ABIDE_fs-6.0.0/0050555/scripts/recon-all.log

Sun Oct  8 01:33:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050555 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050555/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050555
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-924 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:      66074808   52707348   13367460    1741884          0   47644984
-/+ buffers/cache:    5062364   61012444
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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:17-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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: 2017/10/07-23:33:18-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-924  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-6.0.0/0050555

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050555/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Yale/0050555/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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/Yale/0050555/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-6.0.0/0050555/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sun Oct  8 01:33:23 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/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 float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sun Oct  8 01:33:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/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-924 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
Sun Oct  8 01:33:34 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.18371
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18371/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.18371/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.18371/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:33:36 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.18371/nu0.mnc ./tmp.mri_nu_correct.mni.18371/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18371/0/ -iterations 1000 -distance 50
[ntraut@tars-924:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/] [2017-10-08 01:33:37] 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.18371/0/ ./tmp.mri_nu_correct.mni.18371/nu0.mnc ./tmp.mri_nu_correct.mni.18371/nu1.imp

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Number of iterations: 65 
CV of field change: 0.000989566
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.18371/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.18371/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.18371/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...
 
 
Sun Oct  8 01:35:09 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 Sun Oct 8 01:35:09 CEST 2017
Ended   at Sun Oct  8 01:35:50 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sun Oct  8 01:35:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6591, pval=0.3663 >= 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-6.0.0/0050555/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/transforms/talairach_avi.log 

TalAviQA: 0.97294
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sun Oct  8 01:35:53 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-6.0.0/0050555/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-924 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
Sun Oct  8 01:35:53 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.19450
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.19450/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.19450/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.19450/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sun Oct  8 01:35:55 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.19450/nu0.mnc ./tmp.mri_nu_correct.mni.19450/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.19450/0/
[ntraut@tars-924:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/] [2017-10-08 01:35:55] 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.19450/0/ ./tmp.mri_nu_correct.mni.19450/nu0.mnc ./tmp.mri_nu_correct.mni.19450/nu1.imp

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Number of iterations: 39 
CV of field change: 0.000975336
 
 
--------------------------------------------------------
Iteration 2 Sun Oct  8 01:36:46 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.19450/nu1.mnc ./tmp.mri_nu_correct.mni.19450/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.19450/1/
[ntraut@tars-924:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/] [2017-10-08 01:36:46] 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.19450/1/ ./tmp.mri_nu_correct.mni.19450/nu1.mnc ./tmp.mri_nu_correct.mni.19450/nu2.imp

Processing:.................................................................Done
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Number of iterations: 24 
CV of field change: 0.000980245
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.19450/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19450/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-6.0.0/0050555/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.19450/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.19450/ones.mgz 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.19450/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.19450/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.19450/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19450/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.19450/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.19450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19450/input.mean.dat 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.19450/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.19450/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.19450/ones.mgz --i ./tmp.mri_nu_correct.mni.19450/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19450/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.19450/ones.mgz --i ./tmp.mri_nu_correct.mni.19450/nu2.mnc --sum ./tmp.mri_nu_correct.mni.19450/sum.junk --avgwf ./tmp.mri_nu_correct.mni.19450/output.mean.dat 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.19450/ones.mgz
Loading ./tmp.mri_nu_correct.mni.19450/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.19450/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.19450/nu2.mnc ./tmp.mri_nu_correct.mni.19450/nu2.mnc mul 1.03858740709496312888
Saving result to './tmp.mri_nu_correct.mni.19450/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.19450/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.19450/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.19450/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, 121) to ( 3, 110)
 
 
Sun Oct  8 01:38:08 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sun Oct  8 01:38:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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
 1.08974   0.02599  -0.01370  -26.25880;
-0.03747   0.93261   0.31278   24.69901;
 0.01201  -0.25512   1.01138  -15.52162;
 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 = 16
Starting OpenSpline(): npoints = 16
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 53 (53), valley at 21 (21)
csf peak at 27, setting threshold to 44
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 57 (57), valley at 22 (22)
csf peak at 29, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 51 seconds.
#--------------------------------------------
#@# Skull Stripping Sun Oct  8 01:40:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 

aligning to atlas containing skull, setting unknown_nbr_spacing = 5

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca'...
average std = 22.9   using min determinant for regularization = 52.6
0 singular and 9002 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 8.7 or > 569.1 
total sample mean = 77.6 (1399 zeros)
************************************************
spacing=8, using 3243 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=15.0
skull bounding box = (47, 50, 28) --> (209, 213, 236)
using (101, 104, 132) as brain centroid...
mean wm in atlas = 108, using box (81,84,106) --> (120, 124,157) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.2
after smoothing, mri peak at 108, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.470
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.237741 @ (-9.091, -9.091, -27.273)
max log p =    -4.048698 @ (4.545, -4.545, 4.545)
max log p =    -4.014425 @ (2.273, 2.273, 2.273)
max log p =    -4.014425 @ (0.000, 0.000, 0.000)
max log p =    -3.997747 @ (-1.705, -1.705, -2.841)
max log p =    -3.997747 @ (0.000, 0.000, 0.000)
Found translation: (-4.0, -13.1, -23.3): log p = -3.998
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.773, old_max_log_p =-3.998 (thresh=-4.0)
 1.06375   0.00000   0.00000  -12.19162;
 0.00000   1.03837   0.27823  -48.86860;
 0.00000  -0.25882   0.96593   21.45762;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.773, old_max_log_p =-3.773 (thresh=-3.8)
 1.06375   0.00000   0.00000  -12.19162;
 0.00000   1.03837   0.27823  -48.86860;
 0.00000  -0.25882   0.96593   21.45762;
 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=-3.705, old_max_log_p =-3.773 (thresh=-3.8)
 1.08295   0.00000   0.00000  -14.66524;
 0.00000   1.03761   0.34696  -57.85685;
 0.00000  -0.31983   0.92726   35.63758;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.703, old_max_log_p =-3.705 (thresh=-3.7)
 1.08295   0.00000   0.00000  -14.66524;
 0.00000   1.01816   0.34045  -54.10627;
 0.00000  -0.31983   0.92726   35.63758;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.681, old_max_log_p =-3.703 (thresh=-3.7)
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.681, old_max_log_p =-3.681 (thresh=-3.7)
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3243 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.681 (old=-4.470)
transform before final EM align:
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 364799 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    4.1  tol 0.000000
final transform:
 1.08534   0.01678   0.00533  -17.23446;
-0.01766   1.01952   0.32405  -50.79836;
 0.00000  -0.30207   0.92943   31.77548;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1104.180139
mri_em_register stimesec    1.042841
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   157610
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    120
mri_em_register ru_nivcsw   1827
registration took 9 minutes and 38 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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=129 y=123 z=127 r=71
      first estimation of the main basin volume: 1545738 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=151, y=104, z=94, Imax=255
      CSF=18, 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=9304336729 voxels, voxel volume =1.000 
                     = 9304336729 mmm3 = 9304336.384 cm3
done.
PostAnalyze...Basin Prior
 39 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=128,y=130, z=122, r=10355 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = 43949
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1031259014
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = -1035545167
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=38 , nb = 1103858362
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=9, CSF_MAX=40 , nb = 1078557332
    OTHER      CSF_MIN=9, CSF_intensity=23, CSF_MAX=56 , nb = 1076358602
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    40,      31,        23,   52
  after  analyzing :    25,      31,        31,   36
   RIGHT_CER   
  before analyzing :    24,      23,        23,   71
  after  analyzing :    23,      24,        25,   35
   LEFT_CER    
  before analyzing :    24,      24,        24,   62
  after  analyzing :    16,      24,        25,   33
  RIGHT_BRAIN  
  before analyzing :    38,      31,        25,   51
  after  analyzing :    25,      31,        31,   36
  LEFT_BRAIN   
  before analyzing :    40,      31,        23,   52
  after  analyzing :    25,      31,        31,   36
     OTHER     
  before analyzing :    56,      67,        73,   91
  after  analyzing :    56,      71,        73,   76
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...69 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.011
curvature mean = 74.455, std = 8.076

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.04, sigma = 3.12
      after  rotation: sse = 2.04, sigma = 3.12
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.06, its var is  2.58   
      before Erosion-Dilatation  0.06% 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...41 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1974612 voxels, voxel volume = 1.000 mm3
           = 1974612 mmm3 = 1974.612 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    24.321302
mri_watershed stimesec    0.400939
mri_watershed ru_maxrss   822836
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213045
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  3056
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1334
mri_watershed ru_nivcsw   46
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct  8 01:50:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=22.0
skull bounding box = (58, 65, 41) --> (198, 213, 216)
using (105, 114, 129) as brain centroid...
mean wm in atlas = 107, using box (88,96,107) --> (122, 132,150) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.7
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
initial log_p = -4.260
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.010068 @ (-9.091, -9.091, -9.091)
max log p =    -3.781242 @ (4.545, -4.545, -13.636)
max log p =    -3.659349 @ (2.273, 2.273, 2.273)
max log p =    -3.635463 @ (-1.136, 1.136, 3.409)
max log p =    -3.614100 @ (1.705, -1.705, -1.705)
max log p =    -3.614100 @ (0.000, 0.000, 0.000)
Found translation: (-1.7, -11.9, -18.8): log p = -3.614
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.302, old_max_log_p =-3.614 (thresh=-3.6)
 1.07500   0.00000   0.00000  -11.33768;
 0.00000   1.03837   0.27823  -51.52150;
 0.00000  -0.23941   0.89348   25.89452;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.302, old_max_log_p =-3.302 (thresh=-3.3)
 1.07500   0.00000   0.00000  -11.33768;
 0.00000   1.03837   0.27823  -51.52150;
 0.00000  -0.23941   0.89348   25.89452;
 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=-3.155, old_max_log_p =-3.302 (thresh=-3.3)
 1.01420  -0.02279  -0.03902   4.30810;
 0.03447   1.00911   0.30241  -53.23725;
 0.03385  -0.28080   0.91724   25.90282;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.155, old_max_log_p =-3.155 (thresh=-3.2)
 1.01420  -0.02279  -0.03902   4.30810;
 0.03447   1.00911   0.30241  -53.23725;
 0.03385  -0.28080   0.91724   25.90282;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.145, old_max_log_p =-3.155 (thresh=-3.2)
 1.01257  -0.04145  -0.03611   6.12174;
 0.05037   1.00948   0.28576  -52.82841;
 0.02611  -0.26410   0.92234   24.57035;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.144, old_max_log_p =-3.145 (thresh=-3.1)
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 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
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.144 (old=-4.260)
transform before final EM align:
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 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
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =    3.7  tol 0.000000
final transform:
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    936.018703
mri_em_register stimesec    1.055839
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158954
mri_em_register ru_majflt   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    75
mri_em_register ru_nivcsw   1686
registration took 8 minutes and 6 seconds.
#--------------------------------------
#@# CA Normalize Sun Oct  8 01:58:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

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

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=22.0
skull bounding box = (58, 65, 41) --> (198, 213, 216)
using (105, 114, 129) as brain centroid...
mean wm in atlas = 107, using box (88,96,107) --> (122, 132,150) to find MRI wm
before smoothing, mri peak at 108
robust fit to distribution - 108 +- 4.7
after smoothing, mri peak at 108, scaling input intensities by 0.991
scaling channel 0 by 0.990741
using 246344 sample points...
INFO: compute sample coordinates transform
 1.01376  -0.04150  -0.03616   5.98040;
 0.05031   1.00830   0.28543  -52.62671;
 0.02608  -0.26379   0.92126   24.66513;
 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 (126, 65, 43) --> (194, 180, 213)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 7013 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 66, 42) --> (130, 175, 214)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 7415 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 156, 73) --> (179, 195, 129)
Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 132.0
0 of 136 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 156, 72) --> (129, 196, 131)
Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0
10 of 57 (17.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 140, 110) --> (148, 208, 142)
Brain_Stem: limiting intensities to 88.0 --> 132.0
12 of 157 (7.6%) samples deleted
using 14778 total control points for intensity normalization...
bias field = 0.975 +- 0.040
118 of 14756 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 65, 43) --> (194, 180, 213)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
1 of 7296 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 66, 42) --> (130, 175, 214)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 8073 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 156, 73) --> (179, 195, 129)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
24 of 204 (11.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 156, 72) --> (129, 196, 131)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
68 of 134 (50.7%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 140, 110) --> (148, 208, 142)
Brain_Stem: limiting intensities to 88.0 --> 132.0
238 of 263 (90.5%) samples deleted
using 15970 total control points for intensity normalization...
bias field = 1.023 +- 0.038
36 of 15582 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (126, 65, 43) --> (194, 180, 213)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0
1 of 7268 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (64, 66, 42) --> (130, 175, 214)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
2 of 8068 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (130, 156, 73) --> (179, 195, 129)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
48 of 222 (21.6%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (86, 156, 72) --> (129, 196, 131)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
154 of 174 (88.5%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 140, 110) --> (148, 208, 142)
Brain_Stem: limiting intensities to 88.0 --> 132.0
337 of 339 (99.4%) samples deleted
using 16071 total control points for intensity normalization...
bias field = 1.018 +- 0.035
30 of 15372 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 37 seconds.
#--------------------------------------
#@# CA Reg Sun Oct  8 01:59:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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) = 1.02 (predicted orig area = 7.8)
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=0.753, neg=0, invalid=762
0001: dt=202.997183, rms=0.699 (7.189%), neg=0, invalid=762
0002: dt=221.952000, rms=0.688 (1.623%), neg=0, invalid=762
0003: dt=181.600000, rms=0.682 (0.850%), neg=0, invalid=762
0004: dt=129.472000, rms=0.679 (0.414%), neg=0, invalid=762
0005: dt=517.888000, rms=0.673 (0.948%), neg=0, invalid=762
0006: dt=129.472000, rms=0.671 (0.234%), neg=0, invalid=762
0007: dt=129.472000, rms=0.670 (0.153%), neg=0, invalid=762
0008: dt=129.472000, rms=0.668 (0.260%), neg=0, invalid=762
0009: dt=129.472000, rms=0.666 (0.346%), neg=0, invalid=762
0010: dt=129.472000, rms=0.664 (0.371%), neg=0, invalid=762
0011: dt=129.472000, rms=0.661 (0.363%), neg=0, invalid=762
0012: dt=129.472000, rms=0.659 (0.338%), neg=0, invalid=762
0013: dt=129.472000, rms=0.657 (0.276%), neg=0, invalid=762
0014: dt=129.472000, rms=0.656 (0.236%), neg=0, invalid=762
0015: dt=129.472000, rms=0.654 (0.203%), neg=0, invalid=762
0016: dt=129.472000, rms=0.653 (0.188%), neg=0, invalid=762
0017: dt=129.472000, rms=0.652 (0.168%), neg=0, invalid=762
0018: dt=129.472000, rms=0.651 (0.145%), neg=0, invalid=762
0019: dt=129.472000, rms=0.650 (0.125%), neg=0, invalid=762
0020: dt=129.472000, rms=0.649 (0.109%), neg=0, invalid=762
0021: dt=129.472000, rms=0.649 (0.110%), neg=0, invalid=762
0022: dt=129.472000, rms=0.648 (0.103%), neg=0, invalid=762
0023: dt=517.888000, rms=0.648 (0.053%), neg=0, invalid=762
0024: dt=517.888000, rms=0.648 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.648, neg=0, invalid=762
0025: dt=129.472000, rms=0.647 (0.198%), neg=0, invalid=762
0026: dt=369.920000, rms=0.647 (0.059%), neg=0, invalid=762
0027: dt=369.920000, rms=0.646 (0.081%), neg=0, invalid=762
0028: dt=369.920000, rms=0.646 (0.094%), neg=0, invalid=762
0029: dt=369.920000, rms=0.645 (0.052%), neg=0, invalid=762
0030: dt=369.920000, rms=0.645 (0.058%), neg=0, invalid=762
0031: dt=369.920000, rms=0.644 (0.153%), neg=0, invalid=762
0032: dt=369.920000, rms=0.643 (0.087%), neg=0, invalid=762
0033: dt=369.920000, rms=0.643 (0.043%), neg=0, invalid=762
0034: dt=129.472000, rms=0.643 (0.066%), neg=0, invalid=762
0035: dt=2071.552000, rms=0.642 (0.108%), neg=0, invalid=762
0036: dt=129.472000, rms=0.642 (0.047%), neg=0, invalid=762
0037: dt=129.472000, rms=0.642 (0.020%), neg=0, invalid=762
0038: dt=129.472000, rms=0.641 (0.023%), neg=0, invalid=762
0039: dt=129.472000, rms=0.641 (0.017%), neg=0, invalid=762
0040: dt=129.472000, rms=0.641 (0.018%), neg=0, invalid=762
0041: dt=129.472000, rms=0.641 (0.033%), neg=0, invalid=762
0042: dt=129.472000, rms=0.641 (0.040%), neg=0, invalid=762
0043: dt=129.472000, rms=0.640 (0.031%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.645, neg=0, invalid=762
0044: dt=256.000000, rms=0.636 (1.314%), neg=0, invalid=762
0045: dt=116.594059, rms=0.629 (1.037%), neg=0, invalid=762
0046: dt=101.085575, rms=0.626 (0.623%), neg=0, invalid=762
0047: dt=102.878505, rms=0.623 (0.363%), neg=0, invalid=762
0048: dt=124.416000, rms=0.620 (0.449%), neg=0, invalid=762
0049: dt=79.633588, rms=0.619 (0.278%), neg=0, invalid=762
0050: dt=145.152000, rms=0.616 (0.379%), neg=0, invalid=762
0051: dt=73.216000, rms=0.615 (0.214%), neg=0, invalid=762
0052: dt=73.216000, rms=0.614 (0.214%), neg=0, invalid=762
0053: dt=73.216000, rms=0.612 (0.283%), neg=0, invalid=762
0054: dt=73.216000, rms=0.610 (0.413%), neg=0, invalid=762
0055: dt=73.216000, rms=0.607 (0.476%), neg=0, invalid=762
0056: dt=73.216000, rms=0.603 (0.520%), neg=0, invalid=762
0057: dt=73.216000, rms=0.601 (0.473%), neg=0, invalid=762
0058: dt=73.216000, rms=0.598 (0.441%), neg=0, invalid=762
0059: dt=73.216000, rms=0.595 (0.424%), neg=0, invalid=762
0060: dt=73.216000, rms=0.593 (0.397%), neg=0, invalid=762
0061: dt=73.216000, rms=0.591 (0.342%), neg=0, invalid=762
0062: dt=73.216000, rms=0.589 (0.260%), neg=0, invalid=762
0063: dt=73.216000, rms=0.588 (0.253%), neg=0, invalid=762
0064: dt=73.216000, rms=0.587 (0.231%), neg=0, invalid=762
0065: dt=73.216000, rms=0.586 (0.188%), neg=0, invalid=762
0066: dt=73.216000, rms=0.585 (0.161%), neg=0, invalid=762
0067: dt=73.216000, rms=0.584 (0.137%), neg=0, invalid=762
0068: dt=73.216000, rms=0.583 (0.168%), neg=0, invalid=762
0069: dt=73.216000, rms=0.582 (0.122%), neg=0, invalid=762
0070: dt=73.216000, rms=0.582 (0.099%), neg=0, invalid=762
0071: dt=36.288000, rms=0.582 (0.006%), neg=0, invalid=762
0072: dt=36.288000, rms=0.581 (0.007%), neg=0, invalid=762
0073: dt=36.288000, rms=0.581 (0.008%), neg=0, invalid=762
0074: dt=36.288000, rms=0.581 (0.008%), neg=0, invalid=762
0075: dt=36.288000, rms=0.581 (0.012%), neg=0, invalid=762
0076: dt=36.288000, rms=0.581 (0.004%), neg=0, invalid=762
0077: dt=36.288000, rms=0.581 (0.013%), neg=0, invalid=762
0078: dt=36.288000, rms=0.581 (0.006%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.582, neg=0, invalid=762
0079: dt=103.680000, rms=0.580 (0.286%), neg=0, invalid=762
0080: dt=82.944000, rms=0.580 (0.041%), neg=0, invalid=762
0081: dt=82.944000, rms=0.580 (0.038%), neg=0, invalid=762
0082: dt=82.944000, rms=0.580 (0.014%), neg=0, invalid=762
0083: dt=82.944000, rms=0.580 (0.013%), neg=0, invalid=762
0084: dt=82.944000, rms=0.579 (0.018%), neg=0, invalid=762
0085: dt=36.288000, rms=0.579 (0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.601, neg=0, invalid=762
0086: dt=0.400000, rms=0.600 (0.109%), neg=0, invalid=762
0087: dt=0.100000, rms=0.600 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.601, neg=0, invalid=762
0088: dt=0.000000, rms=0.600 (0.108%), neg=0, invalid=762
0089: dt=0.000000, rms=0.600 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.664, neg=0, invalid=762
0090: dt=5.846154, rms=0.641 (3.423%), neg=0, invalid=762
0091: dt=2.742857, rms=0.641 (0.117%), neg=0, invalid=762
0092: dt=2.742857, rms=0.641 (-0.039%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.641, neg=0, invalid=762
0093: dt=0.000000, rms=0.641 (0.093%), neg=0, invalid=762
0094: dt=0.000000, rms=0.641 (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=0.694, neg=0, invalid=762
0095: dt=1.280000, rms=0.690 (0.594%), neg=0, invalid=762
0096: dt=2.265625, rms=0.684 (0.887%), neg=0, invalid=762
0097: dt=0.320000, rms=0.684 (0.018%), neg=0, invalid=762
0098: dt=0.320000, rms=0.683 (0.020%), neg=0, invalid=762
0099: dt=0.320000, rms=0.683 (0.016%), neg=0, invalid=762
0100: dt=0.320000, rms=0.683 (0.013%), neg=0, invalid=762
0101: dt=2.000000, rms=0.681 (0.302%), neg=0, invalid=762
0102: dt=0.000000, rms=0.681 (0.000%), neg=0, invalid=762
0103: dt=0.100000, rms=0.681 (-0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.682, neg=0, invalid=762
0104: dt=0.384000, rms=0.681 (0.107%), neg=0, invalid=762
0105: dt=0.448000, rms=0.681 (0.013%), neg=0, invalid=762
0106: dt=0.448000, rms=0.681 (0.010%), neg=0, invalid=762
0107: dt=0.448000, rms=0.681 (0.010%), neg=0, invalid=762
0108: dt=0.448000, rms=0.681 (0.005%), neg=0, invalid=762
0109: dt=0.448000, rms=0.681 (-0.012%), 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=0.652, neg=0, invalid=762
0110: dt=0.803160, rms=0.636 (2.520%), neg=0, invalid=762
0111: dt=0.080000, rms=0.635 (0.129%), neg=0, invalid=762
0112: dt=0.080000, rms=0.635 (-0.092%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.636, neg=0, invalid=762
0113: dt=0.020000, rms=0.635 (0.111%), neg=0, invalid=762
0114: dt=0.001500, rms=0.635 (0.001%), neg=0, invalid=762
0115: dt=0.001500, rms=0.635 (0.000%), neg=0, invalid=762
0116: dt=0.001500, rms=0.635 (-0.000%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.09378 (11)
Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1022 voxels, overlap=0.378)
Left_Lateral_Ventricle (4): linear fit = 0.55 x + 0.0 (1022 voxels, peak = 11), gca=10.9
gca peak = 0.15565 (16)
mri peak = 0.10676 (11)
Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (1109 voxels, overlap=0.696)
Right_Lateral_Ventricle (43): linear fit = 0.69 x + 0.0 (1109 voxels, peak = 11), gca=11.0
gca peak = 0.26829 (96)
mri peak = 0.08560 (93)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1159 voxels, overlap=1.004)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (1159 voxels, peak = 97), gca=97.4
gca peak = 0.20183 (93)
mri peak = 0.09175 (98)
Left_Pallidum (13): linear fit = 1.03 x + 0.0 (1078 voxels, overlap=1.005)
Left_Pallidum (13): linear fit = 1.03 x + 0.0 (1078 voxels, peak = 96), gca=96.3
gca peak = 0.21683 (55)
mri peak = 0.08393 (62)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (877 voxels, overlap=0.999)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (877 voxels, peak = 57), gca=57.5
gca peak = 0.30730 (58)
mri peak = 0.07777 (63)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1026 voxels, overlap=0.998)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1026 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.10997 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (82673 voxels, overlap=0.619)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (82673 voxels, peak = 106), gca=105.5
gca peak = 0.12076 (102)
mri peak = 0.11274 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (83090 voxels, overlap=0.587)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (83090 voxels, peak = 107), gca=106.6
gca peak = 0.14995 (59)
mri peak = 0.03375 (46)
Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (47187 voxels, overlap=0.566)
Left_Cerebral_Cortex (3): linear fit = 0.89 x + 0.0 (47187 voxels, peak = 53), gca=52.8
gca peak = 0.15082 (58)
mri peak = 0.03593 (52)
Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (44312 voxels, overlap=0.875)
Right_Cerebral_Cortex (42): linear fit = 0.89 x + 0.0 (44312 voxels, peak = 52), gca=51.9
gca peak = 0.14161 (67)
mri peak = 0.10712 (68)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1303 voxels, overlap=0.987)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1303 voxels, peak = 68), gca=68.0
gca peak = 0.15243 (71)
mri peak = 0.11043 (69)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (1292 voxels, overlap=0.747)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (1292 voxels, peak = 67), gca=67.1
gca peak = 0.13336 (57)
mri peak = 0.03652 (56)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (40469 voxels, overlap=0.977)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (40469 voxels, peak = 60), gca=59.6
gca peak = 0.13252 (56)
mri peak = 0.04914 (60)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (40966 voxels, overlap=0.964)
Right_Cerebellum_Cortex (47): linear fit = 1.04 x + 0.0 (40966 voxels, peak = 59), gca=58.5
gca peak = 0.18181 (84)
mri peak = 0.08412 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (11135 voxels, overlap=0.730)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (11135 voxels, peak = 89), gca=89.5
gca peak = 0.20573 (83)
mri peak = 0.07148 (83)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (10261 voxels, overlap=0.972)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (10261 voxels, peak = 82), gca=81.8
gca peak = 0.21969 (57)
mri peak = 0.07067 (71)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (570 voxels, overlap=0.296)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (570 voxels, peak = 70), gca=69.8
gca peak = 0.39313 (56)
mri peak = 0.08221 (61)
Right_Amygdala (54): linear fit = 1.07 x + 0.0 (676 voxels, overlap=0.851)
Right_Amygdala (54): linear fit = 1.07 x + 0.0 (676 voxels, peak = 60), gca=59.6
gca peak = 0.14181 (85)
mri peak = 0.05735 (87)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6715 voxels, overlap=0.962)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6715 voxels, peak = 86), gca=86.3
gca peak = 0.11978 (83)
mri peak = 0.07985 (84)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5987 voxels, overlap=0.920)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5987 voxels, peak = 84), gca=84.2
gca peak = 0.13399 (79)
mri peak = 0.05152 (79)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (3068 voxels, overlap=0.921)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (3068 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.07075 (84)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (3076 voxels, overlap=0.973)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (3076 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.17572 (80)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (15538 voxels, overlap=0.401)
Brain_Stem (16): linear fit = 1.05 x + 0.0 (15538 voxels, peak = 84), gca=84.4
gca peak = 0.13281 (86)
mri peak = 0.10328 (84)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1984 voxels, overlap=0.657)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1984 voxels, peak = 85), gca=84.7
gca peak = 0.12801 (89)
mri peak = 0.07914 (87)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (2030 voxels, overlap=0.796)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (2030 voxels, peak = 90), gca=90.3
gca peak = 0.20494 (23)
mri peak = 0.06065 (18)
gca peak = 0.15061 (21)
mri peak = 0.11804 (12)
Fourth_Ventricle (15): linear fit = 0.52 x + 0.0 (485 voxels, overlap=0.285)
Fourth_Ventricle (15): linear fit = 0.52 x + 0.0 (485 voxels, peak = 11), gca=11.0
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 Fourth_Ventricle = 0.15061 (21)
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 1.04 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.62 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=0.668, neg=0, invalid=762
0117: dt=221.952000, rms=0.662 (0.956%), neg=0, invalid=762
0118: dt=369.920000, rms=0.658 (0.512%), neg=0, invalid=762
0119: dt=129.472000, rms=0.657 (0.201%), neg=0, invalid=762
0120: dt=517.888000, rms=0.655 (0.291%), neg=0, invalid=762
0121: dt=92.480000, rms=0.654 (0.156%), neg=0, invalid=762
0122: dt=517.888000, rms=0.653 (0.187%), neg=0, invalid=762
0123: dt=129.472000, rms=0.652 (0.088%), neg=0, invalid=762
0124: dt=129.472000, rms=0.652 (0.055%), neg=0, invalid=762
0125: dt=369.920000, rms=0.652 (0.079%), neg=0, invalid=762
0126: dt=110.976000, rms=0.651 (0.066%), neg=0, invalid=762
0127: dt=295.936000, rms=0.651 (0.054%), neg=0, invalid=762
0128: dt=110.976000, rms=0.650 (0.054%), neg=0, invalid=762
0129: dt=295.936000, rms=0.650 (0.051%), neg=0, invalid=762
0130: dt=110.976000, rms=0.650 (0.042%), neg=0, invalid=762
0131: dt=110.976000, rms=0.650 (0.026%), neg=0, invalid=762
0132: dt=110.976000, rms=0.649 (0.040%), neg=0, invalid=762
0133: dt=110.976000, rms=0.649 (0.059%), neg=0, invalid=762
0134: dt=110.976000, rms=0.649 (0.064%), neg=0, invalid=762
0135: dt=110.976000, rms=0.648 (0.075%), neg=0, invalid=762
0136: dt=110.976000, rms=0.648 (0.079%), neg=0, invalid=762
0137: dt=110.976000, rms=0.647 (0.075%), neg=0, invalid=762
0138: dt=110.976000, rms=0.647 (0.072%), neg=0, invalid=762
0139: dt=110.976000, rms=0.646 (0.066%), neg=0, invalid=762
0140: dt=110.976000, rms=0.646 (0.063%), neg=0, invalid=762
0141: dt=110.976000, rms=0.645 (0.058%), neg=0, invalid=762
0142: dt=110.976000, rms=0.645 (0.053%), neg=0, invalid=762
0143: dt=110.976000, rms=0.645 (0.046%), neg=0, invalid=762
0144: dt=110.976000, rms=0.645 (0.041%), neg=0, invalid=762
0145: dt=110.976000, rms=0.644 (0.043%), neg=0, invalid=762
0146: dt=110.976000, rms=0.644 (0.043%), neg=0, invalid=762
0147: dt=110.976000, rms=0.644 (0.043%), neg=0, invalid=762
0148: dt=110.976000, rms=0.643 (0.043%), neg=0, invalid=762
0149: dt=110.976000, rms=0.643 (0.039%), neg=0, invalid=762
0150: dt=110.976000, rms=0.643 (0.041%), neg=0, invalid=762
0151: dt=110.976000, rms=0.643 (0.038%), neg=0, invalid=762
0152: dt=110.976000, rms=0.642 (0.039%), neg=0, invalid=762
0153: dt=110.976000, rms=0.642 (0.037%), neg=0, invalid=762
0154: dt=110.976000, rms=0.642 (0.039%), neg=0, invalid=762
0155: dt=110.976000, rms=0.642 (0.038%), neg=0, invalid=762
0156: dt=110.976000, rms=0.641 (0.037%), neg=0, invalid=762
0157: dt=110.976000, rms=0.641 (0.039%), neg=0, invalid=762
0158: dt=110.976000, rms=0.641 (0.038%), neg=0, invalid=762
0159: dt=110.976000, rms=0.641 (0.036%), neg=0, invalid=762
0160: dt=110.976000, rms=0.640 (0.037%), neg=0, invalid=762
0161: dt=110.976000, rms=0.640 (0.035%), neg=0, invalid=762
0162: dt=110.976000, rms=0.640 (0.035%), neg=0, invalid=762
0163: dt=110.976000, rms=0.640 (0.029%), neg=0, invalid=762
0164: dt=110.976000, rms=0.640 (0.034%), neg=0, invalid=762
0165: dt=110.976000, rms=0.639 (0.031%), neg=0, invalid=762
0166: dt=110.976000, rms=0.639 (0.032%), neg=0, invalid=762
0167: dt=110.976000, rms=0.639 (0.032%), neg=0, invalid=762
0168: dt=110.976000, rms=0.639 (0.027%), neg=0, invalid=762
0169: dt=110.976000, rms=0.639 (0.024%), neg=0, invalid=762
0170: dt=110.976000, rms=0.638 (0.030%), neg=0, invalid=762
0171: dt=110.976000, rms=0.638 (0.032%), neg=0, invalid=762
0172: dt=110.976000, rms=0.638 (0.029%), neg=0, invalid=762
0173: dt=110.976000, rms=0.638 (0.024%), neg=0, invalid=762
0174: dt=110.976000, rms=0.638 (0.023%), neg=0, invalid=762
0175: dt=517.888000, rms=0.638 (0.019%), neg=0, invalid=762
0176: dt=517.888000, rms=0.638 (-0.238%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.638, neg=0, invalid=762
0177: dt=110.976000, rms=0.637 (0.148%), neg=0, invalid=762
0178: dt=443.904000, rms=0.637 (0.067%), neg=0, invalid=762
0179: dt=295.936000, rms=0.637 (0.049%), neg=0, invalid=762
0180: dt=295.936000, rms=0.637 (0.016%), neg=0, invalid=762
0181: dt=295.936000, rms=0.637 (0.000%), neg=0, invalid=762
0182: dt=295.936000, rms=0.636 (0.121%), neg=0, invalid=762
0183: dt=295.936000, rms=0.636 (0.055%), neg=0, invalid=762
0184: dt=295.936000, rms=0.636 (-0.032%), neg=0, invalid=762
0185: dt=8.092000, rms=0.636 (0.000%), neg=0, invalid=762
0186: dt=4.624000, rms=0.636 (-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=0.637, neg=0, invalid=762
0187: dt=190.358974, rms=0.631 (0.940%), neg=0, invalid=762
0188: dt=98.311787, rms=0.626 (0.765%), neg=0, invalid=762
0189: dt=74.516432, rms=0.623 (0.446%), neg=0, invalid=762
0190: dt=124.416000, rms=0.621 (0.420%), neg=0, invalid=762
0191: dt=72.741463, rms=0.618 (0.391%), neg=0, invalid=762
0192: dt=124.416000, rms=0.616 (0.357%), neg=0, invalid=762
0193: dt=73.423313, rms=0.614 (0.310%), neg=0, invalid=762
0194: dt=124.416000, rms=0.612 (0.306%), neg=0, invalid=762
0195: dt=69.659864, rms=0.611 (0.250%), neg=0, invalid=762
0196: dt=124.416000, rms=0.609 (0.251%), neg=0, invalid=762
0197: dt=72.393443, rms=0.608 (0.228%), neg=0, invalid=762
0198: dt=103.680000, rms=0.607 (0.197%), neg=0, invalid=762
0199: dt=87.111111, rms=0.605 (0.193%), neg=0, invalid=762
0200: dt=82.944000, rms=0.605 (0.155%), neg=0, invalid=762
0201: dt=103.680000, rms=0.603 (0.183%), neg=0, invalid=762
0202: dt=36.288000, rms=0.603 (0.122%), neg=0, invalid=762
0203: dt=580.608000, rms=0.598 (0.756%), neg=0, invalid=762
0204: dt=36.288000, rms=0.597 (0.240%), neg=0, invalid=762
0205: dt=145.152000, rms=0.596 (0.106%), neg=0, invalid=762
0206: dt=82.944000, rms=0.595 (0.162%), neg=0, invalid=762
0207: dt=62.208000, rms=0.595 (0.072%), neg=0, invalid=762
0208: dt=145.152000, rms=0.594 (0.125%), neg=0, invalid=762
0209: dt=36.288000, rms=0.593 (0.081%), neg=0, invalid=762
0210: dt=580.608000, rms=0.591 (0.374%), neg=0, invalid=762
0211: dt=36.288000, rms=0.590 (0.172%), neg=0, invalid=762
0212: dt=145.152000, rms=0.589 (0.131%), neg=0, invalid=762
0213: dt=36.288000, rms=0.589 (0.055%), neg=0, invalid=762
0214: dt=580.608000, rms=0.588 (0.196%), neg=0, invalid=762
0215: dt=74.154982, rms=0.586 (0.252%), neg=0, invalid=762
0216: dt=36.288000, rms=0.586 (0.028%), neg=0, invalid=762
0217: dt=36.288000, rms=0.586 (0.020%), neg=0, invalid=762
0218: dt=36.288000, rms=0.586 (0.038%), neg=0, invalid=762
0219: dt=36.288000, rms=0.586 (0.057%), neg=0, invalid=762
0220: dt=36.288000, rms=0.585 (0.074%), neg=0, invalid=762
0221: dt=36.288000, rms=0.585 (0.091%), neg=0, invalid=762
0222: dt=36.288000, rms=0.584 (0.095%), neg=0, invalid=762
0223: dt=36.288000, rms=0.584 (0.100%), neg=0, invalid=762
0224: dt=36.288000, rms=0.583 (0.106%), neg=0, invalid=762
0225: dt=36.288000, rms=0.582 (0.113%), neg=0, invalid=762
0226: dt=36.288000, rms=0.582 (0.120%), neg=0, invalid=762
0227: dt=36.288000, rms=0.581 (0.120%), neg=0, invalid=762
0228: dt=36.288000, rms=0.580 (0.119%), neg=0, invalid=762
0229: dt=36.288000, rms=0.580 (0.112%), neg=0, invalid=762
0230: dt=36.288000, rms=0.579 (0.111%), neg=0, invalid=762
0231: dt=36.288000, rms=0.578 (0.114%), neg=0, invalid=762
0232: dt=36.288000, rms=0.578 (0.109%), neg=0, invalid=762
0233: dt=36.288000, rms=0.577 (0.106%), neg=0, invalid=762
0234: dt=36.288000, rms=0.576 (0.102%), neg=0, invalid=762
0235: dt=36.288000, rms=0.576 (0.096%), neg=0, invalid=762
0236: dt=36.288000, rms=0.575 (0.090%), neg=0, invalid=762
0237: dt=36.288000, rms=0.575 (0.088%), neg=0, invalid=762
0238: dt=36.288000, rms=0.574 (0.086%), neg=0, invalid=762
0239: dt=36.288000, rms=0.574 (0.009%), neg=0, invalid=762
0240: dt=36.288000, rms=0.574 (0.016%), neg=0, invalid=762
0241: dt=36.288000, rms=0.574 (0.018%), neg=0, invalid=762
0242: dt=36.288000, rms=0.574 (0.025%), neg=0, invalid=762
0243: dt=36.288000, rms=0.574 (0.028%), neg=0, invalid=762
0244: dt=36.288000, rms=0.574 (0.033%), neg=0, invalid=762
0245: dt=36.288000, rms=0.573 (0.036%), neg=0, invalid=762
0246: dt=36.288000, rms=0.573 (0.043%), neg=0, invalid=762
0247: dt=36.288000, rms=0.573 (0.038%), neg=0, invalid=762
0248: dt=36.288000, rms=0.573 (0.044%), neg=0, invalid=762
0249: dt=36.288000, rms=0.572 (0.046%), neg=0, invalid=762
0250: dt=36.288000, rms=0.572 (0.046%), neg=0, invalid=762
0251: dt=36.288000, rms=0.572 (0.048%), neg=0, invalid=762
0252: dt=36.288000, rms=0.572 (0.051%), neg=0, invalid=762
0253: dt=36.288000, rms=0.571 (0.052%), neg=0, invalid=762
0254: dt=36.288000, rms=0.571 (0.051%), neg=0, invalid=762
0255: dt=36.288000, rms=0.571 (0.051%), neg=0, invalid=762
0256: dt=36.288000, rms=0.570 (0.054%), neg=0, invalid=762
0257: dt=36.288000, rms=0.570 (0.047%), neg=0, invalid=762
0258: dt=36.288000, rms=0.570 (0.048%), neg=0, invalid=762
0259: dt=36.288000, rms=0.570 (0.048%), neg=0, invalid=762
0260: dt=36.288000, rms=0.569 (0.044%), neg=0, invalid=762
0261: dt=36.288000, rms=0.569 (0.051%), neg=0, invalid=762
0262: dt=36.288000, rms=0.569 (0.053%), neg=0, invalid=762
0263: dt=36.288000, rms=0.568 (0.050%), neg=0, invalid=762
0264: dt=36.288000, rms=0.568 (0.048%), neg=0, invalid=762
0265: dt=36.288000, rms=0.568 (0.045%), neg=0, invalid=762
0266: dt=36.288000, rms=0.568 (0.044%), neg=0, invalid=762
0267: dt=36.288000, rms=0.567 (0.045%), neg=0, invalid=762
0268: dt=36.288000, rms=0.567 (0.042%), neg=0, invalid=762
0269: dt=36.288000, rms=0.567 (0.045%), neg=0, invalid=762
0270: dt=36.288000, rms=0.567 (0.041%), neg=0, invalid=762
0271: dt=36.288000, rms=0.566 (0.042%), neg=0, invalid=762
0272: dt=36.288000, rms=0.566 (0.038%), neg=0, invalid=762
0273: dt=36.288000, rms=0.566 (0.040%), neg=0, invalid=762
0274: dt=36.288000, rms=0.566 (0.040%), neg=0, invalid=762
0275: dt=36.288000, rms=0.566 (0.043%), neg=0, invalid=762
0276: dt=36.288000, rms=0.565 (0.038%), neg=0, invalid=762
0277: dt=36.288000, rms=0.565 (0.038%), neg=0, invalid=762
0278: dt=36.288000, rms=0.565 (0.039%), neg=0, invalid=762
0279: dt=36.288000, rms=0.565 (0.036%), neg=0, invalid=762
0280: dt=36.288000, rms=0.564 (0.035%), neg=0, invalid=762
0281: dt=36.288000, rms=0.564 (0.033%), neg=0, invalid=762
0282: dt=36.288000, rms=0.564 (0.030%), neg=0, invalid=762
0283: dt=36.288000, rms=0.564 (0.034%), neg=0, invalid=762
0284: dt=36.288000, rms=0.564 (0.037%), neg=0, invalid=762
0285: dt=36.288000, rms=0.564 (0.033%), neg=0, invalid=762
0286: dt=36.288000, rms=0.563 (0.029%), neg=0, invalid=762
0287: dt=36.288000, rms=0.563 (0.026%), neg=0, invalid=762
0288: dt=36.288000, rms=0.563 (0.024%), neg=0, invalid=762
0289: dt=36.288000, rms=0.563 (0.029%), neg=0, invalid=762
0290: dt=36.288000, rms=0.563 (0.033%), neg=0, invalid=762
0291: dt=36.288000, rms=0.563 (0.031%), neg=0, invalid=762
0292: dt=36.288000, rms=0.562 (0.028%), neg=0, invalid=762
0293: dt=36.288000, rms=0.562 (0.030%), neg=0, invalid=762
0294: dt=36.288000, rms=0.562 (0.021%), neg=0, invalid=762
0295: dt=36.288000, rms=0.562 (0.021%), neg=0, invalid=762
0296: dt=36.288000, rms=0.562 (0.029%), neg=0, invalid=762
0297: dt=36.288000, rms=0.562 (0.025%), neg=0, invalid=762
0298: dt=36.288000, rms=0.562 (0.024%), neg=0, invalid=762
0299: dt=36.288000, rms=0.562 (0.003%), neg=0, invalid=762
0300: dt=36.288000, rms=0.562 (0.005%), neg=0, invalid=762
0301: dt=36.288000, rms=0.562 (0.004%), neg=0, invalid=762
0302: dt=36.288000, rms=0.561 (0.008%), neg=0, invalid=762
0303: dt=36.288000, rms=0.561 (0.007%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.562, neg=0, invalid=762
0304: dt=124.416000, rms=0.560 (0.458%), neg=0, invalid=762
0305: dt=62.208000, rms=0.559 (0.081%), neg=0, invalid=762
0306: dt=145.152000, rms=0.559 (0.104%), neg=0, invalid=762
0307: dt=36.288000, rms=0.558 (0.035%), neg=0, invalid=762
0308: dt=36.288000, rms=0.558 (0.024%), neg=0, invalid=762
0309: dt=36.288000, rms=0.558 (0.032%), neg=0, invalid=762
0310: dt=36.288000, rms=0.558 (0.043%), neg=0, invalid=762
0311: dt=36.288000, rms=0.558 (0.049%), neg=0, invalid=762
0312: dt=36.288000, rms=0.557 (0.054%), neg=0, invalid=762
0313: dt=36.288000, rms=0.557 (0.044%), neg=0, invalid=762
0314: dt=36.288000, rms=0.557 (0.050%), neg=0, invalid=762
0315: dt=36.288000, rms=0.556 (0.041%), neg=0, invalid=762
0316: dt=36.288000, rms=0.556 (0.038%), neg=0, invalid=762
0317: dt=36.288000, rms=0.556 (0.042%), neg=0, invalid=762
0318: dt=36.288000, rms=0.556 (0.036%), neg=0, invalid=762
0319: dt=36.288000, rms=0.556 (0.035%), neg=0, invalid=762
0320: dt=36.288000, rms=0.555 (0.037%), neg=0, invalid=762
0321: dt=36.288000, rms=0.555 (0.032%), neg=0, invalid=762
0322: dt=36.288000, rms=0.555 (0.037%), neg=0, invalid=762
0323: dt=36.288000, rms=0.555 (0.038%), neg=0, invalid=762
0324: dt=36.288000, rms=0.555 (0.032%), neg=0, invalid=762
0325: dt=36.288000, rms=0.554 (0.039%), neg=0, invalid=762
0326: dt=36.288000, rms=0.554 (0.040%), neg=0, invalid=762
0327: dt=36.288000, rms=0.554 (0.038%), neg=0, invalid=762
0328: dt=36.288000, rms=0.554 (0.036%), neg=0, invalid=762
0329: dt=36.288000, rms=0.554 (0.032%), neg=0, invalid=762
0330: dt=36.288000, rms=0.553 (0.032%), neg=0, invalid=762
0331: dt=36.288000, rms=0.553 (0.031%), neg=0, invalid=762
0332: dt=36.288000, rms=0.553 (0.027%), neg=0, invalid=762
0333: dt=36.288000, rms=0.553 (0.026%), neg=0, invalid=762
0334: dt=36.288000, rms=0.553 (0.029%), neg=0, invalid=762
0335: dt=36.288000, rms=0.553 (0.026%), neg=0, invalid=762
0336: dt=36.288000, rms=0.553 (0.024%), neg=0, invalid=762
0337: dt=36.288000, rms=0.552 (0.028%), neg=0, invalid=762
0338: dt=36.288000, rms=0.552 (0.019%), neg=0, invalid=762
0339: dt=36.288000, rms=0.552 (0.024%), neg=0, invalid=762
0340: dt=36.288000, rms=0.552 (0.023%), neg=0, invalid=762
0341: dt=124.416000, rms=0.552 (0.003%), neg=0, invalid=762
0342: dt=124.416000, rms=0.552 (0.002%), neg=0, invalid=762
0343: dt=124.416000, rms=0.552 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.562, neg=0, invalid=762
0344: dt=38.400000, rms=0.559 (0.495%), neg=0, invalid=762
0345: dt=44.800000, rms=0.555 (0.632%), neg=0, invalid=762
0346: dt=44.800000, rms=0.554 (0.288%), neg=0, invalid=762
0347: dt=44.286920, rms=0.550 (0.570%), neg=0, invalid=762
0348: dt=2.800000, rms=0.550 (0.063%), neg=0, invalid=762
0349: dt=2.800000, rms=0.550 (0.057%), neg=0, invalid=762
0350: dt=0.700000, rms=0.550 (0.017%), neg=0, invalid=762
0351: dt=0.700000, rms=0.550 (0.013%), neg=0, invalid=762
0352: dt=0.350000, rms=0.550 (0.005%), neg=0, invalid=762
0353: dt=0.087500, rms=0.550 (0.002%), neg=0, invalid=762
0354: dt=0.043750, rms=0.550 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.550, neg=0, invalid=762
0355: dt=55.204678, rms=0.546 (0.756%), neg=0, invalid=762
0356: dt=28.745763, rms=0.544 (0.439%), neg=0, invalid=762
0357: dt=32.000000, rms=0.542 (0.279%), neg=0, invalid=762
0358: dt=25.600000, rms=0.541 (0.220%), neg=0, invalid=762
0359: dt=32.000000, rms=0.540 (0.191%), neg=0, invalid=762
0360: dt=25.600000, rms=0.539 (0.185%), neg=0, invalid=762
0361: dt=32.000000, rms=0.538 (0.162%), neg=0, invalid=762
0362: dt=25.600000, rms=0.537 (0.164%), neg=0, invalid=762
0363: dt=32.000000, rms=0.536 (0.138%), neg=0, invalid=762
0364: dt=25.600000, rms=0.536 (0.147%), neg=0, invalid=762
0365: dt=32.000000, rms=0.535 (0.130%), neg=0, invalid=762
0366: dt=25.600000, rms=0.534 (0.127%), neg=0, invalid=762
0367: dt=25.600000, rms=0.534 (0.118%), neg=0, invalid=762
0368: dt=32.000000, rms=0.533 (0.116%), neg=0, invalid=762
0369: dt=25.600000, rms=0.532 (0.112%), neg=0, invalid=762
0370: dt=25.600000, rms=0.532 (0.105%), neg=0, invalid=762
0371: dt=32.000000, rms=0.531 (0.096%), neg=0, invalid=762
0372: dt=25.600000, rms=0.531 (0.104%), neg=0, invalid=762
0373: dt=25.600000, rms=0.530 (0.085%), neg=0, invalid=762
0374: dt=32.000000, rms=0.530 (0.093%), neg=0, invalid=762
0375: dt=25.600000, rms=0.529 (0.076%), neg=0, invalid=762
0376: dt=32.000000, rms=0.529 (0.102%), neg=0, invalid=762
0377: dt=19.200000, rms=0.529 (0.070%), neg=0, invalid=762
0378: dt=44.800000, rms=0.528 (0.114%), neg=0, invalid=762
0379: dt=25.600000, rms=0.528 (0.065%), neg=0, invalid=762
0380: dt=25.600000, rms=0.527 (0.079%), neg=0, invalid=762
0381: dt=32.000000, rms=0.527 (0.062%), neg=0, invalid=762
0382: dt=25.600000, rms=0.526 (0.081%), neg=0, invalid=762
0383: dt=25.600000, rms=0.526 (0.050%), neg=0, invalid=762
0384: dt=32.000000, rms=0.526 (0.068%), neg=0, invalid=762
0385: dt=19.200000, rms=0.525 (0.058%), neg=0, invalid=762
0386: dt=44.800000, rms=0.525 (0.085%), neg=0, invalid=762
0387: dt=19.200000, rms=0.525 (0.049%), neg=0, invalid=762
0388: dt=19.200000, rms=0.525 (0.045%), neg=0, invalid=762
0389: dt=19.200000, rms=0.524 (0.070%), neg=0, invalid=762
0390: dt=19.200000, rms=0.524 (0.100%), neg=0, invalid=762
0391: dt=19.200000, rms=0.523 (0.117%), neg=0, invalid=762
0392: dt=19.200000, rms=0.522 (0.150%), neg=0, invalid=762
0393: dt=19.200000, rms=0.521 (0.153%), neg=0, invalid=762
0394: dt=19.200000, rms=0.521 (0.169%), neg=0, invalid=762
0395: dt=19.200000, rms=0.520 (0.173%), neg=0, invalid=762
0396: dt=19.200000, rms=0.519 (0.174%), neg=0, invalid=762
0397: dt=19.200000, rms=0.518 (0.180%), neg=0, invalid=762
0398: dt=19.200000, rms=0.517 (0.173%), neg=0, invalid=762
0399: dt=19.200000, rms=0.516 (0.166%), neg=0, invalid=762
0400: dt=19.200000, rms=0.515 (0.153%), neg=0, invalid=762
0401: dt=19.200000, rms=0.515 (0.147%), neg=0, invalid=762
0402: dt=19.200000, rms=0.514 (0.140%), neg=0, invalid=762
0403: dt=19.200000, rms=0.513 (0.125%), neg=0, invalid=762
0404: dt=19.200000, rms=0.513 (0.121%), neg=0, invalid=762
0405: dt=19.200000, rms=0.512 (0.114%), neg=0, invalid=762
0406: dt=19.200000, rms=0.511 (0.098%), neg=0, invalid=762
0407: dt=19.200000, rms=0.511 (0.096%), neg=0, invalid=762
0408: dt=19.200000, rms=0.511 (0.089%), neg=0, invalid=762
0409: dt=19.200000, rms=0.510 (0.078%), neg=0, invalid=762
0410: dt=19.200000, rms=0.510 (0.083%), neg=0, invalid=762
0411: dt=19.200000, rms=0.509 (0.069%), neg=0, invalid=762
0412: dt=19.200000, rms=0.509 (0.068%), neg=0, invalid=762
0413: dt=19.200000, rms=0.509 (0.065%), neg=0, invalid=762
0414: dt=19.200000, rms=0.508 (0.060%), neg=0, invalid=762
0415: dt=19.200000, rms=0.508 (0.041%), neg=0, invalid=762
0416: dt=19.200000, rms=0.508 (0.055%), neg=0, invalid=762
0417: dt=19.200000, rms=0.508 (0.043%), neg=0, invalid=762
0418: dt=19.200000, rms=0.507 (0.047%), neg=0, invalid=762
0419: dt=19.200000, rms=0.507 (0.037%), neg=0, invalid=762
0420: dt=19.200000, rms=0.507 (0.034%), neg=0, invalid=762
0421: dt=19.200000, rms=0.507 (0.042%), neg=0, invalid=762
0422: dt=19.200000, rms=0.507 (0.048%), neg=0, invalid=762
0423: dt=19.200000, rms=0.506 (0.031%), neg=0, invalid=762
0424: dt=19.200000, rms=0.506 (0.025%), neg=0, invalid=762
0425: dt=19.200000, rms=0.506 (0.037%), neg=0, invalid=762
0426: dt=19.200000, rms=0.506 (0.043%), neg=0, invalid=762
0427: dt=19.200000, rms=0.506 (0.029%), neg=0, invalid=762
0428: dt=19.200000, rms=0.506 (0.033%), neg=0, invalid=762
0429: dt=19.200000, rms=0.506 (0.003%), neg=0, invalid=762
0430: dt=19.200000, rms=0.506 (-0.001%), neg=0, invalid=762
0431: dt=2.000000, rms=0.506 (0.000%), neg=0, invalid=762
0432: dt=2.800000, rms=0.506 (0.002%), neg=0, invalid=762
0433: dt=2.800000, rms=0.506 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0434: dt=0.000000, rms=0.527 (0.123%), neg=0, invalid=762
0435: dt=0.000000, rms=0.527 (0.000%), neg=0, invalid=762
0436: dt=0.150000, rms=0.527 (-0.018%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.528, neg=0, invalid=762
0437: dt=0.000000, rms=0.527 (0.123%), neg=0, invalid=762
0438: dt=0.000000, rms=0.527 (0.000%), neg=0, invalid=762
0439: dt=0.150000, rms=0.527 (-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=0.570, neg=0, invalid=762
0440: dt=1.280000, rms=0.566 (0.721%), neg=0, invalid=762
0441: dt=0.320000, rms=0.566 (0.016%), neg=0, invalid=762
0442: dt=0.320000, rms=0.566 (-0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.566, neg=0, invalid=762
0443: dt=0.448000, rms=0.566 (0.151%), neg=0, invalid=762
0444: dt=0.096000, rms=0.566 (0.001%), neg=0, invalid=762
0445: dt=0.096000, rms=0.566 (-0.002%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.517, neg=0, invalid=762
0446: dt=0.448000, rms=0.503 (2.674%), neg=0, invalid=762
0447: dt=0.384000, rms=0.500 (0.564%), neg=0, invalid=762
0448: dt=0.448000, rms=0.498 (0.391%), neg=0, invalid=762
0449: dt=0.448000, rms=0.497 (0.221%), neg=0, invalid=762
0450: dt=0.448000, rms=0.496 (0.151%), neg=0, invalid=762
0451: dt=0.448000, rms=0.496 (0.112%), neg=0, invalid=762
0452: dt=0.384000, rms=0.495 (0.072%), neg=0, invalid=762
0453: dt=0.384000, rms=0.495 (0.062%), neg=0, invalid=762
0454: dt=0.384000, rms=0.495 (0.054%), neg=0, invalid=762
0455: dt=0.384000, rms=0.494 (0.043%), neg=0, invalid=762
0456: dt=0.384000, rms=0.494 (0.039%), neg=0, invalid=762
0457: dt=0.384000, rms=0.494 (0.063%), neg=0, invalid=762
0458: dt=0.192000, rms=0.494 (0.010%), neg=0, invalid=762
0459: dt=0.192000, rms=0.494 (0.021%), neg=0, invalid=762
0460: dt=0.192000, rms=0.494 (0.030%), neg=0, invalid=762
0461: dt=0.192000, rms=0.493 (0.033%), neg=0, invalid=762
0462: dt=0.192000, rms=0.493 (0.034%), neg=0, invalid=762
0463: dt=0.192000, rms=0.493 (0.012%), neg=0, invalid=762
0464: dt=0.192000, rms=0.493 (0.003%), neg=0, invalid=762
0465: dt=0.320000, rms=0.493 (0.008%), neg=0, invalid=762
0466: dt=0.112000, rms=0.493 (0.005%), neg=0, invalid=762
0467: dt=0.112000, rms=0.493 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.494, neg=0, invalid=762
0468: dt=0.320000, rms=0.491 (0.631%), neg=0, invalid=762
0469: dt=0.448000, rms=0.490 (0.236%), neg=0, invalid=762
0470: dt=0.448000, rms=0.489 (0.033%), neg=0, invalid=762
0471: dt=0.448000, rms=0.489 (0.016%), neg=0, invalid=762
0472: dt=0.448000, rms=0.489 (0.007%), neg=0, invalid=762
0473: dt=0.448000, rms=0.489 (0.015%), neg=0, invalid=762
0474: dt=0.224000, rms=0.489 (0.001%), neg=0, invalid=762
0475: dt=0.112000, rms=0.489 (0.000%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.488, neg=0, invalid=762
0476: dt=0.000000, rms=0.487 (0.159%), neg=0, invalid=762
0477: dt=0.000000, rms=0.487 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.488, neg=0, invalid=762
0478: dt=129.472000, rms=0.487 (0.176%), neg=0, invalid=762
0479: dt=129.472000, rms=0.487 (0.010%), neg=0, invalid=762
0480: dt=129.472000, rms=0.487 (0.010%), neg=0, invalid=762
0481: dt=129.472000, rms=0.487 (0.016%), neg=0, invalid=762
0482: dt=129.472000, rms=0.487 (0.022%), neg=0, invalid=762
0483: dt=129.472000, rms=0.487 (0.016%), neg=0, invalid=762
0484: dt=129.472000, rms=0.487 (0.016%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.487, neg=0, invalid=762
0485: dt=31.104000, rms=0.486 (0.194%), neg=0, invalid=762
0486: dt=36.288000, rms=0.486 (0.020%), neg=0, invalid=762
0487: dt=36.288000, rms=0.486 (0.017%), neg=0, invalid=762
0488: dt=36.288000, rms=0.486 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.487, neg=0, invalid=762
0489: dt=103.680000, rms=0.485 (0.444%), neg=0, invalid=762
0490: dt=36.288000, rms=0.484 (0.103%), neg=0, invalid=762
0491: dt=36.288000, rms=0.484 (0.054%), neg=0, invalid=762
0492: dt=36.288000, rms=0.484 (0.078%), neg=0, invalid=762
0493: dt=36.288000, rms=0.483 (0.093%), neg=0, invalid=762
0494: dt=36.288000, rms=0.483 (0.108%), neg=0, invalid=762
0495: dt=36.288000, rms=0.482 (0.113%), neg=0, invalid=762
0496: dt=36.288000, rms=0.482 (0.103%), neg=0, invalid=762
0497: dt=36.288000, rms=0.481 (0.091%), neg=0, invalid=762
0498: dt=82.944000, rms=0.481 (0.014%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0499: dt=38.400000, rms=0.479 (0.639%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 2 iterations, nbhd size=0, neg = 0
0500: dt=66.604651, rms=0.477 (0.492%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0501: dt=21.073171, rms=0.476 (0.284%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0502: dt=44.800000, rms=0.474 (0.294%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0503: dt=19.200000, rms=0.474 (0.113%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0504: dt=19.200000, rms=0.473 (0.110%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0505: dt=19.200000, rms=0.472 (0.151%), neg=0, invalid=762
0506: dt=19.200000, rms=0.472 (0.178%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=0, neg = 0
0507: dt=19.200000, rms=0.471 (0.179%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0508: dt=19.200000, rms=0.470 (0.185%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 0 iterations, nbhd size=0, neg = 0
0509: dt=19.200000, rms=0.469 (0.179%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 4 iterations, nbhd size=0, neg = 0
0510: dt=19.200000, rms=0.468 (0.163%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 2 iterations, nbhd size=0, neg = 0
0511: dt=19.200000, rms=0.468 (0.127%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 4 iterations, nbhd size=0, neg = 0
0512: dt=19.200000, rms=0.467 (0.131%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 8 iterations, nbhd size=0, neg = 0
0513: dt=19.200000, rms=0.466 (0.138%), neg=0, invalid=762
iter 0, gcam->neg = 13
after 15 iterations, nbhd size=1, neg = 0
0514: dt=19.200000, rms=0.466 (0.109%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 7 iterations, nbhd size=0, neg = 0
0515: dt=19.200000, rms=0.465 (0.108%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 3 iterations, nbhd size=0, neg = 0
0516: dt=38.400000, rms=0.465 (0.052%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0517: dt=38.400000, rms=0.465 (-0.112%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0518: dt=44.800000, rms=0.463 (0.664%), neg=0, invalid=762
0519: dt=24.935065, rms=0.461 (0.282%), neg=0, invalid=762
0520: dt=25.491525, rms=0.461 (0.136%), neg=0, invalid=762
0521: dt=25.491525, rms=0.460 (0.120%), neg=0, invalid=762
0522: dt=25.491525, rms=0.459 (0.156%), neg=0, invalid=762
0523: dt=25.491525, rms=0.459 (0.104%), neg=0, invalid=762
0524: dt=25.491525, rms=0.458 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 10 iterations, nbhd size=1, neg = 0
0525: dt=25.491525, rms=0.458 (0.013%), neg=0, invalid=762
0526: dt=11.200000, rms=0.458 (0.042%), neg=0, invalid=762
0527: dt=11.200000, rms=0.458 (0.023%), neg=0, invalid=762
0528: dt=11.200000, rms=0.458 (0.006%), neg=0, invalid=762
0529: dt=11.200000, rms=0.458 (0.017%), neg=0, invalid=762
0530: dt=11.200000, rms=0.458 (0.017%), neg=0, invalid=762
0531: dt=11.200000, rms=0.458 (0.026%), neg=0, invalid=762
0532: dt=11.200000, rms=0.458 (0.030%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0533: dt=11.200000, rms=0.457 (0.035%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0534: dt=11.200000, rms=0.457 (0.041%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0535: dt=11.200000, rms=0.457 (0.029%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 4 iterations, nbhd size=0, neg = 0
0536: dt=11.200000, rms=0.457 (0.016%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.463, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0537: dt=0.576000, rms=0.463 (0.174%), neg=0, invalid=762
0538: dt=0.180000, rms=0.463 (0.001%), neg=0, invalid=762
0539: dt=0.180000, rms=0.463 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.463, neg=0, invalid=762
0540: dt=2.461538, rms=0.462 (0.189%), neg=0, invalid=762
0541: dt=1.008000, rms=0.462 (0.002%), neg=0, invalid=762
0542: dt=1.008000, rms=0.462 (0.010%), neg=0, invalid=762
0543: dt=1.008000, rms=0.462 (-0.005%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.473, neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0544: dt=1.280000, rms=0.471 (0.303%), neg=0, invalid=762
0545: dt=0.320000, rms=0.471 (0.013%), neg=0, invalid=762
0546: dt=0.320000, rms=0.471 (-0.006%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.472, neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0547: dt=1.792000, rms=0.470 (0.338%), neg=0, invalid=762
0548: dt=1.024000, rms=0.470 (0.023%), neg=0, invalid=762
0549: dt=1.024000, rms=0.470 (-0.003%), 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=0.463, neg=0, invalid=762
iter 0, gcam->neg = 521
after 16 iterations, nbhd size=1, neg = 0
0550: dt=2.244622, rms=0.433 (6.512%), neg=0, invalid=762
0551: dt=0.096000, rms=0.433 (0.073%), neg=0, invalid=762
0552: dt=0.096000, rms=0.433 (-0.074%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.434, neg=0, invalid=762
0553: dt=0.064000, rms=0.433 (0.239%), neg=0, invalid=762
0554: dt=0.000000, rms=0.433 (0.001%), neg=0, invalid=762
0555: dt=0.050000, rms=0.433 (-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=0.418, neg=0, invalid=762
0556: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0557: dt=73.984000, rms=0.418 (0.010%), neg=0, invalid=762
0558: dt=295.936000, rms=0.418 (0.014%), neg=0, invalid=762
0559: dt=32.368000, rms=0.418 (0.002%), neg=0, invalid=762
0560: dt=32.368000, rms=0.418 (0.001%), neg=0, invalid=762
0561: dt=32.368000, rms=0.418 (0.000%), neg=0, invalid=762
0562: dt=32.368000, rms=0.418 (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=0.418, neg=0, invalid=762
0563: dt=0.000000, rms=0.418 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0564: dt=145.152000, rms=0.418 (0.096%), neg=0, invalid=762
0565: dt=82.944000, rms=0.418 (0.025%), neg=0, invalid=762
0566: dt=82.944000, rms=0.418 (0.028%), neg=0, invalid=762
0567: dt=82.944000, rms=0.418 (0.043%), neg=0, invalid=762
0568: dt=82.944000, rms=0.418 (0.029%), neg=0, invalid=762
0569: dt=82.944000, rms=0.417 (0.040%), neg=0, invalid=762
0570: dt=82.944000, rms=0.417 (0.023%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0571: dt=11.200000, rms=0.418 (0.060%), neg=0, invalid=762
0572: dt=11.200000, rms=0.418 (0.020%), neg=0, invalid=762
0573: dt=11.200000, rms=0.418 (0.009%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0574: dt=11.200000, rms=0.418 (-0.036%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.418, neg=0, invalid=762
0575: dt=59.914894, rms=0.415 (0.506%), neg=0, invalid=762
0576: dt=23.333333, rms=0.414 (0.260%), neg=0, invalid=762
0577: dt=44.800000, rms=0.414 (0.145%), neg=0, invalid=762
0578: dt=44.800000, rms=0.414 (0.000%), neg=0, invalid=762
0579: dt=44.800000, rms=0.412 (0.404%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 2 iterations, nbhd size=0, neg = 0
0580: dt=44.800000, rms=0.411 (0.232%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0581: dt=44.800000, rms=0.410 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0582: dt=44.800000, rms=0.409 (0.335%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0583: dt=44.800000, rms=0.409 (0.126%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 1 iterations, nbhd size=0, neg = 0
0584: dt=44.800000, rms=0.408 (0.114%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 9 iterations, nbhd size=0, neg = 0
0585: dt=44.800000, rms=0.407 (0.175%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 10 iterations, nbhd size=1, neg = 0
0586: dt=44.800000, rms=0.407 (-0.013%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0587: dt=25.600000, rms=0.407 (0.009%), neg=0, invalid=762
0588: dt=0.125000, rms=0.407 (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=0.412, neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0589: dt=1.008000, rms=0.412 (0.006%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 9 iterations, nbhd size=1, neg = 0
0590: dt=0.864000, rms=0.412 (-0.028%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.412, neg=0, invalid=762
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0591: dt=4.032000, rms=0.412 (0.007%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0592: dt=2.880000, rms=0.412 (0.009%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0593: dt=1.728000, rms=0.412 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0594: dt=0.000050, rms=0.421 (0.000%), neg=0, invalid=762
0595: dt=0.000000, rms=0.421 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0596: dt=0.000000, rms=0.421 (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=0.406, neg=0, invalid=762
iter 0, gcam->neg = 578
after 19 iterations, nbhd size=1, neg = 0
0597: dt=1.377327, rms=0.396 (2.443%), neg=0, invalid=762
0598: dt=0.000023, rms=0.396 (0.000%), neg=0, invalid=762
0599: dt=0.000023, rms=0.396 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.396, neg=0, invalid=762
0600: dt=0.048000, rms=0.396 (0.014%), neg=0, invalid=762
0601: dt=0.016000, rms=0.396 (0.001%), neg=0, invalid=762
0602: dt=0.016000, rms=0.396 (-0.000%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 58 minutes and 56 seconds.
mri_ca_register utimesec    11751.542493
mri_ca_register stimesec    9.289587
mri_ca_register ru_maxrss   1352800
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4969927
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  62800
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    4070
mri_ca_register ru_nivcsw   16297
FSRUNTIME@ mri_ca_register  2.9823 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 04:58:41 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-924
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-6.0.0/0050555/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 7.84
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 = 0.10285 (11)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (978 voxels, overlap=0.235)
Left_Lateral_Ventricle (4): linear fit = 0.50 x + 0.0 (978 voxels, peak = 10), gca=9.9
gca peak = 0.17677 (13)
mri peak = 0.09166 (11)
Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (996 voxels, overlap=0.626)
Right_Lateral_Ventricle (43): linear fit = 0.77 x + 0.0 (996 voxels, peak = 10), gca=10.1
gca peak = 0.28129 (95)
mri peak = 0.10924 (97)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (714 voxels, overlap=1.013)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (714 voxels, peak = 96), gca=96.4
gca peak = 0.16930 (96)
mri peak = 0.09455 (101)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (825 voxels, overlap=0.870)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (825 voxels, peak = 100), gca=100.3
gca peak = 0.24553 (55)
mri peak = 0.07814 (58)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (963 voxels, overlap=1.009)
Right_Hippocampus (53): linear fit = 1.04 x + 0.0 (963 voxels, peak = 57), gca=57.5
gca peak = 0.30264 (59)
mri peak = 0.07834 (61)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (872 voxels, overlap=1.012)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (872 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.11746 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (59626 voxels, overlap=0.597)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (59626 voxels, peak = 105), gca=104.5
gca peak = 0.07714 (104)
mri peak = 0.12010 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (61910 voxels, overlap=0.465)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (61910 voxels, peak = 108), gca=107.6
gca peak = 0.09712 (58)
mri peak = 0.03703 (49)
Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (56400 voxels, overlap=0.725)
Left_Cerebral_Cortex (3): linear fit = 0.92 x + 0.0 (56400 voxels, peak = 53), gca=53.1
gca peak = 0.11620 (58)
mri peak = 0.04045 (51)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (53417 voxels, overlap=0.858)
Right_Cerebral_Cortex (42): linear fit = 0.92 x + 0.0 (53417 voxels, peak = 53), gca=53.1
gca peak = 0.30970 (66)
mri peak = 0.12124 (68)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1294 voxels, overlap=1.003)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1294 voxels, peak = 67), gca=67.0
gca peak = 0.15280 (69)
mri peak = 0.12516 (69)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (1178 voxels, overlap=0.587)
Left_Caudate (11): linear fit = 0.93 x + 0.0 (1178 voxels, peak = 64), gca=63.8
gca peak = 0.13902 (56)
mri peak = 0.05013 (57)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (33025 voxels, overlap=0.993)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (33025 voxels, peak = 59), gca=58.5
gca peak = 0.14777 (55)
mri peak = 0.05933 (60)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35580 voxels, overlap=0.971)
Right_Cerebellum_Cortex (47): linear fit = 1.07 x + 0.0 (35580 voxels, peak = 59), gca=58.6
gca peak = 0.16765 (84)
mri peak = 0.10916 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7621 voxels, overlap=0.729)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (7621 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.09806 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (8291 voxels, overlap=0.968)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (8291 voxels, peak = 85), gca=85.3
gca peak = 0.29869 (57)
mri peak = 0.08187 (61)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (424 voxels, overlap=1.000)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (424 voxels, peak = 60), gca=59.6
gca peak = 0.33601 (57)
mri peak = 0.11318 (61)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (591 voxels, overlap=0.998)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (591 voxels, peak = 60), gca=59.6
gca peak = 0.11131 (90)
mri peak = 0.07570 (87)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (5500 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (5500 voxels, peak = 89), gca=88.7
gca peak = 0.11793 (83)
mri peak = 0.08056 (84)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (6068 voxels, overlap=0.978)
Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (6068 voxels, peak = 84), gca=84.2
gca peak = 0.08324 (81)
mri peak = 0.06947 (79)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2303 voxels, overlap=0.905)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2303 voxels, peak = 83), gca=83.0
gca peak = 0.10360 (77)
mri peak = 0.07555 (81)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2740 voxels, overlap=0.996)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (2740 voxels, peak = 78), gca=78.2
gca peak = 0.08424 (78)
mri peak = 0.17284 (80)
Brain_Stem: unreasonable value (79.2/80.0), not in range [80, 110] - rejecting
gca peak = 0.12631 (89)
mri peak = 0.08207 (84)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1868 voxels, overlap=0.823)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1868 voxels, peak = 88), gca=87.7
gca peak = 0.14500 (87)
mri peak = 0.07662 (87)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1842 voxels, overlap=0.916)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1842 voxels, peak = 89), gca=89.2
gca peak = 0.14975 (24)
mri peak = 0.06257 (25)
Third_Ventricle (14): linear fit = 1.22 x + 0.0 (56 voxels, overlap=0.939)
Third_Ventricle (14): linear fit = 1.22 x + 0.0 (56 voxels, peak = 29), gca=29.2
gca peak = 0.19357 (14)
mri peak = 0.12970 (13)
Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (526 voxels, overlap=0.403)
Fourth_Ventricle (15): linear fit = 0.74 x + 0.0 (526 voxels, peak = 10), gca=10.3
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Brain_Stem = 0.08424 (78)
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 1.00 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 0.81 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.28825 (10)
mri peak = 0.10285 (11)
Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (978 voxels, overlap=1.000)
Left_Lateral_Ventricle (4): linear fit = 1.07 x + 0.0 (978 voxels, peak = 11), gca=10.7
gca peak = 0.23161 (10)
mri peak = 0.09166 (11)
Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (996 voxels, overlap=0.841)
Right_Lateral_Ventricle (43): linear fit = 0.88 x + 0.0 (996 voxels, peak =  9), gca=8.9
gca peak = 0.25969 (97)
mri peak = 0.10924 (97)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (714 voxels, overlap=1.013)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (714 voxels, peak = 97), gca=96.5
gca peak = 0.17104 (100)
mri peak = 0.09455 (101)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (825 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (825 voxels, peak = 100), gca=100.5
gca peak = 0.28858 (58)
mri peak = 0.07814 (58)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (963 voxels, overlap=1.008)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (963 voxels, peak = 57), gca=57.1
gca peak = 0.31664 (59)
mri peak = 0.07834 (61)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (872 voxels, overlap=1.009)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (872 voxels, peak = 60), gca=60.5
gca peak = 0.07771 (104)
mri peak = 0.11746 (104)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (59626 voxels, overlap=0.666)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (59626 voxels, peak = 104), gca=104.0
gca peak = 0.07684 (108)
mri peak = 0.12010 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61910 voxels, overlap=0.630)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61910 voxels, peak = 108), gca=108.0
gca peak = 0.10691 (53)
mri peak = 0.03703 (49)
Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (56400 voxels, overlap=0.996)
Left_Cerebral_Cortex (3): linear fit = 0.96 x + 0.0 (56400 voxels, peak = 51), gca=51.1
gca peak = 0.12609 (53)
mri peak = 0.04045 (51)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (53417 voxels, overlap=0.995)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (53417 voxels, peak = 52), gca=52.2
gca peak = 0.29570 (67)
mri peak = 0.12124 (68)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1294 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1294 voxels, peak = 67), gca=67.0
gca peak = 0.13199 (64)
mri peak = 0.12516 (69)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1178 voxels, overlap=0.873)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (1178 voxels, peak = 65), gca=65.0
gca peak = 0.13438 (57)
mri peak = 0.05013 (57)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (33025 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (33025 voxels, peak = 58), gca=58.4
gca peak = 0.13706 (58)
mri peak = 0.05933 (60)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (35580 voxels, overlap=0.994)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (35580 voxels, peak = 58), gca=58.0
gca peak = 0.15873 (90)
mri peak = 0.10916 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7621 voxels, overlap=0.957)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7621 voxels, peak = 90), gca=89.6
gca peak = 0.15633 (85)
mri peak = 0.09806 (83)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8291 voxels, overlap=0.983)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8291 voxels, peak = 85), gca=85.0
gca peak = 0.26844 (61)
mri peak = 0.08187 (61)
Left_Amygdala (18): linear fit = 1.03 x + 0.0 (424 voxels, overlap=1.033)
Left_Amygdala (18): linear fit = 1.03 x + 0.0 (424 voxels, peak = 63), gca=63.1
gca peak = 0.29016 (60)
mri peak = 0.11318 (61)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (591 voxels, overlap=1.020)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (591 voxels, peak = 62), gca=61.5
gca peak = 0.10107 (87)
mri peak = 0.07570 (87)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5500 voxels, overlap=0.997)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5500 voxels, peak = 87), gca=86.6
gca peak = 0.11233 (82)
mri peak = 0.08056 (84)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6068 voxels, overlap=0.987)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6068 voxels, peak = 82), gca=81.6
gca peak = 0.09216 (77)
mri peak = 0.06947 (79)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2303 voxels, overlap=0.972)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (2303 voxels, peak = 76), gca=75.8
gca peak = 0.08217 (78)
mri peak = 0.07555 (81)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2740 voxels, overlap=0.991)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2740 voxels, peak = 78), gca=78.0
gca peak = 0.08773 (80)
mri peak = 0.17284 (80)
Brain_Stem: unreasonable value (78.8/80.0), not in range [80, 110] - rejecting
gca peak = 0.11710 (87)
mri peak = 0.08207 (84)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1868 voxels, overlap=0.802)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1868 voxels, peak = 87), gca=86.6
gca peak = 0.14406 (89)
mri peak = 0.07662 (87)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1842 voxels, overlap=0.945)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1842 voxels, peak = 89), gca=88.6
gca peak = 0.17284 (31)
mri peak = 0.06257 (25)
Third_Ventricle (14): linear fit = 0.79 x + 0.0 (56 voxels, overlap=1.018)
Third_Ventricle (14): linear fit = 0.79 x + 0.0 (56 voxels, peak = 24), gca=24.3
gca peak = 0.22767 (12)
mri peak = 0.12970 (13)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (526 voxels, overlap=0.802)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (526 voxels, peak = 12), gca=12.4
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.17154 (28)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Brain_Stem = 0.08773 (80)
gca peak CSF = 0.27400 (29)
gca peak Left_Accumbens_area = 0.54646 (57)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.74536 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.22003 (24)
gca peak Right_Accumbens_area = 0.45042 (66)
gca peak Right_vessel = 0.82280 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.54107 (26)
gca peak WM_hypointensities = 0.07126 (78)
gca peak non_WM_hypointensities = 0.07502 (56)
gca peak Optic_Chiasm = 0.71110 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.94 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
58004 voxels changed in iteration 0 of unlikely voxel relabeling
151 voxels changed in iteration 1 of unlikely voxel relabeling
12 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
32521 gm and wm labels changed (%22 to gray, %78 to white out of all changed labels)
269 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 74313 changed. image ll: -2.150, PF=0.500
pass 2: 21985 changed. image ll: -2.149, PF=0.500
pass 3: 8354 changed.
pass 4: 3526 changed.
35455 voxels changed in iteration 0 of unlikely voxel relabeling
234 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6063 voxels changed in iteration 0 of unlikely voxel relabeling
87 voxels changed in iteration 1 of unlikely voxel relabeling
4 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5106 voxels changed in iteration 0 of unlikely voxel relabeling
34 voxels changed in iteration 1 of unlikely voxel relabeling
1 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
5667 voxels changed in iteration 0 of unlikely voxel relabeling
33 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
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    3554.942566
mri_ca_label stimesec    1.309800
mri_ca_label ru_maxrss   2111044
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   696958
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  512
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    263
mri_ca_label ru_nivcsw   4924
auto-labeling took 58 minutes and 31 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/transforms/cc_up.lta 0050555 

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-6.0.0/0050555/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/norm.mgz
43433 voxels in left wm, 70643 in right wm, xrange [123, 133]
searching rotation angles z=[-6  8], y=[-9  5]

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  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.5  
searching scale 1 Z rot 7.8  global minimum found at slice 128.5, rotations (-1.63, 1.02)
final transformation (x=128.5, yr=-1.631, zr=1.020):
 0.99944  -0.01780  -0.02846   4.88406;
 0.01779   0.99984  -0.00051   13.79026;
 0.02846   0.00000   0.99959   7.38979;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 112 117
eigenvectors:
-0.00069   0.00106   1.00000;
-0.06779  -0.99770   0.00101;
 0.99770  -0.06779   0.00076;
error in mid anterior detected - correcting...
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.0 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 05:58:14 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 05:58:14 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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...
2110 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 54 (54), valley at 19 (19)
csf peak at 27, setting threshold to 45
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 57 (57), valley at  0 (-1)
csf peak at 28, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 2 minutes and 57 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 06:01:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1936810 voxels in mask (pct= 11.54)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 06:01:15 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): 104.5 +- 5.2 [79.0 --> 125.0]
GM (71.0) : 69.5 +- 9.1 [30.0 --> 95.0]
setting bottom of white matter range to 78.5
setting top of gray matter range to 87.6
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...
3364 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4347 filled
3111 bright non-wm voxels segmented.
1545 diagonally connected voxels added...
white matter segmentation took 1.6 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.49 minutes
reading wm segmentation from wm.seg.mgz...
57 voxels added to wm to prevent paths from MTL structures to cortex
3277 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 45406 voxels turned on, 52564 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  12 found -  12 modified     |    TOTAL:  12
pass   2 (xy+):   0 found -  12 modified     |    TOTAL:  12
pass   1 (xy-):  11 found -  11 modified     |    TOTAL:  23
pass   2 (xy-):   0 found -  11 modified     |    TOTAL:  23
pass   1 (yz+):  19 found -  19 modified     |    TOTAL:  42
pass   2 (yz+):   0 found -  19 modified     |    TOTAL:  42
pass   1 (yz-):  16 found -  16 modified     |    TOTAL:  58
pass   2 (yz-):   0 found -  16 modified     |    TOTAL:  58
pass   1 (xz+):  13 found -  13 modified     |    TOTAL:  71
pass   2 (xz+):   0 found -  13 modified     |    TOTAL:  71
pass   1 (xz-):  21 found -  21 modified     |    TOTAL:  92
pass   2 (xz-):   0 found -  21 modified     |    TOTAL:  92
Iteration Number : 1
pass   1 (+++):  23 found -  23 modified     |    TOTAL:  23
pass   2 (+++):   0 found -  23 modified     |    TOTAL:  23
pass   1 (+++):  14 found -  14 modified     |    TOTAL:  37
pass   2 (+++):   0 found -  14 modified     |    TOTAL:  37
pass   1 (+++):  26 found -  26 modified     |    TOTAL:  63
pass   2 (+++):   0 found -  26 modified     |    TOTAL:  63
pass   1 (+++):  22 found -  22 modified     |    TOTAL:  85
pass   2 (+++):   0 found -  22 modified     |    TOTAL:  85
Iteration Number : 1
pass   1 (++):  42 found -  42 modified     |    TOTAL:  42
pass   2 (++):   0 found -  42 modified     |    TOTAL:  42
pass   1 (+-):  30 found -  30 modified     |    TOTAL:  72
pass   2 (+-):   0 found -  30 modified     |    TOTAL:  72
pass   1 (--):  55 found -  55 modified     |    TOTAL: 127
pass   2 (--):   0 found -  55 modified     |    TOTAL: 127
pass   1 (-+):  43 found -  43 modified     |    TOTAL: 170
pass   2 (-+):   0 found -  43 modified     |    TOTAL: 170
Iteration Number : 2
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:   6
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:   6
pass   1 (yz+):   6 found -   6 modified     |    TOTAL:  12
pass   2 (yz+):   0 found -   6 modified     |    TOTAL:  12
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  14
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  14
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  17
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  17
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  19
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  19
Iteration Number : 2
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
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   1 found -   1 modified     |    TOTAL:   3
pass   2 (--):   0 found -   1 modified     |    TOTAL:   3
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   5
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   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 = 377 (out of 689072: 0.054711)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 06:03:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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
 1.01376  -0.04150  -0.03616   5.98039;
 0.05031   1.00830   0.28543  -52.62672;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.01376  -0.04150  -0.03616   5.98039;
 0.05031   1.00830   0.28543  -52.62672;
 0.02608  -0.26379   0.92126   24.66513;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2376 (min = 350, max = 1400), aspect = 1.14 (min = 0.10, max = 0.75)
need search nearby
using seed (128, 109, 89), TAL = (0.0, -39.0, 19.0)
talairach voxel to voxel transform
 0.98349   0.04678   0.02410  -4.01419;
-0.03810   0.91560  -0.28517   55.44657;
-0.03875   0.26084   1.00314  -10.78340;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (128,  109,  89) --> (0.0, -39.0, 19.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (0.00, -39.00, 19.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(18.00, -39.00, 19.00) SRC: (111.41, 125.68, 102.66)
search lh wm seed point around talairach space (-18.00, -39.00, 19.00), SRC: (146.82, 124.30, 101.27)
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 06:04:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   3
pass   1 (yz+):   6 found -   6 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   6 modified     |    TOTAL:   9
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  12
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  12
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  16
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  16
pass   1 (xz-):   4 found -   4 modified     |    TOTAL:  20
pass   2 (xz-):   0 found -   4 modified     |    TOTAL:  20
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (--):   0 found -   0 modified     |    TOTAL:   3
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   5
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 25 (out of 329168: 0.007595)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 2914 vertices, 3109 faces
slice 60: 10724 vertices, 11061 faces
slice 70: 22047 vertices, 22454 faces
slice 80: 34078 vertices, 34479 faces
slice 90: 45028 vertices, 45418 faces
slice 100: 56400 vertices, 56812 faces
slice 110: 67930 vertices, 68365 faces
slice 120: 79712 vertices, 80116 faces
slice 130: 91103 vertices, 91542 faces
slice 140: 101749 vertices, 102188 faces
slice 150: 113483 vertices, 113899 faces
slice 160: 123164 vertices, 123531 faces
slice 170: 131618 vertices, 131988 faces
slice 180: 139111 vertices, 139414 faces
slice 190: 145760 vertices, 146053 faces
slice 200: 151058 vertices, 151292 faces
slice 210: 154615 vertices, 154776 faces
slice 220: 154968 vertices, 155052 faces
slice 230: 154968 vertices, 155052 faces
slice 240: 154968 vertices, 155052 faces
slice 250: 154968 vertices, 155052 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...
   154968 voxel in cpt #1: X=-84 [v=154968,e=465156,f=310104] located at (-28.198854, -8.854305, 4.758227)
For the whole surface: X=-84 [v=154968,e=465156,f=310104]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 06:04:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   4
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   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 = 9 (out of 334449: 0.002691)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 1747 vertices, 1900 faces
slice 60: 8007 vertices, 8230 faces
slice 70: 17105 vertices, 17481 faces
slice 80: 28272 vertices, 28647 faces
slice 90: 39786 vertices, 40202 faces
slice 100: 51439 vertices, 51854 faces
slice 110: 63446 vertices, 63888 faces
slice 120: 75661 vertices, 76117 faces
slice 130: 87164 vertices, 87587 faces
slice 140: 98726 vertices, 99188 faces
slice 150: 110164 vertices, 110606 faces
slice 160: 121872 vertices, 122279 faces
slice 170: 130939 vertices, 131274 faces
slice 180: 139902 vertices, 140237 faces
slice 190: 147012 vertices, 147295 faces
slice 200: 152653 vertices, 152901 faces
slice 210: 156625 vertices, 156772 faces
slice 220: 157234 vertices, 157304 faces
slice 230: 157234 vertices, 157304 faces
slice 240: 157234 vertices, 157304 faces
slice 250: 157234 vertices, 157304 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...
   157234 voxel in cpt #1: X=-70 [v=157234,e=471912,f=314608] located at (27.428068, -4.971584, 5.411082)
For the whole surface: X=-70 [v=157234,e=471912,f=314608]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 06:04:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 06:04:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

Waiting for PID 2133 of (2133 2136) to complete...
Waiting for PID 2136 of (2133 2136) 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 (2133 2136) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 06:04:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 06:04:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

Waiting for PID 2183 of (2183 2186) to complete...
Waiting for PID 2186 of (2183 2186) 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 = 50.5 mm, total surface area = 83732 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.153 (target=0.015)   
step 005: RMS=0.118 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.076 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.059 (target=0.015)   
step 030: RMS=0.054 (target=0.015)   
step 035: RMS=0.050 (target=0.015)   
step 040: RMS=0.048 (target=0.015)   
step 045: RMS=0.046 (target=0.015)   
step 050: RMS=0.044 (target=0.015)   
step 055: RMS=0.043 (target=0.015)   
step 060: RMS=0.043 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    51.033241
mris_inflate stimesec    0.118981
mris_inflate ru_maxrss   225792
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32368
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10904
mris_inflate ru_oublock  10920
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2186
mris_inflate ru_nivcsw   4273

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 49.9 mm, total surface area = 84974 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.154 (target=0.015)   
step 005: RMS=0.119 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.078 (target=0.015)   
step 020: RMS=0.069 (target=0.015)   
step 025: RMS=0.064 (target=0.015)   
step 030: RMS=0.057 (target=0.015)   
step 035: RMS=0.053 (target=0.015)   
step 040: RMS=0.050 (target=0.015)   
step 045: RMS=0.049 (target=0.015)   
step 050: RMS=0.048 (target=0.015)   
step 055: RMS=0.047 (target=0.015)   
step 060: RMS=0.047 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    51.628151
mris_inflate stimesec    0.114982
mris_inflate ru_maxrss   228652
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32578
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11080
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2167
mris_inflate ru_nivcsw   3940
PIDs (2183 2186) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 06:05:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 06:05:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

Waiting for PID 2251 of (2251 2255) to complete...
Waiting for PID 2255 of (2251 2255) 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 0.92 +- 0.56 (0.00-->6.10) (max @ vno 85199 --> 86317)
face area 0.02 +- 0.03 (-0.24-->0.56)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.294...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.386, avgs=0
005/300: dt: 0.9000, rms radial error=176.126, avgs=0
010/300: dt: 0.9000, rms radial error=175.569, avgs=0
015/300: dt: 0.9000, rms radial error=174.836, avgs=0
020/300: dt: 0.9000, rms radial error=174.000, avgs=0
025/300: dt: 0.9000, rms radial error=173.106, avgs=0
030/300: dt: 0.9000, rms radial error=172.180, avgs=0
035/300: dt: 0.9000, rms radial error=171.235, avgs=0
040/300: dt: 0.9000, rms radial error=170.281, avgs=0
045/300: dt: 0.9000, rms radial error=169.324, avgs=0
050/300: dt: 0.9000, rms radial error=168.368, avgs=0
055/300: dt: 0.9000, rms radial error=167.413, avgs=0
060/300: dt: 0.9000, rms radial error=166.463, avgs=0
065/300: dt: 0.9000, rms radial error=165.524, avgs=0
070/300: dt: 0.9000, rms radial error=164.590, avgs=0
075/300: dt: 0.9000, rms radial error=163.660, avgs=0
080/300: dt: 0.9000, rms radial error=162.735, avgs=0
085/300: dt: 0.9000, rms radial error=161.815, avgs=0
090/300: dt: 0.9000, rms radial error=160.900, avgs=0
095/300: dt: 0.9000, rms radial error=159.991, avgs=0
100/300: dt: 0.9000, rms radial error=159.092, avgs=0
105/300: dt: 0.9000, rms radial error=158.198, avgs=0
110/300: dt: 0.9000, rms radial error=157.309, avgs=0
115/300: dt: 0.9000, rms radial error=156.426, avgs=0
120/300: dt: 0.9000, rms radial error=155.548, avgs=0
125/300: dt: 0.9000, rms radial error=154.675, avgs=0
130/300: dt: 0.9000, rms radial error=153.806, avgs=0
135/300: dt: 0.9000, rms radial error=152.943, avgs=0
140/300: dt: 0.9000, rms radial error=152.084, avgs=0
145/300: dt: 0.9000, rms radial error=151.230, avgs=0
150/300: dt: 0.9000, rms radial error=150.381, avgs=0
155/300: dt: 0.9000, rms radial error=149.537, avgs=0
160/300: dt: 0.9000, rms radial error=148.697, avgs=0
165/300: dt: 0.9000, rms radial error=147.861, avgs=0
170/300: dt: 0.9000, rms radial error=147.031, avgs=0
175/300: dt: 0.9000, rms radial error=146.205, avgs=0
180/300: dt: 0.9000, rms radial error=145.383, avgs=0
185/300: dt: 0.9000, rms radial error=144.566, avgs=0
190/300: dt: 0.9000, rms radial error=143.753, avgs=0
195/300: dt: 0.9000, rms radial error=142.946, avgs=0
200/300: dt: 0.9000, rms radial error=142.142, avgs=0
205/300: dt: 0.9000, rms radial error=141.343, avgs=0
210/300: dt: 0.9000, rms radial error=140.548, avgs=0
215/300: dt: 0.9000, rms radial error=139.758, avgs=0
220/300: dt: 0.9000, rms radial error=138.972, avgs=0
225/300: dt: 0.9000, rms radial error=138.190, avgs=0
230/300: dt: 0.9000, rms radial error=137.413, avgs=0
235/300: dt: 0.9000, rms radial error=136.640, avgs=0
240/300: dt: 0.9000, rms radial error=135.871, avgs=0
245/300: dt: 0.9000, rms radial error=135.107, avgs=0
250/300: dt: 0.9000, rms radial error=134.347, avgs=0
255/300: dt: 0.9000, rms radial error=133.591, avgs=0
260/300: dt: 0.9000, rms radial error=132.839, avgs=0
265/300: dt: 0.9000, rms radial error=132.091, avgs=0
270/300: dt: 0.9000, rms radial error=131.347, avgs=0
275/300: dt: 0.9000, rms radial error=130.608, avgs=0
280/300: dt: 0.9000, rms radial error=129.873, avgs=0
285/300: dt: 0.9000, rms radial error=129.141, avgs=0
290/300: dt: 0.9000, rms radial error=128.414, avgs=0
295/300: dt: 0.9000, rms radial error=127.691, avgs=0
300/300: dt: 0.9000, rms radial error=126.972, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18421.77
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00014
epoch 2 (K=40.0), pass 1, starting sse = 3217.64
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
epoch 3 (K=160.0), pass 1, starting sse = 373.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/11 = 0.00669
epoch 4 (K=640.0), pass 1, starting sse = 30.97
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/13 = 0.00726
final distance error %28.77
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    290.980764
mris_sphere stimesec    0.209968
mris_sphere ru_maxrss   226008
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   32419
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10944
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    12361
mris_sphere ru_nivcsw   23862
FSRUNTIME@ mris_sphere  0.0797 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 0.92 +- 0.55 (0.00-->6.30) (max @ vno 113299 --> 114434)
face area 0.02 +- 0.03 (-0.22-->0.52)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.293...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.501, avgs=0
005/300: dt: 0.9000, rms radial error=176.244, avgs=0
010/300: dt: 0.9000, rms radial error=175.686, avgs=0
015/300: dt: 0.9000, rms radial error=174.951, avgs=0
020/300: dt: 0.9000, rms radial error=174.120, avgs=0
025/300: dt: 0.9000, rms radial error=173.231, avgs=0
030/300: dt: 0.9000, rms radial error=172.311, avgs=0
035/300: dt: 0.9000, rms radial error=171.374, avgs=0
040/300: dt: 0.9000, rms radial error=170.430, avgs=0
045/300: dt: 0.9000, rms radial error=169.483, avgs=0
050/300: dt: 0.9000, rms radial error=168.538, avgs=0
055/300: dt: 0.9000, rms radial error=167.595, avgs=0
060/300: dt: 0.9000, rms radial error=166.656, avgs=0
065/300: dt: 0.9000, rms radial error=165.722, avgs=0
070/300: dt: 0.9000, rms radial error=164.792, avgs=0
075/300: dt: 0.9000, rms radial error=163.867, avgs=0
080/300: dt: 0.9000, rms radial error=162.946, avgs=0
085/300: dt: 0.9000, rms radial error=162.031, avgs=0
090/300: dt: 0.9000, rms radial error=161.120, avgs=0
095/300: dt: 0.9000, rms radial error=160.215, avgs=0
100/300: dt: 0.9000, rms radial error=159.314, avgs=0
105/300: dt: 0.9000, rms radial error=158.418, avgs=0
110/300: dt: 0.9000, rms radial error=157.526, avgs=0
115/300: dt: 0.9000, rms radial error=156.640, avgs=0
120/300: dt: 0.9000, rms radial error=155.758, avgs=0
125/300: dt: 0.9000, rms radial error=154.881, avgs=0
130/300: dt: 0.9000, rms radial error=154.010, avgs=0
135/300: dt: 0.9000, rms radial error=153.143, avgs=0
140/300: dt: 0.9000, rms radial error=152.281, avgs=0
145/300: dt: 0.9000, rms radial error=151.425, avgs=0
150/300: dt: 0.9000, rms radial error=150.573, avgs=0
155/300: dt: 0.9000, rms radial error=149.727, avgs=0
160/300: dt: 0.9000, rms radial error=148.887, avgs=0
165/300: dt: 0.9000, rms radial error=148.052, avgs=0
170/300: dt: 0.9000, rms radial error=147.221, avgs=0
175/300: dt: 0.9000, rms radial error=146.395, avgs=0
180/300: dt: 0.9000, rms radial error=145.573, avgs=0
185/300: dt: 0.9000, rms radial error=144.756, avgs=0
190/300: dt: 0.9000, rms radial error=143.943, avgs=0
195/300: dt: 0.9000, rms radial error=143.135, avgs=0
200/300: dt: 0.9000, rms radial error=142.331, avgs=0
205/300: dt: 0.9000, rms radial error=141.532, avgs=0
210/300: dt: 0.9000, rms radial error=140.737, avgs=0
215/300: dt: 0.9000, rms radial error=139.947, avgs=0
220/300: dt: 0.9000, rms radial error=139.160, avgs=0
225/300: dt: 0.9000, rms radial error=138.378, avgs=0
230/300: dt: 0.9000, rms radial error=137.601, avgs=0
235/300: dt: 0.9000, rms radial error=136.828, avgs=0
240/300: dt: 0.9000, rms radial error=136.059, avgs=0
245/300: dt: 0.9000, rms radial error=135.294, avgs=0
250/300: dt: 0.9000, rms radial error=134.533, avgs=0
255/300: dt: 0.9000, rms radial error=133.777, avgs=0
260/300: dt: 0.9000, rms radial error=133.025, avgs=0
265/300: dt: 0.9000, rms radial error=132.277, avgs=0
270/300: dt: 0.9000, rms radial error=131.533, avgs=0
275/300: dt: 0.9000, rms radial error=130.793, avgs=0
280/300: dt: 0.9000, rms radial error=130.057, avgs=0
285/300: dt: 0.9000, rms radial error=129.326, avgs=0
290/300: dt: 0.9000, rms radial error=128.598, avgs=0
295/300: dt: 0.9000, rms radial error=127.875, avgs=0
300/300: dt: 0.9000, rms radial error=127.156, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 18664.05
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00011
epoch 2 (K=40.0), pass 1, starting sse = 3215.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 3 (K=160.0), pass 1, starting sse = 359.00
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00476
epoch 4 (K=640.0), pass 1, starting sse = 31.74
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/11 = 0.00757
final distance error %27.07
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
mris_sphere utimesec    279.577497
mris_sphere stimesec    0.227965
mris_sphere ru_maxrss   228864
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   33132
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  11064
mris_sphere ru_oublock  11104
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    13630
mris_sphere ru_nivcsw   22268
FSRUNTIME@ mris_sphere  0.0778 hours 1 threads
PIDs (2251 2255) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 06:10:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 06:10:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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


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

#@# Fix Topology lh Sun Oct  8 06:10:01 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050555 lh 

#@# Fix Topology rh Sun Oct  8 06:10:01 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050555 rh 

Waiting for PID 2650 of (2650 2653) to complete...
Waiting for PID 2653 of (2650 2653) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050555 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=-84 (nv=154968, nf=310104, ne=465156, g=43)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 8 iterations
marking ambiguous vertices...
10457 ambiguous faces found in tessellation
segmenting defects...
41 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 22 into 21
      -merging segment 35 into 29
39 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3083  (-4.6542)
      -vertex     loglikelihood: -6.2378  (-3.1189)
      -normal dot loglikelihood: -3.5878  (-3.5878)
      -quad curv  loglikelihood: -6.0187  (-3.0094)
      Total Loglikelihood : -25.1527

CORRECTING DEFECT 0 (vertices=13, convex hull=29, v0=347)
After retessellation of defect 0 (v0=347), euler #=-34 (148892,444853,295927) : difference with theory (-36) = -2 

CORRECTING DEFECT 1 (vertices=19, convex hull=52, v0=5347)
After retessellation of defect 1 (v0=5347), euler #=-33 (148901,444900,295966) : difference with theory (-35) = -2 

CORRECTING DEFECT 2 (vertices=19, convex hull=56, v0=6147)
After retessellation of defect 2 (v0=6147), euler #=-32 (148909,444944,296003) : difference with theory (-34) = -2 

CORRECTING DEFECT 3 (vertices=53, convex hull=97, v0=9855)
After retessellation of defect 3 (v0=9855), euler #=-31 (148944,445089,296114) : difference with theory (-33) = -2 

CORRECTING DEFECT 4 (vertices=205, convex hull=185, v0=9963)
After retessellation of defect 4 (v0=9963), euler #=-30 (148993,445324,296301) : difference with theory (-32) = -2 

CORRECTING DEFECT 5 (vertices=18, convex hull=39, v0=18062)
After retessellation of defect 5 (v0=18062), euler #=-29 (148998,445356,296329) : difference with theory (-31) = -2 

CORRECTING DEFECT 6 (vertices=39, convex hull=52, v0=25321)
After retessellation of defect 6 (v0=25321), euler #=-28 (149007,445404,296369) : difference with theory (-30) = -2 

CORRECTING DEFECT 7 (vertices=26, convex hull=82, v0=35016)
After retessellation of defect 7 (v0=35016), euler #=-27 (149021,445475,296427) : difference with theory (-29) = -2 

CORRECTING DEFECT 8 (vertices=8, convex hull=25, v0=44735)
After retessellation of defect 8 (v0=44735), euler #=-26 (149024,445492,296442) : difference with theory (-28) = -2 

CORRECTING DEFECT 9 (vertices=40, convex hull=64, v0=52366)
After retessellation of defect 9 (v0=52366), euler #=-25 (149043,445574,296506) : difference with theory (-27) = -2 

CORRECTING DEFECT 10 (vertices=77, convex hull=102, v0=53748)
After retessellation of defect 10 (v0=53748), euler #=-24 (149082,445744,296638) : difference with theory (-26) = -2 

CORRECTING DEFECT 11 (vertices=38, convex hull=83, v0=58032)
After retessellation of defect 11 (v0=58032), euler #=-23 (149108,445857,296726) : difference with theory (-25) = -2 

CORRECTING DEFECT 12 (vertices=329, convex hull=203, v0=59381)
After retessellation of defect 12 (v0=59381), euler #=-22 (149169,446138,296947) : difference with theory (-24) = -2 

CORRECTING DEFECT 13 (vertices=16, convex hull=18, v0=63150)
After retessellation of defect 13 (v0=63150), euler #=-21 (149170,446146,296955) : difference with theory (-23) = -2 

CORRECTING DEFECT 14 (vertices=3100, convex hull=989, v0=65011)
XL defect detected...
After retessellation of defect 14 (v0=65011), euler #=-23 (149666,448179,298490) : difference with theory (-22) = 1 

CORRECTING DEFECT 15 (vertices=6, convex hull=18, v0=67501)
After retessellation of defect 15 (v0=67501), euler #=-22 (149668,448189,298499) : difference with theory (-21) = 1 

CORRECTING DEFECT 16 (vertices=7, convex hull=30, v0=68901)
After retessellation of defect 16 (v0=68901), euler #=-21 (149671,448206,298514) : difference with theory (-20) = 1 

CORRECTING DEFECT 17 (vertices=326, convex hull=358, v0=74842)
After retessellation of defect 17 (v0=74842), euler #=-20 (149836,448866,299010) : difference with theory (-19) = 1 

CORRECTING DEFECT 18 (vertices=39, convex hull=74, v0=75958)
After retessellation of defect 18 (v0=75958), euler #=-19 (149860,448968,299089) : difference with theory (-18) = 1 

CORRECTING DEFECT 19 (vertices=27, convex hull=51, v0=90846)
After retessellation of defect 19 (v0=90846), euler #=-18 (149871,449019,299130) : difference with theory (-17) = 1 

CORRECTING DEFECT 20 (vertices=28, convex hull=28, v0=96265)
After retessellation of defect 20 (v0=96265), euler #=-17 (149878,449048,299153) : difference with theory (-16) = 1 

CORRECTING DEFECT 21 (vertices=144, convex hull=92, v0=105847)
After retessellation of defect 21 (v0=105847), euler #=-15 (149908,449183,299260) : difference with theory (-15) = 0 

CORRECTING DEFECT 22 (vertices=34, convex hull=45, v0=109704)
After retessellation of defect 22 (v0=109704), euler #=-14 (149924,449249,299311) : difference with theory (-14) = 0 

CORRECTING DEFECT 23 (vertices=328, convex hull=88, v0=113132)
After retessellation of defect 23 (v0=113132), euler #=-13 (149946,449358,299399) : difference with theory (-13) = 0 

CORRECTING DEFECT 24 (vertices=26, convex hull=50, v0=113186)
After retessellation of defect 24 (v0=113186), euler #=-12 (149955,449398,299431) : difference with theory (-12) = 0 

CORRECTING DEFECT 25 (vertices=11, convex hull=25, v0=116299)
After retessellation of defect 25 (v0=116299), euler #=-11 (149955,449405,299439) : difference with theory (-11) = 0 

CORRECTING DEFECT 26 (vertices=7, convex hull=13, v0=116309)
After retessellation of defect 26 (v0=116309), euler #=-10 (149958,449416,299448) : difference with theory (-10) = 0 

CORRECTING DEFECT 27 (vertices=36, convex hull=61, v0=122028)
After retessellation of defect 27 (v0=122028), euler #=-9 (149971,449475,299495) : difference with theory (-9) = 0 

CORRECTING DEFECT 28 (vertices=247, convex hull=188, v0=123804)
After retessellation of defect 28 (v0=123804), euler #=-8 (150038,449779,299733) : difference with theory (-8) = 0 

CORRECTING DEFECT 29 (vertices=37, convex hull=85, v0=124806)
After retessellation of defect 29 (v0=124806), euler #=-7 (150058,449874,299809) : difference with theory (-7) = 0 

CORRECTING DEFECT 30 (vertices=53, convex hull=33, v0=125199)
After retessellation of defect 30 (v0=125199), euler #=-6 (150070,449920,299844) : difference with theory (-6) = 0 

CORRECTING DEFECT 31 (vertices=124, convex hull=54, v0=126170)
After retessellation of defect 31 (v0=126170), euler #=-5 (150088,449997,299904) : difference with theory (-5) = 0 

CORRECTING DEFECT 32 (vertices=26, convex hull=60, v0=128752)
After retessellation of defect 32 (v0=128752), euler #=-4 (150098,450053,299951) : difference with theory (-4) = 0 

CORRECTING DEFECT 33 (vertices=76, convex hull=86, v0=129390)
After retessellation of defect 33 (v0=129390), euler #=-3 (150136,450208,300069) : difference with theory (-3) = 0 

CORRECTING DEFECT 34 (vertices=169, convex hull=82, v0=133642)
After retessellation of defect 34 (v0=133642), euler #=-2 (150153,450294,300139) : difference with theory (-2) = 0 

CORRECTING DEFECT 35 (vertices=111, convex hull=126, v0=137903)
After retessellation of defect 35 (v0=137903), euler #=-1 (150194,450472,300277) : difference with theory (-1) = 0 

CORRECTING DEFECT 36 (vertices=147, convex hull=114, v0=143833)
After retessellation of defect 36 (v0=143833), euler #=0 (150230,450636,300406) : difference with theory (0) = 0 

CORRECTING DEFECT 37 (vertices=35, convex hull=68, v0=148284)
After retessellation of defect 37 (v0=148284), euler #=1 (150239,450687,300449) : difference with theory (1) = 0 

CORRECTING DEFECT 38 (vertices=29, convex hull=60, v0=153759)
After retessellation of defect 38 (v0=153759), euler #=2 (150248,450738,300492) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.08-->9.26) (max @ vno 139841 --> 143124)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.23 (0.08-->9.26) (max @ vno 139841 --> 143124)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
140 mutations (32.7%), 288 crossovers (67.3%), 380 vertices were eliminated
building final representation...
4720 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=150248, nf=300492, ne=450738, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 41.2 minutes
0 defective edges
removing intersecting faces
000: 299 intersecting
001: 18 intersecting
002: 3 intersecting
mris_fix_topology utimesec    2473.751932
mris_fix_topology stimesec    0.229965
mris_fix_topology ru_maxrss   503788
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   59713
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  10904
mris_fix_topology ru_oublock  14448
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    458
mris_fix_topology ru_nivcsw   13299
FSRUNTIME@ mris_fix_topology lh  0.6871 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050555 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=-70 (nv=157234, nf=314608, ne=471912, g=36)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 8 iterations
marking ambiguous vertices...
10114 ambiguous faces found in tessellation
segmenting defects...
48 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 3 into 2
      -merging segment 18 into 16
      -merging segment 30 into 16
      -merging segment 29 into 27
44 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2953  (-4.6476)
      -vertex     loglikelihood: -6.2185  (-3.1092)
      -normal dot loglikelihood: -3.5542  (-3.5542)
      -quad curv  loglikelihood: -5.7741  (-2.8871)
      Total Loglikelihood : -24.8421

CORRECTING DEFECT 0 (vertices=273, convex hull=164, v0=49)
After retessellation of defect 0 (v0=49), euler #=-42 (151415,452558,301101) : difference with theory (-41) = 1 

CORRECTING DEFECT 1 (vertices=52, convex hull=77, v0=8018)
After retessellation of defect 1 (v0=8018), euler #=-41 (151441,452669,301187) : difference with theory (-40) = 1 

CORRECTING DEFECT 2 (vertices=325, convex hull=264, v0=8197)
After retessellation of defect 2 (v0=8197), euler #=-40 (151570,453184,301574) : difference with theory (-39) = 1 

CORRECTING DEFECT 3 (vertices=55, convex hull=28, v0=16729)
After retessellation of defect 3 (v0=16729), euler #=-39 (151576,453209,301594) : difference with theory (-38) = 1 

CORRECTING DEFECT 4 (vertices=41, convex hull=98, v0=22905)
After retessellation of defect 4 (v0=22905), euler #=-38 (151599,453318,301681) : difference with theory (-37) = 1 

CORRECTING DEFECT 5 (vertices=56, convex hull=56, v0=23402)
After retessellation of defect 5 (v0=23402), euler #=-37 (151607,453362,301718) : difference with theory (-36) = 1 

CORRECTING DEFECT 6 (vertices=59, convex hull=92, v0=27006)
After retessellation of defect 6 (v0=27006), euler #=-36 (151636,453489,301817) : difference with theory (-35) = 1 

CORRECTING DEFECT 7 (vertices=26, convex hull=56, v0=30764)
After retessellation of defect 7 (v0=30764), euler #=-35 (151651,453555,301869) : difference with theory (-34) = 1 

CORRECTING DEFECT 8 (vertices=38, convex hull=77, v0=48663)
After retessellation of defect 8 (v0=48663), euler #=-34 (151677,453668,301957) : difference with theory (-33) = 1 

CORRECTING DEFECT 9 (vertices=66, convex hull=83, v0=50735)
After retessellation of defect 9 (v0=50735), euler #=-33 (151718,453826,302075) : difference with theory (-32) = 1 

CORRECTING DEFECT 10 (vertices=302, convex hull=197, v0=59501)
After retessellation of defect 10 (v0=59501), euler #=-32 (151783,454115,302300) : difference with theory (-31) = 1 

CORRECTING DEFECT 11 (vertices=233, convex hull=199, v0=63384)
After retessellation of defect 11 (v0=63384), euler #=-32 (151873,454496,302591) : difference with theory (-30) = 2 

CORRECTING DEFECT 12 (vertices=6, convex hull=19, v0=65405)
After retessellation of defect 12 (v0=65405), euler #=-31 (151875,454507,302601) : difference with theory (-29) = 2 

CORRECTING DEFECT 13 (vertices=143, convex hull=147, v0=81254)
After retessellation of defect 13 (v0=81254), euler #=-30 (151956,454822,302836) : difference with theory (-28) = 2 

CORRECTING DEFECT 14 (vertices=15, convex hull=21, v0=88167)
After retessellation of defect 14 (v0=88167), euler #=-29 (151957,454832,302846) : difference with theory (-27) = 2 

CORRECTING DEFECT 15 (vertices=1470, convex hull=728, v0=89009)
XL defect detected...
After retessellation of defect 15 (v0=89009), euler #=-27 (152378,456477,304072) : difference with theory (-26) = 1 

CORRECTING DEFECT 16 (vertices=48, convex hull=87, v0=92183)
After retessellation of defect 16 (v0=92183), euler #=-26 (152412,456618,304180) : difference with theory (-25) = 1 

CORRECTING DEFECT 17 (vertices=21, convex hull=22, v0=96059)
After retessellation of defect 17 (v0=96059), euler #=-25 (152415,456631,304191) : difference with theory (-24) = 1 

CORRECTING DEFECT 18 (vertices=28, convex hull=29, v0=99657)
After retessellation of defect 18 (v0=99657), euler #=-24 (152420,456655,304211) : difference with theory (-23) = 1 

CORRECTING DEFECT 19 (vertices=24, convex hull=28, v0=101967)
After retessellation of defect 19 (v0=101967), euler #=-23 (152422,456671,304226) : difference with theory (-22) = 1 

CORRECTING DEFECT 20 (vertices=9, convex hull=30, v0=103197)
After retessellation of defect 20 (v0=103197), euler #=-22 (152425,456690,304243) : difference with theory (-21) = 1 

CORRECTING DEFECT 21 (vertices=18, convex hull=20, v0=107595)
After retessellation of defect 21 (v0=107595), euler #=-21 (152426,456697,304250) : difference with theory (-20) = 1 

CORRECTING DEFECT 22 (vertices=22, convex hull=52, v0=108726)
After retessellation of defect 22 (v0=108726), euler #=-20 (152435,456744,304289) : difference with theory (-19) = 1 

CORRECTING DEFECT 23 (vertices=346, convex hull=110, v0=110143)
After retessellation of defect 23 (v0=110143), euler #=-19 (152453,456846,304374) : difference with theory (-18) = 1 

CORRECTING DEFECT 24 (vertices=142, convex hull=43, v0=112170)
After retessellation of defect 24 (v0=112170), euler #=-18 (152460,456879,304401) : difference with theory (-17) = 1 

CORRECTING DEFECT 25 (vertices=40, convex hull=48, v0=114441)
After retessellation of defect 25 (v0=114441), euler #=-16 (152463,456908,304429) : difference with theory (-16) = 0 

CORRECTING DEFECT 26 (vertices=19, convex hull=23, v0=114458)
After retessellation of defect 26 (v0=114458), euler #=-15 (152464,456917,304438) : difference with theory (-15) = 0 

CORRECTING DEFECT 27 (vertices=896, convex hull=280, v0=116883)
After retessellation of defect 27 (v0=116883), euler #=-14 (152649,457609,304946) : difference with theory (-14) = 0 

CORRECTING DEFECT 28 (vertices=87, convex hull=40, v0=121631)
After retessellation of defect 28 (v0=121631), euler #=-13 (152675,457701,305013) : difference with theory (-13) = 0 

CORRECTING DEFECT 29 (vertices=32, convex hull=68, v0=122028)
After retessellation of defect 29 (v0=122028), euler #=-12 (152694,457783,305077) : difference with theory (-12) = 0 

CORRECTING DEFECT 30 (vertices=40, convex hull=35, v0=124624)
After retessellation of defect 30 (v0=124624), euler #=-11 (152702,457817,305104) : difference with theory (-11) = 0 

CORRECTING DEFECT 31 (vertices=47, convex hull=44, v0=127459)
After retessellation of defect 31 (v0=127459), euler #=-10 (152719,457883,305154) : difference with theory (-10) = 0 

CORRECTING DEFECT 32 (vertices=73, convex hull=127, v0=128376)
After retessellation of defect 32 (v0=128376), euler #=-9 (152761,458068,305298) : difference with theory (-9) = 0 

CORRECTING DEFECT 33 (vertices=207, convex hull=48, v0=130751)
After retessellation of defect 33 (v0=130751), euler #=-8 (152777,458138,305353) : difference with theory (-8) = 0 

CORRECTING DEFECT 34 (vertices=12, convex hull=21, v0=130788)
After retessellation of defect 34 (v0=130788), euler #=-7 (152780,458153,305366) : difference with theory (-7) = 0 

CORRECTING DEFECT 35 (vertices=34, convex hull=55, v0=135210)
After retessellation of defect 35 (v0=135210), euler #=-6 (152796,458221,305419) : difference with theory (-6) = 0 

CORRECTING DEFECT 36 (vertices=176, convex hull=64, v0=136827)
After retessellation of defect 36 (v0=136827), euler #=-5 (152807,458281,305469) : difference with theory (-5) = 0 

CORRECTING DEFECT 37 (vertices=51, convex hull=87, v0=138850)
After retessellation of defect 37 (v0=138850), euler #=-4 (152836,458404,305564) : difference with theory (-4) = 0 

CORRECTING DEFECT 38 (vertices=181, convex hull=39, v0=141919)
After retessellation of defect 38 (v0=141919), euler #=-3 (152847,458453,305603) : difference with theory (-3) = 0 

CORRECTING DEFECT 39 (vertices=20, convex hull=61, v0=151677)
After retessellation of defect 39 (v0=151677), euler #=-2 (152858,458513,305653) : difference with theory (-2) = 0 

CORRECTING DEFECT 40 (vertices=38, convex hull=35, v0=155544)
After retessellation of defect 40 (v0=155544), euler #=-1 (152860,458531,305670) : difference with theory (-1) = 0 

CORRECTING DEFECT 41 (vertices=41, convex hull=33, v0=155698)
After retessellation of defect 41 (v0=155698), euler #=0 (152865,458559,305694) : difference with theory (0) = 0 

CORRECTING DEFECT 42 (vertices=38, convex hull=45, v0=156401)
After retessellation of defect 42 (v0=156401), euler #=1 (152867,458586,305720) : difference with theory (1) = 0 

CORRECTING DEFECT 43 (vertices=14, convex hull=24, v0=156809)
After retessellation of defect 43 (v0=156809), euler #=2 (152869,458601,305734) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.06-->11.86) (max @ vno 1277 --> 1821)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.23 (0.06-->11.86) (max @ vno 1277 --> 1821)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
156 mutations (36.4%), 273 crossovers (63.6%), 124 vertices were eliminated
building final representation...
4365 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=152869, nf=305734, ne=458601, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 29.4 minutes
0 defective edges
removing intersecting faces
000: 395 intersecting
001: 18 intersecting
002: 2 intersecting
mris_fix_topology utimesec    1765.059670
mris_fix_topology stimesec    0.195970
mris_fix_topology ru_maxrss   502420
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   58177
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  0
mris_fix_topology ru_oublock  14680
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    545
mris_fix_topology ru_nivcsw   6293
FSRUNTIME@ mris_fix_topology rh  0.4904 hours 1 threads
PIDs (2650 2653) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 150248 - 450738 + 300492 = 2 --> 0 holes
      F =2V-4:          300492 = 300496-4 (0)
      2E=3F:            901476 = 901476 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 152869 - 458601 + 305734 = 2 --> 0 holes
      F =2V-4:          305734 = 305738-4 (0)
      2E=3F:            917202 = 917202 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 63 intersecting
001: 15 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 132 intersecting
001: 2 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 06:51:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050555 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 06:51:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050555 rh 

Waiting for PID 5165 of (5165 5168) to complete...
Waiting for PID 5168 of (5165 5168) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050555 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-6.0.0/0050555/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
13986 bright wm thresholded.
3252 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.orig...
computing class statistics...
border white:    292054 voxels (1.74%)
border gray      329646 voxels (1.96%)
WM (96.0): 96.5 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 53.6 (was 70)
setting MAX_BORDER_WHITE to 109.5 (was 105)
setting MIN_BORDER_WHITE to 64.0 (was 85)
setting MAX_CSF to 43.2 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.8 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.83 +- 0.22 (0.03-->5.20) (max @ vno 119014 --> 150012)
face area 0.29 +- 0.12 (0.00-->4.00)
mean absolute distance = 0.62 +- 0.77
4198 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.0,    GM=64+-8.7
mean inside = 91.8, mean outside = 73.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=77.8, 103 (103) missing vertices, mean dist 0.3 [0.5 (%36.0)->0.7 (%64.0))]
%71 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 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.25 (0.09-->5.37) (max @ vno 149237 --> 149326)
face area 0.29 +- 0.13 (0.00-->3.32)
mean absolute distance = 0.28 +- 0.53
3209 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3539560.5, rms=10.088
001: dt: 0.5000, sse=2086869.1, rms=7.183 (28.800%)
002: dt: 0.5000, sse=1482525.4, rms=5.533 (22.961%)
003: dt: 0.5000, sse=1198979.8, rms=4.549 (17.796%)
004: dt: 0.5000, sse=1058619.1, rms=3.980 (12.504%)
005: dt: 0.5000, sse=999759.7, rms=3.711 (6.750%)
006: dt: 0.5000, sse=969632.9, rms=3.559 (4.103%)
rms = 3.51, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=960386.6, rms=3.511 (1.354%)
008: dt: 0.2500, sse=755930.1, rms=2.175 (38.045%)
009: dt: 0.2500, sse=722844.2, rms=1.873 (13.905%)
010: dt: 0.2500, sse=714482.9, rms=1.791 (4.346%)
011: dt: 0.2500, sse=708858.1, rms=1.734 (3.213%)
rms = 1.71, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=706859.0, rms=1.711 (1.308%)
013: dt: 0.1250, sse=701105.4, rms=1.648 (3.663%)
rms = 1.63, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=699414.2, rms=1.630 (1.117%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=79.6, 129 (39) missing vertices, mean dist -0.1 [0.3 (%65.4)->0.2 (%34.6))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.24 (0.08-->5.25) (max @ vno 149237 --> 149326)
face area 0.36 +- 0.16 (0.00-->4.20)
mean absolute distance = 0.26 +- 0.43
4075 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1145304.0, rms=3.612
015: dt: 0.5000, sse=982035.4, rms=2.725 (24.549%)
rms = 2.92, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=897751.3, rms=2.110 (22.556%)
017: dt: 0.2500, sse=860871.6, rms=1.778 (15.774%)
018: dt: 0.2500, sse=848123.1, rms=1.645 (7.452%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=843726.9, rms=1.599 (2.798%)
020: dt: 0.1250, sse=838675.9, rms=1.540 (3.721%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=836429.6, rms=1.515 (1.585%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.2, 123 (26) missing vertices, mean dist -0.1 [0.3 (%63.0)->0.2 (%37.0))]
%80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.91 +- 0.24 (0.08-->4.99) (max @ vno 149237 --> 149326)
face area 0.35 +- 0.16 (0.00-->4.06)
mean absolute distance = 0.25 +- 0.37
3638 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=993324.0, rms=2.845
022: dt: 0.5000, sse=940668.8, rms=2.503 (12.031%)
rms = 2.76, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=859890.0, rms=1.854 (25.914%)
024: dt: 0.2500, sse=831316.9, rms=1.565 (15.621%)
025: dt: 0.2500, sse=821751.0, rms=1.456 (6.979%)
026: dt: 0.2500, sse=816750.2, rms=1.398 (3.978%)
rms = 1.38, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=815303.6, rms=1.381 (1.202%)
028: dt: 0.1250, sse=810295.1, rms=1.318 (4.558%)
rms = 1.30, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=808736.7, rms=1.298 (1.474%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=82.0, 114 (21) missing vertices, mean dist -0.0 [0.3 (%54.8)->0.2 (%45.2))]
%83 local maxima, %12 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-6.0.0/0050555/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=844242.6, rms=1.807
030: dt: 0.5000, sse=834767.9, rms=1.727 (4.427%)
rms = 2.16, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=796789.9, rms=1.279 (25.923%)
032: dt: 0.2500, sse=786657.9, rms=1.135 (11.254%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
033: dt: 0.2500, sse=785730.5, rms=1.123 (1.051%)
034: dt: 0.1250, sse=780793.0, rms=1.052 (6.367%)
rms = 1.04, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=778761.6, rms=1.037 (1.427%)
positioning took 0.8 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 8209 vertices
erasing segment 0 (vno[0] = 45432)
erasing segment 2 (vno[0] = 103926)
erasing segment 3 (vno[0] = 103976)
erasing segment 4 (vno[0] = 110336)
erasing segment 5 (vno[0] = 118912)
erasing segment 6 (vno[0] = 123846)
erasing segment 7 (vno[0] = 132483)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.area
vertex spacing 0.91 +- 0.24 (0.04-->4.91) (max @ vno 149237 --> 149326)
face area 0.35 +- 0.16 (0.00-->4.66)
refinement took 6.3 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050555 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-6.0.0/0050555/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
13986 bright wm thresholded.
3252 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.orig...
computing class statistics...
border white:    292054 voxels (1.74%)
border gray      329646 voxels (1.96%)
WM (96.0): 96.5 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 53.6 (was 70)
setting MAX_BORDER_WHITE to 109.5 (was 105)
setting MIN_BORDER_WHITE to 64.0 (was 85)
setting MAX_CSF to 43.2 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.8 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.83 +- 0.22 (0.01-->5.11) (max @ vno 1277 --> 1821)
face area 0.29 +- 0.12 (0.00-->5.90)
mean absolute distance = 0.61 +- 0.74
5116 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-6.1,    GM=64+-9.6
mean inside = 91.9, mean outside = 73.6
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=78.3, 40 (40) missing vertices, mean dist 0.3 [0.4 (%37.5)->0.7 (%62.5))]
%75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.25 (0.09-->5.40) (max @ vno 66905 --> 69268)
face area 0.29 +- 0.13 (0.00-->4.87)
mean absolute distance = 0.28 +- 0.52
3419 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3589655.5, rms=10.052
001: dt: 0.5000, sse=2083905.2, rms=7.071 (29.656%)
002: dt: 0.5000, sse=1451526.9, rms=5.339 (24.495%)
003: dt: 0.5000, sse=1165006.6, rms=4.330 (18.895%)
004: dt: 0.5000, sse=1028628.4, rms=3.750 (13.390%)
005: dt: 0.5000, sse=975965.6, rms=3.499 (6.701%)
006: dt: 0.5000, sse=947799.6, rms=3.352 (4.213%)
rms = 3.32, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=941947.3, rms=3.315 (1.087%)
008: dt: 0.2500, sse=737205.5, rms=1.884 (43.180%)
009: dt: 0.2500, sse=703896.0, rms=1.533 (18.636%)
010: dt: 0.2500, sse=695953.0, rms=1.428 (6.796%)
011: dt: 0.2500, sse=690810.3, rms=1.373 (3.883%)
rms = 1.35, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=689106.0, rms=1.347 (1.896%)
013: dt: 0.1250, sse=684863.1, rms=1.293 (4.042%)
rms = 1.28, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=684287.4, rms=1.283 (0.736%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=80.0, 41 (11) missing vertices, mean dist -0.1 [0.3 (%64.5)->0.2 (%35.5))]
%78 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.24 (0.09-->5.79) (max @ vno 66905 --> 69268)
face area 0.36 +- 0.16 (0.00-->5.83)
mean absolute distance = 0.26 +- 0.43
4108 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1152147.1, rms=3.516
015: dt: 0.5000, sse=973388.9, rms=2.512 (28.563%)
rms = 2.71, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=887666.2, rms=1.834 (26.960%)
017: dt: 0.2500, sse=852808.8, rms=1.427 (22.209%)
018: dt: 0.2500, sse=836027.3, rms=1.265 (11.337%)
019: dt: 0.2500, sse=831597.3, rms=1.203 (4.932%)
rms = 1.16, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=828999.2, rms=1.159 (3.629%)
rms = 1.12, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=825968.5, rms=1.121 (3.297%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.5, 55 (10) missing vertices, mean dist -0.1 [0.3 (%62.3)->0.2 (%37.7))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.24 (0.07-->5.98) (max @ vno 66905 --> 69268)
face area 0.35 +- 0.16 (0.00-->6.10)
mean absolute distance = 0.25 +- 0.37
3991 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=974804.6, rms=2.594
022: dt: 0.5000, sse=924095.2, rms=2.232 (13.985%)
rms = 2.54, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=846094.5, rms=1.525 (31.672%)
024: dt: 0.2500, sse=819834.2, rms=1.179 (22.693%)
025: dt: 0.2500, sse=812137.5, rms=1.071 (9.142%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=810750.6, rms=1.050 (1.978%)
rms = 1.01, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=807114.6, rms=1.011 (3.674%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=82.2, 66 (9) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.2 (%45.5))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=845180.6, rms=1.628
028: dt: 0.5000, sse=833822.4, rms=1.502 (7.743%)
rms = 2.01, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=798091.6, rms=1.018 (32.240%)
030: dt: 0.2500, sse=790021.4, rms=0.896 (12.002%)
031: dt: 0.2500, sse=786482.2, rms=0.841 (6.040%)
rms = 0.86, time step reduction 2 of 3 to 0.125...
rms = 0.82, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=785317.8, rms=0.822 (2.339%)
positioning took 0.7 minutes
generating cortex label...
10 non-cortical segments detected
only using segment with 7823 vertices
erasing segment 1 (vno[0] = 66973)
erasing segment 2 (vno[0] = 106207)
erasing segment 3 (vno[0] = 109235)
erasing segment 4 (vno[0] = 109309)
erasing segment 5 (vno[0] = 110295)
erasing segment 6 (vno[0] = 111260)
erasing segment 7 (vno[0] = 112276)
erasing segment 8 (vno[0] = 113409)
erasing segment 9 (vno[0] = 113550)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.area
vertex spacing 0.91 +- 0.24 (0.03-->6.06) (max @ vno 66905 --> 69268)
face area 0.35 +- 0.16 (0.00-->6.43)
refinement took 6.2 minutes
PIDs (5165 5168) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 06:57:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 06:57:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

Waiting for PID 6405 of (6405 6408) to complete...
Waiting for PID 6408 of (6405 6408) 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 (6405 6408) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 06:57:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 06:57:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 6455 of (6455 6458) to complete...
Waiting for PID 6458 of (6455 6458) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 51.1 mm, total surface area = 94964 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.171 (target=0.015)   
step 005: RMS=0.122 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.060 (target=0.015)   
step 025: RMS=0.050 (target=0.015)   
step 030: RMS=0.042 (target=0.015)   
step 035: RMS=0.036 (target=0.015)   
step 040: RMS=0.031 (target=0.015)   
step 045: RMS=0.027 (target=0.015)   
step 050: RMS=0.025 (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    56.348433
mris_inflate stimesec    0.132979
mris_inflate ru_maxrss   219252
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31889
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10568
mris_inflate ru_oublock  11768
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2133
mris_inflate ru_nivcsw   3983

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 50.0 mm, total surface area = 96664 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=0.123 (target=0.015)   
step 010: RMS=0.091 (target=0.015)   
step 015: RMS=0.075 (target=0.015)   
step 020: RMS=0.062 (target=0.015)   
step 025: RMS=0.053 (target=0.015)   
step 030: RMS=0.044 (target=0.015)   
step 035: RMS=0.037 (target=0.015)   
step 040: RMS=0.033 (target=0.015)   
step 045: RMS=0.030 (target=0.015)   
step 050: RMS=0.027 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    56.641389
mris_inflate stimesec    0.146977
mris_inflate ru_maxrss   222596
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32213
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10760
mris_inflate ru_oublock  11976
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2012
mris_inflate ru_nivcsw   4415
PIDs (6455 6458) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 06:58:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 06:58:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 6558 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6561 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6564 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6567 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6570 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6573 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6576 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6579 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6582 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6585 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6588 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...
Waiting for PID 6591 of (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 19.005*4pi (238.824) --> -18 handles
ICI = 171.4, FI = 1656.9, variation=26282.248
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
247 vertices thresholded to be in k1 ~ [-0.19 0.37], k2 ~ [-0.10 0.05]
total integrated curvature = 0.491*4pi (6.172) --> 1 handles
ICI = 1.4, FI = 9.8, variation=164.299
145 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
180 vertices thresholded to be in [-0.13 0.19]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.021
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 16.698*4pi (209.835) --> -16 handles
ICI = 179.1, FI = 1654.7, variation=26563.111
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
182 vertices thresholded to be in k1 ~ [-0.21 0.48], k2 ~ [-0.08 0.06]
total integrated curvature = 0.481*4pi (6.041) --> 1 handles
ICI = 1.5, FI = 10.3, variation=172.874
138 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
144 vertices thresholded to be in [-0.11 0.20]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.022
done.
PIDs (6558 6561 6564 6567 6570 6573 6576 6579 6582 6585 6588 6591) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 07:00:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050555 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      [ 0050555/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                      [ 270 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.578619
WARN:    S explicit min:                          0.000000	vertex = 95

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 07:00:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050555 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      [ 0050555/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                      [ 286 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.045696
WARN:    S explicit min:                          0.000000	vertex = 205
#--------------------------------------------
#@# Sphere lh Sun Oct  8 07:00:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 07:00:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 6764 of (6764 6767) to complete...
Waiting for PID 6767 of (6764 6767) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0.275...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.65
pass 1: epoch 2 of 3 starting distance error %19.62
unfolding complete - removing small folds...
starting distance error %19.55
removing remaining folds...
final distance error %19.57
MRISunfold() return, current seed 1234
-01: dt=0.0000, 62 negative triangles
187: dt=0.9900, 62 negative triangles
188: dt=0.9900, 9 negative triangles
189: dt=0.9900, 12 negative triangles
190: dt=0.9900, 7 negative triangles
191: dt=0.9900, 4 negative triangles
192: dt=0.9900, 3 negative triangles
193: dt=0.9900, 1 negative triangles
194: dt=0.9900, 1 negative triangles
195: dt=0.9900, 1 negative triangles
196: dt=0.9900, 3 negative triangles
197: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.07 hours
mris_sphere utimesec    3866.413215
mris_sphere stimesec    2.094681
mris_sphere ru_maxrss   308964
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   53932
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10600
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    128626
mris_sphere ru_nivcsw   306845
FSRUNTIME@ mris_sphere  1.0743 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0.275...
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 %20.02
pass 1: epoch 2 of 3 starting distance error %20.02
unfolding complete - removing small folds...
starting distance error %19.98
removing remaining folds...
final distance error %20.00
MRISunfold() return, current seed 1234
-01: dt=0.0000, 137 negative triangles
175: dt=0.9900, 137 negative triangles
176: dt=0.9900, 71 negative triangles
177: dt=0.9900, 55 negative triangles
178: dt=0.9900, 49 negative triangles
179: dt=0.9900, 44 negative triangles
180: dt=0.9900, 41 negative triangles
181: dt=0.9900, 43 negative triangles
182: dt=0.9900, 28 negative triangles
183: dt=0.9900, 35 negative triangles
184: dt=0.9900, 26 negative triangles
185: dt=0.9900, 27 negative triangles
186: dt=0.9900, 24 negative triangles
187: dt=0.9900, 23 negative triangles
188: dt=0.9900, 24 negative triangles
189: dt=0.9900, 22 negative triangles
190: dt=0.9900, 23 negative triangles
191: dt=0.9900, 20 negative triangles
192: dt=0.9900, 24 negative triangles
193: dt=0.9900, 18 negative triangles
194: dt=0.9900, 21 negative triangles
195: dt=0.9900, 24 negative triangles
196: dt=0.9900, 20 negative triangles
197: dt=0.9900, 20 negative triangles
198: dt=0.9900, 19 negative triangles
199: dt=0.9900, 18 negative triangles
200: dt=0.9900, 13 negative triangles
201: dt=0.9900, 15 negative triangles
202: dt=0.9900, 23 negative triangles
203: dt=0.9900, 18 negative triangles
204: dt=0.9900, 14 negative triangles
205: dt=0.9900, 15 negative triangles
206: dt=0.9900, 18 negative triangles
207: dt=0.9900, 16 negative triangles
208: dt=0.9900, 17 negative triangles
209: dt=0.9900, 14 negative triangles
210: dt=0.9900, 12 negative triangles
211: dt=0.9900, 8 negative triangles
212: dt=0.9900, 9 negative triangles
213: dt=0.9900, 6 negative triangles
214: dt=0.9900, 6 negative triangles
215: dt=0.9900, 2 negative triangles
216: dt=0.9900, 8 negative triangles
217: dt=0.9900, 5 negative triangles
218: dt=0.9900, 6 negative triangles
219: dt=0.9900, 6 negative triangles
220: dt=0.9900, 5 negative triangles
221: dt=0.9900, 2 negative triangles
222: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.12 hours
mris_sphere utimesec    4136.766115
mris_sphere stimesec    2.152672
mris_sphere ru_maxrss   313828
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   55154
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10800
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    126212
mris_sphere ru_nivcsw   311853
FSRUNTIME@ mris_sphere  1.1159 hours 1 threads
PIDs (6764 6767) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 08:07:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 08:07:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 9064 of (9064 9067) to complete...
Waiting for PID 9067 of (9064 9067) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 5.700
curvature mean = 0.028, std = 0.819
curvature mean = 0.009, std = 0.857
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 344516.8, tmin=1.2120
  d=32.00 min @ (-8.00, -8.00, 0.00) sse = 265535.4, tmin=2.4384
  d=16.00 min @ (0.00, 4.00, 0.00) sse = 245594.4, tmin=3.6687
  d=8.00 min @ (-2.00, -2.00, 2.00) sse = 228415.8, tmin=4.9316
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 227484.5, tmin=6.1567
  d=2.00 min @ (0.00, 0.50, 0.00) sse = 226822.9, tmin=7.4337
  d=0.50 min @ (-0.12, -0.12, 0.00) sse = 226768.6, tmin=9.9320
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.93 min
curvature mean = -0.002, std = 0.827
curvature mean = 0.003, std = 0.945
curvature mean = -0.006, std = 0.836
curvature mean = 0.001, std = 0.977
curvature mean = -0.007, std = 0.838
curvature mean = 0.000, std = 0.990
2 Reading smoothwm
curvature mean = -0.025, std = 0.254
curvature mean = 0.041, std = 0.247
curvature mean = 0.047, std = 0.382
curvature mean = 0.038, std = 0.304
curvature mean = 0.033, std = 0.581
curvature mean = 0.038, std = 0.331
curvature mean = 0.018, std = 0.727
curvature mean = 0.038, std = 0.341
curvature mean = 0.006, std = 0.832
MRISregister() return, current seed 0
-01: dt=0.0000, 27 negative triangles
123: dt=0.9900, 27 negative triangles
expanding nbhd size to 1
124: dt=0.9900, 40 negative triangles
125: dt=0.9900, 28 negative triangles
126: dt=0.9900, 29 negative triangles
127: dt=0.9900, 28 negative triangles
128: dt=0.9900, 25 negative triangles
129: dt=0.9900, 28 negative triangles
130: dt=0.9900, 22 negative triangles
131: dt=0.9900, 18 negative triangles
132: dt=0.9900, 14 negative triangles
133: dt=0.9900, 13 negative triangles
134: dt=0.9900, 12 negative triangles
135: dt=0.9900, 11 negative triangles
136: dt=0.9900, 9 negative triangles
137: dt=0.9900, 8 negative triangles
138: dt=0.9900, 6 negative triangles
139: dt=0.9900, 7 negative triangles
140: dt=0.9900, 5 negative triangles
141: dt=0.9900, 4 negative triangles
142: dt=0.9900, 4 negative triangles
143: dt=0.9900, 3 negative triangles
144: dt=0.9900, 3 negative triangles
145: dt=0.9900, 3 negative triangles
146: dt=0.9900, 2 negative triangles
147: dt=0.9900, 1 negative triangles
148: dt=0.9900, 1 negative triangles
149: dt=0.9900, 2 negative triangles
150: dt=0.9900, 1 negative triangles
151: dt=0.9900, 1 negative triangles
152: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.41 hours
mris_register utimesec    5115.790281
mris_register stimesec    4.706284
mris_register ru_maxrss   273928
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38940
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10664
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    364804
mris_register ru_nivcsw   235241
FSRUNTIME@ mris_register  1.4134 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 5.794
curvature mean = 0.039, std = 0.818
curvature mean = 0.008, std = 0.856
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 360703.3, tmin=1.2179
  d=32.00 min @ (-8.00, -8.00, 8.00) sse = 292709.0, tmin=2.4501
  d=16.00 min @ (0.00, 4.00, -4.00) sse = 267792.1, tmin=3.6884
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 261369.5, tmin=4.9683
  d=4.00 min @ (1.00, 1.00, 1.00) sse = 258004.0, tmin=6.2101
  d=2.00 min @ (0.50, -0.50, 0.00) sse = 257486.2, tmin=7.4990
  d=1.00 min @ (-0.25, 0.00, -0.25) sse = 257294.4, tmin=8.7501
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 257261.0, tmin=10.0289
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  10.03 min
curvature mean = 0.013, std = 0.825
curvature mean = 0.004, std = 0.945
curvature mean = 0.009, std = 0.834
curvature mean = 0.001, std = 0.978
curvature mean = 0.008, std = 0.835
curvature mean = 0.000, std = 0.991
2 Reading smoothwm
curvature mean = -0.026, std = 0.410
curvature mean = 0.038, std = 0.241
curvature mean = 0.030, std = 0.240
curvature mean = 0.036, std = 0.297
curvature mean = 0.022, std = 0.364
curvature mean = 0.035, std = 0.323
curvature mean = 0.013, std = 0.457
curvature mean = 0.035, std = 0.333
curvature mean = 0.004, std = 0.536
MRISregister() return, current seed 0
-01: dt=0.0000, 64 negative triangles
120: dt=0.9900, 64 negative triangles
expanding nbhd size to 1
121: dt=0.9900, 72 negative triangles
122: dt=0.9900, 53 negative triangles
123: dt=0.9900, 53 negative triangles
124: dt=0.9900, 52 negative triangles
125: dt=0.9900, 47 negative triangles
126: dt=0.9900, 43 negative triangles
127: dt=0.9900, 43 negative triangles
128: dt=0.9900, 36 negative triangles
129: dt=0.9900, 28 negative triangles
130: dt=0.9900, 26 negative triangles
131: dt=0.9900, 22 negative triangles
132: dt=0.9900, 20 negative triangles
133: dt=0.9900, 19 negative triangles
134: dt=0.9900, 12 negative triangles
135: dt=0.9900, 11 negative triangles
136: dt=0.9900, 8 negative triangles
137: dt=0.9900, 8 negative triangles
138: dt=0.9900, 10 negative triangles
139: dt=0.9900, 7 negative triangles
140: dt=0.9900, 9 negative triangles
141: dt=0.9900, 8 negative triangles
142: dt=0.9900, 6 negative triangles
143: dt=0.9900, 5 negative triangles
144: dt=0.9900, 4 negative triangles
145: dt=0.9900, 4 negative triangles
146: dt=0.9900, 2 negative triangles
147: dt=0.9900, 1 negative triangles
148: dt=0.9900, 1 negative triangles
149: dt=0.9900, 1 negative triangles
150: dt=0.9900, 1 negative triangles
151: dt=0.9900, 1 negative triangles
152: dt=0.9900, 1 negative triangles
153: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.40 hours
mris_register utimesec    5030.841195
mris_register stimesec    4.411329
mris_register ru_maxrss   276992
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   39014
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10856
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    353154
mris_register ru_nivcsw   230999
FSRUNTIME@ mris_register  1.3983 hours 1 threads
PIDs (9064 9067) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 09:32:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 09:32:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

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

Waiting for PID 14681 of (14681 14684) to complete...
Waiting for PID 14684 of (14681 14684) 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 (14681 14684) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 09:32:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 09:32:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 14727 of (14727 14730) to complete...
Waiting for PID 14730 of (14727 14730) 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 (14727 14730) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 09:32:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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 09:32:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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 14774 of (14774 14777) to complete...
Waiting for PID 14777 of (14774 14777) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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...
1365 labels changed using aseg
relabeling using gibbs priors...
000:   3411 changed, 150248 examined...
001:    836 changed, 14289 examined...
002:    205 changed, 4647 examined...
003:     62 changed, 1274 examined...
004:     26 changed, 390 examined...
005:      8 changed, 151 examined...
006:      6 changed, 50 examined...
007:      3 changed, 37 examined...
008:      3 changed, 14 examined...
009:      1 changed, 15 examined...
010:      0 changed, 7 examined...
266 labels changed using aseg
000: 136 total segments, 94 labels (413 vertices) changed
001: 43 total segments, 5 labels (13 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1495 vertices marked for relabeling...
1495 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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...
1057 labels changed using aseg
relabeling using gibbs priors...
000:   3059 changed, 152869 examined...
001:    685 changed, 13012 examined...
002:    151 changed, 3834 examined...
003:     50 changed, 918 examined...
004:     18 changed, 300 examined...
005:     12 changed, 117 examined...
006:      3 changed, 77 examined...
007:      1 changed, 21 examined...
008:      0 changed, 7 examined...
176 labels changed using aseg
000: 92 total segments, 49 labels (196 vertices) changed
001: 44 total segments, 2 labels (8 vertices) changed
002: 42 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...
1439 vertices marked for relabeling...
1439 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 16 seconds.
PIDs (14774 14777) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 09:32:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050555 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 09:32:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050555 rh 

Waiting for PID 14830 of (14830 14833) to complete...
Waiting for PID 14833 of (14830 14833) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050555 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-6.0.0/0050555/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
13986 bright wm thresholded.
3252 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.orig...
computing class statistics...
border white:    292054 voxels (1.74%)
border gray      329646 voxels (1.96%)
WM (96.0): 96.5 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 53.6 (was 70)
setting MAX_BORDER_WHITE to 109.5 (was 105)
setting MIN_BORDER_WHITE to 64.0 (was 85)
setting MAX_CSF to 43.2 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.8 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-7.0,    GM=64+-8.7
mean inside = 91.8, mean outside = 73.3
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.91 +- 0.24 (0.04-->4.91) (max @ vno 149237 --> 149326)
face area 0.34 +- 0.16 (0.00-->4.61)
mean absolute distance = 0.45 +- 0.75
3139 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 197 points - only 0.00% unknown
deleting segment 1 with 22 points - only 0.00% unknown
deleting segment 2 with 176 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 76 points - only 0.00% unknown
deleting segment 8 with 22 points - only 0.00% unknown
deleting segment 9 with 19 points - only 0.00% unknown
deleting segment 10 with 12 points - only 8.33% unknown
deleting segment 11 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 9 points - only 0.00% unknown
deleting segment 14 with 7 points - only 0.00% unknown
mean border=77.5, 112 (112) missing vertices, mean dist 0.3 [0.5 (%19.4)->0.4 (%80.6))]
%67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.93 +- 0.26 (0.11-->5.07) (max @ vno 149237 --> 149326)
face area 0.34 +- 0.16 (0.00-->4.11)
mean absolute distance = 0.28 +- 0.56
3232 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1946608.1, rms=6.476
001: dt: 0.5000, sse=1270105.9, rms=4.287 (33.802%)
002: dt: 0.5000, sse=1084520.2, rms=3.470 (19.057%)
003: dt: 0.5000, sse=1065114.9, rms=3.375 (2.743%)
004: dt: 0.5000, sse=1021125.2, rms=3.145 (6.798%)
rms = 3.27, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=879327.6, rms=2.168 (31.068%)
006: dt: 0.2500, sse=829550.9, rms=1.695 (21.808%)
007: dt: 0.2500, sse=818129.5, rms=1.567 (7.564%)
008: dt: 0.2500, sse=813379.4, rms=1.498 (4.387%)
rms = 1.47, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=812788.4, rms=1.467 (2.103%)
010: dt: 0.1250, sse=805271.7, rms=1.400 (4.529%)
rms = 1.38, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=803829.9, rms=1.381 (1.387%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 220 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 2 with 142 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 12 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 12 points - only 0.00% unknown
deleting segment 10 with 19 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
deleting segment 14 with 8 points - only 0.00% unknown
mean border=79.4, 148 (56) missing vertices, mean dist -0.1 [0.3 (%66.1)->0.2 (%33.9))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.92 +- 0.25 (0.08-->4.97) (max @ vno 149237 --> 149326)
face area 0.36 +- 0.17 (0.00-->4.31)
mean absolute distance = 0.27 +- 0.45
3677 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1134731.0, rms=3.461
012: dt: 0.5000, sse=974681.6, rms=2.515 (27.337%)
rms = 2.66, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=890532.2, rms=1.874 (25.476%)
014: dt: 0.2500, sse=852779.5, rms=1.473 (21.412%)
015: dt: 0.2500, sse=839693.4, rms=1.314 (10.770%)
016: dt: 0.2500, sse=833876.7, rms=1.236 (5.963%)
rms = 1.21, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=831669.5, rms=1.206 (2.373%)
018: dt: 0.1250, sse=827832.3, rms=1.148 (4.885%)
rms = 1.14, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=827142.5, rms=1.135 (1.081%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 210 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 2 with 141 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 14 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 14 points - only 0.00% unknown
deleting segment 9 with 19 points - only 0.00% unknown
deleting segment 10 with 20 points - only 15.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 8 points - only 0.00% unknown
mean border=81.1, 127 (43) missing vertices, mean dist -0.1 [0.3 (%63.4)->0.2 (%36.6))]
%80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.91 +- 0.25 (0.11-->4.76) (max @ vno 67980 --> 71466)
face area 0.36 +- 0.17 (0.00-->4.31)
mean absolute distance = 0.25 +- 0.38
3775 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=978515.0, rms=2.688
020: dt: 0.5000, sse=924508.2, rms=2.307 (14.177%)
rms = 2.56, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=843817.0, rms=1.585 (31.302%)
022: dt: 0.2500, sse=815440.7, rms=1.236 (22.049%)
023: dt: 0.2500, sse=808930.7, rms=1.133 (8.326%)
rms = 1.11, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=806181.1, rms=1.109 (2.101%)
025: dt: 0.1250, sse=803052.9, rms=1.038 (6.384%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=800898.1, rms=1.027 (1.087%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 205 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 2 with 150 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 18 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
deleting segment 7 with 15 points - only 0.00% unknown
deleting segment 8 with 19 points - only 0.00% unknown
deleting segment 9 with 21 points - only 14.29% unknown
deleting segment 10 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
deleting segment 13 with 8 points - only 0.00% unknown
mean border=82.0, 151 (37) missing vertices, mean dist -0.1 [0.3 (%55.0)->0.2 (%45.0))]
%83 local maxima, %12 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-6.0.0/0050555/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=837771.2, rms=1.658
027: dt: 0.5000, sse=830331.2, rms=1.576 (4.963%)
rms = 2.06, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=791153.9, rms=1.065 (32.419%)
029: dt: 0.2500, sse=782190.9, rms=0.924 (13.289%)
rms = 0.90, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=780116.9, rms=0.899 (2.655%)
031: dt: 0.1250, sse=776052.3, rms=0.828 (7.917%)
rms = 0.82, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=775187.4, rms=0.818 (1.217%)
positioning took 0.7 minutes
generating cortex label...
8 non-cortical segments detected
only using segment with 8169 vertices
erasing segment 0 (vno[0] = 44292)
erasing segment 2 (vno[0] = 102751)
erasing segment 3 (vno[0] = 103976)
erasing segment 4 (vno[0] = 106247)
erasing segment 5 (vno[0] = 110336)
erasing segment 6 (vno[0] = 118912)
erasing segment 7 (vno[0] = 123846)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.area
vertex spacing 0.91 +- 0.25 (0.04-->4.75) (max @ vno 67980 --> 71466)
face area 0.35 +- 0.16 (0.00-->4.48)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 13 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=52.2, 119 (119) missing vertices, mean dist 1.6 [0.6 (%0.0)->2.4 (%100.0))]
%11 local maxima, %52 large gradients and %33 min vals, 989 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=27166334.0, rms=30.393
001: dt: 0.0500, sse=23990590.0, rms=28.508 (6.202%)
002: dt: 0.0500, sse=21706700.0, rms=27.072 (5.040%)
003: dt: 0.0500, sse=19941342.0, rms=25.906 (4.304%)
004: dt: 0.0500, sse=18498938.0, rms=24.914 (3.831%)
005: dt: 0.0500, sse=17274514.0, rms=24.039 (3.511%)
006: dt: 0.0500, sse=16205883.0, rms=23.248 (3.288%)
007: dt: 0.0500, sse=15253405.0, rms=22.520 (3.131%)
008: dt: 0.0500, sse=14392480.0, rms=21.841 (3.015%)
009: dt: 0.0500, sse=13605815.0, rms=21.202 (2.928%)
010: dt: 0.0500, sse=12881689.0, rms=20.596 (2.860%)
positioning took 1.0 minutes
mean border=52.0, 107 (59) missing vertices, mean dist 1.3 [0.2 (%0.0)->2.0 (%100.0))]
%11 local maxima, %51 large gradients and %33 min vals, 955 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=13666359.0, rms=21.250
011: dt: 0.0500, sse=12991391.0, rms=20.687 (2.650%)
012: dt: 0.0500, sse=12363710.0, rms=20.149 (2.600%)
013: dt: 0.0500, sse=11778180.0, rms=19.634 (2.556%)
014: dt: 0.0500, sse=11231656.0, rms=19.140 (2.513%)
015: dt: 0.0500, sse=10721331.0, rms=18.668 (2.469%)
016: dt: 0.0500, sse=10245329.0, rms=18.216 (2.421%)
017: dt: 0.0500, sse=9801264.0, rms=17.784 (2.372%)
018: dt: 0.0500, sse=9387320.0, rms=17.371 (2.320%)
019: dt: 0.0500, sse=9001078.0, rms=16.977 (2.269%)
020: dt: 0.0500, sse=8640915.0, rms=16.601 (2.215%)
positioning took 1.0 minutes
mean border=51.8, 115 (48) missing vertices, mean dist 1.1 [0.1 (%1.0)->1.7 (%99.0))]
%12 local maxima, %51 large gradients and %32 min vals, 939 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=8749336.0, rms=16.719
021: dt: 0.0500, sse=8401751.0, rms=16.350 (2.205%)
022: dt: 0.0500, sse=8078609.0, rms=16.000 (2.143%)
023: dt: 0.0500, sse=7775840.5, rms=15.664 (2.097%)
024: dt: 0.0500, sse=7494593.5, rms=15.346 (2.032%)
025: dt: 0.0500, sse=7233107.0, rms=15.044 (1.969%)
026: dt: 0.0500, sse=6989332.5, rms=14.756 (1.910%)
027: dt: 0.0500, sse=6760887.5, rms=14.482 (1.861%)
028: dt: 0.0500, sse=6544729.5, rms=14.217 (1.828%)
029: dt: 0.0500, sse=6339761.0, rms=13.961 (1.799%)
030: dt: 0.0500, sse=6145181.0, rms=13.714 (1.772%)
positioning took 1.0 minutes
mean border=51.8, 135 (39) missing vertices, mean dist 0.9 [0.1 (%16.4)->1.6 (%83.6))]
%12 local maxima, %51 large gradients and %32 min vals, 946 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=6216801.0, rms=13.802
031: dt: 0.5000, sse=4865423.5, rms=11.957 (13.363%)
032: dt: 0.5000, sse=3981845.0, rms=10.570 (11.602%)
033: dt: 0.5000, sse=3343302.0, rms=9.443 (10.666%)
034: dt: 0.5000, sse=2897154.5, rms=8.559 (9.353%)
035: dt: 0.5000, sse=2556473.0, rms=7.820 (8.643%)
036: dt: 0.5000, sse=2300407.8, rms=7.209 (7.810%)
037: dt: 0.5000, sse=2087429.1, rms=6.664 (7.565%)
038: dt: 0.5000, sse=1928895.1, rms=6.223 (6.613%)
039: dt: 0.5000, sse=1800856.9, rms=5.847 (6.043%)
040: dt: 0.5000, sse=1714083.0, rms=5.572 (4.693%)
041: dt: 0.5000, sse=1643728.0, rms=5.345 (4.082%)
042: dt: 0.5000, sse=1604591.0, rms=5.209 (2.545%)
043: dt: 0.5000, sse=1567098.5, rms=5.081 (2.450%)
044: dt: 0.5000, sse=1548807.2, rms=5.013 (1.352%)
045: dt: 0.5000, sse=1525325.6, rms=4.931 (1.625%)
rms = 4.90, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1516952.6, rms=4.897 (0.700%)
047: dt: 0.2500, sse=1457379.4, rms=4.641 (5.217%)
048: dt: 0.2500, sse=1443487.0, rms=4.586 (1.192%)
rms = 4.58, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1441871.1, rms=4.578 (0.179%)
rms = 4.54, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1432494.9, rms=4.537 (0.877%)
positioning took 2.6 minutes
mean border=51.1, 2307 (12) missing vertices, mean dist 0.2 [0.2 (%55.8)->0.8 (%44.2))]
%20 local maxima, %45 large gradients and %28 min vals, 460 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=1640730.9, rms=4.490
051: dt: 0.5000, sse=1536672.1, rms=4.068 (9.391%)
052: dt: 0.5000, sse=1493271.9, rms=3.899 (4.146%)
rms = 3.87, time step reduction 1 of 3 to 0.250...
053: dt: 0.5000, sse=1485722.1, rms=3.875 (0.629%)
054: dt: 0.2500, sse=1429194.4, rms=3.556 (8.242%)
055: dt: 0.2500, sse=1414072.9, rms=3.478 (2.169%)
rms = 3.47, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1411657.9, rms=3.467 (0.326%)
057: dt: 0.1250, sse=1401510.0, rms=3.410 (1.659%)
rms = 3.40, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1398862.6, rms=3.397 (0.376%)
positioning took 1.2 minutes
mean border=50.3, 2761 (6) missing vertices, mean dist 0.2 [0.2 (%53.9)->0.7 (%46.1))]
%30 local maxima, %36 large gradients and %27 min vals, 524 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=1496420.8, rms=3.756
059: dt: 0.5000, sse=1475188.4, rms=3.662 (2.508%)
rms = 3.69, time step reduction 1 of 3 to 0.250...
060: dt: 0.2500, sse=1441294.1, rms=3.488 (4.762%)
061: dt: 0.2500, sse=1426980.6, rms=3.422 (1.894%)
rms = 3.40, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1421677.6, rms=3.397 (0.719%)
063: dt: 0.1250, sse=1412394.8, rms=3.344 (1.554%)
rms = 3.33, time step reduction 3 of 3 to 0.062...
064: dt: 0.1250, sse=1408383.9, rms=3.325 (0.569%)
positioning took 1.0 minutes
mean border=49.5, 5130 (6) missing vertices, mean dist 0.1 [0.2 (%50.3)->0.5 (%49.7))]
%38 local maxima, %28 large gradients and %26 min vals, 598 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-6.0.0/0050555/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1461598.5, rms=3.514
065: dt: 0.5000, sse=1439116.1, rms=3.413 (2.879%)
rms = 3.38, time step reduction 1 of 3 to 0.250...
066: dt: 0.5000, sse=1423557.0, rms=3.382 (0.914%)
067: dt: 0.2500, sse=1378298.0, rms=3.098 (8.398%)
068: dt: 0.2500, sse=1365461.2, rms=3.029 (2.234%)
rms = 3.02, time step reduction 2 of 3 to 0.125...
069: dt: 0.2500, sse=1362884.0, rms=3.018 (0.365%)
070: dt: 0.1250, sse=1350321.4, rms=2.938 (2.636%)
rms = 2.92, time step reduction 3 of 3 to 0.062...
071: dt: 0.1250, sse=1346651.4, rms=2.920 (0.623%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.area.pial
vertex spacing 1.06 +- 0.46 (0.06-->8.97) (max @ vno 72589 --> 67980)
face area 0.45 +- 0.35 (0.00-->8.72)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 150248 vertices processed
25000 of 150248 vertices processed
50000 of 150248 vertices processed
75000 of 150248 vertices processed
100000 of 150248 vertices processed
125000 of 150248 vertices processed
150000 of 150248 vertices processed
0 of 150248 vertices processed
25000 of 150248 vertices processed
50000 of 150248 vertices processed
75000 of 150248 vertices processed
100000 of 150248 vertices processed
125000 of 150248 vertices processed
150000 of 150248 vertices processed
thickness calculation complete, 272:1931 truncations.
36997 vertices at 0 distance
108349 vertices at 1 distance
88997 vertices at 2 distance
35255 vertices at 3 distance
11101 vertices at 4 distance
3420 vertices at 5 distance
1152 vertices at 6 distance
455 vertices at 7 distance
203 vertices at 8 distance
94 vertices at 9 distance
62 vertices at 10 distance
47 vertices at 11 distance
34 vertices at 12 distance
25 vertices at 13 distance
26 vertices at 14 distance
23 vertices at 15 distance
9 vertices at 16 distance
5 vertices at 17 distance
7 vertices at 18 distance
7 vertices at 19 distance
8 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.thickness
positioning took 17.0 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050555 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-6.0.0/0050555/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
13986 bright wm thresholded.
3252 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.orig...
computing class statistics...
border white:    292054 voxels (1.74%)
border gray      329646 voxels (1.96%)
WM (96.0): 96.5 +- 8.5 [70.0 --> 110.0]
GM (70.0) : 69.1 +- 10.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 53.6 (was 70)
setting MAX_BORDER_WHITE to 109.5 (was 105)
setting MIN_BORDER_WHITE to 64.0 (was 85)
setting MAX_CSF to 43.2 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 32.8 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=101+-6.1,    GM=64+-9.6
mean inside = 91.9, mean outside = 73.6
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 0.91 +- 0.24 (0.03-->6.06) (max @ vno 66905 --> 69268)
face area 0.35 +- 0.16 (0.00-->6.36)
mean absolute distance = 0.44 +- 0.73
3961 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 57 points - only 0.00% unknown
deleting segment 2 with 24 points - only 0.00% unknown
deleting segment 4 with 30 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 127 points - only 0.00% unknown
deleting segment 8 with 6 points - only 0.00% unknown
mean border=77.8, 46 (46) missing vertices, mean dist 0.3 [0.4 (%20.8)->0.4 (%79.2))]
%71 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 0.94 +- 0.26 (0.07-->6.30) (max @ vno 66905 --> 69268)
face area 0.35 +- 0.16 (0.00-->5.77)
mean absolute distance = 0.29 +- 0.55
3539 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1997994.0, rms=6.514
001: dt: 0.5000, sse=1278282.8, rms=4.219 (35.231%)
002: dt: 0.5000, sse=1093010.0, rms=3.405 (19.301%)
003: dt: 0.5000, sse=1065055.0, rms=3.263 (4.176%)
004: dt: 0.5000, sse=1024326.9, rms=3.052 (6.461%)
rms = 3.15, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=884857.8, rms=2.074 (32.034%)
006: dt: 0.2500, sse=836669.3, rms=1.591 (23.294%)
007: dt: 0.2500, sse=823238.4, rms=1.434 (9.849%)
008: dt: 0.2500, sse=818793.9, rms=1.379 (3.888%)
rms = 1.34, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=816661.8, rms=1.339 (2.859%)
rms = 1.30, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=813057.4, rms=1.295 (3.274%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
deleting segment 1 with 54 points - only 0.00% unknown
deleting segment 2 with 24 points - only 0.00% unknown
deleting segment 3 with 38 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 28 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 17 points - only 0.00% unknown
deleting segment 10 with 7 points - only 0.00% unknown
mean border=79.8, 58 (16) missing vertices, mean dist -0.1 [0.3 (%65.9)->0.2 (%34.1))]
%77 local maxima, %18 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 0.92 +- 0.25 (0.08-->6.37) (max @ vno 66905 --> 69268)
face area 0.37 +- 0.17 (0.00-->6.15)
mean absolute distance = 0.26 +- 0.44
4193 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1174796.8, rms=3.537
011: dt: 0.5000, sse=992288.5, rms=2.497 (29.396%)
rms = 2.64, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=908886.1, rms=1.847 (26.038%)
013: dt: 0.2500, sse=868000.6, rms=1.426 (22.791%)
014: dt: 0.2500, sse=853131.8, rms=1.241 (12.997%)
015: dt: 0.2500, sse=848529.5, rms=1.170 (5.720%)
rms = 1.12, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=845040.5, rms=1.120 (4.241%)
rms = 1.08, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=844372.9, rms=1.084 (3.214%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
deleting segment 1 with 56 points - only 0.00% unknown
deleting segment 2 with 27 points - only 0.00% unknown
deleting segment 3 with 29 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 5 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 35 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 17 points - only 0.00% unknown
deleting segment 10 with 21 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
mean border=81.4, 61 (9) missing vertices, mean dist -0.1 [0.3 (%63.0)->0.2 (%37.0))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.92 +- 0.25 (0.06-->6.41) (max @ vno 66905 --> 69268)
face area 0.36 +- 0.17 (0.00-->6.29)
mean absolute distance = 0.26 +- 0.38
4131 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=987135.8, rms=2.610
018: dt: 0.5000, sse=931614.0, rms=2.206 (15.467%)
rms = 2.49, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=851770.8, rms=1.490 (32.470%)
020: dt: 0.2500, sse=824449.9, rms=1.131 (24.118%)
021: dt: 0.2500, sse=827437.2, rms=1.028 (9.055%)
rms = 1.02, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=816097.9, rms=1.018 (0.981%)
rms = 0.97, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=813430.8, rms=0.974 (4.331%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
deleting segment 1 with 56 points - only 0.00% unknown
deleting segment 2 with 27 points - only 0.00% unknown
deleting segment 3 with 34 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 36 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 17 points - only 0.00% unknown
deleting segment 9 with 21 points - only 0.00% unknown
deleting segment 10 with 9 points - only 0.00% unknown
mean border=82.2, 71 (8) missing vertices, mean dist -0.1 [0.3 (%54.7)->0.2 (%45.3))]
%85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=850559.6, rms=1.621
024: dt: 0.5000, sse=840757.8, rms=1.506 (7.122%)
rms = 1.99, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=803735.9, rms=1.008 (33.093%)
026: dt: 0.2500, sse=795000.6, rms=0.867 (13.993%)
027: dt: 0.2500, sse=791791.0, rms=0.815 (6.003%)
rms = 0.83, time step reduction 2 of 3 to 0.125...
rms = 0.80, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=790324.1, rms=0.796 (2.300%)
positioning took 0.7 minutes
generating cortex label...
14 non-cortical segments detected
only using segment with 7813 vertices
erasing segment 1 (vno[0] = 48736)
erasing segment 2 (vno[0] = 52547)
erasing segment 3 (vno[0] = 65736)
erasing segment 4 (vno[0] = 68180)
erasing segment 5 (vno[0] = 106201)
erasing segment 6 (vno[0] = 107256)
erasing segment 7 (vno[0] = 109235)
erasing segment 8 (vno[0] = 109309)
erasing segment 9 (vno[0] = 110295)
erasing segment 10 (vno[0] = 111260)
erasing segment 11 (vno[0] = 112276)
erasing segment 12 (vno[0] = 113409)
erasing segment 13 (vno[0] = 113550)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.area
vertex spacing 0.91 +- 0.25 (0.03-->6.43) (max @ vno 66905 --> 69268)
face area 0.35 +- 0.16 (0.00-->6.36)
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=52.6, 60 (60) missing vertices, mean dist 1.5 [2.9 (%0.0)->2.5 (%100.0))]
%10 local maxima, %49 large gradients and %37 min vals, 973 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=27475514.0, rms=30.263
001: dt: 0.0500, sse=24289566.0, rms=28.401 (6.152%)
002: dt: 0.0500, sse=21996460.0, rms=26.981 (4.999%)
003: dt: 0.0500, sse=20225636.0, rms=25.831 (4.261%)
004: dt: 0.0500, sse=18780034.0, rms=24.853 (3.786%)
005: dt: 0.0500, sse=17552914.0, rms=23.992 (3.467%)
006: dt: 0.0500, sse=16480530.0, rms=23.212 (3.248%)
007: dt: 0.0500, sse=15524792.0, rms=22.495 (3.090%)
008: dt: 0.0500, sse=14660157.0, rms=21.826 (2.975%)
009: dt: 0.0500, sse=13869784.0, rms=21.196 (2.888%)
010: dt: 0.0500, sse=13141351.0, rms=20.597 (2.822%)
positioning took 1.0 minutes
mean border=52.4, 48 (29) missing vertices, mean dist 1.3 [2.2 (%0.0)->2.1 (%100.0))]
%10 local maxima, %48 large gradients and %37 min vals, 972 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=14023521.0, rms=21.320
011: dt: 0.0500, sse=13342584.0, rms=20.764 (2.604%)
012: dt: 0.0500, sse=12708980.0, rms=20.234 (2.554%)
013: dt: 0.0500, sse=12117737.0, rms=19.726 (2.510%)
014: dt: 0.0500, sse=11565434.0, rms=19.240 (2.467%)
015: dt: 0.0500, sse=11049285.0, rms=18.773 (2.424%)
016: dt: 0.0500, sse=10567088.0, rms=18.327 (2.378%)
017: dt: 0.0500, sse=10116553.0, rms=17.900 (2.331%)
018: dt: 0.0500, sse=9696297.0, rms=17.491 (2.280%)
019: dt: 0.0500, sse=9303952.0, rms=17.102 (2.229%)
020: dt: 0.0500, sse=8937681.0, rms=16.729 (2.177%)
positioning took 1.0 minutes
mean border=52.2, 58 (26) missing vertices, mean dist 1.1 [0.1 (%0.9)->1.8 (%99.1))]
%11 local maxima, %48 large gradients and %37 min vals, 914 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=9051050.0, rms=16.850
021: dt: 0.0500, sse=8699392.0, rms=16.487 (2.153%)
022: dt: 0.0500, sse=8372846.0, rms=16.143 (2.088%)
023: dt: 0.0500, sse=8067104.5, rms=15.813 (2.040%)
024: dt: 0.0500, sse=7782998.5, rms=15.501 (1.975%)
025: dt: 0.0500, sse=7518758.0, rms=15.205 (1.912%)
026: dt: 0.0500, sse=7272597.0, rms=14.923 (1.852%)
027: dt: 0.0500, sse=7042157.5, rms=14.654 (1.800%)
028: dt: 0.0500, sse=6824433.5, rms=14.396 (1.764%)
029: dt: 0.0500, sse=6617923.0, rms=14.146 (1.734%)
030: dt: 0.0500, sse=6422081.0, rms=13.905 (1.704%)
positioning took 1.0 minutes
mean border=52.1, 92 (22) missing vertices, mean dist 0.9 [0.1 (%14.9)->1.7 (%85.1))]
%11 local maxima, %48 large gradients and %36 min vals, 938 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=6510382.5, rms=14.011
031: dt: 0.5000, sse=5156547.0, rms=12.231 (12.702%)
032: dt: 0.5000, sse=4272932.5, rms=10.905 (10.841%)
033: dt: 0.5000, sse=3633978.5, rms=9.837 (9.801%)
034: dt: 0.5000, sse=3179136.5, rms=8.991 (8.592%)
035: dt: 0.5000, sse=2824124.2, rms=8.273 (7.992%)
036: dt: 0.5000, sse=2540238.5, rms=7.647 (7.567%)
037: dt: 0.5000, sse=2296859.8, rms=7.069 (7.555%)
038: dt: 0.5000, sse=2103708.5, rms=6.573 (7.018%)
039: dt: 0.5000, sse=1945246.1, rms=6.141 (6.581%)
040: dt: 0.5000, sse=1832971.1, rms=5.812 (5.352%)
041: dt: 0.5000, sse=1740892.1, rms=5.532 (4.823%)
042: dt: 0.5000, sse=1683888.2, rms=5.346 (3.348%)
043: dt: 0.5000, sse=1636765.8, rms=5.193 (2.874%)
044: dt: 0.5000, sse=1610593.6, rms=5.101 (1.757%)
045: dt: 0.5000, sse=1585331.4, rms=5.016 (1.677%)
rms = 4.97, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1574156.9, rms=4.974 (0.834%)
047: dt: 0.2500, sse=1519729.2, rms=4.747 (4.566%)
048: dt: 0.2500, sse=1504075.6, rms=4.688 (1.245%)
rms = 4.68, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1501575.9, rms=4.677 (0.228%)
rms = 4.65, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1493917.6, rms=4.645 (0.686%)
positioning took 2.8 minutes
mean border=51.6, 2994 (12) missing vertices, mean dist 0.2 [0.2 (%56.1)->0.8 (%43.9))]
%18 local maxima, %42 large gradients and %33 min vals, 403 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=1686944.5, rms=4.465
051: dt: 0.5000, sse=1598702.1, rms=4.119 (7.743%)
052: dt: 0.5000, sse=1562582.9, rms=3.988 (3.197%)
rms = 3.97, time step reduction 1 of 3 to 0.250...
053: dt: 0.5000, sse=1556294.6, rms=3.972 (0.390%)
054: dt: 0.2500, sse=1500949.4, rms=3.672 (7.553%)
055: dt: 0.2500, sse=1485796.5, rms=3.599 (1.980%)
rms = 3.59, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1482862.9, rms=3.586 (0.378%)
057: dt: 0.1250, sse=1472953.9, rms=3.532 (1.494%)
rms = 3.52, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1469394.0, rms=3.516 (0.465%)
positioning took 1.3 minutes
mean border=50.9, 3333 (6) missing vertices, mean dist 0.1 [0.2 (%52.8)->0.6 (%47.2))]
%27 local maxima, %34 large gradients and %32 min vals, 521 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=1552022.1, rms=3.809
rms = 3.76, time step reduction 1 of 3 to 0.250...
059: dt: 0.5000, sse=1539887.9, rms=3.763 (1.214%)
060: dt: 0.2500, sse=1500758.4, rms=3.576 (4.980%)
rms = 3.53, time step reduction 2 of 3 to 0.125...
061: dt: 0.2500, sse=1491242.1, rms=3.532 (1.231%)
rms = 3.49, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1484357.6, rms=3.493 (1.085%)
positioning took 0.7 minutes
mean border=50.3, 6158 (5) missing vertices, mean dist 0.1 [0.2 (%49.9)->0.5 (%50.1))]
%34 local maxima, %27 large gradients and %31 min vals, 520 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-6.0.0/0050555/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1524251.2, rms=3.632
063: dt: 0.5000, sse=1507581.1, rms=3.573 (1.647%)
rms = 3.55, time step reduction 1 of 3 to 0.250...
064: dt: 0.5000, sse=1492875.0, rms=3.549 (0.664%)
065: dt: 0.2500, sse=1447565.6, rms=3.282 (7.525%)
066: dt: 0.2500, sse=1436060.4, rms=3.224 (1.755%)
rms = 3.18, time step reduction 2 of 3 to 0.125...
067: dt: 0.2500, sse=1427240.4, rms=3.181 (1.341%)
068: dt: 0.1250, sse=1416558.1, rms=3.116 (2.040%)
rms = 3.10, time step reduction 3 of 3 to 0.062...
069: dt: 0.1250, sse=1412629.9, rms=3.097 (0.602%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.area.pial
vertex spacing 1.06 +- 0.47 (0.07-->8.12) (max @ vno 105220 --> 105219)
face area 0.45 +- 0.36 (0.00-->8.92)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 152869 vertices processed
25000 of 152869 vertices processed
50000 of 152869 vertices processed
75000 of 152869 vertices processed
100000 of 152869 vertices processed
125000 of 152869 vertices processed
150000 of 152869 vertices processed
0 of 152869 vertices processed
25000 of 152869 vertices processed
50000 of 152869 vertices processed
75000 of 152869 vertices processed
100000 of 152869 vertices processed
125000 of 152869 vertices processed
150000 of 152869 vertices processed
thickness calculation complete, 398:2343 truncations.
38040 vertices at 0 distance
110551 vertices at 1 distance
89517 vertices at 2 distance
36435 vertices at 3 distance
11855 vertices at 4 distance
3461 vertices at 5 distance
1079 vertices at 6 distance
369 vertices at 7 distance
171 vertices at 8 distance
111 vertices at 9 distance
55 vertices at 10 distance
50 vertices at 11 distance
28 vertices at 12 distance
26 vertices at 13 distance
23 vertices at 14 distance
22 vertices at 15 distance
7 vertices at 16 distance
9 vertices at 17 distance
12 vertices at 18 distance
2 vertices at 19 distance
13 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.thickness
positioning took 16.9 minutes
PIDs (14830 14833) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 09:49:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/lh.cortex.label
Total face volume 286076
Total vertex volume 282380 (mask=0)
#@# 0050555 lh 282380
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 09:49:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/rh.cortex.label
Total face volume 296431
Total vertex volume 293693 (mask=0)
#@# 0050555 rh 293693
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 09:49:46 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 

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 = 289
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/ribbon.mgz
mris_volmask took 14.63 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 10:04:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 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 0050555 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 10:04:24 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 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 0050555 rh pial 

Waiting for PID 17352 of (17352 17355 17358 17362) to complete...
Waiting for PID 17355 of (17352 17355 17358 17362) to complete...
Waiting for PID 17358 of (17352 17355 17358 17362) to complete...
Waiting for PID 17362 of (17352 17355 17358 17362) 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 0050555 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 286076
Total vertex volume 282380 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1609   1104   2742  2.391 0.637     0.105     0.021       16     1.2  bankssts
  979    635   1553  2.233 0.668     0.134     0.018       15     0.7  caudalanteriorcingulate
 3800   2627   8164  2.735 0.730     0.108     0.018       30     2.8  caudalmiddlefrontal
 2548   1746   4061  2.215 0.548     0.143     0.036       28     3.7  cuneus
  473    358   1680  3.372 0.931     0.125     0.030        4     0.6  entorhinal
 5000   3471  10855  2.675 0.732     0.120     0.023       52     5.1  fusiform
 7491   5273  15286  2.457 0.675     0.130     0.027       93     9.3  inferiorparietal
 4948   3540  10277  2.236 0.755     0.138     0.036       88     8.1  inferiortemporal
 1966   1336   3719  2.336 0.870     0.121     0.026       22     2.0  isthmuscingulate
 8710   5913  14596  2.255 0.644     0.138     0.030      105    10.7  lateraloccipital
 4034   2882   9694  2.725 0.905     0.125     0.026       40     4.6  lateralorbitofrontal
 5134   3676   8045  2.113 0.561     0.145     0.036       69     7.6  lingual
 2672   1883   5435  2.452 0.782     0.128     0.026       33     2.8  medialorbitofrontal
 4215   3062   9618  2.383 0.794     0.132     0.030       64     5.3  middletemporal
 1013    695   2441  2.969 0.835     0.092     0.018        6     0.7  parahippocampal
 2354   1572   4116  2.366 0.613     0.102     0.018       15     1.8  paracentral
 2026   1467   4684  2.534 0.776     0.117     0.021       17     1.8  parsopercularis
  974    683   2529  2.397 0.878     0.137     0.030       14     1.3  parsorbitalis
 2042   1436   5078  2.545 0.895     0.113     0.016       19     1.4  parstriangularis
 2277   1634   2827  1.881 0.522     0.132     0.030       23     2.8  pericalcarine
 7773   5104  13392  2.229 0.725     0.103     0.021       73     6.5  postcentral
 1781   1266   3831  2.730 0.861     0.143     0.032       25     2.4  posteriorcingulate
 8452   5564  15742  2.513 0.634     0.108     0.020       63     7.5  precentral
 6220   4474  12458  2.466 0.716     0.124     0.025       59     6.3  precuneus
 1322    883   2330  2.193 0.871     0.148     0.043       21     2.7  rostralanteriorcingulate
 9672   6806  18973  2.260 0.691     0.138     0.033      139    14.0  rostralmiddlefrontal
13759   9470  32203  2.819 0.751     0.121     0.025      132    13.9  superiorfrontal
 9618   6632  18018  2.369 0.712     0.115     0.021       83     8.1  superiorparietal
 6329   4470  12979  2.346 0.698     0.121     0.026       74     7.3  superiortemporal
 6336   4439  11744  2.223 0.669     0.125     0.028       82     8.0  supramarginal
  414    299   1113  2.427 0.779     0.154     0.046        6     0.8  frontalpole
  778    591   3029  3.376 0.898     0.152     0.036       11     1.3  temporalpole
  777    530   1621  2.468 0.681     0.136     0.034       15     1.1  transversetemporal
 3710   2527   7497  2.941 0.723     0.119     0.028       36     4.3  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab 0050555 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 286076
Total vertex volume 282380 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1609   1164   2742  2.391 0.637     0.159     0.046       23     3.6  bankssts
  979    754   1553  2.233 0.668     0.171     0.049       26     2.2  caudalanteriorcingulate
 3800   3233   8164  2.735 0.730     0.129     0.027       42     4.6  caudalmiddlefrontal
 2548   1945   4061  2.215 0.548     0.141     0.036       29     4.3  cuneus
  473    657   1680  3.372 0.931     0.216     0.045       11     0.9  entorhinal
 5000   4527  10855  2.675 0.732     0.157     0.036       72     8.6  fusiform
 7491   7089  15286  2.457 0.675     0.165     0.036       96    13.2  inferiorparietal
 4948   5413  10277  2.236 0.755     0.194     0.040       66    10.1  inferiortemporal
 1966   1683   3719  2.336 0.870     0.143     0.034       36     3.1  isthmuscingulate
 8710   6987  14596  2.255 0.644     0.137     0.032      105    12.8  lateraloccipital
 4034   4048   9694  2.725 0.905     0.173     0.039       55     7.4  lateralorbitofrontal
 5134   4162   8045  2.113 0.561     0.146     0.036       82     8.5  lingual
 2672   2464   5435  2.452 0.782     0.168     0.040       39     4.7  medialorbitofrontal
 4215   4618   9618  2.383 0.794     0.188     0.039       49     8.4  middletemporal
 1013    982   2441  2.969 0.835     0.162     0.037       12     2.0  parahippocampal
 2354   1947   4116  2.366 0.613     0.132     0.031       24     3.4  paracentral
 2026   2052   4684  2.534 0.776     0.174     0.036       24     3.5  parsopercularis
  974   1272   2529  2.397 0.878     0.221     0.044       12     2.3  parsorbitalis
 2042   2271   5078  2.545 0.895     0.185     0.034       29     3.4  parstriangularis
 2277   1476   2827  1.881 0.522     0.123     0.030       24     3.0  pericalcarine
 7773   6865  13392  2.229 0.725     0.138     0.028       70    10.5  postcentral
 1781   1451   3831  2.730 0.861     0.166     0.046       48     3.6  posteriorcingulate
 8452   6782  15742  2.513 0.634     0.130     0.028      118    11.1  precentral
 6220   5455  12458  2.466 0.716     0.155     0.036       99    10.0  precuneus
 1322   1256   2330  2.193 0.871     0.210     0.075       36     4.2  rostralanteriorcingulate
 9672   9441  18973  2.260 0.691     0.178     0.040      127    19.1  rostralmiddlefrontal
13759  12794  32203  2.819 0.751     0.156     0.036      172    23.2  superiorfrontal
 9618   8102  18018  2.369 0.712     0.138     0.028      110    12.5  superiorparietal
 6329   6404  12979  2.346 0.698     0.195     0.046      102    14.4  superiortemporal
 6336   5808  11744  2.223 0.669     0.173     0.040       92    12.3  supramarginal
  414    565   1113  2.427 0.779     0.232     0.048        5     1.1  frontalpole
  778   1164   3029  3.376 0.898     0.256     0.055       12     2.6  temporalpole
  777    837   1621  2.468 0.681     0.185     0.047       10     1.6  transversetemporal
 3710   2564   7497  2.941 0.723     0.162     0.048       64     8.7  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 0050555 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 296431
Total vertex volume 293693 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1318    963   2329  2.263 0.583     0.108     0.016       10     0.9  bankssts
 1107    806   2376  2.396 0.776     0.129     0.024       15     1.1  caudalanteriorcingulate
 3932   2687   8119  2.627 0.684     0.113     0.019       35     3.0  caudalmiddlefrontal
 2649   1854   4045  1.984 0.531     0.139     0.031       30     3.4  cuneus
  425    318   1395  3.201 0.886     0.124     0.021        3     0.3  entorhinal
 5243   3667  12638  2.836 0.742     0.140     0.028       66     5.9  fusiform
 7284   5066  15023  2.409 0.701     0.124     0.028       84     8.3  inferiorparietal
 5601   4001  12276  2.383 0.833     0.131     0.031       89     8.1  inferiortemporal
 1757   1212   3401  2.436 0.870     0.128     0.026       22     1.6  isthmuscingulate
 9407   6452  15724  2.258 0.603     0.133     0.028      100    11.1  lateraloccipital
 4113   2852   9307  2.635 0.836     0.134     0.044       55     7.9  lateralorbitofrontal
 5545   3882   9543  2.286 0.690     0.144     0.035       66     8.5  lingual
 2811   2011   6984  2.472 0.842     0.130     0.033       40     3.7  medialorbitofrontal
 5540   3896  13046  2.529 0.827     0.125     0.027       65     6.7  middletemporal
 1026    692   2335  2.827 0.880     0.100     0.020        7     0.7  parahippocampal
 2372   1646   4092  2.371 0.529     0.120     0.021       20     2.1  paracentral
 2111   1478   4720  2.493 0.681     0.118     0.022       23     1.8  parsopercularis
 1211    876   3193  2.596 0.965     0.144     0.035       18     1.7  parsorbitalis
 2135   1525   5072  2.537 0.876     0.129     0.025       26     2.4  parstriangularis
 2671   1855   2794  1.700 0.402     0.135     0.027       27     2.9  pericalcarine
 7268   4901  11710  2.049 0.661     0.106     0.020       54     6.0  postcentral
 1796   1245   3456  2.455 0.685     0.132     0.024       24     1.7  posteriorcingulate
 9463   6341  17328  2.452 0.688     0.110     0.022       67     8.5  precentral
 7458   5324  14658  2.474 0.689     0.128     0.031       78     9.8  precuneus
  808    557   1633  2.485 0.791     0.143     0.037       14     1.1  rostralanteriorcingulate
 8923   6364  18303  2.238 0.755     0.139     0.035      123    13.6  rostralmiddlefrontal
12582   8564  29536  2.873 0.752     0.118     0.024      112    12.8  superiorfrontal
10334   7062  19434  2.354 0.694     0.120     0.026      101    10.5  superiorparietal
 6465   4429  15817  2.904 0.887     0.111     0.019       56     5.2  superiortemporal
 5982   4227  11616  2.268 0.700     0.122     0.024       63     5.7  supramarginal
  547    426   1526  2.460 0.806     0.207     0.068       13     1.8  frontalpole
  600    438   2662  3.884 1.105     0.119     0.031        5     0.6  temporalpole
  672    403   1109  2.189 0.603     0.154     0.076       19     2.3  transversetemporal
 3396   2295   6470  2.837 0.653     0.117     0.028       28     4.0  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050555 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 296431
Total vertex volume 293693 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1318   1039   2329  2.263 0.583     0.149     0.037       18     2.0  bankssts
 1107   1081   2376  2.396 0.776     0.171     0.039       22     2.0  caudalanteriorcingulate
 3932   3314   8119  2.627 0.684     0.132     0.026       37     4.5  caudalmiddlefrontal
 2649   2297   4045  1.984 0.531     0.142     0.035       30     4.1  cuneus
  425    493   1395  3.201 0.886     0.198     0.058        9     1.1  entorhinal
 5243   4937  12638  2.836 0.742     0.157     0.037       83     8.8  fusiform
 7284   7022  15023  2.409 0.701     0.162     0.035       82    12.3  inferiorparietal
 5601   5808  12276  2.383 0.833     0.179     0.041       71    11.3  inferiortemporal
 1757   1466   3401  2.436 0.870     0.138     0.033       29     2.2  isthmuscingulate
 9407   7586  15724  2.258 0.603     0.132     0.030      116    12.9  lateraloccipital
 4113   4096   9307  2.635 0.836     0.207     0.071      142    14.6  lateralorbitofrontal
 5545   4677   9543  2.286 0.690     0.148     0.036       71     9.6  lingual
 2811   3221   6984  2.472 0.842     0.215     0.051       44     7.3  medialorbitofrontal
 5540   5982  13046  2.529 0.827     0.189     0.041       68    11.1  middletemporal
 1026    921   2335  2.827 0.880     0.150     0.038       12     1.9  parahippocampal
 2372   1884   4092  2.371 0.529     0.123     0.029       32     2.9  paracentral
 2111   2075   4720  2.493 0.681     0.178     0.034       29     3.7  parsopercularis
 1211   1426   3193  2.596 0.965     0.190     0.044       16     2.3  parsorbitalis
 2135   2289   5072  2.537 0.876     0.195     0.038       36     4.1  parstriangularis
 2671   1638   2794  1.700 0.402     0.120     0.031       35     3.5  pericalcarine
 7268   6320  11710  2.049 0.661     0.137     0.028       65     9.8  postcentral
 1796   1536   3456  2.455 0.685     0.157     0.040       29     3.1  posteriorcingulate
 9463   7435  17328  2.452 0.688     0.122     0.026       98    11.9  precentral
 7458   6393  14658  2.474 0.689     0.156     0.037      109    13.6  precuneus
  808    787   1633  2.485 0.791     0.193     0.049       25     2.0  rostralanteriorcingulate
 8923   9430  18303  2.238 0.755     0.189     0.039      114    17.9  rostralmiddlefrontal
12582  11392  29536  2.873 0.752     0.150     0.034      161    20.0  superiorfrontal
10334   8953  19434  2.354 0.694     0.145     0.032      120    14.9  superiorparietal
 6465   6174  15817  2.904 0.887     0.167     0.041       78    13.2  superiortemporal
 5982   5633  11616  2.268 0.700     0.170     0.038       73    11.2  supramarginal
  547    762   1526  2.460 0.806     0.283     0.070       10     2.0  frontalpole
  600    900   2662  3.884 1.105     0.218     0.040        6     1.3  temporalpole
  672    626   1109  2.189 0.603     0.174     0.051       10     1.5  transversetemporal
 3396   2324   6470  2.837 0.653     0.162     0.044       59     7.6  insula
PIDs (17352 17355 17358 17362) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 10:05:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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 10:05:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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 17451 of (17451 17454) to complete...
Waiting for PID 17454 of (17451 17454) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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...
100 labels changed using aseg
relabeling using gibbs priors...
000:   9338 changed, 150248 examined...
001:   2183 changed, 36672 examined...
002:    651 changed, 11482 examined...
003:    254 changed, 3671 examined...
004:    123 changed, 1438 examined...
005:     57 changed, 730 examined...
006:     28 changed, 320 examined...
007:     13 changed, 161 examined...
008:      6 changed, 73 examined...
009:      1 changed, 36 examined...
010:      0 changed, 5 examined...
12 labels changed using aseg
000: 282 total segments, 197 labels (2264 vertices) changed
001: 100 total segments, 16 labels (141 vertices) changed
002: 88 total segments, 4 labels (34 vertices) changed
003: 85 total segments, 1 labels (2 vertices) changed
004: 84 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...
851 vertices marked for relabeling...
851 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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...
82 labels changed using aseg
relabeling using gibbs priors...
000:   9941 changed, 152869 examined...
001:   2324 changed, 38830 examined...
002:    692 changed, 12337 examined...
003:    283 changed, 3994 examined...
004:    143 changed, 1582 examined...
005:     79 changed, 812 examined...
006:     43 changed, 451 examined...
007:     21 changed, 245 examined...
008:      7 changed, 128 examined...
009:      5 changed, 48 examined...
010:      2 changed, 29 examined...
011:      0 changed, 14 examined...
51 labels changed using aseg
000: 263 total segments, 177 labels (2632 vertices) changed
001: 96 total segments, 12 labels (47 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 52 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1036 vertices marked for relabeling...
1036 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (17451 17454) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 10:06:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 10:06:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 rh white 

Waiting for PID 17511 of (17511 17515) to complete...
Waiting for PID 17515 of (17511 17515) 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 0050555 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 286076
Total vertex volume 282380 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1393    980   2481  2.061 0.730     0.152     0.043       25     2.4  G&S_frontomargin
 2139   1438   4576  2.642 0.699     0.129     0.024       25     2.1  G&S_occipital_inf
 1681   1122   3319  2.280 0.702     0.106     0.021       11     1.4  G&S_paracentral
 1690   1157   3331  2.207 0.737     0.119     0.024       23     1.6  G&S_subcentral
  882    630   2229  2.396 0.761     0.175     0.050       17     2.3  G&S_transv_frontopol
 2632   1807   4653  2.371 0.739     0.127     0.030       27     3.6  G&S_cingul-Ant
 1427   1001   2730  2.601 0.689     0.123     0.019       15     1.1  G&S_cingul-Mid-Ant
 1568   1069   3342  2.867 0.697     0.131     0.030       16     2.0  G&S_cingul-Mid-Post
  712    523   2450  3.210 0.636     0.161     0.041       10     1.3  G_cingul-Post-dorsal
  366    253    805  2.676 0.726     0.131     0.026        4     0.4  G_cingul-Post-ventral
 2428   1684   4238  2.182 0.600     0.152     0.040       30     3.9  G_cuneus
 1329    963   4240  3.025 0.702     0.133     0.027       17     1.7  G_front_inf-Opercular
  486    320   1717  3.201 0.600     0.136     0.024        9     0.4  G_front_inf-Orbital
 1118    809   3707  2.993 0.808     0.127     0.019       12     0.9  G_front_inf-Triangul
 5289   3694  14009  2.711 0.771     0.142     0.035       89     7.7  G_front_middle
 9072   6208  24563  3.022 0.738     0.131     0.029      104    10.7  G_front_sup
  810    559   1784  3.107 0.883     0.146     0.053       12     1.7  G_Ins_lg&S_cent_ins
  800    514   2206  3.315 0.613     0.116     0.026       10     0.9  G_insular_short
 2369   1681   5354  2.467 0.688     0.149     0.033       35     3.7  G_occipital_middle
 1634   1097   2963  2.399 0.574     0.132     0.028       18     1.8  G_occipital_sup
 2061   1397   5320  2.911 0.642     0.136     0.031       33     2.7  G_oc-temp_lat-fusifor
 3580   2588   6152  2.150 0.624     0.167     0.045       59     6.8  G_oc-temp_med-Lingual
 1229    866   3738  3.240 0.829     0.111     0.026       11     1.1  G_oc-temp_med-Parahip
 2474   1821   7562  2.796 0.858     0.136     0.032       32     3.6  G_orbital
 2882   2036   6871  2.510 0.685     0.144     0.036       51     4.5  G_pariet_inf-Angular
 3056   2196   7235  2.358 0.737     0.149     0.037       57     5.6  G_pariet_inf-Supramar
 3725   2588   8876  2.589 0.809     0.129     0.027       42     4.2  G_parietal_sup
 3083   1895   6204  2.535 0.779     0.115     0.029       36     3.6  G_postcentral
 3232   2015   6993  2.703 0.638     0.109     0.026       26     3.6  G_precentral
 2905   2223   7987  2.682 0.749     0.146     0.032       36     4.0  G_precuneus
  928    688   2574  2.567 0.873     0.166     0.044       18     1.7  G_rectus
  283    198    600  2.960 0.930     0.111     0.036        2     0.3  G_subcallosal
  764    516   1877  2.510 0.675     0.146     0.041       18     1.5  G_temp_sup-G_T_transv
 2274   1678   6325  2.545 0.758     0.160     0.040       47     4.1  G_temp_sup-Lateral
  721    529   1731  2.768 0.804     0.095     0.031        5     0.6  G_temp_sup-Plan_polar
 1037    743   2204  2.390 0.750     0.102     0.017        8     0.8  G_temp_sup-Plan_tempo
 2587   1888   6206  2.321 0.729     0.165     0.050       73     6.0  G_temporal_inf
 2271   1694   6114  2.482 0.741     0.157     0.044       52     4.1  G_temporal_middle
  363    240    476  2.018 0.490     0.078     0.011        1     0.1  Lat_Fis-ant-Horizont
  302    220    342  1.700 0.416     0.086     0.011        1     0.1  Lat_Fis-ant-Vertical
 1332    881   1761  2.445 0.644     0.109     0.018        9     1.0  Lat_Fis-post
 2820   1882   4053  2.012 0.555     0.153     0.039       38     4.5  Pole_occipital
 1696   1261   6348  3.078 0.994     0.166     0.042       29     3.4  Pole_temporal
 2762   1963   3552  2.093 0.636     0.107     0.019       20     2.2  S_calcarine
 3389   2335   4350  2.025 0.569     0.100     0.016       18     2.2  S_central
 1068    733   1589  2.411 0.585     0.093     0.014        5     0.6  S_cingul-Marginalis
  529    375   1018  2.982 0.617     0.091     0.013        2     0.3  S_circular_insula_ant
 1405    945   2107  2.402 0.655     0.092     0.013        6     0.8  S_circular_insula_inf
 1853   1280   2700  2.473 0.572     0.104     0.017       10     1.4  S_circular_insula_sup
 1047    727   1883  2.640 0.683     0.097     0.016        5     0.6  S_collat_transv_ant
  544    368    598  1.929 0.407     0.085     0.014        2     0.3  S_collat_transv_post
 2253   1564   3124  2.069 0.525     0.106     0.017       15     1.5  S_front_inf
 1957   1352   2927  2.039 0.590     0.121     0.025       20     2.1  S_front_middle
 4199   2933   6565  2.341 0.506     0.097     0.016       22     2.7  S_front_sup
  573    386    724  2.151 0.536     0.105     0.020        3     0.5  S_interm_prim-Jensen
 2908   1995   4161  2.283 0.594     0.106     0.018       20     1.9  S_intrapariet&P_trans
 1384    953   1847  2.015 0.483     0.124     0.025       14     1.3  S_oc_middle&Lunatus
 1797   1251   2306  2.088 0.449     0.101     0.017       11     1.1  S_oc_sup&transversal
  640    451    850  2.200 0.528     0.131     0.028        6     0.6  S_occipital_ant
 1109    787   1569  1.918 0.609     0.096     0.013        5     0.7  S_oc-temp_lat
 2357   1651   3664  2.406 0.616     0.101     0.016       14     1.5  S_oc-temp_med&Lingual
  280    195    282  1.452 0.300     0.115     0.016        2     0.2  S_orbital_lateral
  672    477   1137  2.260 0.880     0.122     0.019        7     0.5  S_orbital_med-olfact
 1590   1091   2944  2.415 1.002     0.114     0.023       12     1.6  S_orbital-H_Shaped
 2683   1863   3722  2.169 0.592     0.116     0.023       22     2.4  S_parieto_occipital
 1582    988   1246  1.687 0.556     0.118     0.020       24     1.2  S_pericallosal
 4127   2780   5567  2.112 0.517     0.093     0.013       25     2.1  S_postcentral
 1859   1268   2831  2.362 0.526     0.108     0.017       13     1.2  S_precentral-inf-part
 1487   1034   2141  2.375 0.507     0.094     0.012        7     0.7  S_precentral-sup-part
  891    596   1319  2.369 0.611     0.101     0.015        8     0.6  S_suborbital
 1126    774   1571  2.186 0.610     0.107     0.018        7     0.8  S_subparietal
 1483   1023   1742  1.784 0.515     0.102     0.015        8     1.0  S_temporal_inf
 5854   4076   9613  2.295 0.652     0.102     0.017       40     4.3  S_temporal_sup
  404    295    479  1.866 0.375     0.120     0.010        4     0.2  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050555 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 296431
Total vertex volume 293693 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
  938    739   2272  2.210 0.706     0.183     0.060       18     2.4  G&S_frontomargin
 1236    843   2754  2.693 0.688     0.118     0.023       11     1.2  G&S_occipital_inf
 1469    999   2630  2.163 0.655     0.125     0.025       13     1.6  G&S_paracentral
 1551   1129   3637  2.474 0.636     0.133     0.026       18     1.7  G&S_subcentral
 1444   1088   3420  2.226 0.768     0.188     0.062       29     4.4  G&S_transv_frontopol
 3029   2104   6233  2.533 0.701     0.123     0.029       34     3.5  G&S_cingul-Ant
 1564   1148   3358  2.835 0.564     0.111     0.021       11     1.4  G&S_cingul-Mid-Ant
 1699   1163   3303  2.702 0.432     0.119     0.020       16     1.2  G&S_cingul-Mid-Post
  712    513   2114  2.983 0.623     0.155     0.035        9     1.1  G_cingul-Post-dorsal
  417    289    881  2.411 0.749     0.138     0.033        5     0.5  G_cingul-Post-ventral
 2521   1749   3938  1.946 0.587     0.141     0.032       30     3.5  G_cuneus
 1336    969   3830  2.740 0.671     0.146     0.032       23     1.7  G_front_inf-Opercular
  589    422   1731  2.873 0.896     0.186     0.055       18     1.5  G_front_inf-Orbital
  773    546   2400  2.862 0.918     0.141     0.029       11     1.0  G_front_inf-Triangul
 4522   3115  12343  2.804 0.737     0.144     0.036       75     6.9  G_front_middle
 8320   5524  22315  3.027 0.780     0.128     0.028       98     9.6  G_front_sup
  716    464   1516  2.950 0.681     0.125     0.041        8     1.3  G_Ins_lg&S_cent_ins
  679    448   1683  2.899 0.795     0.131     0.039        8     1.1  G_insular_short
 2786   1905   6729  2.619 0.654     0.154     0.041       46     5.0  G_occipital_middle
 2391   1610   4572  2.380 0.701     0.121     0.029       26     2.8  G_occipital_sup
 2528   1771   6456  2.871 0.668     0.152     0.032       39     3.1  G_oc-temp_lat-fusifor
 3325   2373   6178  2.287 0.727     0.158     0.043       45     6.2  G_oc-temp_med-Lingual
 1143    787   3738  3.261 0.948     0.120     0.028       11     1.2  G_oc-temp_med-Parahip
 2530   1876   8621  3.047 0.843     0.157     0.050       43     5.5  G_orbital
 2511   1673   6509  2.648 0.753     0.133     0.034       36     3.3  G_pariet_inf-Angular
 2533   1848   6615  2.527 0.780     0.144     0.030       36     3.2  G_pariet_inf-Supramar
 3431   2339   8055  2.558 0.785     0.133     0.030       42     4.0  G_parietal_sup
 2649   1745   4525  2.057 0.646     0.118     0.024       24     2.7  G_postcentral
 3731   2447   8675  2.666 0.767     0.111     0.024       28     3.8  G_precentral
 3068   2293   7900  2.640 0.719     0.145     0.035       43     4.8  G_precuneus
  731    576   3205  3.073 0.709     0.169     0.049       14     1.5  G_rectus
  649    388    936  2.269 1.052     0.099     0.059        9     1.3  G_subcallosal
  621    375   1127  2.275 0.714     0.166     0.083       19     2.4  G_temp_sup-G_T_transv
 2294   1591   7389  3.239 0.915     0.138     0.025       32     2.4  G_temp_sup-Lateral
 1237    822   2906  3.232 0.929     0.092     0.030       10     1.9  G_temp_sup-Plan_polar
  899    653   1988  2.515 0.728     0.101     0.021        6     0.7  G_temp_sup-Plan_tempo
 3184   2324   8649  2.522 0.922     0.154     0.043       72     6.3  G_temporal_inf
 2986   2153   8103  2.588 0.841     0.144     0.038       50     5.0  G_temporal_middle
  393    278    600  2.315 0.617     0.105     0.013        2     0.2  Lat_Fis-ant-Horizont
  262    193    403  1.984 0.497     0.095     0.012        1     0.1  Lat_Fis-ant-Vertical
 1588   1077   2271  2.425 0.510     0.107     0.017       10     1.1  Lat_Fis-post
 4003   2824   6131  2.031 0.584     0.144     0.031       46     5.1  Pole_occipital
 1745   1241   7169  3.547 0.997     0.136     0.032       24     2.2  Pole_temporal
 3240   2199   3851  2.028 0.726     0.124     0.023       31     3.2  S_calcarine
 3791   2578   4346  1.909 0.506     0.099     0.017       20     2.6  S_central
 1145    817   1820  2.302 0.493     0.109     0.018        8     0.8  S_cingul-Marginalis
  713    484   1081  2.535 0.719     0.098     0.018        4     0.6  S_circular_insula_ant
 1083    727   1510  2.358 0.576     0.090     0.011        5     0.4  S_circular_insula_inf
 1561   1054   2352  2.461 0.596     0.106     0.018        8     1.1  S_circular_insula_sup
 1188    828   1979  2.453 0.697     0.110     0.020        8     0.9  S_collat_transv_ant
  646    418    878  2.434 0.463     0.123     0.021        5     0.6  S_collat_transv_post
 1959   1330   3389  2.231 0.714     0.108     0.018       14     1.5  S_front_inf
 2456   1734   3308  1.881 0.526     0.105     0.016       16     1.7  S_front_middle
 3185   2244   4780  2.273 0.515     0.089     0.013       13     1.6  S_front_sup
  763    505    744  1.687 0.402     0.090     0.015        4     0.4  S_interm_prim-Jensen
 3735   2588   5609  2.144 0.534     0.112     0.023       29     3.4  S_intrapariet&P_trans
 1386    955   1675  2.094 0.413     0.118     0.021       10     1.2  S_oc_middle&Lunatus
 1789   1266   2575  2.257 0.472     0.118     0.018       15     1.3  S_oc_sup&transversal
 1110    756   1399  2.145 0.390     0.125     0.022       10     1.1  S_occipital_ant
 1427    989   1929  2.166 0.443     0.100     0.015        8     0.9  S_oc-temp_lat
 2178   1508   3799  2.639 0.603     0.108     0.018       16     1.4  S_oc-temp_med&Lingual
  468    346    646  1.951 0.490     0.139     0.025        4     0.6  S_orbital_lateral
  562    414   1097  2.562 0.598     0.105     0.019        3     0.3  S_orbital_med-olfact
 1512   1052   2614  2.211 0.788     0.121     0.026       12     1.7  S_orbital-H_Shaped
 3017   2104   4676  2.281 0.582     0.122     0.028       27     3.2  S_parieto_occipital
 1505    945   1171  1.682 0.534     0.124     0.018       27     0.9  S_pericallosal
 3326   2268   4206  2.032 0.528     0.093     0.016       18     2.2  S_postcentral
 1794   1217   2507  2.118 0.511     0.106     0.016       11     1.2  S_precentral-inf-part
 2274   1564   3569  2.523 0.549     0.098     0.016       10     1.5  S_precentral-sup-part
  342    247    438  2.036 0.529     0.124     0.015        3     0.2  S_suborbital
 1753   1230   2856  2.369 0.591     0.117     0.029       14     2.1  S_subparietal
 1512   1027   1900  1.938 0.529     0.106     0.017        9     1.2  S_temporal_inf
 6179   4334  10805  2.332 0.628     0.103     0.018       46     4.5  S_temporal_sup
  224    169    376  3.046 0.608     0.127     0.023        2     0.1  S_temporal_transverse
PIDs (17511 17515) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 10:06:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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 10:06:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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 17601 of (17601 17604) to complete...
Waiting for PID 17604 of (17601 17604) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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...
1488 labels changed using aseg
relabeling using gibbs priors...
000:   2132 changed, 150248 examined...
001:    474 changed, 9870 examined...
002:    127 changed, 2717 examined...
003:     54 changed, 720 examined...
004:     35 changed, 328 examined...
005:     22 changed, 200 examined...
006:     17 changed, 121 examined...
007:     17 changed, 92 examined...
008:     13 changed, 78 examined...
009:      9 changed, 71 examined...
010:     10 changed, 61 examined...
011:      7 changed, 62 examined...
012:      5 changed, 48 examined...
013:      7 changed, 26 examined...
014:     11 changed, 30 examined...
015:      8 changed, 46 examined...
016:      6 changed, 30 examined...
017:      6 changed, 32 examined...
018:      3 changed, 32 examined...
019:      1 changed, 20 examined...
020:      0 changed, 7 examined...
286 labels changed using aseg
000: 58 total segments, 25 labels (189 vertices) changed
001: 34 total segments, 1 labels (5 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 4 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
757 vertices marked for relabeling...
757 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050555 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...
1606 labels changed using aseg
relabeling using gibbs priors...
000:   2103 changed, 152869 examined...
001:    470 changed, 9943 examined...
002:    132 changed, 2738 examined...
003:     59 changed, 805 examined...
004:     30 changed, 348 examined...
005:     28 changed, 166 examined...
006:     31 changed, 162 examined...
007:     22 changed, 142 examined...
008:     13 changed, 108 examined...
009:     15 changed, 72 examined...
010:     10 changed, 57 examined...
011:     10 changed, 51 examined...
012:      9 changed, 50 examined...
013:      4 changed, 43 examined...
014:      2 changed, 22 examined...
015:      2 changed, 14 examined...
016:      2 changed, 14 examined...
017:      1 changed, 13 examined...
018:      0 changed, 7 examined...
330 labels changed using aseg
000: 55 total segments, 22 labels (178 vertices) changed
001: 33 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...
743 vertices marked for relabeling...
743 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (17601 17604) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 10:07:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 10:07:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 rh white 

Waiting for PID 17661 of (17661 17664) to complete...
Waiting for PID 17664 of (17661 17664) 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 0050555 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 286076
Total vertex volume 282380 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1708   1162   3334  2.508 0.778     0.131     0.021       22     1.4  caudalanteriorcingulate
 4159   2861   8766  2.706 0.722     0.110     0.019       33     3.3  caudalmiddlefrontal
 3524   2428   5651  2.194 0.585     0.135     0.033       36     4.7  cuneus
  444    335   1502  3.440 0.886     0.109     0.023        3     0.3  entorhinal
 4631   3200   9522  2.655 0.696     0.116     0.023       46     4.4  fusiform
 7566   5299  15247  2.436 0.672     0.131     0.028       97     9.7  inferiorparietal
 4981   3600  11133  2.297 0.793     0.141     0.037       89     8.7  inferiortemporal
 1922   1311   3694  2.370 0.862     0.122     0.026       21     2.0  isthmuscingulate
 8883   6038  14943  2.254 0.639     0.140     0.031      109    11.1  lateraloccipital
 4513   3233  11054  2.694 0.940     0.134     0.032       54     6.3  lateralorbitofrontal
 5235   3753   8158  2.108 0.562     0.147     0.036       71     7.9  lingual
 2200   1574   4793  2.451 0.805     0.131     0.028       30     2.6  medialorbitofrontal
 5808   4168  12370  2.358 0.760     0.128     0.027       80     6.8  middletemporal
 1096    757   2635  2.954 0.834     0.093     0.019        7     0.7  parahippocampal
 2733   1814   4952  2.429 0.613     0.103     0.018       18     2.1  paracentral
 1897   1362   4333  2.534 0.787     0.117     0.022       17     1.7  parsopercularis
 1045    722   2603  2.642 0.799     0.104     0.018        9     0.7  parsorbitalis
 2309   1648   5595  2.502 0.876     0.114     0.017       21     1.7  parstriangularis
 2190   1570   2728  1.892 0.509     0.129     0.029       21     2.5  pericalcarine
 9081   5978  15327  2.229 0.710     0.103     0.020       80     7.3  postcentral
 2004   1406   4181  2.697 0.847     0.144     0.032       27     2.8  posteriorcingulate
 8284   5438  15468  2.515 0.639     0.108     0.021       63     7.5  precentral
 6044   4349  12601  2.504 0.730     0.126     0.025       59     6.3  precuneus
 1813   1208   3072  2.289 0.861     0.142     0.037       25     3.1  rostralanteriorcingulate
 6966   4864  13980  2.289 0.710     0.135     0.032       97     9.5  rostralmiddlefrontal
14963  10383  33835  2.704 0.782     0.125     0.027      159    16.8  superiorfrontal
 7491   5182  14069  2.362 0.715     0.113     0.021       65     6.0  superiorparietal
 8216   5819  18042  2.472 0.779     0.121     0.027       96     9.3  superiortemporal
 5697   4000  10718  2.248 0.677     0.125     0.028       72     7.2  supramarginal
  789    528   1611  2.469 0.678     0.137     0.034       16     1.1  transversetemporal
 3050   2075   6460  2.993 0.687     0.118     0.026       30     3.3  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 0050555 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 296431
Total vertex volume 293693 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1205    876   2558  2.400 0.764     0.129     0.024       16     1.2  caudalanteriorcingulate
 4183   2852   8434  2.606 0.679     0.114     0.019       37     3.3  caudalmiddlefrontal
 3340   2305   5182  2.006 0.581     0.135     0.029       37     4.0  cuneus
  450    330   1449  3.230 0.915     0.121     0.020        3     0.3  entorhinal
 4787   3369  10951  2.798 0.676     0.139     0.028       59     5.1  fusiform
 7377   5103  14988  2.406 0.698     0.125     0.028       86     8.3  inferiorparietal
 6015   4262  13914  2.453 0.887     0.132     0.031       95     8.6  inferiortemporal
 1705   1178   3280  2.428 0.846     0.128     0.027       21     1.6  isthmuscingulate
 9478   6493  15616  2.233 0.600     0.133     0.028      102    11.2  lateraloccipital
 4277   3078  10324  2.612 0.844     0.149     0.048       66     9.4  lateralorbitofrontal
 5400   3775   9318  2.295 0.689     0.145     0.036       64     8.3  lingual
 1989   1443   5426  2.599 0.819     0.140     0.042       32     3.4  medialorbitofrontal
 6617   4691  15187  2.503 0.796     0.124     0.026       75     7.6  middletemporal
 1090    738   2495  2.834 0.873     0.101     0.020        8     0.8  parahippocampal
 2518   1735   4543  2.421 0.562     0.119     0.021       21     2.3  paracentral
 2288   1621   5115  2.481 0.687     0.117     0.021       24     1.9  parsopercularis
 1095    768   2595  2.451 0.930     0.143     0.037       17     1.6  parsorbitalis
 2129   1518   5061  2.543 0.877     0.132     0.026       27     2.4  parstriangularis
 2606   1815   2727  1.692 0.388     0.133     0.027       26     2.8  pericalcarine
 8039   5446  12894  2.052 0.653     0.107     0.020       59     6.8  postcentral
 1949   1341   3857  2.515 0.722     0.131     0.024       26     1.8  posteriorcingulate
 8902   6003  16532  2.432 0.692     0.111     0.021       64     7.9  precentral
 7681   5492  15309  2.478 0.689     0.129     0.031       83    10.0  precuneus
 1109    756   1905  2.262 0.872     0.127     0.028       14     1.2  rostralanteriorcingulate
 6096   4256  12542  2.322 0.784     0.130     0.029       74     7.6  rostralmiddlefrontal
16274  11209  37045  2.726 0.794     0.123     0.028      168    19.4  superiorfrontal
 8515   5846  16504  2.405 0.693     0.120     0.026       84     9.2  superiorparietal
 7965   5494  19868  2.909 0.949     0.110     0.020       66     6.5  superiortemporal
 5679   3998  10932  2.271 0.706     0.121     0.024       59     5.4  supramarginal
  684    412   1140  2.190 0.589     0.159     0.076       19     2.4  transversetemporal
 3114   2115   6004  2.822 0.647     0.116     0.027       25     3.5  insula
PIDs (17661 17664) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 10:07:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 pctsurfcon --s 0050555 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 10:07:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts

 pctsurfcon --s 0050555 --rh-only 

Waiting for PID 17722 of (17722 17734) to complete...
Waiting for PID 17734 of (17722 17734) to complete...

 pctsurfcon --s 0050555 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts/pctsurfcon.log
Sun Oct  8 10:07:52 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-6.0.0/0050555/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-924 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-6.0.0/0050555/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17722/lh.wm.mgh --regheader 0050555 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 88585
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17722/lh.wm.mgh
Dim: 150248 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17722/lh.gm.mgh --projfrac 0.3 --regheader 0050555 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 102186
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17722/lh.gm.mgh
Dim: 150248 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17722/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17722/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.w-g.pct.mgh --annot 0050555 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/lh.w-g.pct.mgh --annot 0050555 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/lh.w-g.pct.mgh
Vertex Area is 0.692667 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 0050555 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/scripts/pctsurfcon.log
Sun Oct  8 10:07:52 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-6.0.0/0050555/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-924 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-6.0.0/0050555/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17734/rh.wm.mgh --regheader 0050555 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 89968
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17734/rh.wm.mgh
Dim: 152869 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17734/rh.gm.mgh --projfrac 0.3 --regheader 0050555 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 104125
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17734/rh.gm.mgh
Dim: 152869 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17734/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/tmp.pctsurfcon.17734/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.w-g.pct.mgh --annot 0050555 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.w-g.pct.mgh --annot 0050555 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.w-g.pct.mgh
Vertex Area is 0.693134 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 (17722 17734) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 10:07:58 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2722 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2164 voxels changed to hypointensity...
5253 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 10:08:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555

 mri_aparc2aseg --s 0050555 --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 10:08:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555

 mri_aparc2aseg --s 0050555 --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 10:08:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555

 mri_aparc2aseg --s 0050555 --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 17898 of (17898 17901 17905) to complete...
Waiting for PID 17901 of (17898 17901 17905) to complete...
Waiting for PID 17905 of (17898 17901 17905) to complete...

 mri_aparc2aseg --s 0050555 --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 0050555
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/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-6.0.0/0050555/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 7.84
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 108
rescaling Left_Cerebral_Cortex from 61 --> 51
rescaling Left_Lateral_Ventricle from 13 --> 11
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 94
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 65
rescaling Left_Putamen from 80 --> 76
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 12
rescaling Brain_Stem from 81 --> 80
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 63
rescaling CSF from 32 --> 27
rescaling Left_Accumbens_area from 62 --> 58
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 52
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 85
rescaling Right_Cerebellum_Cortex from 59 --> 58
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 67
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 57
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 66
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 25
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  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 = 572895
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 134 changed.
pass 2: 9 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050555 --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 0050555
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/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-6.0.0/0050555/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 7.84
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 108
rescaling Left_Cerebral_Cortex from 61 --> 51
rescaling Left_Lateral_Ventricle from 13 --> 11
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 94
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 65
rescaling Left_Putamen from 80 --> 76
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 12
rescaling Brain_Stem from 81 --> 80
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 63
rescaling CSF from 32 --> 27
rescaling Left_Accumbens_area from 62 --> 58
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 52
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 85
rescaling Right_Cerebellum_Cortex from 59 --> 58
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 67
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 57
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 66
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 25
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  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 = 572868
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 134 changed.
pass 2: 9 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050555 --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 0050555
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/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-6.0.0/0050555/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 7.84
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 108
rescaling Left_Cerebral_Cortex from 61 --> 51
rescaling Left_Lateral_Ventricle from 13 --> 11
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 58
rescaling Left_Thalamus from 94 --> 94
rescaling Left_Thalamus_Proper from 84 --> 87
rescaling Left_Caudate from 75 --> 65
rescaling Left_Putamen from 80 --> 76
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 24
rescaling Fourth_Ventricle from 22 --> 12
rescaling Brain_Stem from 81 --> 80
rescaling Left_Hippocampus from 57 --> 60
rescaling Left_Amygdala from 56 --> 63
rescaling CSF from 32 --> 27
rescaling Left_Accumbens_area from 62 --> 58
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 104
rescaling Right_Cerebral_Cortex from 58 --> 52
rescaling Right_Lateral_Ventricle from 13 -->  9
rescaling Right_Inf_Lat_Vent from 25 --> 24
rescaling Right_Cerebellum_White_Matter from 87 --> 85
rescaling Right_Cerebellum_Cortex from 59 --> 58
rescaling Right_Thalamus_Proper from 85 --> 82
rescaling Right_Caudate from 62 --> 67
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 97
rescaling Right_Hippocampus from 53 --> 57
rescaling Right_Amygdala from 55 --> 62
rescaling Right_Accumbens_area from 65 --> 66
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 25
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 56
  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 = 572868
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 134 changed.
pass 2: 9 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (17898 17901 17905) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 10:15:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri

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

Sun Oct  8 10:15:20 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-6.0.0/0050555/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-924 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-6.0.0/0050555/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-924
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 10:15:20 CEST 2017 
Ended   at Sun Oct  8 10:15:26 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 10:15:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555

 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 0050555 


$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 0050555 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1745712 mm^3    (det: 1.115938 )
Computing euler number
orig.nofix lheno =  -84, rheno = -70
orig.nofix lhholes =   43, rhholes = 36
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
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 10:17:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555

 mri_aparc2aseg --s 0050555 --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 0050555
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-6.0.0/0050555/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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-6.0.0/0050555/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 9042 vertices from left hemi
Ripped 8317 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-6.0.0/0050555/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 = 1175921
Used brute-force search on 727 voxels
Fixing Parahip LH WM
  Found 3 clusters
     0 k 1.000000
     1 k 6.000000
     2 k 1812.000000
Fixing Parahip RH WM
  Found 5 clusters
     0 k 1.000000
     1 k 11.000000
     2 k 1908.000000
     3 k 1.000000
     4 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050555 --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 0050555 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-924
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1745712 mm^3    (det: 1.115938 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
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-6.0.0/0050555/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 10:26:31 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 18773 of (18773 18779 18785 18790 18797) to complete...
Waiting for PID 18779 of (18773 18779 18785 18790 18797) to complete...
Waiting for PID 18785 of (18773 18779 18785 18790 18797) to complete...
Waiting for PID 18790 of (18773 18779 18785 18790 18797) to complete...
Waiting for PID 18797 of (18773 18779 18785 18790 18797) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 702
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4831
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 1281
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9190
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 256
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4333
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 589
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6572
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 571
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6355
mri_label2label: Done

PIDs (18773 18779 18785 18790 18797) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 18839 of (18839 18845 18851 18857) to complete...
Waiting for PID 18845 of (18839 18845 18851 18857) to complete...
Waiting for PID 18851 of (18839 18845 18851 18857) to complete...
Waiting for PID 18857 of (18839 18845 18851 18857) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 280
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4350
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 2022
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15611
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 294
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4475
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 512
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 3934
mri_label2label: Done

PIDs (18839 18845 18851 18857) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 18911 of (18911 18917 18923 18928 18935) to complete...
Waiting for PID 18917 of (18911 18917 18923 18928 18935) to complete...
Waiting for PID 18923 of (18911 18917 18923 18928 18935) to complete...
Waiting for PID 18928 of (18911 18917 18923 18928 18935) to complete...
Waiting for PID 18935 of (18911 18917 18923 18928 18935) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 1675
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6316
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 3661
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11775
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 509
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2527
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 113
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1403
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 123
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1322
mri_label2label: Done

PIDs (18911 18917 18923 18928 18935) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 18989 of (18989 18995 19001 19007 19013) to complete...
Waiting for PID 18995 of (18989 18995 19001 19007 19013) to complete...
Waiting for PID 19001 of (18989 18995 19001 19007 19013) to complete...
Waiting for PID 19007 of (18989 18995 19001 19007 19013) to complete...
Waiting for PID 19013 of (18989 18995 19001 19007 19013) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 278
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1292
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 464
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2556
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 59
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1563
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 132
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2128
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 153
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2472
mri_label2label: Done

PIDs (18989 18995 19001 19007 19013) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 19062 of (19062 19068 19074 19078) to complete...
Waiting for PID 19068 of (19062 19068 19074 19078) to complete...
Waiting for PID 19074 of (19062 19068 19074 19078) to complete...
Waiting for PID 19078 of (19062 19068 19074 19078) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1612
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 819
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7854
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 94
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2006
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 202
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1353
mri_label2label: Done

PIDs (19062 19068 19074 19078) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 19133 of (19133 19139 19145 19150 19157) to complete...
Waiting for PID 19139 of (19133 19139 19145 19150 19157) to complete...
Waiting for PID 19145 of (19133 19139 19145 19150 19157) to complete...
Waiting for PID 19150 of (19133 19139 19145 19150 19157) to complete...
Waiting for PID 19157 of (19133 19139 19145 19150 19157) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 1131
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4536
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 1672
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5006
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 618
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 38
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 508
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 150248
Number of reverse mapping hits = 48
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 498
mri_label2label: Done

PIDs (19133 19139 19145 19150 19157) completed and logs appended.

 mris_label2annot --s 0050555 --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-6.0.0/0050555/label
cmdline mris_label2annot --s 0050555 --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-924
machine  x86_64
user     ntraut

subject 0050555
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-6.0.0/0050555/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 103318 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050555 --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-6.0.0/0050555/label
cmdline mris_label2annot --s 0050555 --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-924
machine  x86_64
user     ntraut

subject 0050555
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-6.0.0/0050555/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 123170 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 286076
Total vertex volume 282380 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1483    870   2855  2.444 0.651     0.118     0.032       19     1.8  BA1_exvivo
 5360   3592   8624  2.253 0.680     0.103     0.017       46     3.9  BA2_exvivo
 1145    794   1255  1.911 0.467     0.125     0.023        8     1.1  BA3a_exvivo
 2705   1810   4127  1.930 0.600     0.100     0.020       28     2.2  BA3b_exvivo
 1792   1154   3362  2.493 0.634     0.097     0.018        9     1.3  BA4a_exvivo
 1336    945   2009  2.223 0.505     0.102     0.019        7     1.0  BA4p_exvivo
11126   7471  25442  2.851 0.722     0.110     0.021       86     9.4  BA6_exvivo
 2115   1513   5004  2.614 0.724     0.117     0.022       20     2.1  BA44_exvivo
 2891   2029   6881  2.467 0.858     0.119     0.018       30     2.1  BA45_exvivo
 3928   2818   5157  1.840 0.483     0.138     0.033       43     5.1  V1_exvivo
 9524   6525  15283  2.235 0.607     0.145     0.036      122    14.2  V2_exvivo
 2169   1482   4238  2.463 0.710     0.136     0.028       26     2.6  MT_exvivo
  590    418   1595  3.317 0.921     0.115     0.026        7     0.5  perirhinal_exvivo
  766    544   2292  3.059 0.833     0.123     0.029        7     1.0  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 0050555 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 286076
Total vertex volume 282380 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1091    580   2177  2.647 0.685     0.118     0.035       18     1.6  BA1_exvivo
 2215   1499   3994  2.428 0.778     0.098     0.018       16     1.6  BA2_exvivo
  910    617    953  1.929 0.462     0.131     0.024        7     0.9  BA3a_exvivo
 1539   1059   2003  1.728 0.469     0.079     0.013        7     0.8  BA3b_exvivo
 1673   1077   3241  2.541 0.620     0.095     0.018        9     1.3  BA4a_exvivo
 1051    756   1601  2.221 0.540     0.108     0.020        6     0.9  BA4p_exvivo
 6038   3984  13330  2.797 0.705     0.106     0.022       43     5.5  BA6_exvivo
 1246    909   3416  2.707 0.757     0.124     0.025       13     1.5  BA44_exvivo
 1153    832   3218  2.637 0.922     0.127     0.019       12     0.9  BA45_exvivo
 4187   3008   5520  1.831 0.488     0.139     0.034       46     5.8  V1_exvivo
 4763   3243   7211  2.186 0.609     0.151     0.039       64     7.7  V2_exvivo
  529    369   1334  2.802 0.685     0.151     0.030        8     0.6  MT_exvivo
  291    212    948  3.389 0.783     0.073     0.011        1     0.1  perirhinal_exvivo
  392    285   1225  3.436 0.711     0.131     0.025        3     0.4  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 10:29:44 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 19272 of (19272 19278 19284 19288 19295) to complete...
Waiting for PID 19278 of (19272 19278 19284 19288 19295) to complete...
Waiting for PID 19284 of (19272 19278 19284 19288 19295) to complete...
Waiting for PID 19288 of (19272 19278 19284 19288 19295) to complete...
Waiting for PID 19295 of (19272 19278 19284 19288 19295) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 439
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4401
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 633
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7320
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 253
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4233
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 354
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4876
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 788
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6535
mri_label2label: Done

PIDs (19272 19278 19284 19288 19295) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 19361 of (19361 19367 19373 19378) to complete...
Waiting for PID 19367 of (19361 19367 19373 19378) to complete...
Waiting for PID 19373 of (19361 19367 19373 19378) to complete...
Waiting for PID 19378 of (19361 19367 19373 19378) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 349
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4822
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 2341
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14597
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 529
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7441
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 669
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6024
mri_label2label: Done

PIDs (19361 19367 19373 19378) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 19437 of (19437 19443 19449 19455 19460) to complete...
Waiting for PID 19443 of (19437 19443 19449 19455 19460) to complete...
Waiting for PID 19449 of (19437 19443 19449 19455 19460) to complete...
Waiting for PID 19455 of (19437 19443 19449 19455 19460) to complete...
Waiting for PID 19460 of (19437 19443 19449 19455 19460) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 2158
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6885
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 4067
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12083
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 694
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2626
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 121
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1159
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 78
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 830
mri_label2label: Done

PIDs (19437 19443 19449 19455 19460) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 19508 of (19508 19514 19520 19525 19531) to complete...
Waiting for PID 19514 of (19508 19514 19520 19525 19531) to complete...
Waiting for PID 19520 of (19508 19514 19520 19525 19531) to complete...
Waiting for PID 19525 of (19508 19514 19520 19525 19531) to complete...
Waiting for PID 19531 of (19508 19514 19520 19525 19531) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 134
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1010
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 254
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2942
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 121
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1819
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 185
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2368
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1475
mri_label2label: Done

PIDs (19508 19514 19520 19525 19531) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 19582 of (19582 19588 19594 19600) to complete...
Waiting for PID 19588 of (19582 19588 19594 19600) to complete...
Waiting for PID 19594 of (19582 19588 19594 19600) to complete...
Waiting for PID 19600 of (19582 19588 19594 19600) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1622
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 1544
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8503
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 127
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1139
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 114
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1292
mri_label2label: Done

PIDs (19582 19588 19594 19600) 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 0050555 --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 0050555 --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 0050555 --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 0050555 --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 0050555 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 19651 of (19651 19657 19663 19669 19675) to complete...
Waiting for PID 19657 of (19651 19657 19663 19669 19675) to complete...
Waiting for PID 19663 of (19651 19657 19663 19669 19675) to complete...
Waiting for PID 19669 of (19651 19657 19663 19669 19675) to complete...
Waiting for PID 19675 of (19651 19657 19663 19669 19675) 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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 1412
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4644
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 1808
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5245
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 75
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 343
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 66
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 760
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 0050555 --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 = 0050555
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-6.0.0/0050555/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 152869
Number of reverse mapping hits = 30
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 321
mri_label2label: Done

PIDs (19651 19657 19663 19669 19675) completed and logs appended.

 mris_label2annot --s 0050555 --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-6.0.0/0050555/label
cmdline mris_label2annot --s 0050555 --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-924
machine  x86_64
user     ntraut

subject 0050555
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-6.0.0/0050555/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 104648 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050555 --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-6.0.0/0050555/label
cmdline mris_label2annot --s 0050555 --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-924
machine  x86_64
user     ntraut

subject 0050555
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-6.0.0/0050555/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 124958 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/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 0050555 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 296431
Total vertex volume 293693 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
 1139    714   2307  2.374 0.665     0.134     0.033       12     1.5  BA1_exvivo
 3861   2630   5742  2.080 0.595     0.096     0.017       24     2.6  BA2_exvivo
 1338    880   1258  1.836 0.426     0.125     0.025       11     1.1  BA3a_exvivo
 2198   1529   3044  1.729 0.536     0.105     0.018       15     1.7  BA3b_exvivo
 1715   1166   2829  2.218 0.554     0.107     0.021       11     1.6  BA4a_exvivo
 1498   1050   2148  2.168 0.487     0.098     0.018        7     1.1  BA4p_exvivo
11166   7384  25299  2.882 0.695     0.107     0.021       80     9.4  BA6_exvivo
 3639   2543   7319  2.384 0.668     0.119     0.021       37     3.2  BA44_exvivo
 3813   2742   9492  2.572 0.872     0.137     0.029       49     4.5  BA45_exvivo
 4620   3252   6190  1.878 0.552     0.144     0.033       54     6.0  V1_exvivo
 9822   6810  14938  2.115 0.597     0.140     0.031      111    13.1  V2_exvivo
 2435   1643   4198  2.402 0.601     0.129     0.026       26     2.7  MT_exvivo
  606    432   1949  3.292 0.895     0.140     0.035        7     1.0  perirhinal_exvivo
  371    250   1183  3.382 0.966     0.102     0.019        3     0.2  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 0050555 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050555/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 296431
Total vertex volume 293693 (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) = 1745712 mm^3    (det: 1.115938 )
lhCtxGM: 282446.943 282330.000  diff=  116.9  pctdiff= 0.041
rhCtxGM: 292180.576 292072.000  diff=  108.6  pctdiff= 0.037
lhCtxWM: 300318.813 300374.500  diff=  -55.7  pctdiff=-0.019
rhCtxWM: 304600.553 305501.500  diff= -900.9  pctdiff=-0.296
SubCortGMVol  66848.000
SupraTentVol  1262477.885 (1260448.000) diff=2029.885 pctdiff=0.161
SupraTentVolNotVent  1249161.885 (1247132.000) diff=2029.885 pctdiff=0.162
BrainSegVol  1427450.000 (1424106.000) diff=3344.000 pctdiff=0.234
BrainSegVolNotVent  1409336.000 (1408497.885) diff=838.115 pctdiff=0.059
BrainSegVolNotVent  1409336.000
CerebellumVol 162097.000
VentChorVol   13316.000
3rd4th5thCSF   4798.000
CSFVol  1454.000, OptChiasmVol   107.000
MaskVol 1964270.000
  777    486   1602  2.327 0.618     0.139     0.036       10     1.1  BA1_exvivo
 2224   1482   3388  2.096 0.614     0.082     0.013       10     1.3  BA2_exvivo
 1238    817   1078  1.829 0.378     0.134     0.028       11     1.4  BA3a_exvivo
 1763   1225   1968  1.541 0.318     0.090     0.014        9     1.0  BA3b_exvivo
  959    646   1532  2.150 0.597     0.127     0.030        8     1.3  BA4a_exvivo
 1238    856   1701  2.126 0.465     0.095     0.016        5     0.8  BA4p_exvivo
 7429   4853  16326  2.838 0.677     0.108     0.021       52     6.7  BA6_exvivo
  917    692   2542  2.614 0.729     0.128     0.024       13     1.0  BA44_exvivo
  975    707   2781  2.699 0.894     0.141     0.030       14     1.2  BA45_exvivo
 4435   3115   5741  1.864 0.542     0.142     0.031       50     5.6  V1_exvivo
 5029   3566   7731  1.995 0.598     0.150     0.036       63     7.9  V2_exvivo
  318    211    644  2.517 0.533     0.129     0.035        4     0.5  MT_exvivo
  357    250   1347  3.361 0.914     0.106     0.024        3     0.3  perirhinal_exvivo
  252    191    654  3.217 0.920     0.138     0.021        2     0.2  entorhinal_exvivo

Started at Sun Oct 8 01:33:17 CEST 2017 
Ended   at Sun Oct 8 10:32:59 CEST 2017
#@#%# recon-all-run-time-hours 8.995
recon-all -s 0050555 finished without error at Sun Oct  8 10:33:00 CEST 2017