ABIDE_fs-6.0.0/0051140/scripts/recon-all.log

Sat Oct  7 20:21:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0051140 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0051140/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0051140
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-963 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:      66074836   63170964    2903872    1766272          0   55925536
-/+ buffers/cache:    7245428   58829408
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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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: 2017/10/07-18:21:59-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-963  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-6.0.0/0051140

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0051140/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0051140/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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/Trinity/0051140/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-6.0.0/0051140/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 20:22:01 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/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-6.0.0/0051140/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 20:22:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/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-963 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 20:22:10 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.24536
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.24536/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.24536/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.24536/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 20:22:12 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.24536/nu0.mnc ./tmp.mri_nu_correct.mni.24536/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.24536/0/ -iterations 1000 -distance 50
[ntraut@tars-963:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/] [2017-10-07 20:22:12] 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.24536/0/ ./tmp.mri_nu_correct.mni.24536/nu0.mnc ./tmp.mri_nu_correct.mni.24536/nu1.imp

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Number of iterations: 68 
CV of field change: 0.00098316
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.24536/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.24536/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.24536/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 20:23:40 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 20:23:40 CEST 2017
Ended   at Sat Oct  7 20:24:15 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 20:24:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7100, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/transforms/talairach_avi.log 

TalAviQA: 0.97371
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 20:24:17 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-6.0.0/0051140/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-963 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 20:24:17 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.25677
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25677/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.25677/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.25677/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 20:24:20 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.25677/nu0.mnc ./tmp.mri_nu_correct.mni.25677/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25677/0/
[ntraut@tars-963:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/] [2017-10-07 20:24:20] 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.25677/0/ ./tmp.mri_nu_correct.mni.25677/nu0.mnc ./tmp.mri_nu_correct.mni.25677/nu1.imp

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Number of iterations: 50 
CV of field change: 0.000964998
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 20:25:14 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.25677/nu1.mnc ./tmp.mri_nu_correct.mni.25677/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25677/1/
[ntraut@tars-963:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/] [2017-10-07 20:25:14] 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.25677/1/ ./tmp.mri_nu_correct.mni.25677/nu1.mnc ./tmp.mri_nu_correct.mni.25677/nu2.imp

Processing:.................................................................Done
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Number of iterations: 16 
CV of field change: 0.000965967
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.25677/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25677/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-6.0.0/0051140/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.25677/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25677/ones.mgz 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.25677/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.25677/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.25677/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25677/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.25677/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25677/input.mean.dat 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.25677/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.25677/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25677/ones.mgz --i ./tmp.mri_nu_correct.mni.25677/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25677/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.25677/ones.mgz --i ./tmp.mri_nu_correct.mni.25677/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25677/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25677/output.mean.dat 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.25677/ones.mgz
Loading ./tmp.mri_nu_correct.mni.25677/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.25677/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.25677/nu2.mnc ./tmp.mri_nu_correct.mni.25677/nu2.mnc mul .84294828192562988670
Saving result to './tmp.mri_nu_correct.mni.25677/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.25677/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.25677/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.25677/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 ( 5, 151) to ( 3, 110)
 
 
Sat Oct  7 20:26:25 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 20:26:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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
 1.00460   0.00804  -0.03860  -7.43092;
-0.01477   0.95861   0.09263  -2.96787;
 0.02103  -0.06474   1.11087  -7.12317;
 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 73 (73), valley at 35 (35)
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 72 (72), valley at 34 (34)
csf peak at 37, setting threshold to 60
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 9 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 20:28:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=9.0
skull bounding box = (47, 19, 0) --> (208, 171, 223)
using (101, 70, 112) as brain centroid...
mean wm in atlas = 108, using box (81,51,84) --> (120, 88,139) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.4
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.525
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.230908 @ (-9.091, 27.273, -9.091)
max log p =    -4.074083 @ (4.545, -4.545, 4.545)
max log p =    -4.021574 @ (2.273, -2.273, -2.273)
max log p =    -4.005552 @ (1.136, 3.409, 1.136)
max log p =    -3.990278 @ (0.568, -0.568, 0.568)
max log p =    -3.990278 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, 23.3, -5.1): log p = -3.990
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.902, old_max_log_p =-3.990 (thresh=-4.0)
 1.00000   0.00000   0.00000  -0.56818;
 0.00000   1.15000   0.00000   5.46364;
 0.00000   0.00000   0.92500   3.58912;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.902, old_max_log_p =-3.902 (thresh=-3.9)
 1.00000   0.00000   0.00000  -0.56818;
 0.00000   1.15000   0.00000   5.46364;
 0.00000   0.00000   0.92500   3.58912;
 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=-3.800, old_max_log_p =-3.902 (thresh=-3.9)
 1.00000   0.00000   0.00000  -2.44318;
 0.00000   1.19313   0.00000   5.96199;
 0.00000   0.00000   0.90701   3.80211;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.788, old_max_log_p =-3.800 (thresh=-3.8)
 1.00000   0.00000   0.00000  -2.44318;
 0.00000   1.19249  -0.02968   7.66482;
 0.00000   0.03977   0.92352  -2.68827;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.788, old_max_log_p =-3.788 (thresh=-3.8)
 1.00000   0.00000   0.00000  -2.44318;
 0.00000   1.19249  -0.02968   7.66482;
 0.00000   0.03977   0.92352  -2.68827;
 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=-3.777, old_max_log_p =-3.788 (thresh=-3.8)
 0.99883   0.00000   0.00000  -1.82523;
 0.00000   1.18969  -0.02961   8.44883;
 0.00000   0.03977   0.92352  -2.68827;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.776, old_max_log_p =-3.777 (thresh=-3.8)
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 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
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.776 (old=-4.525)
transform before final EM align:
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 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
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.2  tol 0.000000
final transform:
 0.99762   0.00972  -0.00018  -2.77283;
-0.00818   1.19133  -0.02208   8.40832;
 0.00000   0.03007   0.92481  -1.72229;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1179.414701
mri_em_register stimesec    1.001847
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   157571
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    82
mri_em_register ru_nivcsw   1953
registration took 10 minutes and 19 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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=127 y=94 z=117 r=72
      first estimation of the main basin volume: 1578811 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=103, y=75, z=83, 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=9404667613 voxels, voxel volume =1.000 
                     = 9404667613 mmm3 = 9404667.904 cm3
done.
PostAnalyze...Basin Prior
 85 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=127,y=97, z=108, r=10667 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=5, CSF_MAX=30 , nb = 43928
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = -1034962501
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = -1044568968
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=30 , nb = 1090439600
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=5, CSF_MAX=29 , nb = 1078798046
    OTHER      CSF_MIN=0, CSF_intensity=23, CSF_MAX=47 , nb = 1068359100
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    30,      43,        52,   67
  after  analyzing :    30,      49,        52,   53
   RIGHT_CER   
  before analyzing :    15,      29,        49,   67
  after  analyzing :    15,      42,        49,   48
   LEFT_CER    
  before analyzing :    14,      24,        46,   69
  after  analyzing :    14,      38,        46,   45
  RIGHT_BRAIN  
  before analyzing :    30,      42,        52,   67
  after  analyzing :    30,      48,        52,   52
  LEFT_BRAIN   
  before analyzing :    29,      42,        51,   67
  after  analyzing :    29,      48,        51,   52
     OTHER     
  before analyzing :    47,      49,        54,   91
  after  analyzing :    47,      52,        54,   61
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...66 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.010
curvature mean = 73.344, std = 9.773

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.59, sigma = 3.58
      after  rotation: sse = 2.59, sigma = 3.58
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.69, its var is  3.31   
      before Erosion-Dilatation  0.16% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...48 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1963574 voxels, voxel volume = 1.000 mm3
           = 1963574 mmm3 = 1963.574 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    24.348298
mri_watershed stimesec    0.382941
mri_watershed ru_maxrss   823952
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213326
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  3096
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1307
mri_watershed ru_nivcsw   46
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 20:39:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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=26.1
skull bounding box = (58, 37, 19) --> (196, 162, 207)
using (104, 79, 113) as brain centroid...
mean wm in atlas = 107, using box (87,64,90) --> (120, 94,136) to find MRI wm
before smoothing, mri peak at 106
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 = -4.512
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.061225 @ (-9.091, 27.273, -9.091)
max log p =    -3.797736 @ (4.545, -4.545, 4.545)
max log p =    -3.687985 @ (2.273, 2.273, -2.273)
max log p =    -3.650681 @ (1.136, -3.409, -1.136)
max log p =    -3.650681 @ (0.000, 0.000, 0.000)
max log p =    -3.638929 @ (0.852, 1.420, 1.989)
Found translation: (-0.3, 23.0, -6.0): log p = -3.639
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.518, old_max_log_p =-3.639 (thresh=-3.6)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.15000   0.00000   8.56956;
 0.00000   0.00000   0.91375   3.64322;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.518, old_max_log_p =-3.518 (thresh=-3.5)
 1.00000   0.00000   0.00000  -0.28409;
 0.00000   1.15000   0.00000   8.56956;
 0.00000   0.00000   0.91375   3.64322;
 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=-3.405, old_max_log_p =-3.518 (thresh=-3.5)
 1.01602  -0.06969  -0.03607   8.40804;
 0.06537   1.09933   0.08519  -4.34646;
 0.03272  -0.11125   0.90894   12.60968;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.405 (thresh=-3.4)
 1.01602  -0.06969  -0.03607   8.40804;
 0.06537   1.09933   0.08519  -4.34646;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.401, old_max_log_p =-3.401 (thresh=-3.4)
 1.01602  -0.06969  -0.03607   8.40804;
 0.06537   1.09933   0.08519  -4.34646;
 0.03211  -0.10917   0.89189   14.35033;
 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=-3.401, old_max_log_p =-3.401 (thresh=-3.4)
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 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
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.401 (old=-4.512)
transform before final EM align:
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 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
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    3.9  tol 0.000000
final transform:
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    873.104267
mri_em_register stimesec    0.981850
mri_em_register ru_maxrss   600972
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   159436
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    93
mri_em_register ru_nivcsw   1409
registration took 7 minutes and 34 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 20:46:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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=26.1
skull bounding box = (58, 37, 19) --> (196, 162, 207)
using (104, 79, 113) as brain centroid...
mean wm in atlas = 107, using box (87,64,90) --> (120, 94,136) to find MRI wm
before smoothing, mri peak at 106
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
 1.01602  -0.06969  -0.03607   8.40804;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 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, 35, 21) --> (192, 140, 208)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0
0 of 2261 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 37, 22) --> (129, 144, 209)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 2100 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 116, 49) --> (178, 153, 110)
Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 132.0
0 of 40 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 116, 48) --> (128, 155, 113)
Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 32 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 106, 90) --> (147, 170, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
0 of 52 (0.0%) samples deleted
using 4485 total control points for intensity normalization...
bias field = 0.967 +- 0.048
38 of 4485 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 35, 21) --> (192, 140, 208)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 2805 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 37, 22) --> (129, 144, 209)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 2690 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 116, 49) --> (178, 153, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
11 of 140 (7.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 116, 48) --> (128, 155, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 80 (2.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 106, 90) --> (147, 170, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
14 of 127 (11.0%) samples deleted
using 5842 total control points for intensity normalization...
bias field = 1.030 +- 0.049
24 of 5729 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (124, 35, 21) --> (192, 140, 208)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 2801 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (62, 37, 22) --> (129, 144, 209)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
4 of 2686 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (128, 116, 49) --> (178, 153, 110)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
150 of 218 (68.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 116, 48) --> (128, 155, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
23 of 143 (16.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (112, 106, 90) --> (147, 170, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
91 of 182 (50.0%) samples deleted
using 6030 total control points for intensity normalization...
bias field = 1.030 +- 0.044
22 of 5685 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 45 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 20:48:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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) = 1.01 (predicted orig area = 7.9)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.789, neg=0, invalid=762
0001: dt=259.373970, rms=0.723 (8.307%), neg=0, invalid=762
0002: dt=172.398524, rms=0.708 (2.151%), neg=0, invalid=762
0003: dt=295.936000, rms=0.698 (1.461%), neg=0, invalid=762
0004: dt=159.632184, rms=0.693 (0.715%), neg=0, invalid=762
0005: dt=295.936000, rms=0.689 (0.490%), neg=0, invalid=762
0006: dt=129.753425, rms=0.687 (0.379%), neg=0, invalid=762
0007: dt=517.888000, rms=0.683 (0.548%), neg=0, invalid=762
0008: dt=129.472000, rms=0.681 (0.214%), neg=0, invalid=762
0009: dt=129.472000, rms=0.681 (0.113%), neg=0, invalid=762
0010: dt=129.472000, rms=0.679 (0.184%), neg=0, invalid=762
0011: dt=129.472000, rms=0.678 (0.236%), neg=0, invalid=762
0012: dt=129.472000, rms=0.676 (0.240%), neg=0, invalid=762
0013: dt=129.472000, rms=0.674 (0.257%), neg=0, invalid=762
0014: dt=129.472000, rms=0.673 (0.263%), neg=0, invalid=762
0015: dt=129.472000, rms=0.671 (0.221%), neg=0, invalid=762
0016: dt=129.472000, rms=0.670 (0.185%), neg=0, invalid=762
0017: dt=129.472000, rms=0.669 (0.154%), neg=0, invalid=762
0018: dt=129.472000, rms=0.668 (0.133%), neg=0, invalid=762
0019: dt=129.472000, rms=0.667 (0.119%), neg=0, invalid=762
0020: dt=129.472000, rms=0.666 (0.100%), neg=0, invalid=762
0021: dt=369.920000, rms=0.666 (0.045%), neg=0, invalid=762
0022: dt=369.920000, rms=0.666 (-0.068%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.667, neg=0, invalid=762
0023: dt=295.936000, rms=0.664 (0.373%), neg=0, invalid=762
0024: dt=129.472000, rms=0.664 (0.074%), neg=0, invalid=762
0025: dt=129.472000, rms=0.663 (0.038%), neg=0, invalid=762
0026: dt=129.472000, rms=0.663 (0.068%), neg=0, invalid=762
0027: dt=129.472000, rms=0.662 (0.084%), neg=0, invalid=762
0028: dt=129.472000, rms=0.662 (0.089%), neg=0, invalid=762
0029: dt=129.472000, rms=0.661 (0.094%), neg=0, invalid=762
0030: dt=129.472000, rms=0.661 (0.093%), neg=0, invalid=762
0031: dt=129.472000, rms=0.660 (0.091%), neg=0, invalid=762
0032: dt=1183.744000, rms=0.660 (0.047%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.664, neg=0, invalid=762
0033: dt=150.234742, rms=0.659 (0.758%), neg=0, invalid=762
0034: dt=237.609195, rms=0.650 (1.291%), neg=0, invalid=762
0035: dt=63.492063, rms=0.647 (0.543%), neg=0, invalid=762
0036: dt=145.152000, rms=0.644 (0.334%), neg=0, invalid=762
0037: dt=115.736527, rms=0.642 (0.337%), neg=0, invalid=762
0038: dt=70.652330, rms=0.641 (0.230%), neg=0, invalid=762
0039: dt=70.652330, rms=0.639 (0.204%), neg=0, invalid=762
0040: dt=70.652330, rms=0.638 (0.285%), neg=0, invalid=762
0041: dt=70.652330, rms=0.635 (0.399%), neg=0, invalid=762
0042: dt=70.652330, rms=0.632 (0.412%), neg=0, invalid=762
0043: dt=70.652330, rms=0.629 (0.479%), neg=0, invalid=762
0044: dt=70.652330, rms=0.627 (0.450%), neg=0, invalid=762
0045: dt=70.652330, rms=0.624 (0.417%), neg=0, invalid=762
0046: dt=70.652330, rms=0.622 (0.377%), neg=0, invalid=762
0047: dt=70.652330, rms=0.619 (0.345%), neg=0, invalid=762
0048: dt=70.652330, rms=0.617 (0.336%), neg=0, invalid=762
0049: dt=70.652330, rms=0.616 (0.273%), neg=0, invalid=762
0050: dt=70.652330, rms=0.614 (0.214%), neg=0, invalid=762
0051: dt=70.652330, rms=0.613 (0.196%), neg=0, invalid=762
0052: dt=70.652330, rms=0.612 (0.195%), neg=0, invalid=762
0053: dt=70.652330, rms=0.611 (0.156%), neg=0, invalid=762
0054: dt=70.652330, rms=0.610 (0.111%), neg=0, invalid=762
0055: dt=70.652330, rms=0.610 (0.097%), neg=0, invalid=762
0056: dt=145.152000, rms=0.609 (0.054%), neg=0, invalid=762
0057: dt=145.152000, rms=0.609 (-0.108%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.610, neg=0, invalid=762
0058: dt=114.871795, rms=0.607 (0.415%), neg=0, invalid=762
0059: dt=103.680000, rms=0.606 (0.198%), neg=0, invalid=762
0060: dt=103.680000, rms=0.606 (-0.025%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.631, neg=0, invalid=762
0061: dt=9.600000, rms=0.630 (0.211%), neg=0, invalid=762
0062: dt=2.800000, rms=0.630 (0.016%), neg=0, invalid=762
0063: dt=2.800000, rms=0.630 (0.007%), neg=0, invalid=762
0064: dt=2.800000, rms=0.630 (-0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.630, neg=0, invalid=762
0065: dt=2.800000, rms=0.630 (0.097%), neg=0, invalid=762
0066: dt=2.800000, rms=0.630 (0.010%), neg=0, invalid=762
0067: dt=2.800000, rms=0.630 (0.001%), neg=0, invalid=762
0068: dt=2.800000, rms=0.630 (-0.028%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.684, neg=0, invalid=762
0069: dt=6.093897, rms=0.668 (2.267%), neg=0, invalid=762
0070: dt=4.032000, rms=0.668 (0.136%), neg=0, invalid=762
0071: dt=4.032000, rms=0.668 (-0.027%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.668, neg=0, invalid=762
0072: dt=0.000000, rms=0.668 (0.062%), neg=0, invalid=762
0073: dt=0.000000, rms=0.668 (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=0.718, neg=0, invalid=762
0074: dt=0.448000, rms=0.717 (0.160%), neg=0, invalid=762
0075: dt=0.768000, rms=0.716 (0.114%), neg=0, invalid=762
0076: dt=0.768000, rms=0.715 (0.165%), neg=0, invalid=762
0077: dt=0.768000, rms=0.714 (0.154%), neg=0, invalid=762
0078: dt=0.768000, rms=0.714 (-0.009%), neg=0, invalid=762
0079: dt=3.403846, rms=0.711 (0.370%), neg=0, invalid=762
0080: dt=0.448000, rms=0.711 (0.009%), neg=0, invalid=762
0081: dt=0.448000, rms=0.711 (0.010%), neg=0, invalid=762
0082: dt=0.448000, rms=0.711 (0.012%), neg=0, invalid=762
0083: dt=0.448000, rms=0.711 (0.020%), neg=0, invalid=762
0084: dt=0.448000, rms=0.710 (0.022%), neg=0, invalid=762
0085: dt=0.448000, rms=0.710 (0.022%), neg=0, invalid=762
0086: dt=0.448000, rms=0.710 (0.002%), neg=0, invalid=762
0087: dt=1.792000, rms=0.710 (0.015%), neg=0, invalid=762
0088: dt=1.280000, rms=0.710 (0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.711, neg=0, invalid=762
0089: dt=1.280000, rms=0.709 (0.163%), neg=0, invalid=762
0090: dt=0.000000, rms=0.709 (0.000%), neg=0, invalid=762
0091: dt=0.100000, rms=0.709 (-0.002%), 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=0.684, neg=0, invalid=762
0092: dt=0.751238, rms=0.668 (2.305%), neg=0, invalid=762
0093: dt=0.064000, rms=0.668 (0.084%), neg=0, invalid=762
0094: dt=0.064000, rms=0.668 (-0.055%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.668, neg=0, invalid=762
0095: dt=0.028000, rms=0.668 (0.079%), neg=0, invalid=762
0096: dt=0.006000, rms=0.668 (0.001%), neg=0, invalid=762
0097: dt=0.006000, rms=0.668 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.11290 (27)
Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (1036 voxels, overlap=0.454)
Left_Lateral_Ventricle (4): linear fit = 1.27 x + 0.0 (1036 voxels, peak = 26), gca=25.5
gca peak = 0.15565 (16)
mri peak = 0.10152 (28)
Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (1075 voxels, overlap=0.260)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1075 voxels, peak = 26), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.07293 (94)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1095 voxels, overlap=1.000)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1095 voxels, peak = 96), gca=95.5
gca peak = 0.20183 (93)
mri peak = 0.08245 (91)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (1050 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (1050 voxels, peak = 90), gca=89.7
gca peak = 0.21683 (55)
mri peak = 0.07969 (67)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1193 voxels, overlap=0.224)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1193 voxels, peak = 66), gca=66.3
gca peak = 0.30730 (58)
mri peak = 0.08703 (67)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1241 voxels, overlap=0.973)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1241 voxels, peak = 65), gca=64.7
gca peak = 0.11430 (101)
mri peak = 0.11446 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (78617 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (78617 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.10338 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (76956 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (76956 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.04369 (69)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (31285 voxels, overlap=0.684)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (31285 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.05412 (67)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (32114 voxels, overlap=0.245)
Right_Cerebral_Cortex (42): linear fit = 1.16 x + 0.0 (32114 voxels, peak = 68), gca=67.6
gca peak = 0.14161 (67)
mri peak = 0.11964 (81)
Right_Caudate (50): linear fit = 1.16 x + 0.0 (1023 voxels, overlap=0.135)
Right_Caudate (50): linear fit = 1.16 x + 0.0 (1023 voxels, peak = 78), gca=78.1
gca peak = 0.15243 (71)
mri peak = 0.10951 (79)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (1295 voxels, overlap=0.348)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (1295 voxels, peak = 77), gca=77.0
gca peak = 0.13336 (57)
mri peak = 0.04471 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26350 voxels, overlap=0.647)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (26350 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.04428 (69)
Right_Cerebellum_Cortex (47): linear fit = 1.22 x + 0.0 (26670 voxels, overlap=0.182)
Right_Cerebellum_Cortex (47): linear fit = 1.22 x + 0.0 (26670 voxels, peak = 68), gca=68.0
gca peak = 0.18181 (84)
mri peak = 0.11615 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (11075 voxels, overlap=0.843)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (11075 voxels, peak = 86), gca=86.1
gca peak = 0.20573 (83)
mri peak = 0.11537 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9961 voxels, overlap=0.580)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (9961 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.06922 (63)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (550 voxels, overlap=0.682)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (550 voxels, peak = 64), gca=63.6
gca peak = 0.39313 (56)
mri peak = 0.09462 (69)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (607 voxels, overlap=0.033)
Right_Amygdala (54): linear fit = 1.21 x + 0.0 (607 voxels, peak = 67), gca=67.5
gca peak = 0.14181 (85)
mri peak = 0.06624 (90)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6733 voxels, overlap=0.804)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6733 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.06393 (92)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5679 voxels, overlap=0.722)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5679 voxels, peak = 90), gca=90.1
gca peak = 0.13399 (79)
mri peak = 0.08354 (84)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (2954 voxels, overlap=0.773)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (2954 voxels, peak = 85), gca=84.9
gca peak = 0.14159 (79)
mri peak = 0.08488 (87)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2917 voxels, overlap=0.564)
Right_Putamen (51): linear fit = 1.10 x + 0.0 (2917 voxels, peak = 87), gca=86.5
gca peak = 0.10025 (80)
mri peak = 0.09819 (87)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (15019 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (15019 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.08023 (93)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1541 voxels, overlap=0.650)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1541 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.07192 (93)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2028 voxels, overlap=0.704)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2028 voxels, peak = 95), gca=94.8
gca peak = 0.20494 (23)
mri peak = 1.00000 (19)
gca peak = 0.15061 (21)
mri peak = 0.14827 (23)
Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (504 voxels, overlap=0.681)
Fourth_Ventricle (15): linear fit = 1.16 x + 0.0 (504 voxels, peak = 24), gca=24.5
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 1.16 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.31 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=0.662, neg=0, invalid=762
0098: dt=139.051546, rms=0.647 (2.292%), neg=0, invalid=762
0099: dt=369.920000, rms=0.639 (1.184%), neg=0, invalid=762
0100: dt=129.472000, rms=0.637 (0.264%), neg=0, invalid=762
0101: dt=369.920000, rms=0.635 (0.342%), neg=0, invalid=762
0102: dt=110.976000, rms=0.634 (0.230%), neg=0, invalid=762
0103: dt=369.920000, rms=0.633 (0.180%), neg=0, invalid=762
0104: dt=110.976000, rms=0.632 (0.151%), neg=0, invalid=762
0105: dt=517.888000, rms=0.631 (0.165%), neg=0, invalid=762
0106: dt=110.976000, rms=0.630 (0.152%), neg=0, invalid=762
0107: dt=295.936000, rms=0.629 (0.069%), neg=0, invalid=762
0108: dt=129.472000, rms=0.629 (0.088%), neg=0, invalid=762
0109: dt=221.952000, rms=0.628 (0.043%), neg=0, invalid=762
0110: dt=221.952000, rms=0.628 (0.072%), neg=0, invalid=762
0111: dt=221.952000, rms=0.627 (0.125%), neg=0, invalid=762
0112: dt=221.952000, rms=0.626 (0.103%), neg=0, invalid=762
0113: dt=221.952000, rms=0.625 (0.183%), neg=0, invalid=762
0114: dt=221.952000, rms=0.624 (0.142%), neg=0, invalid=762
0115: dt=221.952000, rms=0.624 (0.095%), neg=0, invalid=762
0116: dt=221.952000, rms=0.623 (0.125%), neg=0, invalid=762
0117: dt=221.952000, rms=0.622 (0.096%), neg=0, invalid=762
0118: dt=221.952000, rms=0.622 (0.084%), neg=0, invalid=762
0119: dt=221.952000, rms=0.621 (0.098%), neg=0, invalid=762
0120: dt=221.952000, rms=0.621 (0.074%), neg=0, invalid=762
0121: dt=221.952000, rms=0.621 (0.062%), neg=0, invalid=762
0122: dt=221.952000, rms=0.620 (0.063%), neg=0, invalid=762
0123: dt=221.952000, rms=0.620 (0.081%), neg=0, invalid=762
0124: dt=221.952000, rms=0.619 (0.075%), neg=0, invalid=762
0125: dt=221.952000, rms=0.619 (0.062%), neg=0, invalid=762
0126: dt=221.952000, rms=0.618 (0.073%), neg=0, invalid=762
0127: dt=221.952000, rms=0.618 (0.057%), neg=0, invalid=762
0128: dt=221.952000, rms=0.618 (0.056%), neg=0, invalid=762
0129: dt=221.952000, rms=0.617 (0.062%), neg=0, invalid=762
0130: dt=221.952000, rms=0.617 (0.073%), neg=0, invalid=762
0131: dt=221.952000, rms=0.616 (0.066%), neg=0, invalid=762
0132: dt=221.952000, rms=0.616 (0.052%), neg=0, invalid=762
0133: dt=221.952000, rms=0.616 (0.056%), neg=0, invalid=762
0134: dt=221.952000, rms=0.615 (0.054%), neg=0, invalid=762
0135: dt=221.952000, rms=0.615 (0.042%), neg=0, invalid=762
0136: dt=221.952000, rms=0.615 (0.034%), neg=0, invalid=762
0137: dt=221.952000, rms=0.615 (0.033%), neg=0, invalid=762
0138: dt=221.952000, rms=0.614 (0.042%), neg=0, invalid=762
0139: dt=221.952000, rms=0.614 (0.040%), neg=0, invalid=762
0140: dt=221.952000, rms=0.614 (0.028%), neg=0, invalid=762
0141: dt=221.952000, rms=0.614 (0.028%), neg=0, invalid=762
0142: dt=221.952000, rms=0.614 (0.033%), neg=0, invalid=762
0143: dt=221.952000, rms=0.613 (0.032%), neg=0, invalid=762
0144: dt=221.952000, rms=0.613 (0.026%), neg=0, invalid=762
0145: dt=221.952000, rms=0.613 (0.027%), neg=0, invalid=762
0146: dt=221.952000, rms=0.613 (0.031%), neg=0, invalid=762
0147: dt=221.952000, rms=0.613 (0.032%), neg=0, invalid=762
0148: dt=221.952000, rms=0.613 (0.028%), neg=0, invalid=762
0149: dt=221.952000, rms=0.612 (0.027%), neg=0, invalid=762
0150: dt=221.952000, rms=0.612 (0.032%), neg=0, invalid=762
0151: dt=221.952000, rms=0.612 (0.031%), neg=0, invalid=762
0152: dt=221.952000, rms=0.612 (0.024%), neg=0, invalid=762
0153: dt=221.952000, rms=0.612 (0.021%), neg=0, invalid=762
0154: dt=295.936000, rms=0.612 (0.009%), neg=0, invalid=762
0155: dt=295.936000, rms=0.612 (-0.029%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.612, neg=0, invalid=762
0156: dt=369.920000, rms=0.611 (0.237%), neg=0, invalid=762
0157: dt=110.976000, rms=0.610 (0.079%), neg=0, invalid=762
0158: dt=517.888000, rms=0.610 (0.055%), neg=0, invalid=762
0159: dt=129.472000, rms=0.610 (0.035%), neg=0, invalid=762
0160: dt=129.472000, rms=0.609 (0.016%), neg=0, invalid=762
0161: dt=129.472000, rms=0.609 (0.026%), neg=0, invalid=762
0162: dt=129.472000, rms=0.609 (0.028%), neg=0, invalid=762
0163: dt=129.472000, rms=0.609 (0.028%), neg=0, invalid=762
0164: dt=129.472000, rms=0.609 (0.028%), neg=0, invalid=762
0165: dt=129.472000, rms=0.609 (0.028%), neg=0, invalid=762
0166: dt=129.472000, rms=0.608 (0.028%), neg=0, invalid=762
0167: dt=129.472000, rms=0.608 (0.027%), neg=0, invalid=762
0168: dt=129.472000, rms=0.608 (0.027%), neg=0, invalid=762
0169: dt=129.472000, rms=0.608 (0.025%), neg=0, invalid=762
0170: dt=129.472000, rms=0.608 (0.023%), neg=0, invalid=762
0171: dt=129.472000, rms=0.608 (0.026%), neg=0, invalid=762
0172: dt=129.472000, rms=0.608 (0.022%), neg=0, invalid=762
0173: dt=129.472000, rms=0.607 (0.020%), neg=0, invalid=762
0174: dt=517.888000, rms=0.607 (0.008%), neg=0, invalid=762
0175: dt=517.888000, rms=0.607 (-0.012%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.609, neg=0, invalid=762
0176: dt=81.892473, rms=0.607 (0.274%), neg=0, invalid=762
0177: dt=331.776000, rms=0.603 (0.704%), neg=0, invalid=762
0178: dt=75.555556, rms=0.600 (0.435%), neg=0, invalid=762
0179: dt=145.152000, rms=0.597 (0.560%), neg=0, invalid=762
0180: dt=36.288000, rms=0.596 (0.155%), neg=0, invalid=762
0181: dt=248.832000, rms=0.595 (0.244%), neg=0, invalid=762
0182: dt=88.070796, rms=0.592 (0.495%), neg=0, invalid=762
0183: dt=36.288000, rms=0.591 (0.087%), neg=0, invalid=762
0184: dt=414.720000, rms=0.590 (0.245%), neg=0, invalid=762
0185: dt=73.600000, rms=0.586 (0.624%), neg=0, invalid=762
0186: dt=36.288000, rms=0.586 (0.055%), neg=0, invalid=762
0187: dt=414.720000, rms=0.584 (0.237%), neg=0, invalid=762
0188: dt=79.304348, rms=0.582 (0.463%), neg=0, invalid=762
0189: dt=36.288000, rms=0.581 (0.044%), neg=0, invalid=762
0190: dt=36.288000, rms=0.581 (0.030%), neg=0, invalid=762
0191: dt=36.288000, rms=0.581 (0.054%), neg=0, invalid=762
0192: dt=36.288000, rms=0.580 (0.096%), neg=0, invalid=762
0193: dt=36.288000, rms=0.579 (0.147%), neg=0, invalid=762
0194: dt=36.288000, rms=0.578 (0.181%), neg=0, invalid=762
0195: dt=36.288000, rms=0.577 (0.196%), neg=0, invalid=762
0196: dt=36.288000, rms=0.576 (0.193%), neg=0, invalid=762
0197: dt=36.288000, rms=0.575 (0.182%), neg=0, invalid=762
0198: dt=36.288000, rms=0.574 (0.173%), neg=0, invalid=762
0199: dt=36.288000, rms=0.573 (0.172%), neg=0, invalid=762
0200: dt=36.288000, rms=0.572 (0.185%), neg=0, invalid=762
0201: dt=36.288000, rms=0.571 (0.184%), neg=0, invalid=762
0202: dt=36.288000, rms=0.570 (0.178%), neg=0, invalid=762
0203: dt=36.288000, rms=0.569 (0.163%), neg=0, invalid=762
0204: dt=36.288000, rms=0.568 (0.151%), neg=0, invalid=762
0205: dt=36.288000, rms=0.567 (0.144%), neg=0, invalid=762
0206: dt=36.288000, rms=0.567 (0.137%), neg=0, invalid=762
0207: dt=36.288000, rms=0.566 (0.143%), neg=0, invalid=762
0208: dt=36.288000, rms=0.565 (0.149%), neg=0, invalid=762
0209: dt=36.288000, rms=0.564 (0.145%), neg=0, invalid=762
0210: dt=36.288000, rms=0.563 (0.129%), neg=0, invalid=762
0211: dt=36.288000, rms=0.563 (0.114%), neg=0, invalid=762
0212: dt=36.288000, rms=0.562 (0.106%), neg=0, invalid=762
0213: dt=36.288000, rms=0.562 (0.100%), neg=0, invalid=762
0214: dt=36.288000, rms=0.561 (0.101%), neg=0, invalid=762
0215: dt=36.288000, rms=0.560 (0.109%), neg=0, invalid=762
0216: dt=36.288000, rms=0.560 (0.107%), neg=0, invalid=762
0217: dt=36.288000, rms=0.559 (0.101%), neg=0, invalid=762
0218: dt=36.288000, rms=0.559 (0.094%), neg=0, invalid=762
0219: dt=36.288000, rms=0.558 (0.088%), neg=0, invalid=762
0220: dt=36.288000, rms=0.558 (0.083%), neg=0, invalid=762
0221: dt=36.288000, rms=0.557 (0.082%), neg=0, invalid=762
0222: dt=36.288000, rms=0.557 (0.083%), neg=0, invalid=762
0223: dt=36.288000, rms=0.556 (0.082%), neg=0, invalid=762
0224: dt=36.288000, rms=0.556 (0.080%), neg=0, invalid=762
0225: dt=36.288000, rms=0.556 (0.070%), neg=0, invalid=762
0226: dt=36.288000, rms=0.555 (0.063%), neg=0, invalid=762
0227: dt=36.288000, rms=0.555 (0.057%), neg=0, invalid=762
0228: dt=36.288000, rms=0.555 (0.054%), neg=0, invalid=762
0229: dt=36.288000, rms=0.554 (0.053%), neg=0, invalid=762
0230: dt=36.288000, rms=0.554 (0.053%), neg=0, invalid=762
0231: dt=36.288000, rms=0.554 (0.058%), neg=0, invalid=762
0232: dt=36.288000, rms=0.553 (0.058%), neg=0, invalid=762
0233: dt=36.288000, rms=0.553 (0.052%), neg=0, invalid=762
0234: dt=36.288000, rms=0.553 (0.047%), neg=0, invalid=762
0235: dt=36.288000, rms=0.553 (0.044%), neg=0, invalid=762
0236: dt=36.288000, rms=0.552 (0.042%), neg=0, invalid=762
0237: dt=36.288000, rms=0.552 (0.042%), neg=0, invalid=762
0238: dt=36.288000, rms=0.552 (0.042%), neg=0, invalid=762
0239: dt=36.288000, rms=0.552 (0.041%), neg=0, invalid=762
0240: dt=36.288000, rms=0.551 (0.041%), neg=0, invalid=762
0241: dt=36.288000, rms=0.551 (0.039%), neg=0, invalid=762
0242: dt=36.288000, rms=0.551 (0.038%), neg=0, invalid=762
0243: dt=36.288000, rms=0.551 (0.035%), neg=0, invalid=762
0244: dt=36.288000, rms=0.551 (0.032%), neg=0, invalid=762
0245: dt=36.288000, rms=0.550 (0.034%), neg=0, invalid=762
0246: dt=36.288000, rms=0.550 (0.038%), neg=0, invalid=762
0247: dt=36.288000, rms=0.550 (0.032%), neg=0, invalid=762
0248: dt=36.288000, rms=0.550 (0.033%), neg=0, invalid=762
0249: dt=36.288000, rms=0.550 (0.035%), neg=0, invalid=762
0250: dt=36.288000, rms=0.549 (0.034%), neg=0, invalid=762
0251: dt=36.288000, rms=0.549 (0.028%), neg=0, invalid=762
0252: dt=36.288000, rms=0.549 (0.023%), neg=0, invalid=762
0253: dt=36.288000, rms=0.549 (0.020%), neg=0, invalid=762
0254: dt=331.776000, rms=0.549 (0.037%), neg=0, invalid=762
0255: dt=15.552000, rms=0.549 (0.005%), neg=0, invalid=762
0256: dt=15.552000, rms=0.549 (0.001%), neg=0, invalid=762
0257: dt=15.552000, rms=0.549 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.549, neg=0, invalid=762
0258: dt=145.152000, rms=0.546 (0.541%), neg=0, invalid=762
0259: dt=36.288000, rms=0.546 (0.110%), neg=0, invalid=762
0260: dt=145.152000, rms=0.545 (0.096%), neg=0, invalid=762
0261: dt=82.944000, rms=0.545 (0.084%), neg=0, invalid=762
0262: dt=103.680000, rms=0.545 (0.046%), neg=0, invalid=762
0263: dt=103.680000, rms=0.544 (0.040%), neg=0, invalid=762
0264: dt=103.680000, rms=0.544 (0.091%), neg=0, invalid=762
0265: dt=103.680000, rms=0.543 (0.066%), neg=0, invalid=762
0266: dt=103.680000, rms=0.543 (0.081%), neg=0, invalid=762
0267: dt=103.680000, rms=0.543 (0.060%), neg=0, invalid=762
0268: dt=103.680000, rms=0.542 (0.090%), neg=0, invalid=762
0269: dt=103.680000, rms=0.542 (0.057%), neg=0, invalid=762
0270: dt=103.680000, rms=0.542 (0.056%), neg=0, invalid=762
0271: dt=103.680000, rms=0.541 (0.095%), neg=0, invalid=762
0272: dt=103.680000, rms=0.541 (0.068%), neg=0, invalid=762
0273: dt=103.680000, rms=0.540 (0.075%), neg=0, invalid=762
0274: dt=103.680000, rms=0.540 (0.072%), neg=0, invalid=762
0275: dt=103.680000, rms=0.539 (0.093%), neg=0, invalid=762
0276: dt=103.680000, rms=0.539 (0.067%), neg=0, invalid=762
0277: dt=103.680000, rms=0.539 (0.038%), neg=0, invalid=762
0278: dt=103.680000, rms=0.538 (0.067%), neg=0, invalid=762
0279: dt=103.680000, rms=0.538 (0.064%), neg=0, invalid=762
0280: dt=103.680000, rms=0.538 (0.058%), neg=0, invalid=762
0281: dt=103.680000, rms=0.538 (0.055%), neg=0, invalid=762
0282: dt=103.680000, rms=0.537 (0.053%), neg=0, invalid=762
0283: dt=103.680000, rms=0.537 (0.053%), neg=0, invalid=762
0284: dt=103.680000, rms=0.537 (0.053%), neg=0, invalid=762
0285: dt=103.680000, rms=0.536 (0.068%), neg=0, invalid=762
0286: dt=103.680000, rms=0.536 (0.059%), neg=0, invalid=762
0287: dt=103.680000, rms=0.536 (0.052%), neg=0, invalid=762
0288: dt=103.680000, rms=0.535 (0.055%), neg=0, invalid=762
0289: dt=103.680000, rms=0.535 (0.057%), neg=0, invalid=762
0290: dt=103.680000, rms=0.535 (0.050%), neg=0, invalid=762
0291: dt=103.680000, rms=0.535 (0.045%), neg=0, invalid=762
0292: dt=103.680000, rms=0.534 (0.054%), neg=0, invalid=762
0293: dt=103.680000, rms=0.534 (0.037%), neg=0, invalid=762
0294: dt=103.680000, rms=0.534 (0.035%), neg=0, invalid=762
0295: dt=103.680000, rms=0.534 (0.046%), neg=0, invalid=762
0296: dt=103.680000, rms=0.534 (0.033%), neg=0, invalid=762
0297: dt=103.680000, rms=0.533 (0.031%), neg=0, invalid=762
0298: dt=103.680000, rms=0.533 (0.047%), neg=0, invalid=762
0299: dt=103.680000, rms=0.533 (0.038%), neg=0, invalid=762
0300: dt=103.680000, rms=0.533 (0.030%), neg=0, invalid=762
0301: dt=103.680000, rms=0.532 (0.049%), neg=0, invalid=762
0302: dt=103.680000, rms=0.532 (0.044%), neg=0, invalid=762
0303: dt=103.680000, rms=0.532 (0.035%), neg=0, invalid=762
0304: dt=103.680000, rms=0.532 (0.040%), neg=0, invalid=762
0305: dt=103.680000, rms=0.532 (0.039%), neg=0, invalid=762
0306: dt=103.680000, rms=0.531 (0.037%), neg=0, invalid=762
0307: dt=103.680000, rms=0.531 (0.032%), neg=0, invalid=762
0308: dt=103.680000, rms=0.531 (0.035%), neg=0, invalid=762
0309: dt=103.680000, rms=0.531 (0.027%), neg=0, invalid=762
0310: dt=103.680000, rms=0.531 (0.034%), neg=0, invalid=762
0311: dt=103.680000, rms=0.531 (0.029%), neg=0, invalid=762
0312: dt=103.680000, rms=0.530 (0.025%), neg=0, invalid=762
0313: dt=103.680000, rms=0.530 (0.025%), neg=0, invalid=762
0314: dt=103.680000, rms=0.530 (0.030%), neg=0, invalid=762
0315: dt=103.680000, rms=0.530 (0.016%), neg=0, invalid=762
0316: dt=103.680000, rms=0.530 (0.031%), neg=0, invalid=762
0317: dt=103.680000, rms=0.530 (0.029%), neg=0, invalid=762
0318: dt=103.680000, rms=0.530 (0.018%), neg=0, invalid=762
0319: dt=103.680000, rms=0.530 (0.032%), neg=0, invalid=762
0320: dt=103.680000, rms=0.529 (0.019%), neg=0, invalid=762
0321: dt=103.680000, rms=0.529 (0.025%), neg=0, invalid=762
0322: dt=103.680000, rms=0.529 (0.021%), neg=0, invalid=762
0323: dt=103.680000, rms=0.529 (0.022%), neg=0, invalid=762
0324: dt=103.680000, rms=0.529 (0.024%), neg=0, invalid=762
0325: dt=103.680000, rms=0.529 (0.024%), neg=0, invalid=762
0326: dt=103.680000, rms=0.529 (0.013%), neg=0, invalid=762
0327: dt=36.288000, rms=0.529 (0.010%), neg=0, invalid=762
0328: dt=36.288000, rms=0.529 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.539, neg=0, invalid=762
0329: dt=9.600000, rms=0.538 (0.116%), neg=0, invalid=762
0330: dt=6.400000, rms=0.538 (0.011%), neg=0, invalid=762
0331: dt=6.400000, rms=0.538 (0.007%), neg=0, invalid=762
0332: dt=6.400000, rms=0.538 (-0.012%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.539, neg=0, invalid=762
0333: dt=32.000000, rms=0.537 (0.331%), neg=0, invalid=762
0334: dt=32.000000, rms=0.536 (0.213%), neg=0, invalid=762
0335: dt=32.000000, rms=0.535 (0.173%), neg=0, invalid=762
0336: dt=32.000000, rms=0.534 (0.190%), neg=0, invalid=762
0337: dt=25.600000, rms=0.533 (0.156%), neg=0, invalid=762
0338: dt=38.400000, rms=0.532 (0.184%), neg=0, invalid=762
0339: dt=24.510638, rms=0.531 (0.143%), neg=0, invalid=762
0340: dt=38.400000, rms=0.530 (0.168%), neg=0, invalid=762
0341: dt=23.434343, rms=0.529 (0.141%), neg=0, invalid=762
0342: dt=44.800000, rms=0.529 (0.172%), neg=0, invalid=762
0343: dt=21.714286, rms=0.528 (0.136%), neg=0, invalid=762
0344: dt=44.800000, rms=0.527 (0.175%), neg=0, invalid=762
0345: dt=23.409396, rms=0.526 (0.103%), neg=0, invalid=762
0346: dt=38.400000, rms=0.526 (0.148%), neg=0, invalid=762
0347: dt=19.200000, rms=0.525 (0.091%), neg=0, invalid=762
0348: dt=128.000000, rms=0.524 (0.271%), neg=0, invalid=762
0349: dt=11.200000, rms=0.523 (0.174%), neg=0, invalid=762
0350: dt=25.600000, rms=0.522 (0.110%), neg=0, invalid=762
0351: dt=32.000000, rms=0.522 (0.123%), neg=0, invalid=762
0352: dt=25.600000, rms=0.521 (0.061%), neg=0, invalid=762
0353: dt=38.400000, rms=0.521 (0.111%), neg=0, invalid=762
0354: dt=19.200000, rms=0.520 (0.067%), neg=0, invalid=762
0355: dt=179.200000, rms=0.519 (0.289%), neg=0, invalid=762
0356: dt=22.555874, rms=0.518 (0.177%), neg=0, invalid=762
0357: dt=32.000000, rms=0.517 (0.125%), neg=0, invalid=762
0358: dt=19.200000, rms=0.517 (0.057%), neg=0, invalid=762
0359: dt=102.400000, rms=0.516 (0.141%), neg=0, invalid=762
0360: dt=11.200000, rms=0.516 (0.072%), neg=0, invalid=762
0361: dt=25.600000, rms=0.516 (0.055%), neg=0, invalid=762
0362: dt=38.400000, rms=0.515 (0.055%), neg=0, invalid=762
0363: dt=19.200000, rms=0.515 (0.048%), neg=0, invalid=762
0364: dt=19.200000, rms=0.515 (0.046%), neg=0, invalid=762
0365: dt=19.200000, rms=0.514 (0.060%), neg=0, invalid=762
0366: dt=19.200000, rms=0.514 (0.083%), neg=0, invalid=762
0367: dt=19.200000, rms=0.514 (0.107%), neg=0, invalid=762
0368: dt=19.200000, rms=0.513 (0.129%), neg=0, invalid=762
0369: dt=19.200000, rms=0.512 (0.137%), neg=0, invalid=762
0370: dt=19.200000, rms=0.511 (0.148%), neg=0, invalid=762
0371: dt=19.200000, rms=0.511 (0.149%), neg=0, invalid=762
0372: dt=19.200000, rms=0.510 (0.156%), neg=0, invalid=762
0373: dt=19.200000, rms=0.509 (0.163%), neg=0, invalid=762
0374: dt=19.200000, rms=0.508 (0.155%), neg=0, invalid=762
0375: dt=19.200000, rms=0.507 (0.151%), neg=0, invalid=762
0376: dt=19.200000, rms=0.507 (0.143%), neg=0, invalid=762
0377: dt=19.200000, rms=0.506 (0.142%), neg=0, invalid=762
0378: dt=19.200000, rms=0.506 (0.011%), neg=0, invalid=762
0379: dt=19.200000, rms=0.506 (0.017%), neg=0, invalid=762
0380: dt=19.200000, rms=0.506 (0.021%), neg=0, invalid=762
0381: dt=19.200000, rms=0.506 (0.026%), neg=0, invalid=762
0382: dt=19.200000, rms=0.505 (0.029%), neg=0, invalid=762
0383: dt=19.200000, rms=0.505 (0.039%), neg=0, invalid=762
0384: dt=19.200000, rms=0.505 (0.038%), neg=0, invalid=762
0385: dt=19.200000, rms=0.505 (0.043%), neg=0, invalid=762
0386: dt=19.200000, rms=0.505 (0.050%), neg=0, invalid=762
0387: dt=19.200000, rms=0.504 (0.055%), neg=0, invalid=762
0388: dt=19.200000, rms=0.504 (0.057%), neg=0, invalid=762
0389: dt=19.200000, rms=0.504 (0.059%), neg=0, invalid=762
0390: dt=19.200000, rms=0.503 (0.068%), neg=0, invalid=762
0391: dt=19.200000, rms=0.503 (0.064%), neg=0, invalid=762
0392: dt=19.200000, rms=0.503 (0.065%), neg=0, invalid=762
0393: dt=19.200000, rms=0.502 (0.069%), neg=0, invalid=762
0394: dt=19.200000, rms=0.502 (0.009%), neg=0, invalid=762
0395: dt=19.200000, rms=0.502 (0.015%), neg=0, invalid=762
0396: dt=19.200000, rms=0.502 (0.006%), neg=0, invalid=762
0397: dt=11.200000, rms=0.502 (0.003%), neg=0, invalid=762
0398: dt=11.200000, rms=0.502 (0.008%), neg=0, invalid=762
0399: dt=5.600000, rms=0.502 (0.001%), neg=0, invalid=762
0400: dt=2.800000, rms=0.502 (0.001%), neg=0, invalid=762
0401: dt=0.350000, rms=0.502 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.521, neg=0, invalid=762
0402: dt=0.000000, rms=0.521 (0.075%), neg=0, invalid=762
0403: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762
0404: dt=0.150000, rms=0.521 (-0.019%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.521, neg=0, invalid=762
0405: dt=0.000000, rms=0.521 (0.075%), neg=0, invalid=762
0406: dt=0.000000, rms=0.521 (0.000%), neg=0, invalid=762
0407: dt=0.150000, rms=0.521 (-0.019%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.559, neg=0, invalid=762
0408: dt=1.024000, rms=0.557 (0.394%), neg=0, invalid=762
0409: dt=0.256000, rms=0.557 (0.011%), neg=0, invalid=762
0410: dt=0.256000, rms=0.557 (-0.012%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.557, neg=0, invalid=762
0411: dt=0.448000, rms=0.556 (0.138%), neg=0, invalid=762
0412: dt=0.384000, rms=0.556 (0.021%), neg=0, invalid=762
0413: dt=0.384000, rms=0.556 (-0.009%), 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=0.510, neg=0, invalid=762
0414: dt=0.448000, rms=0.498 (2.496%), neg=0, invalid=762
0415: dt=0.384000, rms=0.495 (0.450%), neg=0, invalid=762
0416: dt=0.448000, rms=0.494 (0.328%), neg=0, invalid=762
0417: dt=0.448000, rms=0.493 (0.191%), neg=0, invalid=762
0418: dt=0.448000, rms=0.492 (0.140%), neg=0, invalid=762
0419: dt=0.448000, rms=0.492 (0.095%), neg=0, invalid=762
0420: dt=0.448000, rms=0.491 (0.082%), neg=0, invalid=762
0421: dt=0.448000, rms=0.491 (0.054%), neg=0, invalid=762
0422: dt=0.448000, rms=0.491 (0.054%), neg=0, invalid=762
0423: dt=0.448000, rms=0.491 (0.034%), neg=0, invalid=762
0424: dt=0.448000, rms=0.490 (0.040%), neg=0, invalid=762
0425: dt=0.448000, rms=0.490 (0.055%), neg=0, invalid=762
0426: dt=0.224000, rms=0.490 (0.013%), neg=0, invalid=762
0427: dt=0.224000, rms=0.490 (0.019%), neg=0, invalid=762
0428: dt=0.224000, rms=0.490 (0.028%), neg=0, invalid=762
0429: dt=0.224000, rms=0.490 (0.028%), neg=0, invalid=762
0430: dt=0.224000, rms=0.489 (0.029%), neg=0, invalid=762
0431: dt=0.224000, rms=0.489 (0.026%), neg=0, invalid=762
0432: dt=0.224000, rms=0.489 (0.023%), neg=0, invalid=762
0433: dt=0.224000, rms=0.489 (0.002%), neg=0, invalid=762
0434: dt=0.112000, rms=0.489 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.490, neg=0, invalid=762
0435: dt=0.112000, rms=0.488 (0.367%), neg=0, invalid=762
0436: dt=0.320000, rms=0.485 (0.606%), neg=0, invalid=762
0437: dt=0.384000, rms=0.484 (0.281%), neg=0, invalid=762
0438: dt=0.384000, rms=0.483 (0.084%), neg=0, invalid=762
0439: dt=0.384000, rms=0.483 (0.031%), neg=0, invalid=762
0440: dt=0.384000, rms=0.483 (0.013%), neg=0, invalid=762
0441: dt=0.384000, rms=0.483 (0.016%), neg=0, invalid=762
0442: dt=0.384000, rms=0.483 (0.005%), neg=0, invalid=762
0443: dt=0.384000, rms=0.483 (0.002%), neg=0, invalid=762
0444: dt=0.384000, rms=0.483 (0.005%), neg=0, invalid=762
0445: dt=0.320000, rms=0.483 (0.007%), neg=0, invalid=762
0446: dt=0.256000, rms=0.483 (0.002%), 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=0.481, neg=0, invalid=762
0447: dt=0.000000, rms=0.481 (0.093%), neg=0, invalid=762
0448: dt=0.000000, rms=0.481 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.481, neg=0, invalid=762
0449: dt=295.936000, rms=0.480 (0.184%), neg=0, invalid=762
0450: dt=73.984000, rms=0.480 (0.007%), neg=0, invalid=762
0451: dt=73.984000, rms=0.480 (0.005%), neg=0, invalid=762
0452: dt=73.984000, rms=0.480 (0.005%), neg=0, invalid=762
0453: dt=73.984000, rms=0.480 (0.010%), neg=0, invalid=762
0454: dt=73.984000, rms=0.480 (0.018%), neg=0, invalid=762
0455: dt=73.984000, rms=0.480 (0.021%), neg=0, invalid=762
0456: dt=73.984000, rms=0.480 (0.017%), neg=0, invalid=762
0457: dt=73.984000, rms=0.480 (0.012%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.480, neg=0, invalid=762
0458: dt=6.480000, rms=0.480 (0.094%), neg=0, invalid=762
0459: dt=1.312500, rms=0.480 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.480, neg=0, invalid=762
0460: dt=331.776000, rms=0.477 (0.618%), neg=0, invalid=762
0461: dt=36.288000, rms=0.477 (0.099%), neg=0, invalid=762
0462: dt=36.288000, rms=0.477 (0.040%), neg=0, invalid=762
0463: dt=36.288000, rms=0.476 (0.041%), neg=0, invalid=762
0464: dt=36.288000, rms=0.476 (0.044%), neg=0, invalid=762
0465: dt=36.288000, rms=0.476 (0.053%), neg=0, invalid=762
0466: dt=36.288000, rms=0.476 (0.081%), neg=0, invalid=762
0467: dt=36.288000, rms=0.475 (0.087%), neg=0, invalid=762
0468: dt=36.288000, rms=0.475 (0.080%), neg=0, invalid=762
0469: dt=36.288000, rms=0.475 (0.072%), neg=0, invalid=762
0470: dt=103.680000, rms=0.474 (0.015%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.475, neg=0, invalid=762
0471: dt=11.200000, rms=0.474 (0.230%), neg=0, invalid=762
0472: dt=11.200000, rms=0.474 (0.070%), neg=0, invalid=762
0473: dt=11.200000, rms=0.474 (0.055%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0474: dt=11.200000, rms=0.473 (0.031%), neg=0, invalid=762
0475: dt=11.200000, rms=0.473 (-0.031%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.474, neg=0, invalid=762
0476: dt=32.000000, rms=0.469 (0.971%), neg=0, invalid=762
0477: dt=22.379747, rms=0.467 (0.367%), neg=0, invalid=762
0478: dt=32.000000, rms=0.466 (0.254%), neg=0, invalid=762
0479: dt=19.946188, rms=0.465 (0.198%), neg=0, invalid=762
0480: dt=19.946188, rms=0.465 (0.148%), neg=0, invalid=762
0481: dt=19.946188, rms=0.464 (0.211%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=0, neg = 0
0482: dt=19.946188, rms=0.462 (0.287%), neg=0, invalid=762
0483: dt=19.946188, rms=0.461 (0.282%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=0, neg = 0
0484: dt=19.946188, rms=0.460 (0.305%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0485: dt=19.946188, rms=0.458 (0.268%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0486: dt=19.946188, rms=0.457 (0.265%), neg=0, invalid=762
0487: dt=19.946188, rms=0.456 (0.246%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0488: dt=19.946188, rms=0.455 (0.208%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 3 iterations, nbhd size=0, neg = 0
0489: dt=19.946188, rms=0.454 (0.192%), neg=0, invalid=762
0490: dt=19.946188, rms=0.454 (0.154%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0491: dt=19.946188, rms=0.453 (0.149%), neg=0, invalid=762
0492: dt=19.946188, rms=0.452 (0.114%), neg=0, invalid=762
0493: dt=19.946188, rms=0.452 (0.099%), neg=0, invalid=762
0494: dt=11.200000, rms=0.452 (0.007%), neg=0, invalid=762
0495: dt=11.200000, rms=0.452 (0.002%), neg=0, invalid=762
0496: dt=11.200000, rms=0.452 (0.007%), neg=0, invalid=762
0497: dt=11.200000, rms=0.452 (0.002%), neg=0, invalid=762
0498: dt=11.200000, rms=0.452 (0.006%), neg=0, invalid=762
0499: dt=11.200000, rms=0.452 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0500: dt=0.000000, rms=0.456 (0.097%), neg=0, invalid=762
0501: dt=0.000000, rms=0.456 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.457, neg=0, invalid=762
0502: dt=1.728000, rms=0.456 (0.107%), neg=0, invalid=762
0503: dt=1.008000, rms=0.456 (0.005%), neg=0, invalid=762
0504: dt=1.008000, rms=0.456 (0.001%), neg=0, invalid=762
0505: dt=1.008000, rms=0.456 (-0.008%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.465, neg=0, invalid=762
0506: dt=0.448000, rms=0.464 (0.133%), neg=0, invalid=762
0507: dt=0.256000, rms=0.464 (0.006%), neg=0, invalid=762
0508: dt=0.256000, rms=0.464 (-0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.464, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0509: dt=1.536000, rms=0.463 (0.306%), neg=0, invalid=762
0510: dt=0.768000, rms=0.463 (0.027%), neg=0, invalid=762
0511: dt=0.768000, rms=0.463 (-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=0.456, neg=0, invalid=762
iter 0, gcam->neg = 449
after 12 iterations, nbhd size=1, neg = 0
0512: dt=2.184244, rms=0.428 (6.031%), neg=0, invalid=762
0513: dt=0.080000, rms=0.428 (0.042%), neg=0, invalid=762
0514: dt=0.080000, rms=0.428 (-0.052%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
0515: dt=0.096000, rms=0.428 (0.189%), neg=0, invalid=762
0516: dt=0.000000, rms=0.428 (0.001%), neg=0, invalid=762
0517: dt=0.050000, rms=0.428 (-0.017%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
label assignment complete, 0 changed (0.00%)
***************** morphing with label term set to 0 *******************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.414, neg=0, invalid=762
0518: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.414, neg=0, invalid=762
0519: dt=5.780000, rms=0.414 (0.000%), neg=0, invalid=762
0520: dt=2.023000, rms=0.414 (0.000%), neg=0, invalid=762
0521: dt=2.023000, rms=0.414 (-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=0.415, neg=0, invalid=762
0522: dt=0.000000, rms=0.415 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0523: dt=36.288000, rms=0.414 (0.028%), neg=0, invalid=762
0524: dt=103.680000, rms=0.414 (0.028%), neg=0, invalid=762
0525: dt=103.680000, rms=0.414 (0.042%), neg=0, invalid=762
0526: dt=103.680000, rms=0.414 (0.037%), neg=0, invalid=762
0527: dt=103.680000, rms=0.414 (0.010%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
0528: dt=2.000000, rms=0.415 (0.003%), neg=0, invalid=762
0529: dt=0.400000, rms=0.415 (0.000%), neg=0, invalid=762
0530: dt=0.400000, rms=0.415 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.415, neg=0, invalid=762
iter 0, gcam->neg = 2
after 6 iterations, nbhd size=1, neg = 0
0531: dt=127.410138, rms=0.412 (0.710%), neg=0, invalid=762
0532: dt=20.401747, rms=0.411 (0.219%), neg=0, invalid=762
0533: dt=20.401747, rms=0.411 (0.042%), neg=0, invalid=762
0534: dt=20.401747, rms=0.410 (0.041%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0535: dt=20.401747, rms=0.410 (0.074%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0536: dt=20.401747, rms=0.410 (0.077%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0537: dt=20.401747, rms=0.409 (0.150%), neg=0, invalid=762
0538: dt=20.401747, rms=0.408 (0.158%), neg=0, invalid=762
0539: dt=20.401747, rms=0.408 (0.139%), neg=0, invalid=762
0540: dt=20.401747, rms=0.407 (0.122%), neg=0, invalid=762
0541: dt=20.401747, rms=0.407 (0.091%), neg=0, invalid=762
0542: dt=19.200000, rms=0.407 (0.010%), neg=0, invalid=762
0543: dt=19.200000, rms=0.407 (0.008%), neg=0, invalid=762
0544: dt=19.200000, rms=0.407 (0.011%), neg=0, invalid=762
0545: dt=19.200000, rms=0.407 (0.014%), neg=0, invalid=762
0546: dt=19.200000, rms=0.407 (0.018%), neg=0, invalid=762
0547: dt=19.200000, rms=0.407 (0.025%), neg=0, invalid=762
0548: dt=19.200000, rms=0.407 (0.031%), neg=0, invalid=762
0549: dt=19.200000, rms=0.406 (0.034%), neg=0, invalid=762
0550: dt=19.200000, rms=0.406 (0.035%), neg=0, invalid=762
0551: dt=19.200000, rms=0.406 (0.036%), neg=0, invalid=762
0552: dt=19.200000, rms=0.406 (0.039%), neg=0, invalid=762
0553: dt=19.200000, rms=0.406 (0.041%), neg=0, invalid=762
0554: dt=19.200000, rms=0.406 (0.043%), neg=0, invalid=762
0555: dt=19.200000, rms=0.405 (0.045%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0556: dt=19.200000, rms=0.405 (0.046%), neg=0, invalid=762
0557: dt=19.200000, rms=0.405 (0.049%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0558: dt=19.200000, rms=0.405 (0.047%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0559: dt=19.200000, rms=0.405 (0.042%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.409, neg=0, invalid=762
0560: dt=0.000090, rms=0.409 (0.000%), neg=0, invalid=762
0561: 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
0562: dt=0.864000, rms=0.409 (0.001%), neg=0, invalid=762
0563: dt=0.250000, rms=0.409 (0.000%), neg=0, invalid=762
0564: dt=0.250000, rms=0.409 (0.000%), neg=0, invalid=762
0565: dt=0.250000, rms=0.409 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.416, neg=0, invalid=762
0566: dt=0.000000, rms=0.416 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.416, neg=0, invalid=762
0567: dt=0.000000, rms=0.416 (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=0.403, neg=0, invalid=762
iter 0, gcam->neg = 376
after 15 iterations, nbhd size=1, neg = 0
0568: dt=1.297719, rms=0.395 (2.145%), neg=0, invalid=762
0569: dt=0.000016, rms=0.395 (0.000%), neg=0, invalid=762
0570: dt=0.000016, rms=0.395 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.395, neg=0, invalid=762
0571: dt=0.112000, rms=0.394 (0.073%), neg=0, invalid=762
0572: dt=0.096000, rms=0.394 (0.025%), neg=0, invalid=762
0573: dt=0.096000, rms=0.394 (0.014%), neg=0, invalid=762
0574: dt=0.096000, rms=0.394 (-0.027%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 37 minutes and 19 seconds.
mri_ca_register utimesec    10309.896657
mri_ca_register stimesec    6.589998
mri_ca_register ru_maxrss   1349328
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4059287
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63536
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3133
mri_ca_register ru_nivcsw   12943
FSRUNTIME@ mri_ca_register  2.6219 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 23:25:57 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-963
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-6.0.0/0051140/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 7.92
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 = 0.11621 (27)
Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (321 voxels, overlap=0.431)
Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (321 voxels, peak = 26), gca=26.1
gca peak = 0.17677 (13)
mri peak = 0.12903 (28)
Right_Lateral_Ventricle (43): linear fit = 1.96 x + 0.0 (283 voxels, overlap=0.249)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (283 voxels, peak = 25), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.11875 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1065 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1065 voxels, peak = 95), gca=94.5
gca peak = 0.16930 (96)
mri peak = 0.12037 (94)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (991 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 0.96 x + 0.0 (991 voxels, peak = 93), gca=92.6
gca peak = 0.24553 (55)
mri peak = 0.09194 (67)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1235 voxels, overlap=0.282)
Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (1235 voxels, peak = 64), gca=63.5
gca peak = 0.30264 (59)
mri peak = 0.08036 (66)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1139 voxels, overlap=0.855)
Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (1139 voxels, peak = 66), gca=65.8
gca peak = 0.07580 (103)
mri peak = 0.12050 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54552 voxels, overlap=0.641)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54552 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.11326 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51500 voxels, overlap=0.659)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51500 voxels, peak = 104), gca=104.0
gca peak = 0.09712 (58)
mri peak = 0.05044 (68)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (41553 voxels, overlap=0.641)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (41553 voxels, peak = 66), gca=65.8
gca peak = 0.11620 (58)
mri peak = 0.06150 (68)
Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (40366 voxels, overlap=0.432)
Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (40366 voxels, peak = 66), gca=66.4
gca peak = 0.30970 (66)
mri peak = 0.13432 (81)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1288 voxels, overlap=0.021)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1288 voxels, peak = 80), gca=79.5
gca peak = 0.15280 (69)
mri peak = 0.11563 (79)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (1427 voxels, overlap=0.507)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (1427 voxels, peak = 73), gca=73.5
gca peak = 0.13902 (56)
mri peak = 0.05094 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (29301 voxels, overlap=0.721)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (29301 voxels, peak = 64), gca=63.6
gca peak = 0.14777 (55)
mri peak = 0.04935 (67)
Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (28462 voxels, overlap=0.321)
Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (28462 voxels, peak = 66), gca=65.7
gca peak = 0.16765 (84)
mri peak = 0.13447 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (9110 voxels, overlap=0.903)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (9110 voxels, peak = 85), gca=85.3
gca peak = 0.18739 (84)
mri peak = 0.13547 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8737 voxels, overlap=0.556)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (8737 voxels, peak = 89), gca=89.5
gca peak = 0.29869 (57)
mri peak = 0.09993 (63)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (564 voxels, overlap=0.492)
Left_Amygdala (18): linear fit = 1.12 x + 0.0 (564 voxels, peak = 64), gca=63.6
gca peak = 0.33601 (57)
mri peak = 0.11509 (67)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (708 voxels, overlap=0.057)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (708 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.07341 (91)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5693 voxels, overlap=0.910)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (5693 voxels, peak = 92), gca=92.2
gca peak = 0.11793 (83)
mri peak = 0.06841 (91)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5199 voxels, overlap=0.747)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5199 voxels, peak = 90), gca=90.1
gca peak = 0.08324 (81)
mri peak = 0.09435 (84)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (3248 voxels, overlap=0.631)
Left_Putamen (12): linear fit = 1.07 x + 0.0 (3248 voxels, peak = 86), gca=86.3
gca peak = 0.10360 (77)
mri peak = 0.09969 (87)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (3250 voxels, overlap=0.444)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (3250 voxels, peak = 83), gca=82.8
gca peak = 0.08424 (78)
mri peak = 0.10008 (85)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (17639 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (17639 voxels, peak = 83), gca=83.1
gca peak = 0.12631 (89)
mri peak = 0.07790 (93)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (2259 voxels, overlap=0.739)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (2259 voxels, peak = 95), gca=94.8
gca peak = 0.14500 (87)
mri peak = 0.07971 (93)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2422 voxels, overlap=0.863)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (2422 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.08701 (30)
gca peak = 0.19357 (14)
mri peak = 0.14123 (23)
Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (345 voxels, overlap=0.365)
Fourth_Ventricle (15): linear fit = 1.47 x + 0.0 (345 voxels, peak = 21), gca=20.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.14 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.42 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15813 (24)
mri peak = 0.11621 (27)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (321 voxels, overlap=0.782)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (321 voxels, peak = 24), gca=24.4
gca peak = 0.14041 (19)
mri peak = 0.12903 (28)
Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (283 voxels, overlap=0.444)
Right_Lateral_Ventricle (43): linear fit = 1.29 x + 0.0 (283 voxels, peak = 25), gca=24.6
gca peak = 0.26800 (93)
mri peak = 0.11875 (95)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1065 voxels, overlap=1.006)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (1065 voxels, peak = 93), gca=92.5
gca peak = 0.20275 (93)
mri peak = 0.12037 (94)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (991 voxels, overlap=1.000)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (991 voxels, peak = 93), gca=92.5
gca peak = 0.24791 (64)
mri peak = 0.09194 (67)
Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (1235 voxels, overlap=1.005)
Right_Hippocampus (53): linear fit = 1.05 x + 0.0 (1235 voxels, peak = 68), gca=67.5
gca peak = 0.30549 (63)
mri peak = 0.08036 (66)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1139 voxels, overlap=1.009)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (1139 voxels, peak = 62), gca=62.1
gca peak = 0.07580 (103)
mri peak = 0.12050 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54552 voxels, overlap=0.641)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (54552 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.11326 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51500 voxels, overlap=0.659)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51500 voxels, peak = 104), gca=104.0
gca peak = 0.08624 (66)
mri peak = 0.05044 (68)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (41553 voxels, overlap=0.962)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (41553 voxels, peak = 66), gca=66.0
gca peak = 0.10285 (66)
mri peak = 0.06150 (68)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (40366 voxels, overlap=0.939)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (40366 voxels, peak = 66), gca=66.0
gca peak = 0.22228 (80)
mri peak = 0.13432 (81)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1288 voxels, overlap=1.003)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1288 voxels, peak = 80), gca=80.0
gca peak = 0.12679 (73)
mri peak = 0.11563 (79)
Left_Caudate (11): linear fit = 1.05 x + 0.0 (1427 voxels, overlap=0.840)
Left_Caudate (11): linear fit = 1.05 x + 0.0 (1427 voxels, peak = 77), gca=77.0
gca peak = 0.12459 (63)
mri peak = 0.05094 (64)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (29301 voxels, overlap=0.996)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (29301 voxels, peak = 62), gca=62.1
gca peak = 0.12169 (66)
mri peak = 0.04935 (67)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28462 voxels, overlap=0.995)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (28462 voxels, peak = 66), gca=66.0
gca peak = 0.16172 (86)
mri peak = 0.13447 (85)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (9110 voxels, overlap=0.947)
Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (9110 voxels, peak = 85), gca=84.7
gca peak = 0.15153 (90)
mri peak = 0.13547 (88)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8737 voxels, overlap=0.909)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (8737 voxels, peak = 89), gca=88.7
gca peak = 0.28686 (65)
mri peak = 0.09993 (63)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (564 voxels, overlap=1.012)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (564 voxels, peak = 65), gca=65.0
gca peak = 0.29910 (68)
mri peak = 0.11509 (67)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (708 voxels, overlap=1.003)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (708 voxels, peak = 68), gca=68.0
gca peak = 0.10432 (92)
mri peak = 0.07341 (91)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5693 voxels, overlap=0.969)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5693 voxels, peak = 92), gca=91.5
gca peak = 0.10388 (90)
mri peak = 0.06841 (91)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5199 voxels, overlap=0.949)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5199 voxels, peak = 90), gca=89.6
gca peak = 0.08933 (88)
mri peak = 0.09435 (84)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (3248 voxels, overlap=0.808)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (3248 voxels, peak = 88), gca=87.6
gca peak = 0.10536 (81)
mri peak = 0.09969 (87)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (3250 voxels, overlap=0.820)
Right_Putamen (51): linear fit = 1.02 x + 0.0 (3250 voxels, peak = 83), gca=83.0
gca peak = 0.07154 (83)
mri peak = 0.10008 (85)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (17639 voxels, overlap=0.725)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (17639 voxels, peak = 84), gca=84.2
gca peak = 0.11674 (95)
mri peak = 0.07790 (93)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2259 voxels, overlap=0.829)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2259 voxels, peak = 95), gca=94.5
gca peak = 0.15698 (91)
mri peak = 0.07971 (93)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2422 voxels, overlap=0.943)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2422 voxels, peak = 91), gca=90.5
gca peak = 0.14011 (34)
mri peak = 0.08701 (30)
gca peak = 0.14735 (22)
mri peak = 0.14123 (23)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (345 voxels, overlap=0.730)
Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (345 voxels, peak = 23), gca=22.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.15143 (30)
gca peak Left_Thalamus = 0.64095 (101)
gca peak Third_Ventricle = 0.14011 (34)
gca peak CSF = 0.17474 (52)
gca peak Left_Accumbens_area = 0.61676 (66)
gca peak Left_undetermined = 0.96707 (30)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12577 (35)
gca peak Right_Inf_Lat_Vent = 0.18678 (27)
gca peak Right_Accumbens_area = 0.29878 (78)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14506 (37)
gca peak Fifth_Ventricle = 0.75707 (44)
gca peak WM_hypointensities = 0.07941 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.70880 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.11 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
82121 voxels changed in iteration 0 of unlikely voxel relabeling
434 voxels changed in iteration 1 of unlikely voxel relabeling
10 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
50541 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels)
440 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 78239 changed. image ll: -2.145, PF=0.500
pass 2: 22212 changed. image ll: -2.145, PF=0.500
pass 3: 6588 changed.
pass 4: 2563 changed.
59504 voxels changed in iteration 0 of unlikely voxel relabeling
344 voxels changed in iteration 1 of unlikely voxel relabeling
7 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8201 voxels changed in iteration 0 of unlikely voxel relabeling
120 voxels changed in iteration 1 of unlikely voxel relabeling
7 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6362 voxels changed in iteration 0 of unlikely voxel relabeling
71 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
4850 voxels changed in iteration 0 of unlikely voxel relabeling
37 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
1 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    4186.707523
mri_ca_label stimesec    1.522768
mri_ca_label ru_maxrss   2126340
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   670336
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  528
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    294
mri_ca_label ru_nivcsw   5070
auto-labeling took 69 minutes and 2 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/transforms/cc_up.lta 0051140 

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-6.0.0/0051140/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/norm.mgz
23198 voxels in left wm, 59265 in right wm, xrange [121, 129]
searching rotation angles z=[-7  7], y=[-8  6]

searching scale 1 Z rot -6.7  
searching scale 1 Z rot -6.5  
searching scale 1 Z rot -6.2  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.0  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.5  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.0  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.5  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.0  global minimum found at slice 126.0, rotations (-0.66, 0.29)
final transformation (x=126.0, yr=-0.658, zr=0.285):
 0.99992  -0.00498  -0.01148   3.66414;
 0.00498   0.99999  -0.00006   46.37977;
 0.01148   0.00000   0.99993   17.56120;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 81 109
eigenvectors:
 0.00118  -0.00858   0.99996;
 0.01547  -0.99984  -0.00859;
 0.99988   0.01548  -0.00105;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.8 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 00:35:47 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 00:35:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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...
783 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 72 (72), valley at 33 (33)
csf peak at 36, setting threshold to 60
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 72 (72), valley at 33 (33)
csf peak at 36, setting threshold to 60
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 24 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 00:39:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1917080 voxels in mask (pct= 11.43)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 00:39:15 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 103.7 +- 6.9 [79.0 --> 125.0]
GM (72.0) : 71.2 +- 9.3 [30.0 --> 95.0]
setting bottom of white matter range to 80.6
setting top of gray matter range to 89.9
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...
10356 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5926 filled
3188 bright non-wm voxels segmented.
5216 diagonally connected voxels added...
white matter segmentation took 1.8 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 0.51 minutes
reading wm segmentation from wm.seg.mgz...
145 voxels added to wm to prevent paths from MTL structures to cortex
2776 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 29696 voxels turned on, 81389 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  23 found -  23 modified     |    TOTAL:  23
pass   2 (xy+):   0 found -  23 modified     |    TOTAL:  23
pass   1 (xy-):  24 found -  24 modified     |    TOTAL:  47
pass   2 (xy-):   0 found -  24 modified     |    TOTAL:  47
pass   1 (yz+):  29 found -  29 modified     |    TOTAL:  76
pass   2 (yz+):   0 found -  29 modified     |    TOTAL:  76
pass   1 (yz-):  21 found -  21 modified     |    TOTAL:  97
pass   2 (yz-):   0 found -  21 modified     |    TOTAL:  97
pass   1 (xz+):  20 found -  20 modified     |    TOTAL: 117
pass   2 (xz+):   0 found -  20 modified     |    TOTAL: 117
pass   1 (xz-):  19 found -  19 modified     |    TOTAL: 136
pass   2 (xz-):   0 found -  19 modified     |    TOTAL: 136
Iteration Number : 1
pass   1 (+++):  26 found -  26 modified     |    TOTAL:  26
pass   2 (+++):   0 found -  26 modified     |    TOTAL:  26
pass   1 (+++):  29 found -  29 modified     |    TOTAL:  55
pass   2 (+++):   0 found -  29 modified     |    TOTAL:  55
pass   1 (+++):  39 found -  39 modified     |    TOTAL:  94
pass   2 (+++):   0 found -  39 modified     |    TOTAL:  94
pass   1 (+++):  26 found -  26 modified     |    TOTAL: 120
pass   2 (+++):   0 found -  26 modified     |    TOTAL: 120
Iteration Number : 1
pass   1 (++): 198 found - 198 modified     |    TOTAL: 198
pass   2 (++):   0 found - 198 modified     |    TOTAL: 198
pass   1 (+-): 131 found - 131 modified     |    TOTAL: 329
pass   2 (+-):   0 found - 131 modified     |    TOTAL: 329
pass   1 (--): 131 found - 131 modified     |    TOTAL: 460
pass   2 (--):   0 found - 131 modified     |    TOTAL: 460
pass   1 (-+): 122 found - 122 modified     |    TOTAL: 582
pass   2 (-+):   0 found - 122 modified     |    TOTAL: 582
Iteration Number : 2
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   7 found -   7 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   7 modified     |    TOTAL:  11
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:  15
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:  15
pass   1 (yz-):   6 found -   6 modified     |    TOTAL:  21
pass   2 (yz-):   0 found -   6 modified     |    TOTAL:  21
pass   1 (xz+):   5 found -   5 modified     |    TOTAL:  26
pass   2 (xz+):   0 found -   5 modified     |    TOTAL:  26
pass   1 (xz-):  10 found -  10 modified     |    TOTAL:  36
pass   2 (xz-):   0 found -  10 modified     |    TOTAL:  36
Iteration Number : 2
pass   1 (+++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (+++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   7
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   7
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   9
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   9
pass   1 (+++):   4 found -   4 modified     |    TOTAL:  13
pass   2 (+++):   0 found -   4 modified     |    TOTAL:  13
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 (--):   6 found -   6 modified     |    TOTAL:  11
pass   2 (--):   0 found -   6 modified     |    TOTAL:  11
pass   1 (-+):   1 found -   1 modified     |    TOTAL:  12
pass   2 (-+):   0 found -   1 modified     |    TOTAL:  12
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   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 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
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 = 907 (out of 657413: 0.137965)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 00:41:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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
 1.01602  -0.06969  -0.03607   8.40803;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.01602  -0.06969  -0.03607   8.40803;
 0.06529   1.09804   0.08509  -4.20157;
 0.03211  -0.10917   0.89189   14.35033;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 993 (min = 350, max = 1400), aspect = 0.48 (min = 0.10, max = 0.75)
no need to search
using seed (126, 110, 121), TAL = (2.0, -7.0, 18.0)
talairach voxel to voxel transform
 0.97897   0.06544   0.03334  -8.43472;
-0.05496   0.89848  -0.08794   5.49911;
-0.04197   0.10762   1.10925  -15.11302;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (126,  110,  121) --> (2.0, -7.0, 18.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (2.00, -7.00, 18.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, -7.00, 18.00) SRC: (108.53, 87.76, 126.41)
search lh wm seed point around talairach space (-16.00, -7.00, 18.00), SRC: (143.77, 85.78, 124.90)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 00:42:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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


Iteration Number : 1
pass   1 (xy+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (xy+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   8
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   9
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:  10
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:  11
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:  11
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  13
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  13
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 16 (out of 314356: 0.005090)
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 20: 9 vertices, 12 faces
slice 30: 2953 vertices, 3101 faces
slice 40: 9312 vertices, 9595 faces
slice 50: 17617 vertices, 17897 faces
slice 60: 26686 vertices, 27067 faces
slice 70: 37299 vertices, 37665 faces
slice 80: 48590 vertices, 48968 faces
slice 90: 59877 vertices, 60289 faces
slice 100: 73134 vertices, 73566 faces
slice 110: 85393 vertices, 85834 faces
slice 120: 97473 vertices, 97909 faces
slice 130: 109081 vertices, 109523 faces
slice 140: 120964 vertices, 121362 faces
slice 150: 130863 vertices, 131245 faces
slice 160: 139382 vertices, 139729 faces
slice 170: 148178 vertices, 148529 faces
slice 180: 155728 vertices, 156001 faces
slice 190: 161994 vertices, 162254 faces
slice 200: 166068 vertices, 166189 faces
slice 210: 166628 vertices, 166670 faces
slice 220: 166628 vertices, 166670 faces
slice 230: 166628 vertices, 166670 faces
slice 240: 166628 vertices, 166670 faces
slice 250: 166628 vertices, 166670 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...
   166628 voxel in cpt #1: X=-42 [v=166628,e=500010,f=333340] located at (-26.514637, -19.485867, 37.347683)
For the whole surface: X=-42 [v=166628,e=500010,f=333340]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 00:42:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   4
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:   7
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
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
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 = 12 (out of 315113: 0.003808)
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 20: 20 vertices, 27 faces
slice 30: 2078 vertices, 2183 faces
slice 40: 6734 vertices, 6989 faces
slice 50: 14621 vertices, 14918 faces
slice 60: 24063 vertices, 24397 faces
slice 70: 34648 vertices, 35032 faces
slice 80: 45918 vertices, 46336 faces
slice 90: 56960 vertices, 57317 faces
slice 100: 69185 vertices, 69581 faces
slice 110: 81721 vertices, 82186 faces
slice 120: 94258 vertices, 94744 faces
slice 130: 106940 vertices, 107424 faces
slice 140: 119323 vertices, 119802 faces
slice 150: 130245 vertices, 130693 faces
slice 160: 139506 vertices, 139910 faces
slice 170: 148193 vertices, 148571 faces
slice 180: 155921 vertices, 156276 faces
slice 190: 162320 vertices, 162619 faces
slice 200: 166604 vertices, 166824 faces
slice 210: 167600 vertices, 167698 faces
slice 220: 167600 vertices, 167698 faces
slice 230: 167600 vertices, 167698 faces
slice 240: 167600 vertices, 167698 faces
slice 250: 167600 vertices, 167698 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...
   167600 voxel in cpt #1: X=-98 [v=167600,e=503094,f=335396] located at (29.496479, -17.033968, 37.284439)
For the whole surface: X=-98 [v=167600,e=503094,f=335396]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 00:42:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 00:42:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

Waiting for PID 7355 of (7355 7358) to complete...
Waiting for PID 7358 of (7355 7358) 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 (7355 7358) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 00:42:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 00:42:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

Waiting for PID 7410 of (7410 7413) to complete...
Waiting for PID 7413 of (7410 7413) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 50.6 mm, total surface area = 87667 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 1.0 minutes

step 000: RMS=0.154 (target=0.015)   
step 005: RMS=0.116 (target=0.015)   
step 010: RMS=0.086 (target=0.015)   
step 015: RMS=0.073 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.056 (target=0.015)   
step 030: RMS=0.050 (target=0.015)   
step 035: RMS=0.046 (target=0.015)   
step 040: RMS=0.042 (target=0.015)   
step 045: RMS=0.041 (target=0.015)   
step 050: RMS=0.040 (target=0.015)   
step 055: RMS=0.040 (target=0.015)   
step 060: RMS=0.040 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    57.756219
mris_inflate stimesec    0.122981
mris_inflate ru_maxrss   242720
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35067
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11744
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2044
mris_inflate ru_nivcsw   4276

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 50.2 mm, total surface area = 87813 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 1.0 minutes

step 000: RMS=0.156 (target=0.015)   
step 005: RMS=0.118 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.077 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.053 (target=0.015)   
step 035: RMS=0.049 (target=0.015)   
step 040: RMS=0.046 (target=0.015)   
step 045: RMS=0.044 (target=0.015)   
step 050: RMS=0.043 (target=0.015)   
step 055: RMS=0.043 (target=0.015)   
step 060: RMS=0.042 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    58.333132
mris_inflate stimesec    0.131979
mris_inflate ru_maxrss   244476
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34993
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11792
mris_inflate ru_oublock  11808
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2122
mris_inflate ru_nivcsw   4337
PIDs (7410 7413) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 00:43:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 00:43:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

Waiting for PID 7490 of (7490 7494) to complete...
Waiting for PID 7494 of (7490 7494) 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 0.89 +- 0.55 (0.00-->6.49) (max @ vno 94180 --> 95461)
face area 0.02 +- 0.02 (-0.26-->0.76)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.264...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.976, avgs=0
005/300: dt: 0.9000, rms radial error=177.714, avgs=0
010/300: dt: 0.9000, rms radial error=177.153, avgs=0
015/300: dt: 0.9000, rms radial error=176.415, avgs=0
020/300: dt: 0.9000, rms radial error=175.578, avgs=0
025/300: dt: 0.9000, rms radial error=174.684, avgs=0
030/300: dt: 0.9000, rms radial error=173.757, avgs=0
035/300: dt: 0.9000, rms radial error=172.814, avgs=0
040/300: dt: 0.9000, rms radial error=171.862, avgs=0
045/300: dt: 0.9000, rms radial error=170.908, avgs=0
050/300: dt: 0.9000, rms radial error=169.955, avgs=0
055/300: dt: 0.9000, rms radial error=169.004, avgs=0
060/300: dt: 0.9000, rms radial error=168.056, avgs=0
065/300: dt: 0.9000, rms radial error=167.113, avgs=0
070/300: dt: 0.9000, rms radial error=166.174, avgs=0
075/300: dt: 0.9000, rms radial error=165.241, avgs=0
080/300: dt: 0.9000, rms radial error=164.312, avgs=0
085/300: dt: 0.9000, rms radial error=163.387, avgs=0
090/300: dt: 0.9000, rms radial error=162.468, avgs=0
095/300: dt: 0.9000, rms radial error=161.554, avgs=0
100/300: dt: 0.9000, rms radial error=160.644, avgs=0
105/300: dt: 0.9000, rms radial error=159.740, avgs=0
110/300: dt: 0.9000, rms radial error=158.840, avgs=0
115/300: dt: 0.9000, rms radial error=157.945, avgs=0
120/300: dt: 0.9000, rms radial error=157.055, avgs=0
125/300: dt: 0.9000, rms radial error=156.170, avgs=0
130/300: dt: 0.9000, rms radial error=155.290, avgs=0
135/300: dt: 0.9000, rms radial error=154.414, avgs=0
140/300: dt: 0.9000, rms radial error=153.544, avgs=0
145/300: dt: 0.9000, rms radial error=152.678, avgs=0
150/300: dt: 0.9000, rms radial error=151.817, avgs=0
155/300: dt: 0.9000, rms radial error=150.961, avgs=0
160/300: dt: 0.9000, rms radial error=150.110, avgs=0
165/300: dt: 0.9000, rms radial error=149.264, avgs=0
170/300: dt: 0.9000, rms radial error=148.424, avgs=0
175/300: dt: 0.9000, rms radial error=147.588, avgs=0
180/300: dt: 0.9000, rms radial error=146.757, avgs=0
185/300: dt: 0.9000, rms radial error=145.930, avgs=0
190/300: dt: 0.9000, rms radial error=145.108, avgs=0
195/300: dt: 0.9000, rms radial error=144.290, avgs=0
200/300: dt: 0.9000, rms radial error=143.477, avgs=0
205/300: dt: 0.9000, rms radial error=142.669, avgs=0
210/300: dt: 0.9000, rms radial error=141.865, avgs=0
215/300: dt: 0.9000, rms radial error=141.066, avgs=0
220/300: dt: 0.9000, rms radial error=140.271, avgs=0
225/300: dt: 0.9000, rms radial error=139.480, avgs=0
230/300: dt: 0.9000, rms radial error=138.694, avgs=0
235/300: dt: 0.9000, rms radial error=137.912, avgs=0
240/300: dt: 0.9000, rms radial error=137.134, avgs=0
245/300: dt: 0.9000, rms radial error=136.361, avgs=0
250/300: dt: 0.9000, rms radial error=135.592, avgs=0
255/300: dt: 0.9000, rms radial error=134.827, avgs=0
260/300: dt: 0.9000, rms radial error=134.067, avgs=0
265/300: dt: 0.9000, rms radial error=133.311, avgs=0
270/300: dt: 0.9000, rms radial error=132.559, avgs=0
275/300: dt: 0.9000, rms radial error=131.811, avgs=0
280/300: dt: 0.9000, rms radial error=131.068, avgs=0
285/300: dt: 0.9000, rms radial error=130.328, avgs=0
290/300: dt: 0.9000, rms radial error=129.593, avgs=0
295/300: dt: 0.9000, rms radial error=128.862, avgs=0
300/300: dt: 0.9000, rms radial error=128.135, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20415.69
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00017
epoch 2 (K=40.0), pass 1, starting sse = 3749.67
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
epoch 3 (K=160.0), pass 1, starting sse = 464.81
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/11 = 0.00497
epoch 4 (K=640.0), pass 1, starting sse = 36.00
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/13 = 0.00883
final distance error %30.19
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    344.483630
mris_sphere stimesec    0.252961
mris_sphere ru_maxrss   242924
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   35121
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11728
mris_sphere ru_oublock  11768
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    13072
mris_sphere ru_nivcsw   28023
FSRUNTIME@ mris_sphere  0.0958 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 0.90 +- 0.55 (0.00-->7.40) (max @ vno 65163 --> 66506)
face area 0.02 +- 0.02 (-0.20-->0.68)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.265...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=177.998, avgs=0
005/300: dt: 0.9000, rms radial error=177.737, avgs=0
010/300: dt: 0.9000, rms radial error=177.176, avgs=0
015/300: dt: 0.9000, rms radial error=176.440, avgs=0
020/300: dt: 0.9000, rms radial error=175.602, avgs=0
025/300: dt: 0.9000, rms radial error=174.706, avgs=0
030/300: dt: 0.9000, rms radial error=173.777, avgs=0
035/300: dt: 0.9000, rms radial error=172.831, avgs=0
040/300: dt: 0.9000, rms radial error=171.877, avgs=0
045/300: dt: 0.9000, rms radial error=170.922, avgs=0
050/300: dt: 0.9000, rms radial error=169.967, avgs=0
055/300: dt: 0.9000, rms radial error=169.015, avgs=0
060/300: dt: 0.9000, rms radial error=168.067, avgs=0
065/300: dt: 0.9000, rms radial error=167.124, avgs=0
070/300: dt: 0.9000, rms radial error=166.187, avgs=0
075/300: dt: 0.9000, rms radial error=165.254, avgs=0
080/300: dt: 0.9000, rms radial error=164.326, avgs=0
085/300: dt: 0.9000, rms radial error=163.403, avgs=0
090/300: dt: 0.9000, rms radial error=162.485, avgs=0
095/300: dt: 0.9000, rms radial error=161.572, avgs=0
100/300: dt: 0.9000, rms radial error=160.664, avgs=0
105/300: dt: 0.9000, rms radial error=159.761, avgs=0
110/300: dt: 0.9000, rms radial error=158.863, avgs=0
115/300: dt: 0.9000, rms radial error=157.970, avgs=0
120/300: dt: 0.9000, rms radial error=157.082, avgs=0
125/300: dt: 0.9000, rms radial error=156.199, avgs=0
130/300: dt: 0.9000, rms radial error=155.320, avgs=0
135/300: dt: 0.9000, rms radial error=154.447, avgs=0
140/300: dt: 0.9000, rms radial error=153.578, avgs=0
145/300: dt: 0.9000, rms radial error=152.714, avgs=0
150/300: dt: 0.9000, rms radial error=151.855, avgs=0
155/300: dt: 0.9000, rms radial error=151.000, avgs=0
160/300: dt: 0.9000, rms radial error=150.151, avgs=0
165/300: dt: 0.9000, rms radial error=149.306, avgs=0
170/300: dt: 0.9000, rms radial error=148.465, avgs=0
175/300: dt: 0.9000, rms radial error=147.630, avgs=0
180/300: dt: 0.9000, rms radial error=146.798, avgs=0
185/300: dt: 0.9000, rms radial error=145.972, avgs=0
190/300: dt: 0.9000, rms radial error=145.150, avgs=0
195/300: dt: 0.9000, rms radial error=144.332, avgs=0
200/300: dt: 0.9000, rms radial error=143.520, avgs=0
205/300: dt: 0.9000, rms radial error=142.711, avgs=0
210/300: dt: 0.9000, rms radial error=141.907, avgs=0
215/300: dt: 0.9000, rms radial error=141.108, avgs=0
220/300: dt: 0.9000, rms radial error=140.313, avgs=0
225/300: dt: 0.9000, rms radial error=139.522, avgs=0
230/300: dt: 0.9000, rms radial error=138.736, avgs=0
235/300: dt: 0.9000, rms radial error=137.954, avgs=0
240/300: dt: 0.9000, rms radial error=137.176, avgs=0
245/300: dt: 0.9000, rms radial error=136.403, avgs=0
250/300: dt: 0.9000, rms radial error=135.634, avgs=0
255/300: dt: 0.9000, rms radial error=134.869, avgs=0
260/300: dt: 0.9000, rms radial error=134.109, avgs=0
265/300: dt: 0.9000, rms radial error=133.353, avgs=0
270/300: dt: 0.9000, rms radial error=132.601, avgs=0
275/300: dt: 0.9000, rms radial error=131.853, avgs=0
280/300: dt: 0.9000, rms radial error=131.110, avgs=0
285/300: dt: 0.9000, rms radial error=130.370, avgs=0
290/300: dt: 0.9000, rms radial error=129.635, avgs=0
295/300: dt: 0.9000, rms radial error=128.904, avgs=0
300/300: dt: 0.9000, rms radial error=128.177, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20518.98
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 2 (K=40.0), pass 1, starting sse = 3752.92
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 456.45
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/11 = 0.00425
epoch 4 (K=640.0), pass 1, starting sse = 34.76
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/12 = 0.00618
final distance error %29.96
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
mris_sphere utimesec    347.007246
mris_sphere stimesec    0.247962
mris_sphere ru_maxrss   244676
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   35041
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11792
mris_sphere ru_oublock  11840
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    16984
mris_sphere ru_nivcsw   26879
FSRUNTIME@ mris_sphere  0.0963 hours 1 threads
PIDs (7490 7494) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 00:49:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 00:49:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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


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

#@# Fix Topology lh Sun Oct  8 00:49:30 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051140 lh 

#@# Fix Topology rh Sun Oct  8 00:49:30 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051140 rh 

Waiting for PID 7729 of (7729 7732) to complete...
Waiting for PID 7732 of (7729 7732) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051140 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=-42 (nv=166628, nf=333340, ne=500010, g=22)
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 11 iterations
marking ambiguous vertices...
6659 ambiguous faces found in tessellation
segmenting defects...
42 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 8 into 6
41 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.5773  (-4.7886)
      -vertex     loglikelihood: -6.1129  (-3.0564)
      -normal dot loglikelihood: -3.6399  (-3.6399)
      -quad curv  loglikelihood: -6.4922  (-3.2461)
      Total Loglikelihood : -25.8223

CORRECTING DEFECT 0 (vertices=22, convex hull=32, v0=10559)
After retessellation of defect 0 (v0=10559), euler #=-39 (162715,487007,324253) : difference with theory (-38) = 1 

CORRECTING DEFECT 1 (vertices=36, convex hull=42, v0=10674)
After retessellation of defect 1 (v0=10674), euler #=-38 (162722,487044,324284) : difference with theory (-37) = 1 

CORRECTING DEFECT 2 (vertices=8, convex hull=34, v0=20535)
After retessellation of defect 2 (v0=20535), euler #=-37 (162724,487060,324299) : difference with theory (-36) = 1 

CORRECTING DEFECT 3 (vertices=354, convex hull=261, v0=21449)
After retessellation of defect 3 (v0=21449), euler #=-36 (162855,487573,324682) : difference with theory (-35) = 1 

CORRECTING DEFECT 4 (vertices=34, convex hull=50, v0=38442)
After retessellation of defect 4 (v0=38442), euler #=-35 (162876,487656,324745) : difference with theory (-34) = 1 

CORRECTING DEFECT 5 (vertices=115, convex hull=57, v0=51560)
After retessellation of defect 5 (v0=51560), euler #=-34 (162904,487761,324823) : difference with theory (-33) = 1 

CORRECTING DEFECT 6 (vertices=367, convex hull=268, v0=58359)
After retessellation of defect 6 (v0=58359), euler #=-32 (163039,488302,325231) : difference with theory (-32) = 0 

CORRECTING DEFECT 7 (vertices=17, convex hull=24, v0=62019)
After retessellation of defect 7 (v0=62019), euler #=-31 (163047,488333,325255) : difference with theory (-31) = 0 

CORRECTING DEFECT 8 (vertices=127, convex hull=89, v0=65004)
After retessellation of defect 8 (v0=65004), euler #=-30 (163095,488521,325396) : difference with theory (-30) = 0 

CORRECTING DEFECT 9 (vertices=44, convex hull=92, v0=69681)
After retessellation of defect 9 (v0=69681), euler #=-29 (163110,488606,325467) : difference with theory (-29) = 0 

CORRECTING DEFECT 10 (vertices=18, convex hull=33, v0=70001)
After retessellation of defect 10 (v0=70001), euler #=-28 (163115,488628,325485) : difference with theory (-28) = 0 

CORRECTING DEFECT 11 (vertices=45, convex hull=34, v0=71803)
After retessellation of defect 11 (v0=71803), euler #=-27 (163124,488665,325514) : difference with theory (-27) = 0 

CORRECTING DEFECT 12 (vertices=23, convex hull=28, v0=72621)
After retessellation of defect 12 (v0=72621), euler #=-26 (163126,488679,325527) : difference with theory (-26) = 0 

CORRECTING DEFECT 13 (vertices=463, convex hull=302, v0=82693)
After retessellation of defect 13 (v0=82693), euler #=-25 (163167,488948,325756) : difference with theory (-25) = 0 

CORRECTING DEFECT 14 (vertices=31, convex hull=24, v0=84142)
After retessellation of defect 14 (v0=84142), euler #=-24 (163172,488971,325775) : difference with theory (-24) = 0 

CORRECTING DEFECT 15 (vertices=42, convex hull=34, v0=86111)
After retessellation of defect 15 (v0=86111), euler #=-23 (163180,489008,325805) : difference with theory (-23) = 0 

CORRECTING DEFECT 16 (vertices=158, convex hull=61, v0=91383)
After retessellation of defect 16 (v0=91383), euler #=-22 (163207,489115,325886) : difference with theory (-22) = 0 

CORRECTING DEFECT 17 (vertices=22, convex hull=21, v0=96973)
After retessellation of defect 17 (v0=96973), euler #=-21 (163212,489136,325903) : difference with theory (-21) = 0 

CORRECTING DEFECT 18 (vertices=12, convex hull=26, v0=100630)
After retessellation of defect 18 (v0=100630), euler #=-20 (163215,489151,325916) : difference with theory (-20) = 0 

CORRECTING DEFECT 19 (vertices=7, convex hull=25, v0=100822)
After retessellation of defect 19 (v0=100822), euler #=-19 (163215,489157,325923) : difference with theory (-19) = 0 

CORRECTING DEFECT 20 (vertices=190, convex hull=69, v0=102202)
After retessellation of defect 20 (v0=102202), euler #=-18 (163234,489242,325990) : difference with theory (-18) = 0 

CORRECTING DEFECT 21 (vertices=19, convex hull=26, v0=105498)
After retessellation of defect 21 (v0=105498), euler #=-17 (163237,489259,326005) : difference with theory (-17) = 0 

CORRECTING DEFECT 22 (vertices=17, convex hull=40, v0=106280)
After retessellation of defect 22 (v0=106280), euler #=-16 (163246,489299,326037) : difference with theory (-16) = 0 

CORRECTING DEFECT 23 (vertices=20, convex hull=39, v0=108466)
After retessellation of defect 23 (v0=108466), euler #=-15 (163253,489335,326067) : difference with theory (-15) = 0 

CORRECTING DEFECT 24 (vertices=36, convex hull=28, v0=108923)
After retessellation of defect 24 (v0=108923), euler #=-14 (163261,489370,326095) : difference with theory (-14) = 0 

CORRECTING DEFECT 25 (vertices=300, convex hull=91, v0=112382)
After retessellation of defect 25 (v0=112382), euler #=-13 (163310,489569,326246) : difference with theory (-13) = 0 

CORRECTING DEFECT 26 (vertices=835, convex hull=263, v0=113396)
After retessellation of defect 26 (v0=113396), euler #=-12 (163412,490019,326595) : difference with theory (-12) = 0 

CORRECTING DEFECT 27 (vertices=15, convex hull=30, v0=117473)
After retessellation of defect 27 (v0=117473), euler #=-11 (163414,490036,326611) : difference with theory (-11) = 0 

CORRECTING DEFECT 28 (vertices=24, convex hull=49, v0=118216)
After retessellation of defect 28 (v0=118216), euler #=-10 (163428,490097,326659) : difference with theory (-10) = 0 

CORRECTING DEFECT 29 (vertices=40, convex hull=85, v0=120671)
After retessellation of defect 29 (v0=120671), euler #=-9 (163453,490205,326743) : difference with theory (-9) = 0 

CORRECTING DEFECT 30 (vertices=6, convex hull=11, v0=122555)
After retessellation of defect 30 (v0=122555), euler #=-8 (163454,490210,326748) : difference with theory (-8) = 0 

CORRECTING DEFECT 31 (vertices=23, convex hull=34, v0=125882)
After retessellation of defect 31 (v0=125882), euler #=-7 (163459,490237,326771) : difference with theory (-7) = 0 

CORRECTING DEFECT 32 (vertices=96, convex hull=49, v0=126695)
After retessellation of defect 32 (v0=126695), euler #=-6 (163470,490287,326811) : difference with theory (-6) = 0 

CORRECTING DEFECT 33 (vertices=20, convex hull=27, v0=135260)
After retessellation of defect 33 (v0=135260), euler #=-5 (163478,490320,326837) : difference with theory (-5) = 0 

CORRECTING DEFECT 34 (vertices=19, convex hull=27, v0=139082)
After retessellation of defect 34 (v0=139082), euler #=-4 (163482,490339,326853) : difference with theory (-4) = 0 

CORRECTING DEFECT 35 (vertices=33, convex hull=52, v0=140827)
After retessellation of defect 35 (v0=140827), euler #=-3 (163491,490385,326891) : difference with theory (-3) = 0 

CORRECTING DEFECT 36 (vertices=64, convex hull=43, v0=147267)
After retessellation of defect 36 (v0=147267), euler #=-2 (163506,490449,326941) : difference with theory (-2) = 0 

CORRECTING DEFECT 37 (vertices=6, convex hull=32, v0=148119)
After retessellation of defect 37 (v0=148119), euler #=-1 (163507,490461,326953) : difference with theory (-1) = 0 

CORRECTING DEFECT 38 (vertices=18, convex hull=32, v0=155722)
After retessellation of defect 38 (v0=155722), euler #=0 (163510,490484,326974) : difference with theory (0) = 0 

CORRECTING DEFECT 39 (vertices=119, convex hull=36, v0=156985)
After retessellation of defect 39 (v0=156985), euler #=1 (163517,490524,327008) : difference with theory (1) = 0 

CORRECTING DEFECT 40 (vertices=66, convex hull=51, v0=163077)
After retessellation of defect 40 (v0=163077), euler #=2 (163524,490566,327044) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.08-->11.55) (max @ vno 57896 --> 66481)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.08-->11.55) (max @ vno 57896 --> 66481)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
134 mutations (33.9%), 261 crossovers (66.1%), 222 vertices were eliminated
building final representation...
3104 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=163524, nf=327044, ne=490566, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 35.8 minutes
0 defective edges
removing intersecting faces
000: 334 intersecting
001: 26 intersecting
mris_fix_topology utimesec    2149.979153
mris_fix_topology stimesec    0.222966
mris_fix_topology ru_maxrss   519636
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   56562
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  15648
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    543
mris_fix_topology ru_nivcsw   5721
FSRUNTIME@ mris_fix_topology lh  0.5972 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0051140 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=-98 (nv=167600, nf=335396, ne=503094, g=50)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 12 iterations
marking ambiguous vertices...
8382 ambiguous faces found in tessellation
segmenting defects...
49 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 14 into 12
      -merging segment 39 into 29
      -merging segment 42 into 41
      -merging segment 43 into 41
45 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3321  (-4.6661)
      -vertex     loglikelihood: -6.0609  (-3.0304)
      -normal dot loglikelihood: -3.5767  (-3.5767)
      -quad curv  loglikelihood: -6.4453  (-3.2227)
      Total Loglikelihood : -25.4151

CORRECTING DEFECT 0 (vertices=128, convex hull=165, v0=1394)
After retessellation of defect 0 (v0=1394), euler #=-40 (162593,486035,323402) : difference with theory (-42) = -2 

CORRECTING DEFECT 1 (vertices=523, convex hull=311, v0=12990)
After retessellation of defect 1 (v0=12990), euler #=-39 (162724,486570,323807) : difference with theory (-41) = -2 

CORRECTING DEFECT 2 (vertices=52, convex hull=23, v0=20135)
After retessellation of defect 2 (v0=20135), euler #=-38 (162728,486589,323823) : difference with theory (-40) = -2 

CORRECTING DEFECT 3 (vertices=31, convex hull=60, v0=21627)
After retessellation of defect 3 (v0=21627), euler #=-37 (162739,486646,323870) : difference with theory (-39) = -2 

CORRECTING DEFECT 4 (vertices=24, convex hull=55, v0=46177)
After retessellation of defect 4 (v0=46177), euler #=-36 (162751,486704,323917) : difference with theory (-38) = -2 

CORRECTING DEFECT 5 (vertices=24, convex hull=62, v0=52526)
After retessellation of defect 5 (v0=52526), euler #=-35 (162763,486766,323968) : difference with theory (-37) = -2 

CORRECTING DEFECT 6 (vertices=205, convex hull=56, v0=53682)
After retessellation of defect 6 (v0=53682), euler #=-34 (162772,486815,324009) : difference with theory (-36) = -2 

CORRECTING DEFECT 7 (vertices=487, convex hull=215, v0=56647)
After retessellation of defect 7 (v0=56647), euler #=-33 (162881,487250,324336) : difference with theory (-35) = -2 

CORRECTING DEFECT 8 (vertices=13, convex hull=23, v0=63714)
After retessellation of defect 8 (v0=63714), euler #=-32 (162887,487275,324356) : difference with theory (-34) = -2 

CORRECTING DEFECT 9 (vertices=188, convex hull=222, v0=63788)
After retessellation of defect 9 (v0=63788), euler #=-31 (162956,487589,324602) : difference with theory (-33) = -2 

CORRECTING DEFECT 10 (vertices=38, convex hull=88, v0=68575)
After retessellation of defect 10 (v0=68575), euler #=-30 (162981,487701,324690) : difference with theory (-32) = -2 

CORRECTING DEFECT 11 (vertices=5, convex hull=24, v0=73623)
After retessellation of defect 11 (v0=73623), euler #=-29 (162983,487713,324701) : difference with theory (-31) = -2 

CORRECTING DEFECT 12 (vertices=961, convex hull=497, v0=76153)
XL defect detected...
After retessellation of defect 12 (v0=76153), euler #=-31 (163197,488633,325405) : difference with theory (-30) = 1 

CORRECTING DEFECT 13 (vertices=6, convex hull=20, v0=80325)
After retessellation of defect 13 (v0=80325), euler #=-30 (163198,488644,325416) : difference with theory (-29) = 1 

CORRECTING DEFECT 14 (vertices=48, convex hull=33, v0=86314)
After retessellation of defect 14 (v0=86314), euler #=-29 (163207,488681,325445) : difference with theory (-28) = 1 

CORRECTING DEFECT 15 (vertices=14, convex hull=21, v0=87134)
After retessellation of defect 15 (v0=87134), euler #=-28 (163210,488697,325459) : difference with theory (-27) = 1 

CORRECTING DEFECT 16 (vertices=94, convex hull=59, v0=91154)
After retessellation of defect 16 (v0=91154), euler #=-27 (163222,488761,325512) : difference with theory (-26) = 1 

CORRECTING DEFECT 17 (vertices=5, convex hull=20, v0=91656)
After retessellation of defect 17 (v0=91656), euler #=-26 (163223,488769,325520) : difference with theory (-25) = 1 

CORRECTING DEFECT 18 (vertices=61, convex hull=66, v0=92924)
After retessellation of defect 18 (v0=92924), euler #=-25 (163249,488872,325598) : difference with theory (-24) = 1 

CORRECTING DEFECT 19 (vertices=26, convex hull=79, v0=94285)
After retessellation of defect 19 (v0=94285), euler #=-24 (163265,488950,325661) : difference with theory (-23) = 1 

CORRECTING DEFECT 20 (vertices=22, convex hull=55, v0=95710)
After retessellation of defect 20 (v0=95710), euler #=-23 (163275,488999,325701) : difference with theory (-22) = 1 

CORRECTING DEFECT 21 (vertices=47, convex hull=35, v0=96424)
After retessellation of defect 21 (v0=96424), euler #=-22 (163286,489042,325734) : difference with theory (-21) = 1 

CORRECTING DEFECT 22 (vertices=74, convex hull=34, v0=99248)
After retessellation of defect 22 (v0=99248), euler #=-21 (163294,489077,325762) : difference with theory (-20) = 1 

CORRECTING DEFECT 23 (vertices=32, convex hull=59, v0=100652)
After retessellation of defect 23 (v0=100652), euler #=-20 (163312,489157,325825) : difference with theory (-19) = 1 

CORRECTING DEFECT 24 (vertices=16, convex hull=30, v0=101335)
After retessellation of defect 24 (v0=101335), euler #=-19 (163313,489170,325838) : difference with theory (-18) = 1 

CORRECTING DEFECT 25 (vertices=24, convex hull=37, v0=102765)
After retessellation of defect 25 (v0=102765), euler #=-18 (163316,489194,325860) : difference with theory (-17) = 1 

CORRECTING DEFECT 26 (vertices=30, convex hull=56, v0=106306)
After retessellation of defect 26 (v0=106306), euler #=-17 (163325,489242,325900) : difference with theory (-16) = 1 

CORRECTING DEFECT 27 (vertices=25, convex hull=32, v0=106558)
After retessellation of defect 27 (v0=106558), euler #=-16 (163330,489268,325922) : difference with theory (-15) = 1 

CORRECTING DEFECT 28 (vertices=538, convex hull=382, v0=108932)
After retessellation of defect 28 (v0=108932), euler #=-15 (163570,490217,326632) : difference with theory (-14) = 1 

CORRECTING DEFECT 29 (vertices=82, convex hull=45, v0=109230)
After retessellation of defect 29 (v0=109230), euler #=-14 (163579,490264,326671) : difference with theory (-13) = 1 

CORRECTING DEFECT 30 (vertices=26, convex hull=70, v0=111617)
After retessellation of defect 30 (v0=111617), euler #=-13 (163588,490316,326715) : difference with theory (-12) = 1 

CORRECTING DEFECT 31 (vertices=41, convex hull=32, v0=112364)
After retessellation of defect 31 (v0=112364), euler #=-12 (163595,490347,326740) : difference with theory (-11) = 1 

CORRECTING DEFECT 32 (vertices=69, convex hull=113, v0=112533)
After retessellation of defect 32 (v0=112533), euler #=-11 (163616,490456,326829) : difference with theory (-10) = 1 

CORRECTING DEFECT 33 (vertices=34, convex hull=29, v0=112709)
After retessellation of defect 33 (v0=112709), euler #=-10 (163625,490493,326858) : difference with theory (-9) = 1 

CORRECTING DEFECT 34 (vertices=59, convex hull=70, v0=114246)
After retessellation of defect 34 (v0=114246), euler #=-9 (163663,490636,326964) : difference with theory (-8) = 1 

CORRECTING DEFECT 35 (vertices=24, convex hull=26, v0=115048)
After retessellation of defect 35 (v0=115048), euler #=-8 (163672,490668,326988) : difference with theory (-7) = 1 

CORRECTING DEFECT 36 (vertices=23, convex hull=41, v0=117637)
After retessellation of defect 36 (v0=117637), euler #=-7 (163681,490708,327020) : difference with theory (-6) = 1 

CORRECTING DEFECT 37 (vertices=10, convex hull=23, v0=119095)
After retessellation of defect 37 (v0=119095), euler #=-6 (163685,490727,327036) : difference with theory (-5) = 1 

CORRECTING DEFECT 38 (vertices=17, convex hull=25, v0=121239)
After retessellation of defect 38 (v0=121239), euler #=-5 (163689,490750,327056) : difference with theory (-4) = 1 

CORRECTING DEFECT 39 (vertices=832, convex hull=433, v0=121342)
L defect detected...
After retessellation of defect 39 (v0=121342), euler #=-3 (163903,491645,327739) : difference with theory (-3) = 0 

CORRECTING DEFECT 40 (vertices=11, convex hull=25, v0=131040)
After retessellation of defect 40 (v0=131040), euler #=-2 (163904,491653,327747) : difference with theory (-2) = 0 

CORRECTING DEFECT 41 (vertices=30, convex hull=26, v0=141223)
After retessellation of defect 41 (v0=141223), euler #=-1 (163908,491672,327763) : difference with theory (-1) = 0 

CORRECTING DEFECT 42 (vertices=37, convex hull=28, v0=149691)
After retessellation of defect 42 (v0=149691), euler #=0 (163909,491690,327781) : difference with theory (0) = 0 

CORRECTING DEFECT 43 (vertices=9, convex hull=27, v0=165872)
After retessellation of defect 43 (v0=165872), euler #=1 (163910,491703,327794) : difference with theory (1) = 0 

CORRECTING DEFECT 44 (vertices=20, convex hull=43, v0=167533)
After retessellation of defect 44 (v0=167533), euler #=2 (163911,491727,327818) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.03-->11.54) (max @ vno 117328 --> 126340)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.03-->11.54) (max @ vno 117328 --> 126340)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
159 mutations (36.2%), 280 crossovers (63.8%), 392 vertices were eliminated
building final representation...
3689 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=163911, nf=327818, ne=491727, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 37.8 minutes
0 defective edges
removing intersecting faces
000: 351 intersecting
001: 12 intersecting
mris_fix_topology utimesec    2266.597424
mris_fix_topology stimesec    0.205968
mris_fix_topology ru_maxrss   530100
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   60036
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  15728
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    418
mris_fix_topology ru_nivcsw   4120
FSRUNTIME@ mris_fix_topology rh  0.6295 hours 1 threads
PIDs (7729 7732) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 163524 - 490566 + 327044 = 2 --> 0 holes
      F =2V-4:          327044 = 327048-4 (0)
      2E=3F:            981132 = 981132 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 163911 - 491727 + 327818 = 2 --> 0 holes
      F =2V-4:          327818 = 327822-4 (0)
      2E=3F:            983454 = 983454 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 98 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 84 intersecting
001: 4 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 01:27:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051140 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 01:27:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051140 rh 

Waiting for PID 12485 of (12485 12488) to complete...
Waiting for PID 12488 of (12485 12488) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051140 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-6.0.0/0051140/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
33724 bright wm thresholded.
3436 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.orig...
computing class statistics...
border white:    306165 voxels (1.82%)
border gray      351388 voxels (2.09%)
WM (100.0): 99.7 +- 8.2 [70.0 --> 110.0]
GM (74.0) : 73.4 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.1 (was 70)
setting MAX_BORDER_WHITE to 113.2 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 51.2 (was 40)
setting MAX_GRAY to 96.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 41.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.01-->4.64) (max @ vno 57896 --> 66481)
face area 0.28 +- 0.12 (0.00-->4.67)
mean absolute distance = 0.66 +- 0.83
4827 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=105+-5.2,    GM=71+-6.1
mean inside = 95.4, mean outside = 76.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=81.9, 28 (28) missing vertices, mean dist 0.2 [0.5 (%38.6)->0.7 (%61.4))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.24 (0.05-->4.70) (max @ vno 57896 --> 66481)
face area 0.28 +- 0.13 (0.00-->4.44)
mean absolute distance = 0.34 +- 0.49
4639 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3589708.0, rms=9.606
001: dt: 0.5000, sse=2003777.0, rms=6.558 (31.731%)
002: dt: 0.5000, sse=1383033.9, rms=4.846 (26.110%)
003: dt: 0.5000, sse=1126262.9, rms=3.921 (19.095%)
004: dt: 0.5000, sse=1010406.9, rms=3.419 (12.802%)
005: dt: 0.5000, sse=970277.0, rms=3.222 (5.753%)
006: dt: 0.5000, sse=948457.2, rms=3.111 (3.438%)
rms = 3.10, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=946088.9, rms=3.095 (0.517%)
008: dt: 0.2500, sse=768225.3, rms=1.857 (40.016%)
009: dt: 0.2500, sse=735445.1, rms=1.537 (17.231%)
010: dt: 0.2500, sse=728468.4, rms=1.460 (4.989%)
rms = 1.42, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=725570.6, rms=1.416 (3.003%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=721395.8, rms=1.374 (2.959%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=85.7, 40 (3) missing vertices, mean dist -0.3 [0.4 (%80.3)->0.2 (%19.7))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.09-->5.05) (max @ vno 59004 --> 60226)
face area 0.34 +- 0.16 (0.00-->6.19)
mean absolute distance = 0.22 +- 0.32
4315 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1601278.5, rms=5.008
013: dt: 0.5000, sse=1094952.0, rms=2.999 (40.129%)
rms = 2.97, time step reduction 1 of 3 to 0.250...
014: dt: 0.5000, sse=1087807.2, rms=2.973 (0.862%)
015: dt: 0.2500, sse=898647.1, rms=1.635 (44.985%)
016: dt: 0.2500, sse=873903.1, rms=1.363 (16.685%)
017: dt: 0.2500, sse=866166.7, rms=1.273 (6.559%)
018: dt: 0.2500, sse=862102.0, rms=1.211 (4.905%)
rms = 1.20, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=862246.9, rms=1.197 (1.118%)
rms = 1.16, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=857752.3, rms=1.157 (3.365%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=87.9, 33 (2) missing vertices, mean dist -0.1 [0.2 (%72.8)->0.2 (%27.2))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.24 (0.01-->5.05) (max @ vno 59004 --> 60226)
face area 0.33 +- 0.15 (0.00-->6.25)
mean absolute distance = 0.18 +- 0.28
4373 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1068063.4, rms=3.013
021: dt: 0.5000, sse=982606.8, rms=2.451 (18.667%)
rms = 2.78, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=870426.1, rms=1.612 (34.226%)
023: dt: 0.2500, sse=840148.7, rms=1.216 (24.595%)
024: dt: 0.2500, sse=824231.6, rms=1.101 (9.410%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=825349.6, rms=1.089 (1.131%)
rms = 1.05, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=820506.6, rms=1.048 (3.719%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=88.5, 53 (2) missing vertices, mean dist -0.0 [0.2 (%56.3)->0.2 (%43.7))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=834365.7, rms=1.375
rms = 1.42, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=805300.7, rms=0.994 (27.687%)
028: dt: 0.2500, sse=797242.2, rms=0.795 (20.032%)
rms = 0.81, time step reduction 2 of 3 to 0.125...
rms = 0.79, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=794542.4, rms=0.792 (0.352%)
positioning took 0.5 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 7849 vertices
erasing segment 1 (vno[0] = 107880)
erasing segment 2 (vno[0] = 111090)
erasing segment 3 (vno[0] = 116892)
erasing segment 4 (vno[0] = 117839)
erasing segment 5 (vno[0] = 163293)
erasing segment 6 (vno[0] = 163333)
erasing segment 7 (vno[0] = 163343)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.area
vertex spacing 0.88 +- 0.24 (0.01-->5.08) (max @ vno 59004 --> 60226)
face area 0.33 +- 0.15 (0.00-->6.23)
refinement took 6.0 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0051140 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-6.0.0/0051140/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
33724 bright wm thresholded.
3436 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.orig...
computing class statistics...
border white:    306165 voxels (1.82%)
border gray      351388 voxels (2.09%)
WM (100.0): 99.7 +- 8.2 [70.0 --> 110.0]
GM (74.0) : 73.4 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.1 (was 70)
setting MAX_BORDER_WHITE to 113.2 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.2 (was 40)
setting MAX_GRAY to 96.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->4.70) (max @ vno 89314 --> 163100)
face area 0.28 +- 0.13 (0.00-->4.73)
mean absolute distance = 0.66 +- 0.86
4912 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=105+-5.2,    GM=72+-6.1
mean inside = 95.5, mean outside = 77.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=82.8, 60 (60) missing vertices, mean dist 0.2 [0.6 (%40.1)->0.7 (%59.9))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.24 (0.07-->5.02) (max @ vno 163138 --> 91801)
face area 0.28 +- 0.13 (0.00-->4.74)
mean absolute distance = 0.35 +- 0.51
4219 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3352315.0, rms=9.192
001: dt: 0.5000, sse=1884375.0, rms=6.237 (32.154%)
002: dt: 0.5000, sse=1317865.9, rms=4.602 (26.215%)
003: dt: 0.5000, sse=1092848.4, rms=3.758 (18.330%)
004: dt: 0.5000, sse=991201.5, rms=3.302 (12.134%)
005: dt: 0.5000, sse=957081.2, rms=3.131 (5.185%)
006: dt: 0.5000, sse=936043.0, rms=3.020 (3.556%)
rms = 3.00, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=933698.1, rms=3.002 (0.578%)
008: dt: 0.2500, sse=766587.3, rms=1.813 (39.619%)
009: dt: 0.2500, sse=735205.2, rms=1.507 (16.844%)
010: dt: 0.2500, sse=729437.2, rms=1.433 (4.932%)
rms = 1.40, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=727679.0, rms=1.399 (2.393%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=724127.5, rms=1.362 (2.615%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=86.4, 67 (12) missing vertices, mean dist -0.3 [0.4 (%80.0)->0.2 (%20.0))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.06-->5.29) (max @ vno 163138 --> 91801)
face area 0.34 +- 0.16 (0.00-->6.03)
mean absolute distance = 0.22 +- 0.34
4339 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1568180.8, rms=4.883
013: dt: 0.5000, sse=1090598.0, rms=2.934 (39.917%)
014: dt: 0.5000, sse=1065988.1, rms=2.835 (3.364%)
rms = 2.84, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=939975.2, rms=1.984 (30.017%)
016: dt: 0.2500, sse=882650.0, rms=1.429 (27.962%)
017: dt: 0.2500, sse=871651.6, rms=1.295 (9.424%)
018: dt: 0.2500, sse=866228.8, rms=1.242 (4.035%)
rms = 1.21, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=864370.0, rms=1.211 (2.489%)
rms = 1.18, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=864315.9, rms=1.180 (2.628%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=88.5, 105 (10) missing vertices, mean dist -0.1 [0.2 (%72.8)->0.2 (%27.2))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.24 (0.07-->5.55) (max @ vno 61331 --> 61340)
face area 0.33 +- 0.15 (0.00-->5.89)
mean absolute distance = 0.18 +- 0.27
4209 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1049602.8, rms=2.870
021: dt: 0.5000, sse=970521.8, rms=2.327 (18.910%)
rms = 2.63, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=869309.9, rms=1.572 (32.425%)
023: dt: 0.2500, sse=838454.6, rms=1.214 (22.797%)
024: dt: 0.2500, sse=829887.1, rms=1.117 (7.949%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=843459.4, rms=1.108 (0.840%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=825048.5, rms=1.074 (3.105%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=89.1, 121 (4) missing vertices, mean dist -0.0 [0.2 (%56.4)->0.2 (%43.6))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=838043.8, rms=1.380
rms = 1.38, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=841308.3, rms=1.379 (0.078%)
028: dt: 0.2500, sse=814802.4, rms=1.063 (22.970%)
029: dt: 0.2500, sse=799211.7, rms=0.884 (16.781%)
rms = 0.95, time step reduction 2 of 3 to 0.125...
rms = 0.86, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=798759.7, rms=0.857 (3.074%)
positioning took 0.6 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7372 vertices
erasing segment 1 (vno[0] = 108002)
erasing segment 2 (vno[0] = 109131)
erasing segment 3 (vno[0] = 111562)
erasing segment 4 (vno[0] = 113766)
erasing segment 5 (vno[0] = 113777)
erasing segment 6 (vno[0] = 113781)
erasing segment 7 (vno[0] = 114964)
erasing segment 8 (vno[0] = 114988)
erasing segment 9 (vno[0] = 116080)
erasing segment 10 (vno[0] = 117206)
erasing segment 11 (vno[0] = 163518)
erasing segment 12 (vno[0] = 163555)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.area
vertex spacing 0.88 +- 0.24 (0.02-->5.73) (max @ vno 61331 --> 61340)
face area 0.32 +- 0.15 (0.00-->5.85)
refinement took 6.1 minutes
PIDs (12485 12488) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 01:33:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 01:33:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

Waiting for PID 13092 of (13092 13095) to complete...
Waiting for PID 13095 of (13092 13095) 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 (13092 13095) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 01:33:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 01:33:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 13138 of (13138 13141) to complete...
Waiting for PID 13141 of (13138 13141) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 50.7 mm, total surface area = 97395 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.172 (target=0.015)   
step 005: RMS=0.121 (target=0.015)   
step 010: RMS=0.089 (target=0.015)   
step 015: RMS=0.073 (target=0.015)   
step 020: RMS=0.059 (target=0.015)   
step 025: RMS=0.051 (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 0.9 minutes
mris_inflate utimesec    55.694533
mris_inflate stimesec    0.131979
mris_inflate ru_maxrss   238468
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34643
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  12800
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    1981
mris_inflate ru_nivcsw   4155

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 50.5 mm, total surface area = 96854 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.172 (target=0.015)   
step 005: RMS=0.120 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.061 (target=0.015)   
step 025: RMS=0.050 (target=0.015)   
step 030: RMS=0.041 (target=0.015)   
step 035: RMS=0.035 (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=0.020 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    56.050479
mris_inflate stimesec    0.131979
mris_inflate ru_maxrss   239236
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34834
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11536
mris_inflate ru_oublock  12840
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2123
mris_inflate ru_nivcsw   4097
PIDs (13138 13141) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 01:34:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 01:34:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 13287 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13290 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13293 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13296 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13299 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13302 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13305 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13308 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13311 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13314 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13317 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...
Waiting for PID 13320 of (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = -0.019*4pi (-0.233) --> 1 handles
ICI = 166.5, FI = 2016.1, variation=30859.600
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
227 vertices thresholded to be in k1 ~ [-0.20 0.49], k2 ~ [-0.11 0.04]
total integrated curvature = 0.544*4pi (6.831) --> 0 handles
ICI = 1.5, FI = 10.9, variation=179.367
147 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
178 vertices thresholded to be in [-0.13 0.15]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = -3.451*4pi (-43.372) --> 4 handles
ICI = 179.8, FI = 2140.5, variation=32931.320
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
232 vertices thresholded to be in k1 ~ [-0.19 0.34], k2 ~ [-0.10 0.06]
total integrated curvature = 0.536*4pi (6.734) --> 0 handles
ICI = 1.5, FI = 10.5, variation=176.569
154 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
179 vertices thresholded to be in [-0.12 0.16]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.021
done.
PIDs (13287 13290 13293 13296 13299 13302 13305 13308 13311 13314 13317 13320) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 01:36:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0051140 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      [ 0051140/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                      [ 315 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.501712
WARN:    S explicit min:                          0.000000	vertex = 337

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 01:36:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0051140 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      [ 0051140/rh.smoothwm ]
                                Reading surface...                       [ ok ]
                                   Setting texture                     [ curv ]
                                Reading texture...                       [ ok ]
                                   Setting texture                     [ sulc ]
                                Reading texture...Gb_filter = 0
                       [ ok ]
      Calculating Discrete Principal Curvatures...
   Determining geometric order for vertex faces... [####################] [ ok ]
                      Determining KH curvatures... [####################] [ ok ]
                    Determining k1k2 curvatures... [####################] [ ok ]
                                   deltaViolations                      [ 287 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.260109
WARN:    S explicit min:                          0.000000	vertex = 780
#--------------------------------------------
#@# Sphere lh Sun Oct  8 01:36:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 01:36:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 13804 of (13804 13808) to complete...
Waiting for PID 13808 of (13804 13808) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0.248...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

singular matrix in quadratic form
--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.28
pass 1: epoch 2 of 3 starting distance error %21.23
unfolding complete - removing small folds...
starting distance error %21.20
removing remaining folds...
final distance error %21.21
MRISunfold() return, current seed 1234
-01: dt=0.0000, 126 negative triangles
171: dt=0.9900, 126 negative triangles
172: dt=0.9900, 56 negative triangles
173: dt=0.9900, 45 negative triangles
174: dt=0.9900, 28 negative triangles
175: dt=0.9900, 33 negative triangles
176: dt=0.9900, 25 negative triangles
177: dt=0.9900, 25 negative triangles
178: dt=0.9900, 26 negative triangles
179: dt=0.9900, 28 negative triangles
180: dt=0.9900, 19 negative triangles
181: dt=0.9900, 21 negative triangles
182: dt=0.9900, 19 negative triangles
183: dt=0.9900, 19 negative triangles
184: dt=0.9900, 14 negative triangles
185: dt=0.9900, 18 negative triangles
186: dt=0.9900, 14 negative triangles
187: dt=0.9900, 19 negative triangles
188: dt=0.9900, 9 negative triangles
189: dt=0.9900, 13 negative triangles
190: dt=0.9900, 8 negative triangles
191: dt=0.9900, 14 negative triangles
192: dt=0.9900, 7 negative triangles
193: dt=0.9900, 7 negative triangles
194: dt=0.9900, 5 negative triangles
195: dt=0.9900, 8 negative triangles
196: dt=0.9900, 4 negative triangles
197: dt=0.9900, 6 negative triangles
198: dt=0.9900, 6 negative triangles
199: dt=0.9900, 6 negative triangles
200: dt=0.9900, 4 negative triangles
201: dt=0.9900, 4 negative triangles
202: dt=0.9900, 5 negative triangles
203: dt=0.9900, 5 negative triangles
204: dt=0.9900, 4 negative triangles
205: dt=0.9900, 3 negative triangles
206: dt=0.9900, 2 negative triangles
207: dt=0.9900, 2 negative triangles
208: dt=0.9900, 2 negative triangles
209: dt=0.9900, 1 negative triangles
210: dt=0.9900, 4 negative triangles
211: dt=0.9900, 1 negative triangles
212: dt=0.9900, 1 negative triangles
213: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.85 hours
mris_sphere utimesec    3778.060647
mris_sphere stimesec    1.365792
mris_sphere ru_maxrss   336032
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   59167
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11552
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    85585
mris_sphere ru_nivcsw   181139
FSRUNTIME@ mris_sphere  0.8485 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0.249...
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 %44.17
pass 1: epoch 2 of 3 starting distance error %21.14
unfolding complete - removing small folds...
starting distance error %21.00
removing remaining folds...
final distance error %21.01
MRISunfold() return, current seed 1234
-01: dt=0.0000, 156 negative triangles
116: dt=0.9900, 156 negative triangles
117: dt=0.9900, 73 negative triangles
118: dt=0.9900, 40 negative triangles
119: dt=0.9900, 16 negative triangles
120: dt=0.9900, 22 negative triangles
121: dt=0.9900, 19 negative triangles
122: dt=0.9900, 13 negative triangles
123: dt=0.9900, 8 negative triangles
124: dt=0.9900, 13 negative triangles
125: dt=0.9900, 8 negative triangles
126: dt=0.9900, 9 negative triangles
127: dt=0.9900, 6 negative triangles
128: dt=0.9900, 4 negative triangles
129: dt=0.9900, 2 negative triangles
130: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.62 hours
mris_sphere utimesec    2240.955323
mris_sphere stimesec    1.127828
mris_sphere ru_maxrss   336968
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   59416
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11568
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    69636
mris_sphere ru_nivcsw   182343
FSRUNTIME@ mris_sphere  0.6228 hours 1 threads
PIDs (13804 13808) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 02:27:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 02:27:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 19473 of (19473 19476) to complete...
Waiting for PID 19476 of (19473 19476) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 5.508
curvature mean = 0.031, std = 0.820
curvature mean = 0.026, std = 0.836
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, 0.00, 16.00) sse = 439469.2, tmin=1.2340
  d=32.00 min @ (8.00, -8.00, -8.00) sse = 318413.2, tmin=2.4861
  d=16.00 min @ (-4.00, 4.00, 0.00) sse = 287593.8, tmin=3.7471
  d=8.00 min @ (0.00, -2.00, 2.00) sse = 270501.0, tmin=5.0245
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 268107.4, tmin=6.3177
  d=2.00 min @ (0.00, 0.50, -0.50) sse = 266987.0, tmin=7.6120
  d=1.00 min @ (0.25, 0.00, 0.00) sse = 266830.4, tmin=8.9018
  d=0.50 min @ (-0.12, -0.12, 0.00) sse = 266826.3, tmin=10.2002
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  10.20 min
curvature mean = -0.005, std = 0.822
curvature mean = 0.009, std = 0.932
curvature mean = -0.012, std = 0.827
curvature mean = 0.004, std = 0.970
curvature mean = -0.015, std = 0.827
curvature mean = 0.001, std = 0.987
2 Reading smoothwm
curvature mean = -0.027, std = 0.307
curvature mean = 0.037, std = 0.246
curvature mean = 0.070, std = 0.307
curvature mean = 0.034, std = 0.303
curvature mean = 0.037, std = 0.490
curvature mean = 0.034, std = 0.329
curvature mean = 0.021, std = 0.631
curvature mean = 0.033, std = 0.341
curvature mean = 0.007, std = 0.744
MRISregister() return, current seed 0
-01: dt=0.0000, 31 negative triangles
123: dt=0.9900, 31 negative triangles
expanding nbhd size to 1
124: dt=0.9900, 46 negative triangles
125: dt=0.9900, 27 negative triangles
126: dt=0.9900, 19 negative triangles
127: dt=0.9900, 22 negative triangles
128: dt=0.9900, 20 negative triangles
129: dt=0.9900, 18 negative triangles
130: dt=0.9900, 15 negative triangles
131: dt=0.9900, 16 negative triangles
132: dt=0.9900, 9 negative triangles
133: dt=0.9900, 10 negative triangles
134: dt=0.9900, 7 negative triangles
135: dt=0.9900, 2 negative triangles
136: dt=0.9900, 2 negative triangles
137: dt=0.9900, 1 negative triangles
138: dt=0.9900, 1 negative triangles
139: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.61 hours
mris_register utimesec    5846.602181
mris_register stimesec    6.099072
mris_register ru_maxrss   296228
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   41321
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  11600
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    431446
mris_register ru_nivcsw   263167
FSRUNTIME@ mris_register  1.6094 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 5.501
curvature mean = 0.032, std = 0.805
curvature mean = 0.028, std = 0.842
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 16.00) sse = 379298.2, tmin=1.2474
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 300866.4, tmin=2.5232
  d=16.00 min @ (-4.00, 0.00, -4.00) sse = 286769.1, tmin=3.8038
  d=8.00 min @ (2.00, 0.00, 2.00) sse = 271736.0, tmin=5.1098
  d=4.00 min @ (0.00, -1.00, -1.00) sse = 270399.7, tmin=6.4305
  d=2.00 min @ (0.00, 0.50, 0.50) sse = 269388.4, tmin=7.7561
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 269290.9, tmin=9.0742
  d=0.50 min @ (-0.12, 0.00, 0.00) sse = 269269.9, tmin=10.4060
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  10.41 min
curvature mean = 0.002, std = 0.809
curvature mean = 0.011, std = 0.938
curvature mean = -0.005, std = 0.813
curvature mean = 0.005, std = 0.974
curvature mean = -0.007, std = 0.811
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.027, std = 0.289
curvature mean = 0.034, std = 0.238
curvature mean = 0.073, std = 0.328
curvature mean = 0.028, std = 0.296
curvature mean = 0.036, std = 0.522
curvature mean = 0.028, std = 0.322
curvature mean = 0.020, std = 0.668
curvature mean = 0.028, std = 0.333
curvature mean = 0.007, std = 0.781
MRISregister() return, current seed 0
-01: dt=0.0000, 44 negative triangles
121: dt=0.9900, 44 negative triangles
expanding nbhd size to 1
122: dt=0.9900, 61 negative triangles
123: dt=0.9900, 46 negative triangles
124: dt=0.9900, 35 negative triangles
125: dt=0.9900, 36 negative triangles
126: dt=0.9900, 34 negative triangles
127: dt=0.9900, 34 negative triangles
128: dt=0.9900, 33 negative triangles
129: dt=0.9900, 27 negative triangles
130: dt=0.9900, 23 negative triangles
131: dt=0.9900, 23 negative triangles
132: dt=0.9900, 25 negative triangles
133: dt=0.9900, 20 negative triangles
134: dt=0.9900, 20 negative triangles
135: dt=0.9900, 14 negative triangles
136: dt=0.9900, 11 negative triangles
137: dt=0.9900, 10 negative triangles
138: dt=0.9900, 8 negative triangles
139: dt=0.9900, 8 negative triangles
140: dt=0.9900, 3 negative triangles
141: dt=0.9900, 3 negative triangles
142: dt=0.9900, 1 negative triangles
143: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.58 hours
mris_register utimesec    5692.726574
mris_register stimesec    6.115070
mris_register ru_maxrss   295492
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   41781
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  11536
mris_register ru_oublock  11632
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    422699
mris_register ru_nivcsw   262308
FSRUNTIME@ mris_register  1.5828 hours 1 threads
PIDs (19473 19476) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 04:03:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 04:03:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

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

Waiting for PID 25213 of (25213 25216) to complete...
Waiting for PID 25216 of (25213 25216) 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 (25213 25216) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 04:03:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 04:04:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 25259 of (25259 25262) to complete...
Waiting for PID 25262 of (25259 25262) 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 (25259 25262) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 04:04:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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 04:04:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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 25309 of (25309 25312) to complete...
Waiting for PID 25312 of (25309 25312) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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...
1779 labels changed using aseg
relabeling using gibbs priors...
000:   3609 changed, 163524 examined...
001:    871 changed, 15237 examined...
002:    241 changed, 4772 examined...
003:     81 changed, 1410 examined...
004:     27 changed, 486 examined...
005:     12 changed, 147 examined...
006:      6 changed, 66 examined...
007:      4 changed, 42 examined...
008:      1 changed, 28 examined...
009:      2 changed, 6 examined...
010:      2 changed, 11 examined...
011:      1 changed, 12 examined...
012:      1 changed, 9 examined...
013:      0 changed, 5 examined...
269 labels changed using aseg
000: 160 total segments, 108 labels (486 vertices) changed
001: 51 total segments, 7 labels (20 vertices) changed
002: 43 total segments, 1 labels (4 vertices) changed
003: 42 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2814 vertices marked for relabeling...
2814 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 18 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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...
1706 labels changed using aseg
relabeling using gibbs priors...
000:   3253 changed, 163911 examined...
001:    748 changed, 13841 examined...
002:    180 changed, 4154 examined...
003:     68 changed, 1097 examined...
004:     15 changed, 412 examined...
005:      6 changed, 104 examined...
006:      2 changed, 44 examined...
007:      3 changed, 12 examined...
008:      0 changed, 18 examined...
159 labels changed using aseg
000: 107 total segments, 69 labels (276 vertices) changed
001: 39 total segments, 2 labels (2 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2431 vertices marked for relabeling...
2431 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 17 seconds.
PIDs (25309 25312) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 04:04:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051140 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 04:04:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051140 rh 

Waiting for PID 25356 of (25356 25359) to complete...
Waiting for PID 25359 of (25356 25359) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051140 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-6.0.0/0051140/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
33724 bright wm thresholded.
3436 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.orig...
computing class statistics...
border white:    306165 voxels (1.82%)
border gray      351388 voxels (2.09%)
WM (100.0): 99.7 +- 8.2 [70.0 --> 110.0]
GM (74.0) : 73.4 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.1 (was 70)
setting MAX_BORDER_WHITE to 113.2 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 51.2 (was 40)
setting MAX_GRAY to 96.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 41.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105+-5.2,    GM=71+-6.1
mean inside = 95.4, mean outside = 76.9
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.24 (0.01-->5.08) (max @ vno 59004 --> 60226)
face area 0.32 +- 0.15 (0.00-->6.21)
mean absolute distance = 0.64 +- 0.81
3550 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
deleting segment 1 with 15 points - only 0.00% unknown
deleting segment 4 with 13 points - only 0.00% unknown
deleting segment 5 with 54 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 48 points - only 0.00% unknown
deleting segment 8 with 81 points - only 1.23% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
mean border=81.7, 72 (72) missing vertices, mean dist 0.4 [0.9 (%11.4)->0.6 (%88.6))]
%68 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.11-->5.04) (max @ vno 59004 --> 60226)
face area 0.32 +- 0.15 (0.00-->6.26)
mean absolute distance = 0.35 +- 0.48
4116 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2929961.2, rms=8.287
001: dt: 0.5000, sse=1456337.1, rms=4.682 (43.498%)
002: dt: 0.5000, sse=1093658.8, rms=3.257 (30.436%)
003: dt: 0.5000, sse=1050612.9, rms=3.051 (6.333%)
004: dt: 0.5000, sse=1005270.4, rms=2.822 (7.520%)
rms = 2.99, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=884656.5, rms=1.967 (30.292%)
006: dt: 0.2500, sse=842307.5, rms=1.560 (20.688%)
007: dt: 0.2500, sse=833583.2, rms=1.430 (8.313%)
rms = 1.40, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=828466.1, rms=1.395 (2.455%)
rms = 1.35, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=824908.6, rms=1.353 (3.014%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 15 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 41 points - only 0.00% unknown
deleting segment 4 with 37 points - only 0.00% unknown
deleting segment 5 with 81 points - only 1.23% unknown
deleting segment 6 with 5 points - only 0.00% unknown
mean border=85.7, 46 (13) missing vertices, mean dist -0.3 [0.4 (%81.2)->0.2 (%18.8))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.06-->5.19) (max @ vno 59004 --> 60226)
face area 0.35 +- 0.16 (0.00-->7.28)
mean absolute distance = 0.22 +- 0.33
4561 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1623856.4, rms=5.050
010: dt: 0.5000, sse=1104001.2, rms=2.976 (41.063%)
011: dt: 0.5000, sse=1084525.1, rms=2.891 (2.875%)
rms = 2.93, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=944247.6, rms=1.950 (32.526%)
013: dt: 0.2500, sse=884691.3, rms=1.342 (31.183%)
014: dt: 0.2500, sse=871376.9, rms=1.198 (10.717%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=871303.6, rms=1.153 (3.769%)
rms = 1.11, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=865332.0, rms=1.113 (3.515%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 8 points - only 0.00% unknown
deleting segment 4 with 44 points - only 0.00% unknown
deleting segment 5 with 36 points - only 0.00% unknown
deleting segment 6 with 95 points - only 1.05% unknown
deleting segment 7 with 9 points - only 0.00% unknown
mean border=87.9, 36 (5) missing vertices, mean dist -0.1 [0.2 (%73.2)->0.2 (%26.8))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.25 (0.09-->5.19) (max @ vno 59004 --> 60226)
face area 0.33 +- 0.16 (0.00-->7.14)
mean absolute distance = 0.18 +- 0.27
4430 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1075597.1, rms=3.025
017: dt: 0.5000, sse=985986.9, rms=2.441 (19.287%)
rms = 2.75, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=875317.9, rms=1.604 (34.292%)
019: dt: 0.2500, sse=838629.3, rms=1.197 (25.383%)
020: dt: 0.2500, sse=830561.5, rms=1.080 (9.792%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=828019.2, rms=1.066 (1.232%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=827135.4, rms=1.028 (3.644%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 points - only 0.00% unknown
deleting segment 1 with 17 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 13 points - only 0.00% unknown
deleting segment 4 with 44 points - only 0.00% unknown
deleting segment 5 with 38 points - only 0.00% unknown
deleting segment 6 with 93 points - only 1.08% unknown
deleting segment 7 with 9 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
mean border=88.5, 45 (3) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=841102.6, rms=1.370
rms = 1.42, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=810196.7, rms=0.985 (28.099%)
024: dt: 0.2500, sse=803298.2, rms=0.780 (20.768%)
rms = 0.79, time step reduction 2 of 3 to 0.125...
rms = 0.78, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=800741.3, rms=0.777 (0.358%)
positioning took 0.5 minutes
generating cortex label...
6 non-cortical segments detected
only using segment with 7903 vertices
erasing segment 1 (vno[0] = 116892)
erasing segment 2 (vno[0] = 117839)
erasing segment 3 (vno[0] = 163293)
erasing segment 4 (vno[0] = 163333)
erasing segment 5 (vno[0] = 163343)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.area
vertex spacing 0.88 +- 0.25 (0.01-->5.19) (max @ vno 59004 --> 60226)
face area 0.33 +- 0.16 (0.00-->7.07)
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 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 24 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=59.4, 75 (75) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.9 (%100.0))]
%15 local maxima, %45 large gradients and %36 min vals, 198 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=28379296.0, rms=29.640
001: dt: 0.0500, sse=24808076.0, rms=27.657 (6.690%)
002: dt: 0.0500, sse=22317788.0, rms=26.185 (5.321%)
003: dt: 0.0500, sse=20448346.0, rms=25.024 (4.437%)
004: dt: 0.0500, sse=18961676.0, rms=24.060 (3.852%)
005: dt: 0.0500, sse=17731854.0, rms=23.232 (3.440%)
006: dt: 0.0500, sse=16684643.0, rms=22.503 (3.137%)
007: dt: 0.0500, sse=15771241.0, rms=21.847 (2.913%)
008: dt: 0.0500, sse=14960745.0, rms=21.249 (2.741%)
009: dt: 0.0500, sse=14233816.0, rms=20.697 (2.597%)
010: dt: 0.0500, sse=13575984.0, rms=20.185 (2.476%)
positioning took 1.1 minutes
mean border=59.2, 54 (33) missing vertices, mean dist 1.5 [0.1 (%0.0)->2.3 (%100.0))]
%16 local maxima, %45 large gradients and %35 min vals, 182 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=14344346.0, rms=20.783
011: dt: 0.0500, sse=13741331.0, rms=20.316 (2.248%)
012: dt: 0.0500, sse=13187544.0, rms=19.878 (2.159%)
013: dt: 0.0500, sse=12677062.0, rms=19.464 (2.079%)
014: dt: 0.0500, sse=12205385.0, rms=19.075 (2.003%)
015: dt: 0.0500, sse=11768540.0, rms=18.706 (1.931%)
016: dt: 0.0500, sse=11363137.0, rms=18.358 (1.863%)
017: dt: 0.0500, sse=10986160.0, rms=18.027 (1.799%)
018: dt: 0.0500, sse=10635276.0, rms=17.715 (1.736%)
019: dt: 0.0500, sse=10307800.0, rms=17.417 (1.678%)
020: dt: 0.0500, sse=10001863.0, rms=17.135 (1.622%)
positioning took 1.1 minutes
mean border=59.2, 70 (23) missing vertices, mean dist 1.3 [0.1 (%0.3)->2.0 (%99.7))]
%16 local maxima, %45 large gradients and %35 min vals, 155 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=10092944.0, rms=17.226
021: dt: 0.0500, sse=9802424.0, rms=16.955 (1.574%)
022: dt: 0.0500, sse=9529950.0, rms=16.696 (1.524%)
023: dt: 0.0500, sse=9273367.0, rms=16.449 (1.480%)
024: dt: 0.0500, sse=9031826.0, rms=16.213 (1.436%)
025: dt: 0.0500, sse=8803367.0, rms=15.986 (1.398%)
026: dt: 0.0500, sse=8586691.0, rms=15.768 (1.364%)
027: dt: 0.0500, sse=8379847.5, rms=15.557 (1.339%)
028: dt: 0.0500, sse=8180901.0, rms=15.351 (1.323%)
029: dt: 0.0500, sse=7988963.5, rms=15.150 (1.312%)
030: dt: 0.0500, sse=7803070.5, rms=14.952 (1.305%)
positioning took 1.1 minutes
mean border=59.1, 110 (18) missing vertices, mean dist 1.1 [0.1 (%4.0)->1.7 (%96.0))]
%16 local maxima, %45 large gradients and %35 min vals, 140 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=7883328.0, rms=15.039
031: dt: 0.5000, sse=6537642.0, rms=13.531 (10.024%)
032: dt: 0.5000, sse=5506088.5, rms=12.245 (9.503%)
033: dt: 0.5000, sse=4662402.5, rms=11.085 (9.480%)
034: dt: 0.5000, sse=3968235.2, rms=10.024 (9.569%)
035: dt: 0.5000, sse=3377964.8, rms=9.026 (9.955%)
036: dt: 0.5000, sse=2863714.5, rms=8.054 (10.765%)
037: dt: 0.5000, sse=2407584.2, rms=7.086 (12.023%)
038: dt: 0.5000, sse=2054666.4, rms=6.233 (12.038%)
039: dt: 0.5000, sse=1808116.9, rms=5.564 (10.739%)
040: dt: 0.5000, sse=1663975.2, rms=5.129 (7.814%)
041: dt: 0.5000, sse=1576609.9, rms=4.850 (5.433%)
042: dt: 0.5000, sse=1537469.2, rms=4.717 (2.759%)
043: dt: 0.5000, sse=1505458.0, rms=4.609 (2.285%)
rms = 4.57, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1495268.2, rms=4.570 (0.841%)
045: dt: 0.2500, sse=1337212.0, rms=3.918 (14.273%)
046: dt: 0.2500, sse=1296867.9, rms=3.747 (4.350%)
rms = 3.73, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1293738.9, rms=3.730 (0.474%)
048: dt: 0.1250, sse=1269408.1, rms=3.617 (3.020%)
rms = 3.60, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1265496.9, rms=3.599 (0.490%)
positioning took 2.8 minutes
mean border=57.7, 2644 (6) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.4 (%55.9))]
%32 local maxima, %32 large gradients and %31 min vals, 129 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=1620102.0, rms=4.192
050: dt: 0.5000, sse=1557429.0, rms=3.953 (5.697%)
rms = 3.95, time step reduction 1 of 3 to 0.250...
051: dt: 0.5000, sse=1545833.8, rms=3.949 (0.100%)
052: dt: 0.2500, sse=1381938.5, rms=3.134 (20.646%)
053: dt: 0.2500, sse=1343398.4, rms=2.931 (6.477%)
rms = 2.89, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1337337.4, rms=2.893 (1.274%)
055: dt: 0.1250, sse=1307080.9, rms=2.710 (6.343%)
rms = 2.68, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1301745.4, rms=2.679 (1.146%)
positioning took 1.3 minutes
mean border=56.8, 2806 (3) missing vertices, mean dist 0.1 [0.1 (%43.8)->0.3 (%56.2))]
%46 local maxima, %18 large gradients and %30 min vals, 138 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=1373686.4, rms=3.094
rms = 3.55, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1324593.8, rms=2.818 (8.916%)
058: dt: 0.2500, sse=1311059.9, rms=2.740 (2.787%)
rms = 2.74, time step reduction 2 of 3 to 0.125...
rms = 2.71, time step reduction 3 of 3 to 0.062...
059: dt: 0.1250, sse=1305883.1, rms=2.707 (1.203%)
positioning took 0.8 minutes
mean border=56.2, 5294 (2) missing vertices, mean dist 0.0 [0.1 (%47.5)->0.2 (%52.5))]
%50 local maxima, %14 large gradients and %29 min vals, 129 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-6.0.0/0051140/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1327933.1, rms=2.838
rms = 3.22, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1305289.5, rms=2.700 (4.837%)
061: dt: 0.2500, sse=1292175.9, rms=2.636 (2.398%)
rms = 2.63, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1289101.4, rms=2.626 (0.370%)
063: dt: 0.1250, sse=1271587.4, rms=2.513 (4.314%)
rms = 2.49, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1266688.9, rms=2.485 (1.087%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.area.pial
vertex spacing 1.00 +- 0.43 (0.04-->6.56) (max @ vno 104229 --> 103182)
face area 0.39 +- 0.31 (0.00-->9.18)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 163524 vertices processed
25000 of 163524 vertices processed
50000 of 163524 vertices processed
75000 of 163524 vertices processed
100000 of 163524 vertices processed
125000 of 163524 vertices processed
150000 of 163524 vertices processed
0 of 163524 vertices processed
25000 of 163524 vertices processed
50000 of 163524 vertices processed
75000 of 163524 vertices processed
100000 of 163524 vertices processed
125000 of 163524 vertices processed
150000 of 163524 vertices processed
thickness calculation complete, 454:843 truncations.
38800 vertices at 0 distance
116721 vertices at 1 distance
98844 vertices at 2 distance
40694 vertices at 3 distance
13115 vertices at 4 distance
3962 vertices at 5 distance
1327 vertices at 6 distance
405 vertices at 7 distance
131 vertices at 8 distance
83 vertices at 9 distance
47 vertices at 10 distance
41 vertices at 11 distance
32 vertices at 12 distance
43 vertices at 13 distance
25 vertices at 14 distance
22 vertices at 15 distance
30 vertices at 16 distance
24 vertices at 17 distance
15 vertices at 18 distance
8 vertices at 19 distance
11 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.thickness
positioning took 17.3 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0051140 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-6.0.0/0051140/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
33724 bright wm thresholded.
3436 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.orig...
computing class statistics...
border white:    306165 voxels (1.82%)
border gray      351388 voxels (2.09%)
WM (100.0): 99.7 +- 8.2 [70.0 --> 110.0]
GM (74.0) : 73.4 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 62.1 (was 70)
setting MAX_BORDER_WHITE to 113.2 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 52.2 (was 40)
setting MAX_GRAY to 96.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 62.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105+-5.2,    GM=72+-6.1
mean inside = 95.5, mean outside = 77.6
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.24 (0.02-->5.73) (max @ vno 61331 --> 61340)
face area 0.32 +- 0.15 (0.00-->5.81)
mean absolute distance = 0.64 +- 0.83
3514 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
deleting segment 3 with 39 points - only 0.00% unknown
deleting segment 4 with 39 points - only 0.00% unknown
deleting segment 5 with 14 points - only 0.00% unknown
deleting segment 6 with 62 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 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
deleting segment 10 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
mean border=82.5, 92 (92) missing vertices, mean dist 0.4 [1.0 (%11.1)->0.6 (%88.9))]
%70 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.08-->6.05) (max @ vno 62493 --> 62505)
face area 0.32 +- 0.15 (0.00-->5.43)
mean absolute distance = 0.35 +- 0.49
4032 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2817000.2, rms=8.047
001: dt: 0.5000, sse=1433665.4, rms=4.584 (43.033%)
002: dt: 0.5000, sse=1088066.2, rms=3.180 (30.635%)
003: dt: 0.5000, sse=1029857.2, rms=2.933 (7.757%)
004: dt: 0.5000, sse=988382.1, rms=2.719 (7.287%)
rms = 2.86, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=878579.5, rms=1.919 (29.441%)
006: dt: 0.2500, sse=839488.3, rms=1.532 (20.146%)
007: dt: 0.2500, sse=829243.0, rms=1.416 (7.600%)
rms = 1.38, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=842557.2, rms=1.384 (2.253%)
rms = 1.35, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=823995.0, rms=1.347 (2.634%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 21 points - only 0.00% unknown
deleting segment 4 with 28 points - only 0.00% unknown
deleting segment 5 with 20 points - only 10.00% unknown
deleting segment 6 with 28 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
mean border=86.4, 68 (22) missing vertices, mean dist -0.3 [0.4 (%81.2)->0.2 (%18.8))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.08-->6.29) (max @ vno 62506 --> 62505)
face area 0.35 +- 0.16 (0.00-->6.08)
mean absolute distance = 0.22 +- 0.34
4302 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1587099.9, rms=4.926
010: dt: 0.5000, sse=1101131.9, rms=2.900 (41.119%)
011: dt: 0.5000, sse=1059424.6, rms=2.746 (5.307%)
rms = 2.77, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=936693.1, rms=1.887 (31.285%)
013: dt: 0.2500, sse=880417.4, rms=1.319 (30.114%)
014: dt: 0.2500, sse=869302.4, rms=1.185 (10.113%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=866989.9, rms=1.153 (2.779%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=864329.8, rms=1.118 (2.992%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 1 with 35 points - only 0.00% unknown
deleting segment 2 with 31 points - only 0.00% unknown
deleting segment 3 with 29 points - only 6.90% unknown
deleting segment 4 with 32 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 10 points - only 0.00% unknown
mean border=88.5, 67 (9) missing vertices, mean dist -0.1 [0.2 (%73.2)->0.2 (%26.8))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.25 (0.10-->6.46) (max @ vno 62506 --> 62505)
face area 0.33 +- 0.16 (0.00-->5.89)
mean absolute distance = 0.18 +- 0.27
4206 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1049815.2, rms=2.875
017: dt: 0.5000, sse=968932.2, rms=2.308 (19.724%)
rms = 2.59, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=871124.4, rms=1.547 (32.971%)
019: dt: 0.2500, sse=838225.3, rms=1.174 (24.072%)
020: dt: 0.2500, sse=832543.1, rms=1.071 (8.778%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=827777.6, rms=1.064 (0.688%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=825350.5, rms=1.030 (3.222%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 1 with 40 points - only 0.00% unknown
deleting segment 2 with 40 points - only 0.00% unknown
deleting segment 3 with 20 points - only 10.00% unknown
deleting segment 4 with 37 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
mean border=89.1, 73 (7) missing vertices, mean dist -0.0 [0.2 (%56.6)->0.2 (%43.4))]
%93 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=837794.6, rms=1.347
rms = 1.36, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=811081.2, rms=0.978 (27.408%)
024: dt: 0.2500, sse=807752.9, rms=0.790 (19.230%)
rms = 0.81, time step reduction 2 of 3 to 0.125...
rms = 0.79, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=799811.9, rms=0.786 (0.475%)
positioning took 0.5 minutes
generating cortex label...
15 non-cortical segments detected
only using segment with 7366 vertices
erasing segment 1 (vno[0] = 107999)
erasing segment 2 (vno[0] = 110369)
erasing segment 3 (vno[0] = 111562)
erasing segment 4 (vno[0] = 113766)
erasing segment 5 (vno[0] = 113777)
erasing segment 6 (vno[0] = 113781)
erasing segment 7 (vno[0] = 113936)
erasing segment 8 (vno[0] = 114965)
erasing segment 9 (vno[0] = 116080)
erasing segment 10 (vno[0] = 117206)
erasing segment 11 (vno[0] = 137731)
erasing segment 12 (vno[0] = 163518)
erasing segment 13 (vno[0] = 163555)
erasing segment 14 (vno[0] = 163680)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.area
vertex spacing 0.88 +- 0.25 (0.02-->6.51) (max @ vno 62505 --> 62506)
face area 0.33 +- 0.16 (0.00-->5.83)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=60.5, 94 (94) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.9 (%100.0))]
%14 local maxima, %42 large gradients and %40 min vals, 189 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=27733738.0, rms=29.223
001: dt: 0.0500, sse=24270588.0, rms=27.283 (6.641%)
002: dt: 0.0500, sse=21856506.0, rms=25.844 (5.275%)
003: dt: 0.0500, sse=20044572.0, rms=24.708 (4.393%)
004: dt: 0.0500, sse=18605370.0, rms=23.768 (3.806%)
005: dt: 0.0500, sse=17415978.0, rms=22.962 (3.392%)
006: dt: 0.0500, sse=16402537.0, rms=22.252 (3.093%)
007: dt: 0.0500, sse=15519379.0, rms=21.614 (2.867%)
008: dt: 0.0500, sse=14736119.0, rms=21.032 (2.693%)
009: dt: 0.0500, sse=14033006.0, rms=20.495 (2.551%)
010: dt: 0.0500, sse=13395601.0, rms=19.996 (2.434%)
positioning took 1.1 minutes
mean border=60.3, 70 (43) missing vertices, mean dist 1.4 [0.1 (%0.0)->2.4 (%100.0))]
%15 local maxima, %42 large gradients and %39 min vals, 209 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=14220471.0, rms=20.640
011: dt: 0.0500, sse=13634081.0, rms=20.185 (2.205%)
012: dt: 0.0500, sse=13095407.0, rms=19.758 (2.117%)
013: dt: 0.0500, sse=12598723.0, rms=19.355 (2.037%)
014: dt: 0.0500, sse=12138932.0, rms=18.975 (1.965%)
015: dt: 0.0500, sse=11712307.0, rms=18.615 (1.896%)
016: dt: 0.0500, sse=11315986.0, rms=18.274 (1.830%)
017: dt: 0.0500, sse=10947184.0, rms=17.951 (1.767%)
018: dt: 0.0500, sse=10603656.0, rms=17.645 (1.706%)
019: dt: 0.0500, sse=10283417.0, rms=17.355 (1.646%)
020: dt: 0.0500, sse=9984518.0, rms=17.079 (1.588%)
positioning took 1.1 minutes
mean border=60.1, 66 (30) missing vertices, mean dist 1.2 [0.1 (%0.4)->2.1 (%99.6))]
%16 local maxima, %42 large gradients and %38 min vals, 178 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=10123481.0, rms=17.214
021: dt: 0.0500, sse=9838336.0, rms=16.949 (1.540%)
022: dt: 0.0500, sse=9571230.0, rms=16.697 (1.488%)
023: dt: 0.0500, sse=9319710.0, rms=16.455 (1.444%)
024: dt: 0.0500, sse=9083210.0, rms=16.225 (1.398%)
025: dt: 0.0500, sse=8860116.0, rms=16.005 (1.356%)
026: dt: 0.0500, sse=8649099.0, rms=15.794 (1.319%)
027: dt: 0.0500, sse=8447963.0, rms=15.590 (1.291%)
028: dt: 0.0500, sse=8255104.5, rms=15.392 (1.271%)
029: dt: 0.0500, sse=8069786.5, rms=15.199 (1.254%)
030: dt: 0.0500, sse=7891031.0, rms=15.011 (1.240%)
positioning took 1.1 minutes
mean border=60.1, 86 (23) missing vertices, mean dist 1.0 [0.1 (%4.1)->1.8 (%95.9))]
%16 local maxima, %42 large gradients and %38 min vals, 167 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=7979184.0, rms=15.105
031: dt: 0.5000, sse=6680033.0, rms=13.666 (9.525%)
032: dt: 0.5000, sse=5667910.0, rms=12.425 (9.086%)
033: dt: 0.5000, sse=4821977.5, rms=11.283 (9.185%)
034: dt: 0.5000, sse=4108697.5, rms=10.218 (9.441%)
035: dt: 0.5000, sse=3492612.5, rms=9.201 (9.949%)
036: dt: 0.5000, sse=2941946.2, rms=8.185 (11.052%)
037: dt: 0.5000, sse=2464906.0, rms=7.193 (12.119%)
038: dt: 0.5000, sse=2097870.0, rms=6.322 (12.108%)
039: dt: 0.5000, sse=1848686.5, rms=5.658 (10.505%)
040: dt: 0.5000, sse=1697486.2, rms=5.210 (7.909%)
041: dt: 0.5000, sse=1603157.9, rms=4.913 (5.695%)
042: dt: 0.5000, sse=1550109.5, rms=4.734 (3.659%)
043: dt: 0.5000, sse=1513199.2, rms=4.609 (2.642%)
044: dt: 0.5000, sse=1489542.1, rms=4.523 (1.859%)
rms = 4.49, time step reduction 1 of 3 to 0.250...
045: dt: 0.5000, sse=1479233.0, rms=4.488 (0.772%)
046: dt: 0.2500, sse=1333443.5, rms=3.872 (13.729%)
047: dt: 0.2500, sse=1291335.8, rms=3.694 (4.585%)
rms = 3.70, time step reduction 2 of 3 to 0.125...
048: dt: 0.1250, sse=1280683.9, rms=3.644 (1.356%)
049: dt: 0.1250, sse=1267182.8, rms=3.578 (1.818%)
rms = 3.57, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1266383.9, rms=3.572 (0.156%)
positioning took 3.1 minutes
mean border=58.9, 3011 (8) missing vertices, mean dist 0.1 [0.2 (%45.2)->0.4 (%54.8))]
%31 local maxima, %30 large gradients and %34 min vals, 93 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=1610495.6, rms=4.142
051: dt: 0.5000, sse=1563447.6, rms=3.968 (4.217%)
052: dt: 0.5000, sse=1536502.0, rms=3.899 (1.734%)
rms = 4.05, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1393444.2, rms=3.203 (17.844%)
054: dt: 0.2500, sse=1355323.5, rms=2.984 (6.842%)
rms = 2.96, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1351902.9, rms=2.964 (0.665%)
056: dt: 0.1250, sse=1322725.9, rms=2.790 (5.871%)
rms = 2.76, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1318189.8, rms=2.765 (0.910%)
positioning took 1.4 minutes
mean border=58.1, 3088 (7) missing vertices, mean dist 0.1 [0.1 (%44.0)->0.3 (%56.0))]
%43 local maxima, %18 large gradients and %33 min vals, 105 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=1383209.9, rms=3.126
rms = 3.58, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1338402.6, rms=2.880 (7.876%)
059: dt: 0.2500, sse=1327906.1, rms=2.823 (1.957%)
rms = 2.83, time step reduction 2 of 3 to 0.125...
rms = 2.79, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1323005.1, rms=2.793 (1.074%)
positioning took 0.8 minutes
mean border=57.6, 5765 (7) missing vertices, mean dist 0.0 [0.1 (%46.8)->0.3 (%53.2))]
%46 local maxima, %14 large gradients and %32 min vals, 105 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-6.0.0/0051140/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1343488.6, rms=2.909
rms = 3.28, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1321285.1, rms=2.780 (4.438%)
062: dt: 0.2500, sse=1308553.1, rms=2.724 (2.022%)
rms = 2.72, time step reduction 2 of 3 to 0.125...
rms = 2.70, time step reduction 3 of 3 to 0.062...
063: dt: 0.1250, sse=1304269.6, rms=2.696 (1.021%)
positioning took 0.8 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.area.pial
vertex spacing 1.00 +- 0.43 (0.05-->6.88) (max @ vno 103454 --> 103435)
face area 0.39 +- 0.30 (0.00-->5.81)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 163911 vertices processed
25000 of 163911 vertices processed
50000 of 163911 vertices processed
75000 of 163911 vertices processed
100000 of 163911 vertices processed
125000 of 163911 vertices processed
150000 of 163911 vertices processed
0 of 163911 vertices processed
25000 of 163911 vertices processed
50000 of 163911 vertices processed
75000 of 163911 vertices processed
100000 of 163911 vertices processed
125000 of 163911 vertices processed
150000 of 163911 vertices processed
thickness calculation complete, 186:1090 truncations.
37810 vertices at 0 distance
115715 vertices at 1 distance
99079 vertices at 2 distance
42419 vertices at 3 distance
14206 vertices at 4 distance
4338 vertices at 5 distance
1390 vertices at 6 distance
442 vertices at 7 distance
138 vertices at 8 distance
75 vertices at 9 distance
62 vertices at 10 distance
43 vertices at 11 distance
43 vertices at 12 distance
39 vertices at 13 distance
19 vertices at 14 distance
20 vertices at 15 distance
28 vertices at 16 distance
37 vertices at 17 distance
14 vertices at 18 distance
8 vertices at 19 distance
11 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.thickness
positioning took 17.7 minutes
PIDs (25356 25359) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 04:22:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label
Total face volume 308447
Total vertex volume 304436 (mask=0)
#@# 0051140 lh 304436
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 04:22:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label
Total face volume 310341
Total vertex volume 306508 (mask=0)
#@# 0051140 rh 306508
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 04:22:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 

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 = 128
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/ribbon.mgz
mris_volmask took 19.37 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 04:41:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 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 0051140 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 04:41:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 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 0051140 rh pial 

Waiting for PID 27513 of (27513 27516 27519 27522) to complete...
Waiting for PID 27516 of (27513 27516 27519 27522) to complete...
Waiting for PID 27519 of (27513 27516 27519 27522) to complete...
Waiting for PID 27522 of (27513 27516 27519 27522) 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 0051140 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 308447
Total vertex volume 304436 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1600   1131   2897  2.627 0.390     0.109     0.017       13     1.1  bankssts
 1304    827   2601  2.730 0.783     0.126     0.020       19     1.0  caudalanteriorcingulate
 4097   2706   7846  2.642 0.472     0.109     0.019       37     3.1  caudalmiddlefrontal
 2491   1556   3035  1.947 0.508     0.144     0.039       34     3.9  cuneus
  918    583   2616  3.469 0.750     0.110     0.026        8     0.9  entorhinal
 6384   4336  14243  2.833 0.615     0.129     0.028       99     7.8  fusiform
 8015   5316  15624  2.583 0.473     0.121     0.023      106     7.3  inferiorparietal
 5649   3751  12192  2.857 0.687     0.117     0.026       75     6.0  inferiortemporal
 2078   1340   3747  2.441 1.007     0.120     0.032       31     2.0  isthmuscingulate
 9627   5863  14630  2.241 0.578     0.126     0.028      114    10.7  lateraloccipital
 5231   3443  10674  2.814 0.567     0.123     0.031       70     6.2  lateralorbitofrontal
 4900   3207   6934  2.011 0.625     0.137     0.033       63     6.4  lingual
 2742   1900   5991  2.750 0.641     0.118     0.023       40     2.4  medialorbitofrontal
 5446   3541  13639  3.093 0.581     0.110     0.020       70     4.5  middletemporal
 1219    770   2741  3.139 0.703     0.102     0.021       12     0.8  parahippocampal
 2263   1320   3857  2.718 0.576     0.103     0.021       19     1.8  paracentral
 2324   1535   4833  2.767 0.488     0.112     0.019       26     1.7  parsopercularis
 1262    794   3371  3.091 0.572     0.121     0.021       18     1.0  parsorbitalis
 2013   1332   4469  2.820 0.529     0.126     0.021       25     1.9  parstriangularis
 2165   1461   2251  1.795 0.457     0.125     0.024       19     2.3  pericalcarine
 7585   4552  11446  2.258 0.663     0.106     0.022       70     6.8  postcentral
 1805   1268   3378  2.421 0.764     0.124     0.021       27     1.3  posteriorcingulate
 9451   5866  17767  2.764 0.500     0.104     0.020       82     7.6  precentral
 6516   4332  12165  2.627 0.507     0.126     0.023       84     6.1  precuneus
 1672   1096   3617  2.970 0.450     0.123     0.026       28     1.7  rostralanteriorcingulate
10139   6670  20238  2.642 0.504     0.128     0.027      145    10.8  rostralmiddlefrontal
13482   8984  30302  3.002 0.574     0.122     0.026      157    13.4  superiorfrontal
 9311   5888  15987  2.420 0.518     0.116     0.024      103     9.4  superiorparietal
 7673   5058  17870  3.107 0.642     0.110     0.022       94     6.2  superiortemporal
 8949   6031  18174  2.717 0.491     0.122     0.025      110     8.7  supramarginal
  393    247    985  2.953 0.449     0.174     0.047       11     0.8  frontalpole
  707    488   2802  3.961 0.698     0.141     0.040       12     1.0  temporalpole
  825    428   1251  2.577 0.552     0.119     0.061       19     2.5  transversetemporal
 5214   3350  10239  3.031 0.844     0.119     0.034       63     6.8  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 0051140 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 308447
Total vertex volume 304436 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1600   1053   2897  2.627 0.390     0.114     0.028       20     1.9  bankssts
 1304   1038   2601  2.730 0.783     0.137     0.032       35     1.6  caudalanteriorcingulate
 4097   3089   7846  2.642 0.472     0.127     0.024       63     4.3  caudalmiddlefrontal
 2491   1681   3035  1.947 0.508     0.130     0.035       42     3.9  cuneus
  918    947   2616  3.469 0.750     0.185     0.049       21     2.1  entorhinal
 6384   5665  14243  2.833 0.615     0.151     0.034       94    10.1  fusiform
 8015   6638  15624  2.583 0.473     0.142     0.028      104     9.7  inferiorparietal
 5649   4707  12192  2.857 0.687     0.140     0.033       72     8.3  inferiortemporal
 2078   1690   3747  2.441 1.007     0.151     0.043       48     3.7  isthmuscingulate
 9627   7175  14630  2.241 0.578     0.129     0.027      123    11.9  lateraloccipital
 5231   4083  10674  2.814 0.567     0.136     0.033       82     7.3  lateralorbitofrontal
 4900   3796   6934  2.011 0.625     0.140     0.034       84     7.8  lingual
 2742   2384   5991  2.750 0.641     0.142     0.033       37     4.0  medialorbitofrontal
 5446   5113  13639  3.093 0.581     0.142     0.029       51     7.0  middletemporal
 1219   1033   2741  3.139 0.703     0.148     0.038       16     2.1  parahippocampal
 2263   1524   3857  2.718 0.576     0.103     0.021       21     2.0  paracentral
 2324   1897   4833  2.767 0.488     0.143     0.030       29     3.3  parsopercularis
 1262   1302   3371  3.091 0.572     0.154     0.029       12     1.6  parsorbitalis
 2013   1785   4469  2.820 0.529     0.147     0.029       26     2.6  parstriangularis
 2165   1145   2251  1.795 0.457     0.105     0.030      118     3.1  pericalcarine
 7585   5564  11446  2.258 0.663     0.119     0.023       70     7.6  postcentral
 1805   1485   3378  2.421 0.764     0.142     0.032       36     2.5  posteriorcingulate
 9451   6925  17767  2.764 0.500     0.114     0.022       93     9.2  precentral
 6516   4792  12165  2.627 0.507     0.131     0.031      129     8.8  precuneus
 1672   1371   3617  2.970 0.450     0.158     0.044       42     3.2  rostralanteriorcingulate
10139   8378  20238  2.642 0.504     0.147     0.031      143    14.5  rostralmiddlefrontal
13482  10785  30302  3.002 0.574     0.135     0.030      181    17.7  superiorfrontal
 9311   7136  15987  2.420 0.518     0.127     0.027      103    11.2  superiorparietal
 7673   6253  17870  3.107 0.642     0.136     0.031       96    10.3  superiortemporal
 8949   7147  18174  2.717 0.491     0.138     0.030      120    12.3  supramarginal
  393    402    985  2.953 0.449     0.178     0.029        5     0.6  frontalpole
  707    945   2802  3.961 0.698     0.199     0.040        8     1.4  temporalpole
  825    562   1251  2.577 0.552     0.127     0.038       11     1.2  transversetemporal
 5214   3467  10239  3.031 0.844     0.142     0.043       99    10.0  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051140 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 310341
Total vertex volume 306508 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1466   1003   3210  3.105 0.502     0.104     0.017       11     1.1  bankssts
 1555    988   3164  2.838 0.729     0.124     0.021       24     1.3  caudalanteriorcingulate
 3487   2339   7006  2.788 0.448     0.113     0.022       39     3.0  caudalmiddlefrontal
 2973   1785   4074  2.068 0.521     0.137     0.035       39     4.3  cuneus
  716    484   2266  3.321 0.889     0.137     0.056        8     1.6  entorhinal
 5304   3530  11201  2.803 0.635     0.117     0.029       65     6.0  fusiform
11005   7239  21253  2.565 0.530     0.120     0.022      145     9.5  inferiorparietal
 5606   3665  12481  2.961 0.689     0.120     0.031       77     6.8  inferiortemporal
 1801   1166   3239  2.375 0.993     0.124     0.029       30     1.6  isthmuscingulate
 9875   6099  15470  2.237 0.574     0.133     0.030      135    11.9  lateraloccipital
 5460   3516  10440  2.750 0.621     0.127     0.037       77     7.7  lateralorbitofrontal
 5573   3492   8698  2.294 0.674     0.135     0.035       82     7.8  lingual
 3024   2005   6009  2.665 0.628     0.117     0.031       45     3.5  medialorbitofrontal
 6112   4103  16363  3.290 0.653     0.120     0.025       74     6.0  middletemporal
 1231    785   2644  2.976 0.597     0.093     0.015        9     0.6  parahippocampal
 2684   1537   4429  2.708 0.509     0.098     0.025       26     2.8  paracentral
 2232   1463   4996  3.018 0.407     0.112     0.020       23     1.8  parsopercularis
 1491    934   3697  3.144 0.525     0.129     0.027       20     1.7  parsorbitalis
 2891   1896   5753  2.787 0.445     0.113     0.020       34     2.0  parstriangularis
 2560   1646   2785  1.919 0.530     0.104     0.024       16     2.5  pericalcarine
 8299   5135  12993  2.292 0.684     0.109     0.024       83     7.9  postcentral
 2106   1452   4063  2.517 0.882     0.128     0.024       33     1.9  posteriorcingulate
 8992   5362  16398  2.811 0.483     0.102     0.022       74     8.1  precentral
 6651   4393  11876  2.576 0.496     0.124     0.025       86     6.6  precuneus
 1413    948   3582  3.015 0.640     0.136     0.029       29     1.5  rostralanteriorcingulate
11109   7419  22068  2.637 0.523     0.124     0.026      151    11.3  rostralmiddlefrontal
13113   8624  28795  2.949 0.515     0.120     0.026      153    12.8  superiorfrontal
 8605   5500  14239  2.341 0.467     0.119     0.023       98     7.6  superiorparietal
 6341   4205  15768  3.378 0.587     0.108     0.021       58     5.2  superiortemporal
 6302   4187  13202  2.833 0.488     0.113     0.020       70     5.1  supramarginal
  457    277   1210  2.976 0.610     0.171     0.060        9     1.4  frontalpole
  723    488   2932  3.927 0.773     0.140     0.036       10     1.1  temporalpole
  612    344   1165  2.725 0.587     0.095     0.035        8     0.8  transversetemporal
 4251   2809   9017  3.134 0.715     0.124     0.038       57     6.4  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0051140 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 310341
Total vertex volume 306508 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1466   1038   3210  3.105 0.502     0.124     0.033       19     2.2  bankssts
 1555   1259   3164  2.838 0.729     0.161     0.040       35     2.6  caudalanteriorcingulate
 3487   2665   7006  2.788 0.448     0.119     0.026       43     3.7  caudalmiddlefrontal
 2973   2174   4074  2.068 0.521     0.135     0.036       43     4.8  cuneus
  716    840   2266  3.321 0.889     0.201     0.046       13     1.6  entorhinal
 5304   4323  11201  2.803 0.635     0.136     0.031       66     7.5  fusiform
11005   8876  21253  2.565 0.530     0.140     0.029      134    14.0  inferiorparietal
 5606   4595  12481  2.961 0.689     0.146     0.033      101     8.5  inferiortemporal
 1801   1476   3239  2.375 0.993     0.146     0.035       37     2.7  isthmuscingulate
 9875   7639  15470  2.237 0.574     0.137     0.031      124    13.4  lateraloccipital
 5460   4004  10440  2.750 0.621     0.136     0.037       76     9.0  lateralorbitofrontal
 5573   4138   8698  2.294 0.674     0.135     0.035       80     8.8  lingual
 3024   2485   6009  2.665 0.628     0.142     0.035       42     4.5  medialorbitofrontal
 6112   5760  16363  3.290 0.653     0.147     0.033       87     9.2  middletemporal
 1231    998   2644  2.976 0.597     0.129     0.026       17     1.5  parahippocampal
 2684   1726   4429  2.708 0.509     0.105     0.031       25     2.7  paracentral
 2232   1834   4996  3.018 0.407     0.142     0.030       35     3.2  parsopercularis
 1491   1391   3697  3.144 0.525     0.148     0.028       16     1.9  parsorbitalis
 2891   2253   5753  2.787 0.445     0.135     0.024       38     3.2  parstriangularis
 2560   1419   2785  1.919 0.530     0.101     0.027       29     2.8  pericalcarine
 8299   6143  12993  2.292 0.684     0.118     0.024       75     8.5  postcentral
 2106   1712   4063  2.517 0.882     0.136     0.030       31     2.8  posteriorcingulate
 8992   6203  16398  2.811 0.483     0.106     0.022       84     8.6  precentral
 6651   4757  11876  2.576 0.496     0.127     0.030       86     8.7  precuneus
 1413   1410   3582  3.015 0.640     0.177     0.042       37     2.7  rostralanteriorcingulate
11109   9030  22068  2.637 0.523     0.140     0.029      140    14.6  rostralmiddlefrontal
13113  10553  28795  2.949 0.515     0.133     0.029      161    16.9  superiorfrontal
 8605   6529  14239  2.341 0.467     0.127     0.026      100     9.5  superiorparietal
 6341   5084  15768  3.378 0.587     0.133     0.031      101     8.6  superiortemporal
 6302   4955  13202  2.833 0.488     0.131     0.028       79     8.0  supramarginal
  457    529   1210  2.976 0.610     0.196     0.039        5     1.0  frontalpole
  723    956   2932  3.927 0.773     0.204     0.043       10     1.5  temporalpole
  612    504   1165  2.725 0.587     0.144     0.053       14     1.7  transversetemporal
 4251   2811   9017  3.134 0.715     0.143     0.045       92     8.7  insula
PIDs (27513 27516 27519 27522) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 04:43:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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 04:43:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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 27721 of (27721 27724) to complete...
Waiting for PID 27724 of (27721 27724) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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...
26 labels changed using aseg
relabeling using gibbs priors...
000:  10639 changed, 163524 examined...
001:   2537 changed, 41102 examined...
002:    775 changed, 13122 examined...
003:    330 changed, 4490 examined...
004:    147 changed, 1921 examined...
005:     66 changed, 813 examined...
006:     38 changed, 378 examined...
007:     13 changed, 198 examined...
008:      7 changed, 86 examined...
009:      6 changed, 35 examined...
010:      5 changed, 31 examined...
011:      2 changed, 25 examined...
012:      3 changed, 18 examined...
013:      2 changed, 18 examined...
014:      1 changed, 13 examined...
015:      0 changed, 6 examined...
1 labels changed using aseg
000: 295 total segments, 211 labels (2885 vertices) changed
001: 97 total segments, 13 labels (39 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 54 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1803 vertices marked for relabeling...
1803 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 22 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 rh ../surf/rh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot

setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading atlas from /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs...
reading color table from GCSA file....
average std = 1.4   using min determinant for regularization = 0.020
0 singular and 719 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
0 labels changed using aseg
relabeling using gibbs priors...
000:  10638 changed, 163911 examined...
001:   2499 changed, 41826 examined...
002:    738 changed, 13062 examined...
003:    319 changed, 4124 examined...
004:    156 changed, 1820 examined...
005:     78 changed, 848 examined...
006:     49 changed, 460 examined...
007:     18 changed, 269 examined...
008:     16 changed, 107 examined...
009:     12 changed, 83 examined...
010:      2 changed, 54 examined...
011:      0 changed, 15 examined...
0 labels changed using aseg
000: 297 total segments, 207 labels (3500 vertices) changed
001: 106 total segments, 18 labels (221 vertices) changed
002: 88 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 38 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1770 vertices marked for relabeling...
1770 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 22 seconds.
PIDs (27721 27724) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 04:43:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 04:43:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 rh white 

Waiting for PID 27772 of (27772 27775) to complete...
Waiting for PID 27775 of (27772 27775) 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 0051140 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 308447
Total vertex volume 304436 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1227    816   2511  2.756 0.458     0.134     0.031       19     1.5  G&S_frontomargin
 2232   1426   4146  2.555 0.717     0.137     0.028       28     2.6  G&S_occipital_inf
 1950   1018   3030  2.524 0.672     0.112     0.034       22     3.0  G&S_paracentral
 1840   1246   4409  3.045 0.489     0.128     0.023       24     1.7  G&S_subcentral
  879    567   2287  2.976 0.603     0.158     0.034       18     1.3  G&S_transv_frontopol
 2766   1858   5779  2.944 0.428     0.119     0.024       35     2.7  G&S_cingul-Ant
 1556   1044   3073  3.004 0.476     0.103     0.016       12     1.0  G&S_cingul-Mid-Ant
 1645   1141   3276  2.695 0.493     0.113     0.017       17     1.1  G&S_cingul-Mid-Post
  701    469   2073  3.211 0.690     0.136     0.032       11     0.8  G_cingul-Post-dorsal
  385    229    827  2.745 0.964     0.133     0.050        9     0.4  G_cingul-Post-ventral
 2332   1441   2958  1.869 0.552     0.141     0.035       33     3.4  G_cuneus
 1451    929   3951  3.029 0.487     0.119     0.021       22     1.3  G_front_inf-Opercular
  490    297   1469  3.268 0.380     0.143     0.026        9     0.5  G_front_inf-Orbital
 1034    648   2750  2.994 0.487     0.131     0.029       17     1.2  G_front_inf-Triangul
 5720   3623  13844  2.822 0.529     0.135     0.030      105     6.7  G_front_middle
 9332   6047  23108  3.135 0.575     0.129     0.030      126    10.6  G_front_sup
  902    577   2229  3.396 0.633     0.123     0.033       13     0.9  G_Ins_lg&S_cent_ins
  992    589   3029  3.587 0.523     0.130     0.030       20     1.2  G_insular_short
 2969   1840   6383  2.573 0.541     0.134     0.029       53     3.2  G_occipital_middle
 1732   1019   2758  2.325 0.561     0.132     0.033       23     2.2  G_occipital_sup
 2829   1891   7004  2.911 0.557     0.124     0.024       48     2.7  G_oc-temp_lat-fusifor
 3628   2306   5390  1.934 0.642     0.147     0.040       53     5.8  G_oc-temp_med-Lingual
 1794   1112   4977  3.368 0.731     0.113     0.031       21     2.3  G_oc-temp_med-Parahip
 3100   1943   7803  2.893 0.649     0.127     0.037       58     4.4  G_orbital
 3439   2254   8328  2.780 0.499     0.136     0.029       64     3.9  G_pariet_inf-Angular
 3959   2647   9375  2.909 0.464     0.131     0.033       68     4.6  G_pariet_inf-Supramar
 3555   2218   7606  2.656 0.513     0.136     0.030       60     4.5  G_parietal_sup
 3095   1583   4680  2.313 0.511     0.099     0.023       30     3.0  G_postcentral
 3773   2092   7604  2.888 0.421     0.103     0.021       39     3.1  G_precentral
 3057   1978   7175  2.808 0.501     0.139     0.029       55     3.3  G_precuneus
 1219    846   3491  2.997 0.605     0.150     0.038       32     1.8  G_rectus
 1139    666   1834  2.485 1.215     0.102     0.043       12     1.6  G_subcallosal
  607    297   1051  2.629 0.561     0.108     0.062       14     1.8  G_temp_sup-G_T_transv
 2642   1697   8064  3.422 0.633     0.139     0.029       51     3.1  G_temp_sup-Lateral
  827    570   2464  3.914 0.645     0.100     0.026        6     0.8  G_temp_sup-Plan_polar
 1991   1335   3974  2.687 0.445     0.107     0.019       22     1.4  G_temp_sup-Plan_tempo
 2846   1836   7382  2.991 0.769     0.129     0.033       54     3.7  G_temporal_inf
 3005   1861   8865  3.233 0.557     0.125     0.027       57     3.1  G_temporal_middle
  320    226    507  2.458 0.509     0.103     0.009        2     0.1  Lat_Fis-ant-Horizont
  271    213    495  2.581 0.312     0.097     0.016        1     0.1  Lat_Fis-ant-Vertical
 1358    888   1873  2.630 0.510     0.113     0.025       12     1.6  Lat_Fis-post
 2703   1457   3490  2.066 0.490     0.123     0.033       35     3.4  Pole_occipital
 1729   1168   5862  3.401 0.823     0.156     0.050       36     3.9  Pole_temporal
 2785   1850   3372  2.134 0.667     0.126     0.024       27     2.8  S_calcarine
 3802   2567   4755  2.083 0.571     0.101     0.018       22     2.7  S_central
 1061    737   1633  2.373 0.384     0.096     0.012        6     0.5  S_cingul-Marginalis
  836    554   1358  2.966 0.375     0.105     0.018        5     0.6  S_circular_insula_ant
 1737   1167   2954  3.029 0.522     0.089     0.013        9     1.0  S_circular_insula_inf
 1866   1274   2957  2.949 0.446     0.105     0.019        8     1.6  S_circular_insula_sup
 1238    855   2260  2.798 0.685     0.110     0.016        9     0.9  S_collat_transv_ant
  545    369    659  2.021 0.488     0.121     0.018        5     0.5  S_collat_transv_post
 2673   1823   4177  2.396 0.410     0.115     0.021       22     2.3  S_front_inf
 2006   1347   3119  2.511 0.398     0.121     0.024       20     1.9  S_front_middle
 3241   2224   5199  2.535 0.386     0.093     0.015       16     2.0  S_front_sup
  962    644   1375  2.524 0.449     0.102     0.017        7     0.6  S_interm_prim-Jensen
 3597   2446   5032  2.307 0.386     0.109     0.017       24     2.5  S_intrapariet&P_trans
 1310    884   1566  2.009 0.371     0.116     0.019        9     1.1  S_oc_middle&Lunatus
 1491    978   1930  2.139 0.433     0.104     0.019       10     1.1  S_oc_sup&transversal
  754    513    926  2.280 0.373     0.108     0.014        4     0.5  S_occipital_ant
 1561   1056   2476  2.643 0.364     0.097     0.018       12     1.0  S_oc-temp_lat
 2422   1672   3796  2.556 0.594     0.118     0.020       24     1.9  S_oc-temp_med&Lingual
  553    393    829  2.382 0.392     0.127     0.020        4     0.6  S_orbital_lateral
  999    715   1489  2.566 0.577     0.117     0.020        9     0.8  S_orbital_med-olfact
 1906   1279   3575  2.803 0.528     0.112     0.020       17     1.4  S_orbital-H_Shaped
 2112   1380   3018  2.439 0.459     0.112     0.024       19     1.9  S_parieto_occipital
 1674   1049   1536  1.659 0.693     0.123     0.024       32     1.1  S_pericallosal
 3555   2404   5329  2.306 0.475     0.105     0.018       24     2.7  S_postcentral
 2238   1510   3908  2.639 0.426     0.100     0.016       18     1.4  S_precentral-inf-part
 1611   1151   2742  2.540 0.444     0.106     0.015       12     1.1  S_precentral-sup-part
  799    547   1133  2.371 0.330     0.100     0.011        5     0.4  S_suborbital
 1744   1193   2729  2.500 0.415     0.117     0.020       15     1.4  S_subparietal
 1726   1212   2757  2.646 0.523     0.107     0.019       14     1.2  S_temporal_inf
 7220   4962  12245  2.642 0.428     0.095     0.015       45     4.2  S_temporal_sup
  264    184    422  2.480 0.274     0.108     0.013        1     0.1  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 0051140 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 310341
Total vertex volume 306508 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1193    802   2380  2.635 0.511     0.143     0.036       19     1.6  G&S_frontomargin
 1649   1017   3265  2.629 0.592     0.137     0.029       28     1.9  G&S_occipital_inf
 1622    838   2479  2.509 0.459     0.103     0.030       16     1.9  G&S_paracentral
 1827   1254   4443  3.162 0.450     0.131     0.025       23     1.8  G&S_subcentral
 1369    861   2857  2.774 0.540     0.142     0.037       23     2.4  G&S_transv_frontopol
 3243   2231   6815  2.875 0.512     0.112     0.021       36     2.6  G&S_cingul-Ant
 2015   1332   4359  3.067 0.511     0.114     0.022       20     1.7  G&S_cingul-Mid-Ant
 1834   1260   3508  2.800 0.500     0.117     0.026       26     2.1  G&S_cingul-Mid-Post
  616    408   1684  3.104 0.818     0.160     0.045       15     0.9  G_cingul-Post-dorsal
  420    259   1048  2.741 0.840     0.138     0.038        9     0.5  G_cingul-Post-ventral
 2859   1701   3767  1.979 0.518     0.133     0.034       37     3.8  G_cuneus
 1458    932   4062  3.177 0.337     0.120     0.026       21     1.4  G_front_inf-Opercular
  297    189    742  2.981 0.426     0.140     0.027        6     0.3  G_front_inf-Orbital
 1251    782   3238  3.030 0.440     0.127     0.027       22     1.2  G_front_inf-Triangul
 4741   3027  11619  2.866 0.507     0.134     0.031       94     5.5  G_front_middle
 9047   5668  22183  3.084 0.502     0.126     0.030      132    10.1  G_front_sup
  901    596   2019  3.061 0.803     0.148     0.056       19     2.1  G_Ins_lg&S_cent_ins
 1065    642   3066  3.367 0.846     0.136     0.047       20     1.9  G_insular_short
 3020   1871   6556  2.644 0.605     0.139     0.031       56     3.5  G_occipital_middle
 1698    980   2572  2.188 0.466     0.129     0.032       23     2.1  G_occipital_sup
 2613   1602   6109  2.819 0.661     0.132     0.038       49     3.8  G_oc-temp_lat-fusifor
 3402   2095   5430  2.172 0.673     0.138     0.037       57     4.9  G_oc-temp_med-Lingual
 1325    830   3645  3.164 0.810     0.112     0.039       13     1.6  G_oc-temp_med-Parahip
 3467   2176   8583  2.968 0.633     0.138     0.037       68     5.3  G_orbital
 4122   2631   9221  2.669 0.556     0.131     0.026       74     4.1  G_pariet_inf-Angular
 3096   1980   7921  3.043 0.498     0.121     0.025       49     2.9  G_pariet_inf-Supramar
 2845   1813   6087  2.584 0.443     0.133     0.029       46     3.1  G_parietal_sup
 3473   1939   5386  2.309 0.572     0.116     0.030       46     3.9  G_postcentral
 3908   2064   8003  2.981 0.398     0.102     0.026       41     3.9  G_precentral
 2969   1878   6498  2.769 0.434     0.131     0.029       50     3.1  G_precuneus
  917    590   2270  2.653 0.676     0.133     0.043       21     1.4  G_rectus
  688    417   1066  2.429 0.958     0.128     0.075       11     1.6  G_subcallosal
  581    321   1286  2.834 0.663     0.103     0.037        9     0.9  G_temp_sup-G_T_transv
 2121   1403   7067  3.741 0.538     0.140     0.033       35     2.7  G_temp_sup-Lateral
 1196    791   2873  3.339 0.857     0.120     0.042       17     2.2  G_temp_sup-Plan_polar
  823    585   1985  3.053 0.542     0.101     0.015        5     0.6  G_temp_sup-Plan_tempo
 2864   1799   7754  3.056 0.822     0.128     0.041       55     4.3  G_temporal_inf
 3426   2222  10561  3.417 0.614     0.133     0.030       55     4.2  G_temporal_middle
  490    330    822  2.730 0.310     0.114     0.014        5     0.2  Lat_Fis-ant-Horizont
  394    272    593  2.788 0.448     0.079     0.013        1     0.2  Lat_Fis-ant-Vertical
 1432    963   2217  2.851 0.396     0.115     0.023       10     1.2  Lat_Fis-post
 4399   2556   6078  2.025 0.636     0.133     0.037       60     6.7  Pole_occipital
 2130   1388   7436  3.466 0.868     0.153     0.049       42     4.2  Pole_temporal
 2791   1828   3509  2.257 0.605     0.116     0.026       24     2.9  S_calcarine
 3600   2331   4209  2.091 0.621     0.100     0.019       18     3.0  S_central
 1418    969   2290  2.398 0.363     0.102     0.018       11     1.0  S_cingul-Marginalis
  843    563   1367  2.959 0.416     0.103     0.017        4     0.7  S_circular_insula_ant
 1426    922   2350  3.118 0.428     0.071     0.011        4     0.6  S_circular_insula_inf
 1686   1149   2853  3.015 0.453     0.102     0.018        7     1.3  S_circular_insula_sup
 1113    761   2056  2.951 0.418     0.088     0.011        4     0.6  S_collat_transv_ant
  447    288    558  2.226 0.417     0.143     0.031        4     0.7  S_collat_transv_post
 2844   1921   4590  2.538 0.436     0.103     0.015       21     1.9  S_front_inf
 2972   2054   5275  2.538 0.513     0.120     0.024       30     2.7  S_front_middle
 3236   2255   5467  2.576 0.387     0.099     0.016       20     2.2  S_front_sup
  614    424   1119  2.708 0.339     0.075     0.008        2     0.2  S_interm_prim-Jensen
 3884   2604   5704  2.299 0.389     0.109     0.018       30     2.9  S_intrapariet&P_trans
 1097    737   1280  1.981 0.404     0.121     0.018        9     0.8  S_oc_middle&Lunatus
 1423    957   1830  2.089 0.375     0.116     0.018       11     1.1  S_oc_sup&transversal
 1141    814   1859  2.432 0.443     0.117     0.018        9     0.9  S_occipital_ant
 1252    907   2004  2.620 0.456     0.093     0.012        5     0.6  S_oc-temp_lat
 2730   1915   4347  2.702 0.448     0.099     0.014       14     1.6  S_oc-temp_med&Lingual
  584    413    816  2.244 0.316     0.097     0.010        3     0.3  S_orbital_lateral
  937    700   1491  2.601 0.479     0.117     0.022        7     0.7  S_orbital_med-olfact
 1929   1254   3584  2.846 0.573     0.117     0.024       18     1.9  S_orbital-H_Shaped
 2235   1480   3093  2.401 0.495     0.112     0.021       19     2.0  S_parieto_occipital
 2058   1313   2005  1.821 0.821     0.121     0.020       33     1.3  S_pericallosal
 3343   2224   4502  2.236 0.439     0.102     0.016       25     2.1  S_postcentral
 1879   1268   3054  2.782 0.355     0.102     0.016       12     1.2  S_precentral-inf-part
 1397    993   2240  2.582 0.403     0.090     0.012        5     0.7  S_precentral-sup-part
  136     99    268  2.771 0.444     0.143     0.023        1     0.2  S_suborbital
 1757   1213   2855  2.486 0.562     0.128     0.023       17     1.8  S_subparietal
 1679   1199   2848  2.856 0.593     0.113     0.018       11     1.2  S_temporal_inf
 8459   5753  15094  2.796 0.557     0.099     0.015       54     5.1  S_temporal_sup
  326    222    437  2.567 0.494     0.128     0.017        3     0.2  S_temporal_transverse
PIDs (27772 27775) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 04:44:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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 04:44:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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 27844 of (27844 27847) to complete...
Waiting for PID 27847 of (27844 27847) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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...
1593 labels changed using aseg
relabeling using gibbs priors...
000:   2269 changed, 163524 examined...
001:    556 changed, 10428 examined...
002:    144 changed, 3100 examined...
003:     65 changed, 873 examined...
004:     29 changed, 386 examined...
005:     18 changed, 161 examined...
006:      8 changed, 109 examined...
007:      7 changed, 62 examined...
008:      5 changed, 41 examined...
009:      0 changed, 30 examined...
205 labels changed using aseg
000: 59 total segments, 26 labels (170 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 10 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1264 vertices marked for relabeling...
1264 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0051140 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...
1550 labels changed using aseg
relabeling using gibbs priors...
000:   2283 changed, 163911 examined...
001:    570 changed, 10693 examined...
002:    155 changed, 3218 examined...
003:     66 changed, 935 examined...
004:     28 changed, 349 examined...
005:      9 changed, 159 examined...
006:      2 changed, 52 examined...
007:      0 changed, 14 examined...
83 labels changed using aseg
000: 55 total segments, 22 labels (115 vertices) changed
001: 35 total segments, 2 labels (2 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1453 vertices marked for relabeling...
1453 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.
PIDs (27844 27847) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 04:44:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 04:44:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 rh white 

Waiting for PID 27909 of (27909 27912) to complete...
Waiting for PID 27912 of (27909 27912) 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 0051140 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 308447
Total vertex volume 304436 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 2293   1487   4771  2.863 0.733     0.120     0.021       29     1.7  caudalanteriorcingulate
 4446   2927   8518  2.637 0.467     0.109     0.020       43     3.5  caudalmiddlefrontal
 3291   2057   4280  2.028 0.534     0.134     0.033       41     4.5  cuneus
  794    506   2367  3.485 0.706     0.099     0.022        5     0.7  entorhinal
 5885   4014  12837  2.840 0.583     0.124     0.024       84     5.8  fusiform
 8312   5522  16145  2.580 0.465     0.121     0.023      107     7.5  inferiorparietal
 5729   3797  13213  2.887 0.703     0.120     0.029       82     6.8  inferiortemporal
 2062   1332   3737  2.458 0.995     0.121     0.032       31     2.0  isthmuscingulate
 9689   5887  14672  2.228 0.572     0.126     0.028      118    10.6  lateraloccipital
 5669   3723  11823  2.811 0.622     0.125     0.034       82     7.3  lateralorbitofrontal
 5090   3313   7131  1.999 0.620     0.138     0.033       65     6.9  lingual
 2855   1889   6098  2.652 0.859     0.115     0.031       43     3.4  medialorbitofrontal
 7026   4651  16275  2.973 0.590     0.109     0.019       82     5.6  middletemporal
 1256    800   2827  3.164 0.684     0.103     0.020       12     0.9  parahippocampal
 2705   1595   4692  2.770 0.572     0.104     0.023       23     2.3  paracentral
 2173   1428   4660  2.822 0.468     0.115     0.020       26     1.7  parsopercularis
 1246    793   2984  3.055 0.490     0.123     0.021       15     1.0  parsorbitalis
 2453   1660   4877  2.672 0.531     0.124     0.023       28     2.3  parstriangularis
 2145   1445   2255  1.821 0.452     0.121     0.024       17     2.2  pericalcarine
 8356   5074  12582  2.270 0.655     0.109     0.023       80     8.0  postcentral
 2093   1450   3881  2.449 0.736     0.121     0.020       30     1.5  posteriorcingulate
 9190   5722  17292  2.767 0.505     0.104     0.020       78     7.5  precentral
 6522   4310  12296  2.636 0.505     0.129     0.024       87     6.4  precuneus
 2317   1529   4573  2.873 0.560     0.117     0.023       33     2.0  rostralanteriorcingulate
 7391   4781  14737  2.640 0.501     0.128     0.026      108     7.7  rostralmiddlefrontal
14502   9696  32873  2.959 0.582     0.125     0.026      180    14.9  superiorfrontal
 7573   4807  13293  2.454 0.507     0.113     0.023       83     7.0  superiorparietal
 9734   6459  22930  3.114 0.705     0.115     0.026      127     9.7  superiortemporal
 8065   5422  16551  2.743 0.492     0.124     0.026      101     8.2  supramarginal
  847    441   1281  2.583 0.554     0.119     0.060       19     2.5  transversetemporal
 3600   2332   7985  3.229 0.562     0.114     0.022       40     3.2  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 0051140 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 310341
Total vertex volume 306508 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1697   1086   3429  2.839 0.719     0.125     0.021       25     1.4  caudalanteriorcingulate
 3671   2451   7283  2.779 0.456     0.114     0.022       41     3.1  caudalmiddlefrontal
 3316   2014   4619  2.088 0.532     0.134     0.033       42     4.5  cuneus
  659    452   2099  3.286 0.885     0.136     0.055        7     1.4  entorhinal
 4874   3234   9896  2.784 0.588     0.114     0.026       57     5.3  fusiform
10810   7098  20735  2.561 0.530     0.120     0.022      141     9.4  inferiorparietal
 6099   3987  13873  2.960 0.711     0.123     0.033       86     7.8  inferiortemporal
 1784   1157   3175  2.378 0.992     0.123     0.029       29     1.6  isthmuscingulate
 9958   6119  15506  2.221 0.572     0.133     0.030      138    12.0  lateraloccipital
 5850   3789  11718  2.770 0.622     0.136     0.038       99     9.2  lateralorbitofrontal
 5389   3399   8383  2.282 0.672     0.135     0.035       77     7.5  lingual
 2607   1711   5470  2.616 0.714     0.126     0.044       47     4.0  medialorbitofrontal
 7165   4858  18546  3.253 0.642     0.119     0.023       80     6.7  middletemporal
 1356    859   2881  2.953 0.614     0.095     0.015       12     0.6  parahippocampal
 2811   1627   4770  2.735 0.523     0.099     0.023       21     2.4  paracentral
 2519   1652   5496  3.013 0.413     0.111     0.020       26     1.9  parsopercularis
 1217    778   2642  2.946 0.509     0.115     0.020       14     0.9  parsorbitalis
 3070   1995   6246  2.773 0.471     0.115     0.021       37     2.4  parstriangularis
 2534   1632   2769  1.922 0.521     0.104     0.024       16     2.5  pericalcarine
 9036   5619  13983  2.289 0.672     0.111     0.024       92     8.4  postcentral
 2226   1526   4229  2.521 0.870     0.127     0.028       40     2.6  posteriorcingulate
 8638   5148  15914  2.822 0.478     0.102     0.022       70     7.8  precentral
 6897   4530  12383  2.579 0.488     0.124     0.025       90     6.8  precuneus
 1730   1155   4048  2.980 0.618     0.132     0.028       32     1.7  rostralanteriorcingulate
 8237   5479  16439  2.638 0.528     0.123     0.025      112     8.2  rostralmiddlefrontal
16075  10578  34378  2.892 0.531     0.119     0.026      185    16.2  superiorfrontal
 7263   4648  12233  2.360 0.468     0.118     0.023       83     6.3  superiorparietal
 8432   5555  21581  3.355 0.655     0.111     0.025       85     8.2  superiortemporal
 5871   3914  12445  2.840 0.488     0.112     0.020       65     4.7  supramarginal
  595    336   1165  2.764 0.575     0.094     0.035        8     0.8  transversetemporal
 3656   2438   8173  3.261 0.618     0.120     0.031       41     4.4  insula
PIDs (27909 27912) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 04:45:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 pctsurfcon --s 0051140 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 04:45:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts

 pctsurfcon --s 0051140 --rh-only 

Waiting for PID 27999 of (27999 28012) to complete...
Waiting for PID 28012 of (27999 28012) to complete...

 pctsurfcon --s 0051140 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts/pctsurfcon.log
Sun Oct  8 04:45:26 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-6.0.0/0051140/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-963 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-6.0.0/0051140/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.27999/lh.wm.mgh --regheader 0051140 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 87381
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.27999/lh.wm.mgh
Dim: 163524 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.27999/lh.gm.mgh --projfrac 0.3 --regheader 0051140 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 107671
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.27999/lh.gm.mgh
Dim: 163524 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.27999/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.27999/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.w-g.pct.mgh --annot 0051140 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/lh.w-g.pct.mgh --annot 0051140 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/lh.w-g.pct.mgh
Vertex Area is 0.650749 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 0051140 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/scripts/pctsurfcon.log
Sun Oct  8 04:45:26 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-6.0.0/0051140/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-963 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-6.0.0/0051140/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.28012/rh.wm.mgh --regheader 0051140 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 87328
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.28012/rh.wm.mgh
Dim: 163911 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.28012/rh.gm.mgh --projfrac 0.3 --regheader 0051140 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 107595
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.28012/rh.gm.mgh
Dim: 163911 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.28012/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/tmp.pctsurfcon.28012/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.w-g.pct.mgh --annot 0051140 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.w-g.pct.mgh --annot 0051140 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.w-g.pct.mgh
Vertex Area is 0.648218 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 (27999 28012) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 04:45:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2127 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
1405 voxels changed to hypointensity...
3501 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 04:45:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140

 mri_aparc2aseg --s 0051140 --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 04:45:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140

 mri_aparc2aseg --s 0051140 --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 04:45:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140

 mri_aparc2aseg --s 0051140 --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 28183 of (28183 28186 28189) to complete...
Waiting for PID 28186 of (28183 28186 28189) to complete...
Waiting for PID 28189 of (28183 28186 28189) to complete...

 mri_aparc2aseg --s 0051140 --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 0051140
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/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-6.0.0/0051140/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 7.92
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 24
rescaling Left_Inf_Lat_Vent from 34 --> 30
rescaling Left_Cerebellum_White_Matter from 86 --> 85
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 92
rescaling Left_Caudate from 75 --> 77
rescaling Left_Putamen from 80 --> 88
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 38
rescaling Fourth_Ventricle from 22 --> 23
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 65
rescaling CSF from 32 --> 58
rescaling Left_Accumbens_area from 62 --> 70
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 66
rescaling Right_Lateral_Ventricle from 13 --> 25
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 68
rescaling Right_Amygdala from 55 --> 68
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 607374
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 9 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0051140 --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 0051140
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/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-6.0.0/0051140/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 7.92
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 24
rescaling Left_Inf_Lat_Vent from 34 --> 30
rescaling Left_Cerebellum_White_Matter from 86 --> 85
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 92
rescaling Left_Caudate from 75 --> 77
rescaling Left_Putamen from 80 --> 88
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 38
rescaling Fourth_Ventricle from 22 --> 23
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 65
rescaling CSF from 32 --> 58
rescaling Left_Accumbens_area from 62 --> 70
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 66
rescaling Right_Lateral_Ventricle from 13 --> 25
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 68
rescaling Right_Amygdala from 55 --> 68
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 607097
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 9 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0051140 --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 0051140
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/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-6.0.0/0051140/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 7.92
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 24
rescaling Left_Inf_Lat_Vent from 34 --> 30
rescaling Left_Cerebellum_White_Matter from 86 --> 85
rescaling Left_Cerebellum_Cortex from 60 --> 62
rescaling Left_Thalamus from 94 --> 102
rescaling Left_Thalamus_Proper from 84 --> 92
rescaling Left_Caudate from 75 --> 77
rescaling Left_Putamen from 80 --> 88
rescaling Left_Pallidum from 98 --> 93
rescaling Third_Ventricle from 25 --> 38
rescaling Fourth_Ventricle from 22 --> 23
rescaling Brain_Stem from 81 --> 84
rescaling Left_Hippocampus from 57 --> 62
rescaling Left_Amygdala from 56 --> 65
rescaling CSF from 32 --> 58
rescaling Left_Accumbens_area from 62 --> 70
rescaling Left_VentralDC from 87 --> 91
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 66
rescaling Right_Lateral_Ventricle from 13 --> 25
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 90
rescaling Right_Caudate from 62 --> 80
rescaling Right_Putamen from 80 --> 83
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 68
rescaling Right_Amygdala from 55 --> 68
rescaling Right_Accumbens_area from 65 --> 78
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 49
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 607097
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 167 changed.
pass 2: 9 changed.
pass 3: 1 changed.
pass 4: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (28183 28186 28189) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 04:54:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri

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

Sun Oct  8 04:54:26 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-6.0.0/0051140/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-963 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-6.0.0/0051140/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-963
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 04:54:26 CEST 2017 
Ended   at Sun Oct  8 04:54:32 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 04:54:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140

 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 0051140 


$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 0051140 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1809324 mm^3    (det: 1.076703 )
Computing euler number
orig.nofix lheno =  -42, rheno = -98
orig.nofix lhholes =   22, rhholes = 50
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
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 04:56:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140

 mri_aparc2aseg --s 0051140 --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 0051140
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-6.0.0/0051140/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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-6.0.0/0051140/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8074 vertices from left hemi
Ripped 7891 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-6.0.0/0051140/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 = 1134245
Used brute-force search on 434 voxels
Fixing Parahip LH WM
  Found 10 clusters
     0 k 2.000000
     1 k 2.000000
     2 k 1841.000000
     3 k 1.000000
     4 k 1.000000
     5 k 4.000000
     6 k 1.000000
     7 k 4.000000
     8 k 14.000000
     9 k 1.000000
Fixing Parahip RH WM
  Found 7 clusters
     0 k 2.000000
     1 k 4.000000
     2 k 1.000000
     3 k 49.000000
     4 k 1913.000000
     5 k 1.000000
     6 k 2.000000
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 0051140 --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 0051140 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-963
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1809324 mm^3    (det: 1.076703 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
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-6.0.0/0051140/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 05:05:35 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 29227 of (29227 29233 29239 29244 29250) to complete...
Waiting for PID 29233 of (29227 29233 29239 29244 29250) to complete...
Waiting for PID 29239 of (29227 29233 29239 29244 29250) to complete...
Waiting for PID 29244 of (29227 29233 29239 29244 29250) to complete...
Waiting for PID 29250 of (29227 29233 29239 29244 29250) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 583
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4712
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 1033
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8942
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 324
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4401
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 654
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6637
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 976
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6760
mri_label2label: Done

PIDs (29227 29233 29239 29244 29250) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 29311 of (29311 29317 29323 29329) to complete...
Waiting for PID 29317 of (29311 29317 29323 29329) to complete...
Waiting for PID 29323 of (29311 29317 29323 29329) to complete...
Waiting for PID 29329 of (29311 29317 29323 29329) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 557
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4627
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 2637
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16226
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 436
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4617
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 801
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4223
mri_label2label: Done

PIDs (29311 29317 29323 29329) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 29374 of (29374 29380 29386 29392 29398) to complete...
Waiting for PID 29380 of (29374 29380 29386 29392 29398) to complete...
Waiting for PID 29386 of (29374 29380 29386 29392 29398) to complete...
Waiting for PID 29392 of (29374 29380 29386 29392 29398) to complete...
Waiting for PID 29398 of (29374 29380 29386 29392 29398) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 1928
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6569
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 4019
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 12133
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 691
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2709
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 245
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1535
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 235
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1434
mri_label2label: Done

PIDs (29374 29380 29386 29392 29398) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 29494 of (29494 29500 29506 29509 29517) to complete...
Waiting for PID 29500 of (29494 29500 29506 29509 29517) to complete...
Waiting for PID 29506 of (29494 29500 29506 29509 29517) to complete...
Waiting for PID 29509 of (29494 29500 29506 29509 29517) to complete...
Waiting for PID 29517 of (29494 29500 29506 29509 29517) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 209
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1223
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 271
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2363
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 81
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1585
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 277
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2273
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 423
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2742
mri_label2label: Done

PIDs (29494 29500 29506 29509 29517) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 29560 of (29560 29566 29572 29577) to complete...
Waiting for PID 29566 of (29560 29566 29572 29577) to complete...
Waiting for PID 29572 of (29560 29566 29572 29577) to complete...
Waiting for PID 29577 of (29560 29566 29572 29577) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 168
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1717
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 1303
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8338
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 125
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2037
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 260
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1411
mri_label2label: Done

PIDs (29560 29566 29572 29577) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 29637 of (29637 29643 29649 29654 29661) to complete...
Waiting for PID 29643 of (29637 29643 29649 29654 29661) to complete...
Waiting for PID 29649 of (29637 29643 29649 29654 29661) to complete...
Waiting for PID 29654 of (29637 29643 29649 29654 29661) to complete...
Waiting for PID 29661 of (29637 29643 29649 29654 29661) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 1341
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4746
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 1827
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5161
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 110
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 623
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 75
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 545
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163524
Number of reverse mapping hits = 108
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 558
mri_label2label: Done

PIDs (29637 29643 29649 29654 29661) completed and logs appended.

 mris_label2annot --s 0051140 --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-6.0.0/0051140/label
cmdline mris_label2annot --s 0051140 --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-963
machine  x86_64
user     ntraut

subject 0051140
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-6.0.0/0051140/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 114340 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/lh.BA_exvivo.annot

 mris_label2annot --s 0051140 --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-6.0.0/0051140/label
cmdline mris_label2annot --s 0051140 --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-963
machine  x86_64
user     ntraut

subject 0051140
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-6.0.0/0051140/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 134667 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 308447
Total vertex volume 304436 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1536    739   2387  2.371 0.541     0.102     0.028       15     1.7  BA1_exvivo
 4519   2881   7381  2.406 0.487     0.105     0.020       38     3.7  BA2_exvivo
 1275    863   1325  1.918 0.424     0.124     0.025        9     1.2  BA3a_exvivo
 2871   1833   4295  2.061 0.658     0.114     0.021       32     2.7  BA3b_exvivo
 2146   1078   3767  2.968 0.440     0.088     0.022       15     2.0  BA4a_exvivo
 1603    982   2591  2.708 0.426     0.091     0.019        8     1.2  BA4p_exvivo
11923   7739  25597  2.909 0.540     0.113     0.022      120    10.3  BA6_exvivo
 2383   1612   5400  2.890 0.481     0.109     0.019       25     1.7  BA44_exvivo
 3167   2093   6401  2.656 0.535     0.126     0.027       39     3.3  BA45_exvivo
 3980   2536   4606  1.836 0.556     0.125     0.027       42     4.7  V1_exvivo
 9731   5936  13085  2.051 0.569     0.139     0.035      127    13.4  V2_exvivo
 2420   1567   4546  2.532 0.545     0.124     0.023       33     2.4  MT_exvivo
  741    441   2231  3.561 0.697     0.090     0.020        6     0.5  perirhinal_exvivo
  889    619   2204  3.345 0.694     0.129     0.027       10     0.8  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 0051140 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 308447
Total vertex volume 304436 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1003    455   1461  2.279 0.434     0.104     0.026       11     1.0  BA1_exvivo
 1814   1078   2793  2.368 0.455     0.098     0.019       14     1.5  BA2_exvivo
 1043    712   1039  1.866 0.414     0.131     0.027        8     1.1  BA3a_exvivo
 1777   1141   2000  1.713 0.411     0.100     0.020       14     1.5  BA3b_exvivo
 2123   1099   3708  2.942 0.454     0.087     0.022       14     1.9  BA4a_exvivo
 1285    798   2006  2.654 0.407     0.092     0.019        6     1.0  BA4p_exvivo
 6699   4243  14029  2.872 0.526     0.112     0.023       68     5.9  BA6_exvivo
 1422    965   3442  2.940 0.457     0.109     0.018       16     1.0  BA44_exvivo
 1189    750   2778  2.836 0.509     0.132     0.029       18     1.4  BA45_exvivo
 4240   2693   5042  1.853 0.562     0.126     0.028       45     5.0  V1_exvivo
 4847   2972   5799  1.877 0.506     0.144     0.038       65     7.5  V2_exvivo
  559    368    843  2.246 0.369     0.101     0.014        4     0.3  MT_exvivo
  358    228   1178  3.532 0.684     0.073     0.011        1     0.2  perirhinal_exvivo
  498    335   1027  3.229 0.531     0.099     0.018        2     0.4  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 05:08:58 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29776 of (29776 29782 29788 29794 29800) to complete...
Waiting for PID 29782 of (29776 29782 29788 29794 29800) to complete...
Waiting for PID 29788 of (29776 29782 29788 29794 29800) to complete...
Waiting for PID 29794 of (29776 29782 29788 29794 29800) to complete...
Waiting for PID 29800 of (29776 29782 29788 29794 29800) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 832
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4794
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1284
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7971
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 235
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4215
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 546
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5068
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1185
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6932
mri_label2label: Done

PIDs (29776 29782 29788 29794 29800) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29846 of (29846 29853 29859 29865) to complete...
Waiting for PID 29853 of (29846 29853 29859 29865) to complete...
Waiting for PID 29859 of (29846 29853 29859 29865) to complete...
Waiting for PID 29865 of (29846 29853 29859 29865) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 560
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5033
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 2035
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14291
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1036
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7948
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1661
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7016
mri_label2label: Done

PIDs (29846 29853 29859 29865) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29922 of (29922 29928 29934 29940 29946) to complete...
Waiting for PID 29928 of (29922 29928 29934 29940 29946) to complete...
Waiting for PID 29934 of (29922 29928 29934 29940 29946) to complete...
Waiting for PID 29940 of (29922 29928 29934 29940 29946) to complete...
Waiting for PID 29946 of (29922 29928 29934 29940 29946) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 2304
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 7031
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.V2_exvivo.label --trgsubject 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 4228
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12244
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1290
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 3222
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 183
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1221
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 148
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 900
mri_label2label: Done

PIDs (29922 29928 29934 29940 29946) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 30011 of (30011 30017 30023 30028 30034) to complete...
Waiting for PID 30017 of (30011 30017 30023 30028 30034) to complete...
Waiting for PID 30023 of (30011 30017 30023 30028 30034) to complete...
Waiting for PID 30028 of (30011 30017 30023 30028 30034) to complete...
Waiting for PID 30034 of (30011 30017 30023 30028 30034) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 262
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1138
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 717
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3405
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 80
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1778
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 195
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2378
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 324
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1712
mri_label2label: Done

PIDs (30011 30017 30023 30028 30034) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 30093 of (30093 30099 30105 30110) to complete...
Waiting for PID 30099 of (30093 30099 30105 30110) to complete...
Waiting for PID 30105 of (30093 30099 30105 30110) to complete...
Waiting for PID 30110 of (30093 30099 30105 30110) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 193
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1682
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1025
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7984
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 181
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1193
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 222
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1400
mri_label2label: Done

PIDs (30093 30099 30105 30110) 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 0051140 --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 0051140 --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 0051140 --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 0051140 --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 0051140 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 30157 of (30157 30163 30169 30172 30181) to complete...
Waiting for PID 30163 of (30157 30163 30169 30172 30181) to complete...
Waiting for PID 30169 of (30157 30163 30169 30172 30181) to complete...
Waiting for PID 30172 of (30157 30163 30169 30172 30181) to complete...
Waiting for PID 30181 of (30157 30163 30169 30172 30181) 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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1522
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4754
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 1928
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5365
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 205
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 473
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 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 121
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 815
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject 0051140 --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 = 0051140
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-6.0.0/0051140/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 163911
Number of reverse mapping hits = 41
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 332
mri_label2label: Done

PIDs (30157 30163 30169 30172 30181) completed and logs appended.

 mris_label2annot --s 0051140 --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-6.0.0/0051140/label
cmdline mris_label2annot --s 0051140 --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-963
machine  x86_64
user     ntraut

subject 0051140
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-6.0.0/0051140/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 112866 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/label/rh.BA_exvivo.annot

 mris_label2annot --s 0051140 --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-6.0.0/0051140/label
cmdline mris_label2annot --s 0051140 --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-963
machine  x86_64
user     ntraut

subject 0051140
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-6.0.0/0051140/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 135284 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/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 0051140 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 310341
Total vertex volume 306508 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
 1302    658   2035  2.367 0.590     0.112     0.034       18     1.6  BA1_exvivo
 4684   2999   6913  2.281 0.503     0.107     0.021       45     3.7  BA2_exvivo
 1200    821   1228  1.946 0.457     0.122     0.027        9     1.2  BA3a_exvivo
 2272   1434   3004  1.857 0.596     0.107     0.023       19     2.3  BA3b_exvivo
 2188   1088   3600  2.808 0.420     0.092     0.024       16     2.1  BA4a_exvivo
 1470    879   2193  2.666 0.372     0.089     0.018        7     1.1  BA4p_exvivo
 9876   6103  21299  2.959 0.514     0.110     0.024      102     9.1  BA6_exvivo
 4009   2621   8524  2.982 0.443     0.109     0.020       39     3.1  BA44_exvivo
 5304   3473  11209  2.800 0.501     0.115     0.020       65     4.1  BA45_exvivo
 4698   2857   6132  2.025 0.691     0.116     0.031       46     6.1  V1_exvivo
 9737   5964  13079  2.061 0.538     0.139     0.036      136    14.1  V2_exvivo
 3157   2075   6053  2.560 0.455     0.134     0.024       46     3.0  MT_exvivo
  685    435   2108  3.327 0.831     0.121     0.050        7     1.3  perirhinal_exvivo
  463    316   1240  3.239 0.671     0.105     0.021        3     0.4  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0051140 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0051140/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 310341
Total vertex volume 306508 (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) = 1809324 mm^3    (det: 1.076703 )
lhCtxGM: 303412.266 302684.000  diff=  728.3  pctdiff= 0.240
rhCtxGM: 306067.185 305189.000  diff=  878.2  pctdiff= 0.287
lhCtxWM: 263753.719 264229.500  diff= -475.8  pctdiff=-0.180
rhCtxWM: 264950.014 265778.500  diff= -828.5  pctdiff=-0.313
SubCortGMVol  73220.000
SupraTentVol  1221760.185 (1219012.000) diff=2748.185 pctdiff=0.225
SupraTentVolNotVent  1213893.185 (1211145.000) diff=2748.185 pctdiff=0.226
BrainSegVol  1411381.000 (1408616.000) diff=2765.000 pctdiff=0.196
BrainSegVolNotVent  1399782.000 (1399959.185) diff=-177.185 pctdiff=-0.013
BrainSegVolNotVent  1399782.000
CerebellumVol 188512.000
VentChorVol    7867.000
3rd4th5thCSF   3732.000
CSFVol   967.000, OptChiasmVol   125.000
MaskVol 1956014.000
  948    455   1347  2.266 0.523     0.112     0.029       12     1.1  BA1_exvivo
 3011   1861   4756  2.343 0.494     0.104     0.021       30     2.4  BA2_exvivo
 1055    714    992  1.930 0.479     0.124     0.029        7     1.1  BA3a_exvivo
 1747   1145   1992  1.675 0.459     0.097     0.020       11     1.5  BA3b_exvivo
 1433    649   2202  2.874 0.509     0.092     0.028       13     1.5  BA4a_exvivo
 1257    775   1864  2.650 0.384     0.091     0.018        6     1.0  BA4p_exvivo
 6235   3864  12960  2.923 0.495     0.111     0.024       58     5.9  BA6_exvivo
 1033    680   2402  2.961 0.474     0.106     0.020       11     0.9  BA44_exvivo
 1194    782   2797  2.943 0.460     0.114     0.021       15     0.9  BA45_exvivo
 4454   2723   5626  2.003 0.673     0.116     0.031       43     5.8  V1_exvivo
 5084   3071   6468  1.948 0.555     0.141     0.040       73     8.2  V2_exvivo
  470    297    963  2.529 0.365     0.144     0.030        8     0.6  MT_exvivo
  427    267   1245  3.273 0.831     0.120     0.055        5     0.9  perirhinal_exvivo
  279    198    685  3.051 0.646     0.109     0.030        2     0.3  entorhinal_exvivo

Started at Sat Oct 7 20:21:59 CEST 2017 
Ended   at Sun Oct 8 05:12:22 CEST 2017
#@#%# recon-all-run-time-hours 8.840
recon-all -s 0051140 finished without error at Sun Oct  8 05:12:22 CEST 2017