ABIDE_fs-6.0.0/0050270/scripts/recon-all.log

Sat Oct  7 20:07:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050270 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050270/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050270
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-388 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:     264648720  258999620    5649100    1734196          0  252772180
-/+ buffers/cache:    6227440  258421280
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-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-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-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-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-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-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-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-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-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-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $  User: ntraut  Machine: tars-388  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-18:07:57-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: ntraut  Machine: tars-388  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-6.0.0/0050270

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050270/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050270/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/Trinity/0050270/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-6.0.0/0050270/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 20:08:00 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, 0)
j_ras = (-0, 1, 0)
k_ras = (-0, -0, 1)
changing data type from short to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 20:08:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/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-388 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 20:08:10 CEST 2017
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.20213
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20213/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.20213/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.20213/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 20:08:12 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.20213/nu0.mnc ./tmp.mri_nu_correct.mni.20213/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20213/0/ -iterations 1000 -distance 50
[ntraut@tars-388:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/] [2017-10-07 20:08:12] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20213/0/ ./tmp.mri_nu_correct.mni.20213/nu0.mnc ./tmp.mri_nu_correct.mni.20213/nu1.imp

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Number of iterations: 64 
CV of field change: 0.000991591
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.20213/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.20213/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.20213/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 20:09:40 CEST 2017
mri_nu_correct.mni done

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 20:09:40 CEST 2017
Ended   at Sat Oct  7 20:10:25 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 20:10:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6790, pval=0.4932 >= threshold=0.0050)

 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/transforms/talairach_avi.log 

TalAviQA: 0.97115
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 20:10:27 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-6.0.0/0050270/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-388 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 20:10:27 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.21301
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.21301/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.21301/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.21301/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 20:10:29 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.21301/nu0.mnc ./tmp.mri_nu_correct.mni.21301/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.21301/0/
[ntraut@tars-388:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/] [2017-10-07 20:10:29] 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.21301/0/ ./tmp.mri_nu_correct.mni.21301/nu0.mnc ./tmp.mri_nu_correct.mni.21301/nu1.imp

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Number of iterations: 50 
CV of field change: 0.0010769
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 20:11:23 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.21301/nu1.mnc ./tmp.mri_nu_correct.mni.21301/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.21301/1/
[ntraut@tars-388:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/] [2017-10-07 20:11:24] 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.21301/1/ ./tmp.mri_nu_correct.mni.21301/nu1.mnc ./tmp.mri_nu_correct.mni.21301/nu2.imp

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Number of iterations: 13 
CV of field change: 0.000972915
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.21301/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.21301/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-6.0.0/0050270/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.21301/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.21301/ones.mgz 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.21301/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.21301/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.21301/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.21301/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21301/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.21301/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.21301/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21301/input.mean.dat 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.21301/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.21301/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.21301/ones.mgz --i ./tmp.mri_nu_correct.mni.21301/nu2.mnc --sum ./tmp.mri_nu_correct.mni.21301/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21301/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.21301/ones.mgz --i ./tmp.mri_nu_correct.mni.21301/nu2.mnc --sum ./tmp.mri_nu_correct.mni.21301/sum.junk --avgwf ./tmp.mri_nu_correct.mni.21301/output.mean.dat 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.21301/ones.mgz
Loading ./tmp.mri_nu_correct.mni.21301/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.21301/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.21301/nu2.mnc ./tmp.mri_nu_correct.mni.21301/nu2.mnc mul .85884289168004793785
Saving result to './tmp.mri_nu_correct.mni.21301/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.21301/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.21301/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.21301/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 9 seconds.
mapping ( 5, 166) to ( 3, 110)
 
 
Sat Oct  7 20:12:36 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 20:12:37 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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
 1.00557   0.01415  -0.00589   10.05454;
 0.02000   0.94609   0.32116   4.57018;
-0.04314  -0.25338   1.06618  -1.06885;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 21
Starting OpenSpline(): npoints = 21
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 76 (76), valley at 36 (36)
csf peak at 38, setting threshold to 63
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 74 (74), valley at 35 (35)
csf peak at 37, setting threshold to 61
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 9 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 20:14:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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=8.0
skull bounding box = (46, 29, 0) --> (209, 185, 219)
using (100, 81, 110) as brain centroid...
mean wm in atlas = 108, using box (80,62,83) --> (120, 100,137) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 107 +- 4.0
after smoothing, mri peak at 107, scaling input intensities by 1.009
scaling channel 0 by 1.00935
initial log_p = -4.317
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.224816 @ (-9.091, 9.091, -9.091)
max log p =    -4.178862 @ (4.545, -4.545, 4.545)
max log p =    -4.128985 @ (-2.273, 6.818, 2.273)
max log p =    -4.112626 @ (3.409, -3.409, -1.136)
max log p =    -4.100922 @ (-1.705, 0.568, 0.568)
max log p =    -4.100922 @ (0.000, 0.000, 0.000)
Found translation: (-5.1, 8.5, -2.8): log p = -4.101
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.031, old_max_log_p =-4.101 (thresh=-4.1)
 1.00000   0.00000   0.00000  -5.11364;
 0.00000   1.03837   0.27823  -20.75816;
 0.00000  -0.25882   0.96593   35.62706;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.977, old_max_log_p =-4.031 (thresh=-4.0)
 1.00000   0.00000   0.00000  -5.11364;
 0.00000   1.10457   0.29597  -31.14511;
 0.00000  -0.25882   0.96593   35.62706;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.977, old_max_log_p =-3.977 (thresh=-4.0)
 1.00000   0.00000   0.00000  -5.11364;
 0.00000   1.10457   0.29597  -31.14511;
 0.00000  -0.25882   0.96593   35.62706;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.887, old_max_log_p =-3.977 (thresh=-4.0)
 1.01657   0.07457   0.01547  -14.64239;
-0.06898   1.16588   0.30739  -29.61289;
 0.00452  -0.25921   0.94601   35.38176;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.887, old_max_log_p =-3.887 (thresh=-3.9)
 1.01657   0.07457   0.01547  -14.64239;
-0.06898   1.16588   0.30739  -29.61289;
 0.00452  -0.25921   0.94601   35.38176;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.858, old_max_log_p =-3.887 (thresh=-3.9)
 1.01583   0.06723   0.00512  -13.40236;
-0.06067   1.16343   0.32325  -31.69651;
 0.01397  -0.27763   0.94095   36.13383;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.853, old_max_log_p =-3.858 (thresh=-3.9)
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.853, old_max_log_p =-3.853 (thresh=-3.8)
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 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
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.853 (old=-4.317)
transform before final EM align:
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 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
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.3  tol 0.000000
final transform:
 1.01463   0.06716   0.00511  -13.23992;
-0.06053   1.16070   0.32250  -31.28900;
 0.01393  -0.27698   0.93874   36.30912;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1452.342210
mri_em_register stimesec    1.356793
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   157592
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    84
mri_em_register ru_nivcsw   2520
registration took 12 minutes and 33 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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=103 z=109 r=72
      first estimation of the main basin volume: 1601260 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=110, y=89, z=75, Imax=255
      CSF=13, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=9656832414 voxels, voxel volume =1.000 
                     = 9656832414 mmm3 = 9656832.000 cm3
done.
PostAnalyze...Basin Prior
 35 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=129,y=109, z=103, r=10458 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=4, CSF_MAX=27 , nb = 44093
  RIGHT_CER    CSF_MIN=0, CSF_intensity=3, CSF_MAX=18 , nb = -1030638247
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=45 , nb = -1041819245
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=7, CSF_MAX=25 , nb = -1054867627
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=4, CSF_MAX=25 , nb = 1077373842
    OTHER      CSF_MIN=0, CSF_intensity=16, CSF_MAX=59 , nb = 1078678570
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    27,      39,        50,   70
  after  analyzing :    27,      46,        50,   52
   RIGHT_CER   
  before analyzing :    18,      30,        51,   77
  after  analyzing :    18,      44,        51,   52
   LEFT_CER    
  before analyzing :    45,      46,        47,   77
  after  analyzing :    45,      46,        47,   53
  RIGHT_BRAIN  
  before analyzing :    25,      36,        49,   70
  after  analyzing :    25,      44,        49,   50
  LEFT_BRAIN   
  before analyzing :    25,      37,        49,   70
  after  analyzing :    25,      45,        49,   51
     OTHER     
  before analyzing :    59,      59,        59,   93
  after  analyzing :    47,      59,        59,   67
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...75 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.012
curvature mean = 71.595, std = 9.060

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.51, sigma = 3.95
      after  rotation: sse = 2.51, sigma = 3.95
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.70, its var is  3.94   
      before Erosion-Dilatation  0.44% 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...51 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1863802 voxels, voxel volume = 1.000 mm3
           = 1863802 mmm3 = 1863.802 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    27.980746
mri_watershed stimesec    0.438933
mri_watershed ru_maxrss   824564
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   213479
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2952
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1521
mri_watershed ru_nivcsw   50
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 20:27:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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=28.9
skull bounding box = (60, 45, 23) --> (195, 185, 197)
using (105, 92, 110) as brain centroid...
mean wm in atlas = 107, using box (88,75,89) --> (121, 109,131) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 4.3
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
initial log_p = -4.098
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.023185 @ (-9.091, 9.091, -9.091)
max log p =    -3.778985 @ (4.545, 4.545, 4.545)
max log p =    -3.778985 @ (0.000, 0.000, 0.000)
max log p =    -3.778985 @ (0.000, 0.000, 0.000)
max log p =    -3.743837 @ (0.568, -1.705, 1.705)
max log p =    -3.743837 @ (0.000, 0.000, 0.000)
Found translation: (-4.0, 11.9, -2.8): log p = -3.744
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.605, old_max_log_p =-3.744 (thresh=-3.7)
 1.00000   0.00000   0.00000  -3.97727;
 0.00000   1.02750   0.27532  -20.83389;
 0.00000  -0.23650   0.88261   42.75995;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.605, old_max_log_p =-3.605 (thresh=-3.6)
 1.00000   0.00000   0.00000  -3.97727;
 0.00000   1.02750   0.27532  -20.83389;
 0.00000  -0.23650   0.88261   42.75995;
 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=-3.529, old_max_log_p =-3.605 (thresh=-3.6)
 0.99954   0.03236   0.00867  -8.33094;
-0.03451   1.04541   0.28012  -20.63920;
 0.00000  -0.24076   0.89854   39.82401;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.522, old_max_log_p =-3.529 (thresh=-3.5)
 1.01774   0.04098  -0.02112  -8.60249;
-0.03516   1.06501   0.28537  -21.38786;
 0.03209  -0.23508   0.88150   34.87743;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.522, old_max_log_p =-3.522 (thresh=-3.5)
 1.01774   0.04098  -0.02112  -8.60249;
-0.03516   1.06501   0.28537  -21.38786;
 0.03209  -0.23508   0.88150   34.87743;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.514, old_max_log_p =-3.522 (thresh=-3.5)
 1.02013   0.04107  -0.02117  -8.91969;
-0.03516   1.06501   0.28537  -21.38786;
 0.03213  -0.23536   0.88253   34.79473;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.513, old_max_log_p =-3.514 (thresh=-3.5)
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 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
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.513 (old=-4.098)
transform before final EM align:
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 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
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.0  tol 0.000000
final transform:
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1101.828496
mri_em_register stimesec    1.157823
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   158976
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    119
mri_em_register ru_nivcsw   1870
registration took 9 minutes and 29 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 20:37:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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=28.9
skull bounding box = (60, 45, 23) --> (195, 185, 197)
using (105, 92, 110) as brain centroid...
mean wm in atlas = 107, using box (88,75,89) --> (121, 109,131) to find MRI wm
before smoothing, mri peak at 107
robust fit to distribution - 106 +- 4.3
after smoothing, mri peak at 107, scaling input intensities by 1.000
scaling channel 0 by 1
using 246344 sample points...
INFO: compute sample coordinates transform
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 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 (127, 48, 22) --> (195, 159, 200)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 132.0
1 of 2961 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 47, 21) --> (134, 149, 201)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
2 of 2619 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (129, 134, 53) --> (176, 174, 111)
Left_Cerebellum_White_Matter: limiting intensities to 96.0 --> 132.0
0 of 50 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 134, 50) --> (129, 170, 113)
Right_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0
0 of 35 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 119, 92) --> (147, 183, 124)
Brain_Stem: limiting intensities to 92.0 --> 132.0
1 of 66 (1.5%) samples deleted
using 5731 total control points for intensity normalization...
bias field = 0.971 +- 0.047
43 of 5727 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (127, 48, 22) --> (195, 159, 200)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 3572 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 47, 21) --> (134, 149, 201)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0
6 of 3590 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (129, 134, 53) --> (176, 174, 111)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 162 (0.6%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 134, 50) --> (129, 170, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 100 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 119, 92) --> (147, 183, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
10 of 140 (7.1%) samples deleted
using 7564 total control points for intensity normalization...
bias field = 1.038 +- 0.050
51 of 7468 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (127, 48, 22) --> (195, 159, 200)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
3 of 3557 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (67, 47, 21) --> (134, 149, 201)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
9 of 3637 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (129, 134, 53) --> (176, 174, 111)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
28 of 191 (14.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (84, 134, 50) --> (129, 170, 113)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
9 of 96 (9.4%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (113, 119, 92) --> (147, 183, 124)
Brain_Stem: limiting intensities to 88.0 --> 132.0
112 of 266 (42.1%) samples deleted
using 7747 total control points for intensity normalization...
bias field = 1.035 +- 0.044
58 of 7441 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 45 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 20:39:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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) = 1.03 (predicted orig area = 7.7)
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=0.855, neg=0, invalid=762
0001: dt=267.883669, rms=0.755 (11.678%), neg=0, invalid=762
0002: dt=135.059952, rms=0.729 (3.552%), neg=0, invalid=762
0003: dt=443.904000, rms=0.716 (1.724%), neg=0, invalid=762
0004: dt=172.666667, rms=0.710 (0.839%), neg=0, invalid=762
0005: dt=221.952000, rms=0.707 (0.349%), neg=0, invalid=762
0006: dt=129.472000, rms=0.705 (0.313%), neg=0, invalid=762
0007: dt=887.808000, rms=0.699 (0.858%), neg=0, invalid=762
0008: dt=110.976000, rms=0.696 (0.409%), neg=0, invalid=762
0009: dt=1479.680000, rms=0.692 (0.685%), neg=0, invalid=762
0010: dt=92.480000, rms=0.689 (0.442%), neg=0, invalid=762
0011: dt=517.888000, rms=0.688 (0.135%), neg=0, invalid=762
0012: dt=517.888000, rms=0.688 (-0.380%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.688, neg=0, invalid=762
0013: dt=221.952000, rms=0.685 (0.428%), neg=0, invalid=762
0014: dt=129.472000, rms=0.684 (0.097%), neg=0, invalid=762
0015: dt=129.472000, rms=0.684 (0.066%), neg=0, invalid=762
0016: dt=129.472000, rms=0.683 (0.106%), neg=0, invalid=762
0017: dt=129.472000, rms=0.682 (0.132%), neg=0, invalid=762
0018: dt=129.472000, rms=0.681 (0.135%), neg=0, invalid=762
0019: dt=129.472000, rms=0.680 (0.144%), neg=0, invalid=762
0020: dt=129.472000, rms=0.679 (0.146%), neg=0, invalid=762
0021: dt=129.472000, rms=0.678 (0.134%), neg=0, invalid=762
0022: dt=129.472000, rms=0.677 (0.141%), neg=0, invalid=762
0023: dt=129.472000, rms=0.676 (0.144%), neg=0, invalid=762
0024: dt=129.472000, rms=0.675 (0.154%), neg=0, invalid=762
0025: dt=129.472000, rms=0.674 (0.149%), neg=0, invalid=762
0026: dt=129.472000, rms=0.674 (0.139%), neg=0, invalid=762
0027: dt=129.472000, rms=0.673 (0.130%), neg=0, invalid=762
0028: dt=129.472000, rms=0.672 (0.139%), neg=0, invalid=762
0029: dt=129.472000, rms=0.671 (0.143%), neg=0, invalid=762
0030: dt=129.472000, rms=0.670 (0.145%), neg=0, invalid=762
0031: dt=129.472000, rms=0.669 (0.138%), neg=0, invalid=762
0032: dt=129.472000, rms=0.668 (0.123%), neg=0, invalid=762
0033: dt=129.472000, rms=0.667 (0.116%), neg=0, invalid=762
0034: dt=517.888000, rms=0.667 (0.040%), neg=0, invalid=762
0035: dt=517.888000, rms=0.667 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.672, neg=0, invalid=762
0036: dt=92.654155, rms=0.669 (0.545%), neg=0, invalid=762
0037: dt=414.720000, rms=0.653 (2.253%), neg=0, invalid=762
0038: dt=59.733333, rms=0.651 (0.333%), neg=0, invalid=762
0039: dt=414.720000, rms=0.644 (1.078%), neg=0, invalid=762
0040: dt=58.666667, rms=0.642 (0.334%), neg=0, invalid=762
0041: dt=145.152000, rms=0.640 (0.303%), neg=0, invalid=762
0042: dt=31.104000, rms=0.640 (0.025%), neg=0, invalid=762
0043: dt=31.104000, rms=0.640 (0.036%), neg=0, invalid=762
0044: dt=31.104000, rms=0.639 (0.066%), neg=0, invalid=762
0045: dt=31.104000, rms=0.639 (0.113%), neg=0, invalid=762
0046: dt=31.104000, rms=0.638 (0.163%), neg=0, invalid=762
0047: dt=31.104000, rms=0.636 (0.198%), neg=0, invalid=762
0048: dt=31.104000, rms=0.635 (0.211%), neg=0, invalid=762
0049: dt=31.104000, rms=0.634 (0.202%), neg=0, invalid=762
0050: dt=31.104000, rms=0.633 (0.193%), neg=0, invalid=762
0051: dt=31.104000, rms=0.631 (0.186%), neg=0, invalid=762
0052: dt=31.104000, rms=0.630 (0.191%), neg=0, invalid=762
0053: dt=31.104000, rms=0.629 (0.198%), neg=0, invalid=762
0054: dt=31.104000, rms=0.628 (0.203%), neg=0, invalid=762
0055: dt=31.104000, rms=0.626 (0.190%), neg=0, invalid=762
0056: dt=31.104000, rms=0.625 (0.176%), neg=0, invalid=762
0057: dt=31.104000, rms=0.624 (0.162%), neg=0, invalid=762
0058: dt=31.104000, rms=0.623 (0.148%), neg=0, invalid=762
0059: dt=31.104000, rms=0.622 (0.144%), neg=0, invalid=762
0060: dt=31.104000, rms=0.622 (0.137%), neg=0, invalid=762
0061: dt=31.104000, rms=0.621 (0.128%), neg=0, invalid=762
0062: dt=31.104000, rms=0.620 (0.119%), neg=0, invalid=762
0063: dt=31.104000, rms=0.619 (0.115%), neg=0, invalid=762
0064: dt=145.152000, rms=0.619 (0.016%), neg=0, invalid=762
0065: dt=145.152000, rms=0.619 (0.045%), neg=0, invalid=762
0066: dt=145.152000, rms=0.619 (-0.055%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.620, neg=0, invalid=762
0067: dt=121.679012, rms=0.617 (0.456%), neg=0, invalid=762
0068: dt=82.944000, rms=0.616 (0.115%), neg=0, invalid=762
0069: dt=82.944000, rms=0.616 (0.057%), neg=0, invalid=762
0070: dt=82.944000, rms=0.615 (0.059%), neg=0, invalid=762
0071: dt=82.944000, rms=0.615 (0.083%), neg=0, invalid=762
0072: dt=82.944000, rms=0.615 (0.024%), neg=0, invalid=762
0073: dt=82.944000, rms=0.615 (0.010%), neg=0, invalid=762
0074: dt=145.152000, rms=0.614 (0.073%), neg=0, invalid=762
0075: dt=36.288000, rms=0.614 (0.008%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.637, neg=0, invalid=762
0076: dt=2.800000, rms=0.637 (0.092%), neg=0, invalid=762
0077: dt=1.200000, rms=0.637 (0.001%), neg=0, invalid=762
0078: dt=1.200000, rms=0.637 (0.000%), neg=0, invalid=762
0079: dt=1.200000, rms=0.637 (-0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.637, neg=0, invalid=762
0080: dt=0.000000, rms=0.637 (0.077%), neg=0, invalid=762
0081: dt=0.000000, rms=0.637 (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=0.703, neg=0, invalid=762
0082: dt=6.206349, rms=0.684 (2.716%), neg=0, invalid=762
0083: dt=4.000000, rms=0.683 (0.143%), neg=0, invalid=762
0084: dt=4.000000, rms=0.683 (-0.014%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.683, neg=0, invalid=762
0085: dt=0.000000, rms=0.683 (0.053%), neg=0, invalid=762
0086: dt=0.000000, rms=0.683 (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=0.748, neg=0, invalid=762
0087: dt=0.448000, rms=0.747 (0.189%), neg=0, invalid=762
0088: dt=1.024000, rms=0.745 (0.193%), neg=0, invalid=762
0089: dt=2.184211, rms=0.742 (0.522%), neg=0, invalid=762
0090: dt=1.792000, rms=0.740 (0.168%), neg=0, invalid=762
0091: dt=1.792000, rms=0.737 (0.398%), neg=0, invalid=762
0092: dt=1.792000, rms=0.737 (0.042%), neg=0, invalid=762
0093: dt=1.792000, rms=0.737 (-0.149%), neg=0, invalid=762
0094: dt=4.096000, rms=0.736 (0.181%), neg=0, invalid=762
0095: dt=0.448000, rms=0.736 (0.024%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.736, neg=0, invalid=762
0096: dt=1.280000, rms=0.735 (0.163%), neg=0, invalid=762
0097: dt=0.448000, rms=0.735 (0.008%), neg=0, invalid=762
0098: dt=0.448000, rms=0.735 (0.004%), neg=0, invalid=762
0099: dt=0.448000, rms=0.735 (0.003%), neg=0, invalid=762
0100: dt=0.448000, rms=0.735 (-0.001%), 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=0.693, neg=0, invalid=762
0101: dt=0.792743, rms=0.677 (2.302%), neg=0, invalid=762
0102: dt=0.080000, rms=0.676 (0.121%), neg=0, invalid=762
0103: dt=0.080000, rms=0.676 (-0.080%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.677, neg=0, invalid=762
0104: dt=0.028000, rms=0.676 (0.075%), neg=0, invalid=762
0105: dt=0.007000, rms=0.676 (0.001%), neg=0, invalid=762
0106: dt=0.007000, rms=0.676 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.12208 (28)
Left_Lateral_Ventricle (4): linear fit = 1.51 x + 0.0 (871 voxels, overlap=0.388)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (871 voxels, peak = 30), gca=30.0
gca peak = 0.15565 (16)
mri peak = 0.10474 (28)
Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (765 voxels, overlap=0.211)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (765 voxels, peak = 26), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.09807 (94)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (1067 voxels, overlap=0.936)
Right_Pallidum (52): linear fit = 0.96 x + 0.0 (1067 voxels, peak = 93), gca=92.6
gca peak = 0.20183 (93)
mri peak = 0.09194 (94)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (976 voxels, overlap=1.006)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (976 voxels, peak = 92), gca=91.6
gca peak = 0.21683 (55)
mri peak = 0.08718 (68)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1179 voxels, overlap=0.177)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1179 voxels, peak = 66), gca=66.3
gca peak = 0.30730 (58)
mri peak = 0.08404 (68)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (968 voxels, overlap=0.041)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (968 voxels, peak = 68), gca=67.6
gca peak = 0.11430 (101)
mri peak = 0.11983 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (72627 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (72627 voxels, peak = 105), gca=104.5
gca peak = 0.12076 (102)
mri peak = 0.11452 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (71793 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (71793 voxels, peak = 105), gca=104.5
gca peak = 0.14995 (59)
mri peak = 0.04163 (68)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (27200 voxels, overlap=0.285)
Left_Cerebral_Cortex (3): linear fit = 1.17 x + 0.0 (27200 voxels, peak = 69), gca=69.3
gca peak = 0.15082 (58)
mri peak = 0.04000 (68)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (29239 voxels, overlap=0.385)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (29239 voxels, peak = 69), gca=69.3
gca peak = 0.14161 (67)
mri peak = 0.10093 (80)
Right_Caudate (50): linear fit = 1.20 x + 0.0 (572 voxels, overlap=0.032)
Right_Caudate (50): linear fit = 1.20 x + 0.0 (572 voxels, peak = 80), gca=80.1
gca peak = 0.15243 (71)
mri peak = 0.08803 (81)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1220 voxels, overlap=0.145)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (1220 voxels, peak = 80), gca=79.9
gca peak = 0.13336 (57)
mri peak = 0.04670 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (22613 voxels, overlap=0.442)
Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (22613 voxels, peak = 68), gca=67.5
gca peak = 0.13252 (56)
mri peak = 0.04275 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (24017 voxels, overlap=0.182)
Right_Cerebellum_Cortex (47): linear fit = 1.18 x + 0.0 (24017 voxels, peak = 66), gca=66.4
gca peak = 0.18181 (84)
mri peak = 0.08869 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9535 voxels, overlap=0.253)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (9535 voxels, peak = 91), gca=91.1
gca peak = 0.20573 (83)
mri peak = 0.08356 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8554 voxels, overlap=0.005)
Right_Cerebellum_White_Matter (46): linear fit = 1.12 x + 0.0 (8554 voxels, peak = 93), gca=92.5
gca peak = 0.21969 (57)
mri peak = 0.09037 (68)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (509 voxels, overlap=0.300)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (509 voxels, peak = 68), gca=67.5
gca peak = 0.39313 (56)
mri peak = 0.09884 (67)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (688 voxels, overlap=0.049)
Right_Amygdala (54): linear fit = 1.13 x + 0.0 (688 voxels, peak = 64), gca=63.6
gca peak = 0.14181 (85)
mri peak = 0.07331 (94)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6451 voxels, overlap=0.738)
Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (6451 voxels, peak = 91), gca=90.5
gca peak = 0.11978 (83)
mri peak = 0.07182 (91)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5344 voxels, overlap=0.651)
Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (5344 voxels, peak = 90), gca=90.1
gca peak = 0.13399 (79)
mri peak = 0.06534 (86)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2909 voxels, overlap=0.773)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2909 voxels, peak = 87), gca=86.5
gca peak = 0.14159 (79)
mri peak = 0.10372 (84)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2822 voxels, overlap=0.564)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2822 voxels, peak = 85), gca=84.9
gca peak = 0.10025 (80)
mri peak = 0.10151 (88)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13561 voxels, overlap=0.303)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (13561 voxels, peak = 88), gca=88.4
gca peak = 0.13281 (86)
mri peak = 0.08881 (87)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1364 voxels, overlap=0.648)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1364 voxels, peak = 89), gca=89.0
gca peak = 0.12801 (89)
mri peak = 0.07853 (89)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1634 voxels, overlap=0.748)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1634 voxels, peak = 92), gca=92.1
gca peak = 0.20494 (23)
mri peak = 0.14373 (25)
gca peak = 0.15061 (21)
mri peak = 0.17543 (26)
Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (545 voxels, overlap=0.391)
Fourth_Ventricle (15): linear fit = 1.41 x + 0.0 (545 voxels, peak = 30), gca=29.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.18 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.47 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=0.666, neg=0, invalid=762
0107: dt=130.301370, rms=0.645 (3.034%), neg=0, invalid=762
0108: dt=295.936000, rms=0.640 (0.825%), neg=0, invalid=762
0109: dt=129.472000, rms=0.638 (0.371%), neg=0, invalid=762
0110: dt=295.936000, rms=0.636 (0.285%), neg=0, invalid=762
0111: dt=129.472000, rms=0.635 (0.203%), neg=0, invalid=762
0112: dt=129.472000, rms=0.634 (0.111%), neg=0, invalid=762
0113: dt=517.888000, rms=0.632 (0.219%), neg=0, invalid=762
0114: dt=92.480000, rms=0.631 (0.171%), neg=0, invalid=762
0115: dt=1479.680000, rms=0.629 (0.316%), neg=0, invalid=762
0116: dt=92.480000, rms=0.628 (0.251%), neg=0, invalid=762
0117: dt=517.888000, rms=0.627 (0.071%), neg=0, invalid=762
0118: dt=110.976000, rms=0.627 (0.071%), neg=0, invalid=762
0119: dt=295.936000, rms=0.627 (0.031%), neg=0, invalid=762
0120: dt=295.936000, rms=0.627 (-0.023%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.627, neg=0, invalid=762
0121: dt=129.472000, rms=0.626 (0.207%), neg=0, invalid=762
0122: dt=517.888000, rms=0.624 (0.241%), neg=0, invalid=762
0123: dt=129.472000, rms=0.624 (0.080%), neg=0, invalid=762
0124: dt=295.936000, rms=0.623 (0.042%), neg=0, invalid=762
0125: dt=295.936000, rms=0.623 (0.017%), neg=0, invalid=762
0126: dt=295.936000, rms=0.623 (0.116%), neg=0, invalid=762
0127: dt=295.936000, rms=0.621 (0.172%), neg=0, invalid=762
0128: dt=295.936000, rms=0.621 (0.090%), neg=0, invalid=762
0129: dt=295.936000, rms=0.620 (0.096%), neg=0, invalid=762
0130: dt=295.936000, rms=0.619 (0.215%), neg=0, invalid=762
0131: dt=295.936000, rms=0.618 (0.116%), neg=0, invalid=762
0132: dt=295.936000, rms=0.618 (0.083%), neg=0, invalid=762
0133: dt=295.936000, rms=0.617 (0.168%), neg=0, invalid=762
0134: dt=295.936000, rms=0.616 (0.103%), neg=0, invalid=762
0135: dt=295.936000, rms=0.615 (0.108%), neg=0, invalid=762
0136: dt=295.936000, rms=0.615 (0.117%), neg=0, invalid=762
0137: dt=295.936000, rms=0.614 (0.060%), neg=0, invalid=762
0138: dt=295.936000, rms=0.613 (0.152%), neg=0, invalid=762
0139: dt=295.936000, rms=0.613 (0.093%), neg=0, invalid=762
0140: dt=295.936000, rms=0.613 (0.033%), neg=0, invalid=762
0141: dt=295.936000, rms=0.612 (0.142%), neg=0, invalid=762
0142: dt=295.936000, rms=0.611 (0.074%), neg=0, invalid=762
0143: dt=295.936000, rms=0.611 (0.042%), neg=0, invalid=762
0144: dt=295.936000, rms=0.611 (0.092%), neg=0, invalid=762
0145: dt=295.936000, rms=0.610 (0.050%), neg=0, invalid=762
0146: dt=295.936000, rms=0.610 (0.063%), neg=0, invalid=762
0147: dt=295.936000, rms=0.609 (0.060%), neg=0, invalid=762
0148: dt=295.936000, rms=0.609 (0.027%), neg=0, invalid=762
0149: dt=295.936000, rms=0.609 (0.071%), neg=0, invalid=762
0150: dt=295.936000, rms=0.609 (0.047%), neg=0, invalid=762
0151: dt=295.936000, rms=0.608 (0.020%), neg=0, invalid=762
0152: dt=295.936000, rms=0.608 (0.068%), neg=0, invalid=762
0153: dt=295.936000, rms=0.608 (0.039%), neg=0, invalid=762
0154: dt=295.936000, rms=0.608 (0.031%), neg=0, invalid=762
0155: dt=295.936000, rms=0.607 (0.062%), neg=0, invalid=762
0156: dt=295.936000, rms=0.607 (0.040%), neg=0, invalid=762
0157: dt=295.936000, rms=0.607 (0.032%), neg=0, invalid=762
0158: dt=295.936000, rms=0.606 (0.052%), neg=0, invalid=762
0159: dt=295.936000, rms=0.606 (0.026%), neg=0, invalid=762
0160: dt=295.936000, rms=0.606 (0.031%), neg=0, invalid=762
0161: dt=295.936000, rms=0.606 (0.045%), neg=0, invalid=762
0162: dt=295.936000, rms=0.606 (0.040%), neg=0, invalid=762
0163: dt=295.936000, rms=0.605 (0.034%), neg=0, invalid=762
0164: dt=295.936000, rms=0.605 (0.036%), neg=0, invalid=762
0165: dt=295.936000, rms=0.605 (0.031%), neg=0, invalid=762
0166: dt=295.936000, rms=0.605 (0.032%), neg=0, invalid=762
0167: dt=295.936000, rms=0.605 (0.036%), neg=0, invalid=762
0168: dt=295.936000, rms=0.604 (0.026%), neg=0, invalid=762
0169: dt=295.936000, rms=0.604 (0.022%), neg=0, invalid=762
0170: dt=295.936000, rms=0.604 (0.030%), neg=0, invalid=762
0171: dt=295.936000, rms=0.604 (0.024%), neg=0, invalid=762
0172: dt=295.936000, rms=0.604 (0.020%), neg=0, invalid=762
0173: dt=443.904000, rms=0.604 (0.010%), neg=0, invalid=762
0174: dt=443.904000, rms=0.604 (-0.077%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.605, neg=0, invalid=762
0175: dt=65.361702, rms=0.604 (0.239%), neg=0, invalid=762
0176: dt=331.776000, rms=0.599 (0.703%), neg=0, invalid=762
0177: dt=186.514286, rms=0.595 (0.731%), neg=0, invalid=762
0178: dt=36.288000, rms=0.592 (0.433%), neg=0, invalid=762
0179: dt=124.416000, rms=0.591 (0.234%), neg=0, invalid=762
0180: dt=82.944000, rms=0.590 (0.136%), neg=0, invalid=762
0181: dt=145.152000, rms=0.588 (0.303%), neg=0, invalid=762
0182: dt=36.288000, rms=0.588 (0.140%), neg=0, invalid=762
0183: dt=103.680000, rms=0.587 (0.128%), neg=0, invalid=762
0184: dt=103.680000, rms=0.586 (0.205%), neg=0, invalid=762
0185: dt=36.288000, rms=0.585 (0.091%), neg=0, invalid=762
0186: dt=145.152000, rms=0.584 (0.165%), neg=0, invalid=762
0187: dt=74.666667, rms=0.583 (0.174%), neg=0, invalid=762
0188: dt=62.208000, rms=0.583 (0.077%), neg=0, invalid=762
0189: dt=145.152000, rms=0.582 (0.199%), neg=0, invalid=762
0190: dt=36.288000, rms=0.581 (0.067%), neg=0, invalid=762
0191: dt=248.832000, rms=0.580 (0.166%), neg=0, invalid=762
0192: dt=36.288000, rms=0.579 (0.149%), neg=0, invalid=762
0193: dt=248.832000, rms=0.578 (0.206%), neg=0, invalid=762
0194: dt=36.288000, rms=0.578 (0.101%), neg=0, invalid=762
0195: dt=62.208000, rms=0.577 (0.058%), neg=0, invalid=762
0196: dt=145.152000, rms=0.576 (0.156%), neg=0, invalid=762
0197: dt=36.288000, rms=0.576 (0.034%), neg=0, invalid=762
0198: dt=36.288000, rms=0.576 (0.035%), neg=0, invalid=762
0199: dt=36.288000, rms=0.576 (0.057%), neg=0, invalid=762
0200: dt=36.288000, rms=0.575 (0.090%), neg=0, invalid=762
0201: dt=36.288000, rms=0.574 (0.114%), neg=0, invalid=762
0202: dt=36.288000, rms=0.574 (0.123%), neg=0, invalid=762
0203: dt=36.288000, rms=0.573 (0.135%), neg=0, invalid=762
0204: dt=36.288000, rms=0.572 (0.143%), neg=0, invalid=762
0205: dt=36.288000, rms=0.571 (0.154%), neg=0, invalid=762
0206: dt=36.288000, rms=0.570 (0.160%), neg=0, invalid=762
0207: dt=36.288000, rms=0.569 (0.163%), neg=0, invalid=762
0208: dt=36.288000, rms=0.569 (0.158%), neg=0, invalid=762
0209: dt=36.288000, rms=0.568 (0.157%), neg=0, invalid=762
0210: dt=36.288000, rms=0.567 (0.156%), neg=0, invalid=762
0211: dt=36.288000, rms=0.566 (0.155%), neg=0, invalid=762
0212: dt=36.288000, rms=0.565 (0.147%), neg=0, invalid=762
0213: dt=36.288000, rms=0.564 (0.139%), neg=0, invalid=762
0214: dt=36.288000, rms=0.564 (0.130%), neg=0, invalid=762
0215: dt=36.288000, rms=0.563 (0.125%), neg=0, invalid=762
0216: dt=36.288000, rms=0.562 (0.122%), neg=0, invalid=762
0217: dt=36.288000, rms=0.561 (0.122%), neg=0, invalid=762
0218: dt=36.288000, rms=0.561 (0.122%), neg=0, invalid=762
0219: dt=36.288000, rms=0.560 (0.113%), neg=0, invalid=762
0220: dt=36.288000, rms=0.560 (0.103%), neg=0, invalid=762
0221: dt=36.288000, rms=0.559 (0.096%), neg=0, invalid=762
0222: dt=36.288000, rms=0.558 (0.093%), neg=0, invalid=762
0223: dt=36.288000, rms=0.558 (0.090%), neg=0, invalid=762
0224: dt=36.288000, rms=0.557 (0.090%), neg=0, invalid=762
0225: dt=36.288000, rms=0.557 (0.089%), neg=0, invalid=762
0226: dt=36.288000, rms=0.557 (0.088%), neg=0, invalid=762
0227: dt=36.288000, rms=0.556 (0.084%), neg=0, invalid=762
0228: dt=36.288000, rms=0.556 (0.079%), neg=0, invalid=762
0229: dt=36.288000, rms=0.555 (0.074%), neg=0, invalid=762
0230: dt=36.288000, rms=0.555 (0.073%), neg=0, invalid=762
0231: dt=36.288000, rms=0.554 (0.068%), neg=0, invalid=762
0232: dt=36.288000, rms=0.554 (0.066%), neg=0, invalid=762
0233: dt=36.288000, rms=0.554 (0.065%), neg=0, invalid=762
0234: dt=36.288000, rms=0.553 (0.064%), neg=0, invalid=762
0235: dt=36.288000, rms=0.553 (0.062%), neg=0, invalid=762
0236: dt=36.288000, rms=0.553 (0.059%), neg=0, invalid=762
0237: dt=36.288000, rms=0.552 (0.053%), neg=0, invalid=762
0238: dt=36.288000, rms=0.552 (0.052%), neg=0, invalid=762
0239: dt=36.288000, rms=0.552 (0.009%), neg=0, invalid=762
0240: dt=36.288000, rms=0.552 (0.013%), neg=0, invalid=762
0241: dt=36.288000, rms=0.552 (0.011%), neg=0, invalid=762
0242: dt=580.608000, rms=0.552 (0.027%), neg=0, invalid=762
0243: dt=103.680000, rms=0.551 (0.080%), neg=0, invalid=762
0244: dt=9.072000, rms=0.551 (-0.006%), neg=0, invalid=762
0245: dt=9.072000, rms=0.551 (0.002%), neg=0, invalid=762
0246: dt=9.072000, rms=0.551 (0.002%), neg=0, invalid=762
0247: dt=9.072000, rms=0.551 (-0.009%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.552, neg=0, invalid=762
0248: dt=124.416000, rms=0.549 (0.446%), neg=0, invalid=762
0249: dt=66.909091, rms=0.549 (0.126%), neg=0, invalid=762
0250: dt=82.944000, rms=0.548 (0.053%), neg=0, invalid=762
0251: dt=62.208000, rms=0.548 (0.073%), neg=0, invalid=762
0252: dt=36.288000, rms=0.548 (0.027%), neg=0, invalid=762
0253: dt=36.288000, rms=0.548 (0.029%), neg=0, invalid=762
0254: dt=36.288000, rms=0.547 (0.042%), neg=0, invalid=762
0255: dt=36.288000, rms=0.547 (0.057%), neg=0, invalid=762
0256: dt=36.288000, rms=0.547 (0.066%), neg=0, invalid=762
0257: dt=36.288000, rms=0.546 (0.067%), neg=0, invalid=762
0258: dt=36.288000, rms=0.546 (0.066%), neg=0, invalid=762
0259: dt=36.288000, rms=0.546 (0.067%), neg=0, invalid=762
0260: dt=36.288000, rms=0.545 (0.065%), neg=0, invalid=762
0261: dt=36.288000, rms=0.545 (0.060%), neg=0, invalid=762
0262: dt=36.288000, rms=0.545 (0.058%), neg=0, invalid=762
0263: dt=36.288000, rms=0.544 (0.053%), neg=0, invalid=762
0264: dt=36.288000, rms=0.544 (0.052%), neg=0, invalid=762
0265: dt=36.288000, rms=0.544 (0.048%), neg=0, invalid=762
0266: dt=36.288000, rms=0.544 (0.006%), neg=0, invalid=762
0267: dt=36.288000, rms=0.544 (0.014%), neg=0, invalid=762
0268: dt=36.288000, rms=0.544 (0.019%), neg=0, invalid=762
0269: dt=36.288000, rms=0.543 (0.008%), neg=0, invalid=762
0270: dt=36.288000, rms=0.543 (0.007%), neg=0, invalid=762
0271: dt=18.144000, rms=0.543 (0.003%), neg=0, invalid=762
0272: dt=9.072000, rms=0.543 (0.001%), neg=0, invalid=762
0273: dt=4.536000, rms=0.543 (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=0.552, neg=0, invalid=762
0274: dt=38.400000, rms=0.550 (0.486%), neg=0, invalid=762
0275: dt=44.800000, rms=0.545 (0.786%), neg=0, invalid=762
0276: dt=110.056075, rms=0.542 (0.626%), neg=0, invalid=762
0277: dt=32.000000, rms=0.537 (0.895%), neg=0, invalid=762
0278: dt=25.600000, rms=0.536 (0.258%), neg=0, invalid=762
0279: dt=76.800000, rms=0.533 (0.444%), neg=0, invalid=762
0280: dt=25.600000, rms=0.532 (0.327%), neg=0, invalid=762
0281: dt=179.200000, rms=0.527 (0.831%), neg=0, invalid=762
0282: dt=25.577855, rms=0.526 (0.249%), neg=0, invalid=762
0283: dt=44.800000, rms=0.524 (0.293%), neg=0, invalid=762
0284: dt=32.000000, rms=0.524 (0.080%), neg=0, invalid=762
0285: dt=44.800000, rms=0.523 (0.188%), neg=0, invalid=762
0286: dt=11.200000, rms=0.523 (0.036%), neg=0, invalid=762
0287: dt=11.200000, rms=0.522 (0.050%), neg=0, invalid=762
0288: dt=11.200000, rms=0.522 (0.047%), neg=0, invalid=762
0289: dt=11.200000, rms=0.522 (0.084%), neg=0, invalid=762
0290: dt=11.200000, rms=0.521 (0.123%), neg=0, invalid=762
0291: dt=11.200000, rms=0.520 (0.140%), neg=0, invalid=762
0292: dt=11.200000, rms=0.520 (0.139%), neg=0, invalid=762
0293: dt=11.200000, rms=0.519 (0.143%), neg=0, invalid=762
0294: dt=11.200000, rms=0.519 (0.019%), neg=0, invalid=762
0295: dt=11.200000, rms=0.519 (0.036%), neg=0, invalid=762
0296: dt=11.200000, rms=0.518 (0.025%), neg=0, invalid=762
0297: dt=11.200000, rms=0.518 (0.022%), neg=0, invalid=762
0298: dt=0.175000, rms=0.518 (0.000%), neg=0, invalid=762
0299: dt=0.175000, rms=0.518 (0.000%), neg=0, invalid=762
0300: dt=0.087500, rms=0.518 (0.000%), neg=0, invalid=762
0301: dt=0.002734, rms=0.518 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.519, neg=0, invalid=762
0302: dt=0.000000, rms=0.518 (0.074%), neg=0, invalid=762
0303: dt=0.000000, rms=0.518 (0.000%), neg=0, invalid=762
0304: dt=0.000244, rms=0.518 (0.000%), neg=0, invalid=762
0305: dt=0.000122, rms=0.518 (0.000%), neg=0, invalid=762
0306: dt=0.000015, rms=0.518 (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=0.543, neg=0, invalid=762
0307: dt=2.880000, rms=0.543 (0.125%), neg=0, invalid=762
0308: dt=1.008000, rms=0.543 (0.008%), neg=0, invalid=762
0309: dt=1.008000, rms=0.543 (0.003%), neg=0, invalid=762
0310: dt=1.008000, rms=0.543 (-0.013%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.543, neg=0, invalid=762
0311: dt=5.333333, rms=0.542 (0.232%), neg=0, invalid=762
0312: dt=3.777778, rms=0.541 (0.037%), neg=0, invalid=762
0313: dt=3.777778, rms=0.541 (0.014%), neg=0, invalid=762
0314: dt=3.777778, rms=0.541 (-0.076%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.572, neg=0, invalid=762
0315: dt=0.384000, rms=0.572 (0.070%), neg=0, invalid=762
0316: dt=0.112000, rms=0.572 (0.001%), neg=0, invalid=762
0317: dt=0.112000, rms=0.572 (0.001%), neg=0, invalid=762
0318: dt=0.112000, rms=0.572 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.572, neg=0, invalid=762
0319: dt=1.792000, rms=0.571 (0.287%), neg=0, invalid=762
0320: dt=1.280000, rms=0.570 (0.060%), neg=0, invalid=762
0321: dt=1.024000, rms=0.570 (0.019%), neg=0, invalid=762
0322: dt=1.024000, rms=0.570 (0.003%), neg=0, invalid=762
0323: dt=1.024000, rms=0.570 (-0.065%), 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=0.540, neg=0, invalid=762
0324: dt=0.448000, rms=0.526 (2.551%), neg=0, invalid=762
0325: dt=0.448000, rms=0.522 (0.696%), neg=0, invalid=762
0326: dt=0.448000, rms=0.520 (0.412%), neg=0, invalid=762
0327: dt=0.448000, rms=0.519 (0.272%), neg=0, invalid=762
0328: dt=0.448000, rms=0.518 (0.204%), neg=0, invalid=762
0329: dt=0.464286, rms=0.517 (0.161%), neg=0, invalid=762
0330: dt=0.448000, rms=0.516 (0.126%), neg=0, invalid=762
0331: dt=0.448000, rms=0.516 (0.102%), neg=0, invalid=762
0332: dt=0.448000, rms=0.515 (0.087%), neg=0, invalid=762
0333: dt=0.448000, rms=0.515 (0.071%), neg=0, invalid=762
0334: dt=0.448000, rms=0.514 (0.064%), neg=0, invalid=762
0335: dt=0.448000, rms=0.514 (0.053%), neg=0, invalid=762
0336: dt=0.448000, rms=0.514 (0.049%), neg=0, invalid=762
0337: dt=0.448000, rms=0.514 (0.040%), neg=0, invalid=762
0338: dt=0.448000, rms=0.513 (0.073%), neg=0, invalid=762
0339: dt=0.448000, rms=0.513 (0.095%), neg=0, invalid=762
0340: dt=0.448000, rms=0.512 (0.097%), neg=0, invalid=762
0341: dt=0.448000, rms=0.512 (0.095%), neg=0, invalid=762
0342: dt=0.448000, rms=0.511 (0.081%), neg=0, invalid=762
0343: dt=0.448000, rms=0.511 (0.063%), neg=0, invalid=762
0344: dt=0.448000, rms=0.511 (0.045%), neg=0, invalid=762
0345: dt=0.448000, rms=0.511 (0.026%), neg=0, invalid=762
0346: dt=0.448000, rms=0.511 (0.013%), neg=0, invalid=762
0347: dt=0.448000, rms=0.511 (-0.003%), neg=0, invalid=762
0348: dt=0.000000, rms=0.511 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.511, neg=0, invalid=762
0349: dt=0.448000, rms=0.506 (1.082%), neg=0, invalid=762
0350: dt=0.448000, rms=0.505 (0.122%), neg=0, invalid=762
0351: dt=0.448000, rms=0.505 (0.025%), neg=0, invalid=762
0352: dt=0.448000, rms=0.505 (-0.004%), neg=0, invalid=762
label assignment complete, 0 changed (0.00%)
********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.502, neg=0, invalid=762
0353: dt=32.368000, rms=0.502 (0.089%), neg=0, invalid=762
0354: dt=32.368000, rms=0.502 (0.003%), neg=0, invalid=762
0355: dt=32.368000, rms=0.502 (0.000%), neg=0, invalid=762
0356: dt=32.368000, rms=0.502 (-0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.502, neg=0, invalid=762
0357: dt=129.472000, rms=0.501 (0.223%), neg=0, invalid=762
0358: dt=129.472000, rms=0.501 (0.027%), neg=0, invalid=762
0359: dt=129.472000, rms=0.501 (0.032%), neg=0, invalid=762
0360: dt=129.472000, rms=0.500 (0.045%), neg=0, invalid=762
0361: dt=129.472000, rms=0.500 (0.031%), neg=0, invalid=762
0362: dt=129.472000, rms=0.500 (0.035%), neg=0, invalid=762
0363: dt=129.472000, rms=0.500 (0.030%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.500, neg=0, invalid=762
0364: dt=31.104000, rms=0.500 (0.133%), neg=0, invalid=762
0365: dt=36.288000, rms=0.500 (0.027%), neg=0, invalid=762
0366: dt=36.288000, rms=0.499 (0.027%), neg=0, invalid=762
0367: dt=36.288000, rms=0.499 (0.011%), neg=0, invalid=762
0368: dt=36.288000, rms=0.499 (-0.030%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.500, neg=0, invalid=762
0369: dt=109.948718, rms=0.497 (0.624%), neg=0, invalid=762
0370: dt=36.288000, rms=0.496 (0.143%), neg=0, invalid=762
0371: dt=36.288000, rms=0.496 (0.060%), neg=0, invalid=762
0372: dt=36.288000, rms=0.495 (0.099%), neg=0, invalid=762
0373: dt=36.288000, rms=0.495 (0.121%), neg=0, invalid=762
0374: dt=36.288000, rms=0.494 (0.143%), neg=0, invalid=762
0375: dt=36.288000, rms=0.493 (0.158%), neg=0, invalid=762
0376: dt=36.288000, rms=0.492 (0.145%), neg=0, invalid=762
0377: dt=36.288000, rms=0.492 (0.128%), neg=0, invalid=762
0378: dt=36.288000, rms=0.491 (0.111%), neg=0, invalid=762
0379: dt=36.288000, rms=0.491 (0.101%), neg=0, invalid=762
0380: dt=82.944000, rms=0.491 (0.031%), neg=0, invalid=762
0381: dt=82.944000, rms=0.491 (-0.062%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.492, neg=0, invalid=762
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=1, neg = 0
0382: dt=36.470588, rms=0.489 (0.612%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 8 iterations, nbhd size=1, neg = 0
0383: dt=44.800000, rms=0.486 (0.613%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0384: dt=25.600000, rms=0.484 (0.407%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0385: dt=44.800000, rms=0.482 (0.376%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0386: dt=23.867403, rms=0.481 (0.202%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0387: dt=23.867403, rms=0.480 (0.196%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0388: dt=23.867403, rms=0.479 (0.269%), neg=0, invalid=762
0389: dt=23.867403, rms=0.477 (0.280%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0390: dt=23.867403, rms=0.476 (0.312%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 11 iterations, nbhd size=1, neg = 0
0391: dt=23.867403, rms=0.474 (0.279%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 1 iterations, nbhd size=0, neg = 0
0392: dt=23.867403, rms=0.473 (0.291%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 1 iterations, nbhd size=0, neg = 0
0393: dt=23.867403, rms=0.472 (0.217%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 10 iterations, nbhd size=1, neg = 0
0394: dt=23.867403, rms=0.471 (0.198%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 10 iterations, nbhd size=1, neg = 0
0395: dt=23.867403, rms=0.470 (0.186%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 12 iterations, nbhd size=1, neg = 0
0396: dt=23.867403, rms=0.469 (0.172%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 3 iterations, nbhd size=0, neg = 0
0397: dt=23.867403, rms=0.469 (0.135%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 5 iterations, nbhd size=0, neg = 0
0398: dt=23.867403, rms=0.468 (0.127%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0399: dt=23.867403, rms=0.467 (0.145%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 3 iterations, nbhd size=0, neg = 0
0400: dt=23.867403, rms=0.467 (0.096%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 4 iterations, nbhd size=0, neg = 0
0401: dt=23.867403, rms=0.467 (0.061%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 3 iterations, nbhd size=0, neg = 0
0402: dt=11.200000, rms=0.467 (0.038%), neg=0, invalid=762
0403: dt=11.200000, rms=0.466 (0.019%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0404: dt=11.200000, rms=0.466 (0.015%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0405: dt=11.200000, rms=0.466 (0.021%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 3 iterations, nbhd size=0, neg = 0
0406: dt=11.200000, rms=0.466 (0.020%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.467, neg=0, invalid=762
0407: dt=64.222222, rms=0.462 (0.926%), neg=0, invalid=762
0408: dt=24.060150, rms=0.461 (0.239%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0409: dt=24.060150, rms=0.461 (0.109%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0410: dt=24.060150, rms=0.460 (0.142%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 8 iterations, nbhd size=1, neg = 0
0411: dt=24.060150, rms=0.460 (0.091%), neg=0, invalid=762
0412: dt=24.060150, rms=0.459 (0.153%), neg=0, invalid=762
0413: dt=24.060150, rms=0.459 (0.060%), neg=0, invalid=762
0414: dt=24.060150, rms=0.459 (0.030%), neg=0, invalid=762
0415: dt=19.200000, rms=0.458 (0.053%), neg=0, invalid=762
0416: dt=32.000000, rms=0.458 (0.040%), neg=0, invalid=762
0417: dt=32.000000, rms=0.458 (0.000%), neg=0, invalid=762
0418: dt=32.000000, rms=0.458 (0.080%), neg=0, invalid=762
0419: dt=32.000000, rms=0.458 (0.029%), neg=0, invalid=762
0420: dt=32.000000, rms=0.457 (0.061%), neg=0, invalid=762
0421: dt=32.000000, rms=0.457 (0.020%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
0422: dt=0.000000, rms=0.465 (0.116%), neg=0, invalid=762
0423: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.466, neg=0, invalid=762
0424: dt=0.000000, rms=0.465 (0.116%), neg=0, invalid=762
0425: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0426: dt=1.280000, rms=0.480 (0.474%), neg=0, invalid=762
0427: dt=0.320000, rms=0.480 (0.016%), neg=0, invalid=762
0428: dt=0.320000, rms=0.480 (-0.006%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.481, neg=0, invalid=762
0429: dt=1.536000, rms=0.479 (0.315%), neg=0, invalid=762
0430: dt=0.448000, rms=0.479 (0.013%), neg=0, invalid=762
0431: dt=0.448000, rms=0.479 (-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=0.466, neg=0, invalid=762
iter 0, gcam->neg = 460
after 13 iterations, nbhd size=1, neg = 0
0432: dt=2.336179, rms=0.437 (6.343%), neg=0, invalid=762
0433: dt=0.112000, rms=0.436 (0.129%), neg=0, invalid=762
0434: dt=0.112000, rms=0.436 (-0.073%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.437, neg=0, invalid=762
0435: dt=0.096000, rms=0.436 (0.186%), neg=0, invalid=762
0436: dt=0.007000, rms=0.436 (0.001%), neg=0, invalid=762
0437: dt=0.007000, rms=0.436 (0.000%), neg=0, invalid=762
0438: dt=0.007000, rms=0.436 (-0.002%), 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=0.421, neg=0, invalid=762
0439: 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
0440: dt=32.368000, rms=0.421 (0.008%), neg=0, invalid=762
0441: dt=32.368000, rms=0.421 (0.003%), neg=0, invalid=762
0442: dt=32.368000, rms=0.421 (0.001%), neg=0, invalid=762
0443: dt=32.368000, rms=0.421 (0.001%), neg=0, invalid=762
0444: dt=32.368000, rms=0.421 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0445: 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
0446: dt=124.416000, rms=0.421 (0.081%), neg=0, invalid=762
0447: dt=124.416000, rms=0.421 (0.072%), neg=0, invalid=762
0448: dt=124.416000, rms=0.421 (-0.032%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.421, neg=0, invalid=762
0449: dt=11.200000, rms=0.421 (0.129%), neg=0, invalid=762
0450: dt=11.200000, rms=0.420 (0.052%), neg=0, invalid=762
0451: dt=11.200000, rms=0.420 (0.024%), neg=0, invalid=762
0452: dt=11.200000, rms=0.420 (-0.028%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0453: dt=56.864865, rms=0.417 (0.760%), neg=0, invalid=762
0454: dt=25.600000, rms=0.416 (0.312%), neg=0, invalid=762
0455: dt=44.800000, rms=0.415 (0.206%), neg=0, invalid=762
0456: dt=44.800000, rms=0.414 (0.124%), neg=0, invalid=762
0457: dt=44.800000, rms=0.413 (0.339%), neg=0, invalid=762
0458: dt=44.800000, rms=0.412 (0.257%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0459: dt=44.800000, rms=0.411 (0.285%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0460: dt=44.800000, rms=0.410 (0.251%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 7 iterations, nbhd size=1, neg = 0
0461: dt=44.800000, rms=0.409 (0.188%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0462: dt=44.800000, rms=0.408 (0.183%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 4 iterations, nbhd size=0, neg = 0
0463: dt=44.800000, rms=0.408 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 9 iterations, nbhd size=1, neg = 0
0464: dt=44.800000, rms=0.407 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0465: dt=44.800000, rms=0.407 (0.095%), neg=0, invalid=762
0466: dt=19.200000, rms=0.407 (0.016%), neg=0, invalid=762
0467: dt=19.200000, rms=0.407 (0.007%), neg=0, invalid=762
0468: dt=19.200000, rms=0.407 (0.009%), neg=0, invalid=762
0469: dt=19.200000, rms=0.407 (0.008%), neg=0, invalid=762
0470: dt=19.200000, rms=0.407 (0.004%), 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
0471: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.412, neg=0, invalid=762
0472: dt=0.576000, rms=0.412 (0.001%), neg=0, invalid=762
0473: dt=0.250000, rms=0.412 (0.000%), neg=0, invalid=762
0474: dt=0.250000, rms=0.412 (0.000%), neg=0, invalid=762
0475: dt=0.250000, rms=0.412 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
0476: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.422, neg=0, invalid=762
0477: dt=0.320000, rms=0.422 (0.015%), neg=0, invalid=762
0478: dt=0.028000, rms=0.422 (0.000%), neg=0, invalid=762
0479: dt=0.028000, rms=0.422 (0.000%), neg=0, invalid=762
0480: dt=0.028000, rms=0.422 (-0.001%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=762
iter 0, gcam->neg = 388
after 16 iterations, nbhd size=1, neg = 0
0481: dt=1.388325, rms=0.397 (2.142%), neg=0, invalid=762
0482: dt=0.000015, rms=0.397 (0.000%), neg=0, invalid=762
0483: dt=0.000015, rms=0.397 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.397, neg=0, invalid=762
0484: dt=0.112000, rms=0.397 (0.079%), neg=0, invalid=762
0485: dt=0.080000, rms=0.397 (0.021%), neg=0, invalid=762
0486: dt=0.080000, rms=0.397 (0.008%), neg=0, invalid=762
0487: dt=0.080000, rms=0.397 (-0.035%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 16 minutes and 31 seconds.
mri_ca_register utimesec    9152.213652
mri_ca_register stimesec    8.777665
mri_ca_register ru_maxrss   1347288
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4196526
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63600
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3983
mri_ca_register ru_nivcsw   12517
FSRUNTIME@ mri_ca_register  2.2754 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 22:55:33 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-388
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-6.0.0/0050270/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 7.73
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 = 0.12476 (26)
Left_Lateral_Ventricle (4): linear fit = 1.37 x + 0.0 (526 voxels, overlap=0.256)
Left_Lateral_Ventricle (4): linear fit = 1.37 x + 0.0 (526 voxels, peak = 27), gca=27.3
gca peak = 0.17677 (13)
mri peak = 0.10855 (27)
Right_Lateral_Ventricle (43): linear fit = 1.88 x + 0.0 (607 voxels, overlap=0.184)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (607 voxels, peak = 25), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.12060 (94)
Right_Pallidum (52): linear fit = 0.98 x + 0.0 (913 voxels, overlap=1.008)
Right_Pallidum (52): linear fit = 0.98 x + 0.0 (913 voxels, peak = 93), gca=92.6
gca peak = 0.16930 (96)
mri peak = 0.13639 (94)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (782 voxels, overlap=1.004)
Left_Pallidum (13): linear fit = 0.99 x + 0.0 (782 voxels, peak = 95), gca=94.6
gca peak = 0.24553 (55)
mri peak = 0.09140 (68)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1210 voxels, overlap=0.062)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1210 voxels, peak = 66), gca=66.3
gca peak = 0.30264 (59)
mri peak = 0.10295 (68)
Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (1132 voxels, overlap=0.135)
Left_Hippocampus (17): linear fit = 1.14 x + 0.0 (1132 voxels, peak = 68), gca=67.6
gca peak = 0.07580 (103)
mri peak = 0.12778 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47132 voxels, overlap=0.641)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47132 voxels, peak = 103), gca=103.0
gca peak = 0.07714 (104)
mri peak = 0.11991 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49598 voxels, overlap=0.658)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49598 voxels, peak = 103), gca=103.5
gca peak = 0.09712 (58)
mri peak = 0.04701 (68)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (34281 voxels, overlap=0.357)
Left_Cerebral_Cortex (3): linear fit = 1.18 x + 0.0 (34281 voxels, peak = 69), gca=68.7
gca peak = 0.11620 (58)
mri peak = 0.04672 (72)
Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (36436 voxels, overlap=0.548)
Right_Cerebral_Cortex (42): linear fit = 1.18 x + 0.0 (36436 voxels, peak = 69), gca=68.7
gca peak = 0.30970 (66)
mri peak = 0.13194 (83)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1006 voxels, overlap=0.018)
Right_Caudate (50): linear fit = 1.21 x + 0.0 (1006 voxels, peak = 80), gca=79.5
gca peak = 0.15280 (69)
mri peak = 0.13515 (83)
Left_Caudate (11): linear fit = 1.15 x + 0.0 (873 voxels, overlap=0.213)
Left_Caudate (11): linear fit = 1.15 x + 0.0 (873 voxels, peak = 80), gca=79.7
gca peak = 0.13902 (56)
mri peak = 0.05384 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (26485 voxels, overlap=0.331)
Left_Cerebellum_Cortex (8): linear fit = 1.21 x + 0.0 (26485 voxels, peak = 67), gca=67.5
gca peak = 0.14777 (55)
mri peak = 0.05176 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (27316 voxels, overlap=0.227)
Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (27316 voxels, peak = 66), gca=66.3
gca peak = 0.16765 (84)
mri peak = 0.13047 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6197 voxels, overlap=0.530)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6197 voxels, peak = 89), gca=89.5
gca peak = 0.18739 (84)
mri peak = 0.11750 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (6212 voxels, overlap=0.326)
Right_Cerebellum_White_Matter (46): linear fit = 1.09 x + 0.0 (6212 voxels, peak = 91), gca=91.1
gca peak = 0.29869 (57)
mri peak = 0.10180 (71)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (668 voxels, overlap=0.049)
Left_Amygdala (18): linear fit = 1.18 x + 0.0 (668 voxels, peak = 68), gca=67.5
gca peak = 0.33601 (57)
mri peak = 0.10919 (67)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (573 voxels, overlap=0.046)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (573 voxels, peak = 68), gca=67.5
gca peak = 0.11131 (90)
mri peak = 0.07194 (91)
Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5557 voxels, overlap=0.878)
Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5557 voxels, peak = 94), gca=94.0
gca peak = 0.11793 (83)
mri peak = 0.08751 (91)
Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4874 voxels, overlap=0.498)
Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4874 voxels, peak = 92), gca=91.7
gca peak = 0.08324 (81)
mri peak = 0.08647 (86)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (2866 voxels, overlap=0.632)
Left_Putamen (12): linear fit = 1.08 x + 0.0 (2866 voxels, peak = 87), gca=87.1
gca peak = 0.10360 (77)
mri peak = 0.10945 (84)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2668 voxels, overlap=0.547)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2668 voxels, peak = 83), gca=82.8
gca peak = 0.08424 (78)
mri peak = 0.10386 (88)
Brain_Stem (16): linear fit = 1.08 x + 0.0 (14299 voxels, overlap=0.414)
Brain_Stem (16): linear fit = 1.08 x + 0.0 (14299 voxels, peak = 84), gca=83.9
gca peak = 0.12631 (89)
mri peak = 0.07705 (93)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1817 voxels, overlap=0.738)
Right_VentralDC (60): linear fit = 1.07 x + 0.0 (1817 voxels, peak = 95), gca=94.8
gca peak = 0.14500 (87)
mri peak = 0.08073 (94)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1831 voxels, overlap=0.863)
Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1831 voxels, peak = 93), gca=92.7
gca peak = 0.14975 (24)
mri peak = 0.17654 (26)
gca peak = 0.19357 (14)
mri peak = 0.15985 (26)
Fourth_Ventricle (15): linear fit = 1.68 x + 0.0 (260 voxels, overlap=0.195)
Fourth_Ventricle (15): linear fit = 1.68 x + 0.0 (260 voxels, peak = 24), gca=23.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.18 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.43 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.16119 (25)
mri peak = 0.12476 (26)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (526 voxels, overlap=0.765)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (526 voxels, peak = 25), gca=25.4
gca peak = 0.13997 (19)
mri peak = 0.10855 (27)
Right_Lateral_Ventricle (43): linear fit = 1.24 x + 0.0 (607 voxels, overlap=0.353)
Right_Lateral_Ventricle (43): linear fit = 1.24 x + 0.0 (607 voxels, peak = 23), gca=23.5
gca peak = 0.25085 (91)
mri peak = 0.12060 (94)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (913 voxels, overlap=1.002)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (913 voxels, peak = 92), gca=92.4
gca peak = 0.18771 (95)
mri peak = 0.13639 (94)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (782 voxels, overlap=1.002)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (782 voxels, peak = 95), gca=94.5
gca peak = 0.28156 (67)
mri peak = 0.09140 (68)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1210 voxels, overlap=0.979)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1210 voxels, peak = 67), gca=67.0
gca peak = 0.22435 (64)
mri peak = 0.10295 (68)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1132 voxels, overlap=1.006)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1132 voxels, peak = 66), gca=65.6
gca peak = 0.07582 (103)
mri peak = 0.12778 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47132 voxels, overlap=0.641)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (47132 voxels, peak = 103), gca=103.0
gca peak = 0.08042 (104)
mri peak = 0.11991 (104)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49598 voxels, overlap=0.638)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49598 voxels, peak = 104), gca=104.0
gca peak = 0.08213 (69)
mri peak = 0.04701 (68)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (34281 voxels, overlap=0.962)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (34281 voxels, peak = 68), gca=68.0
gca peak = 0.09960 (69)
mri peak = 0.04672 (72)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (36436 voxels, overlap=0.954)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (36436 voxels, peak = 68), gca=68.0
gca peak = 0.22228 (80)
mri peak = 0.13194 (83)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1006 voxels, overlap=1.002)
Right_Caudate (50): linear fit = 1.01 x + 0.0 (1006 voxels, peak = 81), gca=81.2
gca peak = 0.15201 (79)
mri peak = 0.13515 (83)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (873 voxels, overlap=0.817)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (873 voxels, peak = 79), gca=79.0
gca peak = 0.11991 (67)
mri peak = 0.05384 (64)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (26485 voxels, overlap=0.996)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (26485 voxels, peak = 66), gca=66.0
gca peak = 0.12579 (66)
mri peak = 0.05176 (65)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27316 voxels, overlap=0.990)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (27316 voxels, peak = 66), gca=66.0
gca peak = 0.15873 (90)
mri peak = 0.13047 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6197 voxels, overlap=0.904)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6197 voxels, peak = 90), gca=89.6
gca peak = 0.15099 (91)
mri peak = 0.11750 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6212 voxels, overlap=0.888)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6212 voxels, peak = 91), gca=90.5
gca peak = 0.29148 (69)
mri peak = 0.10180 (71)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (668 voxels, overlap=1.011)
Left_Amygdala (18): linear fit = 1.01 x + 0.0 (668 voxels, peak = 70), gca=70.0
gca peak = 0.30950 (68)
mri peak = 0.10919 (67)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (573 voxels, overlap=1.004)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (573 voxels, peak = 67), gca=67.0
gca peak = 0.11130 (94)
mri peak = 0.07194 (91)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5557 voxels, overlap=0.982)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5557 voxels, peak = 94), gca=93.5
gca peak = 0.10108 (89)
mri peak = 0.08751 (91)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4874 voxels, overlap=0.949)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4874 voxels, peak = 89), gca=88.6
gca peak = 0.08480 (87)
mri peak = 0.08647 (86)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2866 voxels, overlap=0.865)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2866 voxels, peak = 87), gca=87.0
gca peak = 0.10536 (81)
mri peak = 0.10945 (84)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2668 voxels, overlap=0.847)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2668 voxels, peak = 81), gca=81.0
gca peak = 0.08828 (84)
mri peak = 0.10386 (88)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (14299 voxels, overlap=0.704)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (14299 voxels, peak = 85), gca=85.3
gca peak = 0.11713 (95)
mri peak = 0.07705 (93)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1817 voxels, overlap=0.827)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1817 voxels, peak = 95), gca=94.5
gca peak = 0.14342 (91)
mri peak = 0.08073 (94)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1831 voxels, overlap=0.927)
Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1831 voxels, peak = 89), gca=88.7
gca peak = 0.16782 (37)
mri peak = 0.17654 (26)
gca peak = 0.14598 (23)
mri peak = 0.15985 (26)
Fourth_Ventricle (15): linear fit = 1.20 x + 0.0 (260 voxels, overlap=0.584)
Fourth_Ventricle (15): linear fit = 1.20 x + 0.0 (260 voxels, peak = 27), gca=27.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16611 (31)
gca peak Left_Thalamus = 0.36646 (101)
gca peak Third_Ventricle = 0.16782 (37)
gca peak CSF = 0.17072 (52)
gca peak Left_Accumbens_area = 0.49711 (72)
gca peak Left_undetermined = 0.95280 (31)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12536 (35)
gca peak Right_Inf_Lat_Vent = 0.24202 (28)
gca peak Right_Accumbens_area = 0.29878 (78)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14504 (37)
gca peak Fifth_Ventricle = 0.51669 (44)
gca peak WM_hypointensities = 0.09311 (76)
gca peak non_WM_hypointensities = 0.08645 (43)
gca peak Optic_Chiasm = 0.70622 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.15 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
83675 voxels changed in iteration 0 of unlikely voxel relabeling
430 voxels changed in iteration 1 of unlikely voxel relabeling
15 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
61411 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels)
469 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 77729 changed. image ll: -2.130, PF=0.500
pass 2: 21204 changed. image ll: -2.129, PF=0.500
pass 3: 6189 changed.
pass 4: 2266 changed.
64187 voxels changed in iteration 0 of unlikely voxel relabeling
588 voxels changed in iteration 1 of unlikely voxel relabeling
17 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
8579 voxels changed in iteration 0 of unlikely voxel relabeling
175 voxels changed in iteration 1 of unlikely voxel relabeling
88 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7184 voxels changed in iteration 0 of unlikely voxel relabeling
48 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
5810 voxels changed in iteration 0 of unlikely voxel relabeling
45 voxels changed in iteration 1 of unlikely voxel relabeling
2 voxels changed in iteration 2 of unlikely voxel relabeling
3 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
MRItoUCHAR: min=0, max=85
MRItoUCHAR: converting to UCHAR
writing labeled volume to aseg.auto_noCCseg.mgz
mri_ca_label utimesec    4125.722794
mri_ca_label stimesec    1.702741
mri_ca_label ru_maxrss   2105256
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   652569
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63592
mri_ca_label ru_oublock  520
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    329
mri_ca_label ru_nivcsw   4922
auto-labeling took 68 minutes and 2 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/transforms/cc_up.lta 0050270 

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-6.0.0/0050270/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/norm.mgz
23908 voxels in left wm, 48884 in right wm, xrange [125, 132]
searching rotation angles z=[-8  6], y=[-8  6]

searching scale 1 Z rot -7.8  
searching scale 1 Z rot -7.6  
searching scale 1 Z rot -7.3  
searching scale 1 Z rot -7.1  
searching scale 1 Z rot -6.8  
searching scale 1 Z rot -6.6  
searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.7  global minimum found at slice 129.0, rotations (-0.57, -0.06)
final transformation (x=129.0, yr=-0.566, zr=-0.063):
 0.99995   0.00110  -0.00988  -0.07560;
-0.00110   1.00000   0.00001   37.14058;
 0.00988   0.00000   0.99995   23.73013;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 91 103
eigenvectors:
 0.00078  -0.00604   0.99998;
-0.01362  -0.99989  -0.00602;
 0.99991  -0.01362  -0.00087;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/aseg.auto.mgz...
corpus callosum segmentation took 0.7 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 00:04:19 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 00:04:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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...
909 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 76 (76), valley at 31 (31)
csf peak at 20, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 75 (75), valley at 28 (28)
csf peak at 38, setting threshold to 62
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 28 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 00:07:49 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1818033 voxels in mask (pct= 10.84)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 00:07:51 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 103.7 +- 6.9 [79.0 --> 125.0]
GM (74.0) : 73.3 +- 9.7 [30.0 --> 95.0]
setting bottom of white matter range to 83.0
setting top of gray matter range to 92.6
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...
7612 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5775 filled
1317 bright non-wm voxels segmented.
3954 diagonally connected voxels added...
white matter segmentation took 1.8 minutes
writing output to wm.seg.mgz...
assuming input volume is MGH (Van der Kouwe) MP-RAGE

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

preserving editing changes in input volume...
auto filling took 0.55 minutes
reading wm segmentation from wm.seg.mgz...
82 voxels added to wm to prevent paths from MTL structures to cortex
3027 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 32755 voxels turned on, 53832 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  27 found -  27 modified     |    TOTAL:  27
pass   2 (xy+):   0 found -  27 modified     |    TOTAL:  27
pass   1 (xy-):  23 found -  23 modified     |    TOTAL:  50
pass   2 (xy-):   0 found -  23 modified     |    TOTAL:  50
pass   1 (yz+):  29 found -  29 modified     |    TOTAL:  79
pass   2 (yz+):   0 found -  29 modified     |    TOTAL:  79
pass   1 (yz-):  23 found -  23 modified     |    TOTAL: 102
pass   2 (yz-):   0 found -  23 modified     |    TOTAL: 102
pass   1 (xz+):  14 found -  14 modified     |    TOTAL: 116
pass   2 (xz+):   0 found -  14 modified     |    TOTAL: 116
pass   1 (xz-):  22 found -  22 modified     |    TOTAL: 138
pass   2 (xz-):   0 found -  22 modified     |    TOTAL: 138
Iteration Number : 1
pass   1 (+++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (+++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+++):  12 found -  12 modified     |    TOTAL:  20
pass   2 (+++):   0 found -  12 modified     |    TOTAL:  20
pass   1 (+++):  23 found -  23 modified     |    TOTAL:  43
pass   2 (+++):   0 found -  23 modified     |    TOTAL:  43
pass   1 (+++):  19 found -  19 modified     |    TOTAL:  62
pass   2 (+++):   0 found -  19 modified     |    TOTAL:  62
Iteration Number : 1
pass   1 (++): 208 found - 208 modified     |    TOTAL: 208
pass   2 (++):   0 found - 208 modified     |    TOTAL: 208
pass   1 (+-): 126 found - 126 modified     |    TOTAL: 334
pass   2 (+-):   0 found - 126 modified     |    TOTAL: 334
pass   1 (--): 156 found - 156 modified     |    TOTAL: 490
pass   2 (--):   0 found - 156 modified     |    TOTAL: 490
pass   1 (-+): 141 found - 141 modified     |    TOTAL: 631
pass   2 (-+):   0 found - 141 modified     |    TOTAL: 631
Iteration Number : 2
pass   1 (xy+):   7 found -   7 modified     |    TOTAL:   7
pass   2 (xy+):   0 found -   7 modified     |    TOTAL:   7
pass   1 (xy-):   7 found -   7 modified     |    TOTAL:  14
pass   2 (xy-):   0 found -   7 modified     |    TOTAL:  14
pass   1 (yz+):   5 found -   5 modified     |    TOTAL:  19
pass   2 (yz+):   0 found -   5 modified     |    TOTAL:  19
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  23
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  23
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  27
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  27
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  30
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  30
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 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   3 found -   3 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   3 modified     |    TOTAL:   4
pass   1 (--):   2 found -   2 modified     |    TOTAL:   6
pass   2 (--):   0 found -   2 modified     |    TOTAL:   6
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   7
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+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 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 = 871 (out of 638203: 0.136477)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 00:10:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.02013   0.04107  -0.02117  -8.91969;
-0.03528   1.06875   0.28637  -21.88281;
 0.03217  -0.23564   0.88357   34.71194;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 2224 (min = 350, max = 1400), aspect = 1.39 (min = 0.10, max = 0.75)
need search nearby
using seed (124, 123, 146), TAL = (4.0, 18.0, 5.0)
talairach voxel to voxel transform
 0.97818  -0.03026   0.03325   6.90883;
 0.03904   0.87206  -0.28171   29.20991;
-0.02520   0.23367   1.05544  -31.74773;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (124,  123,  146) --> (4.0, 18.0, 5.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (4.00, 18.00, 5.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(22.00, 18.00, 5.00) SRC: (111.73, 99.48, 148.42)
search lh wm seed point around talairach space (-14.00, 18.00, 5.00), SRC: (146.94, 100.89, 147.51)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sun Oct  8 00:11:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   6
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   7
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 (--):   2 found -   2 modified     |    TOTAL:   3
pass   2 (--):   0 found -   2 modified     |    TOTAL:   3
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 10 (out of 307128: 0.003256)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 30: 1426 vertices, 1586 faces
slice 40: 7513 vertices, 7799 faces
slice 50: 18020 vertices, 18386 faces
slice 60: 30457 vertices, 30892 faces
slice 70: 43490 vertices, 43978 faces
slice 80: 57214 vertices, 57650 faces
slice 90: 70014 vertices, 70437 faces
slice 100: 82821 vertices, 83262 faces
slice 110: 94584 vertices, 95004 faces
slice 120: 106361 vertices, 106777 faces
slice 130: 118422 vertices, 118864 faces
slice 140: 130580 vertices, 131036 faces
slice 150: 140768 vertices, 141144 faces
slice 160: 150274 vertices, 150642 faces
slice 170: 157673 vertices, 158003 faces
slice 180: 165030 vertices, 165300 faces
slice 190: 169897 vertices, 170084 faces
slice 200: 171872 vertices, 171928 faces
slice 210: 171872 vertices, 171928 faces
slice 220: 171872 vertices, 171928 faces
slice 230: 171872 vertices, 171928 faces
slice 240: 171872 vertices, 171928 faces
slice 250: 171872 vertices, 171928 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...
   171872 voxel in cpt #1: X=-56 [v=171872,e=515784,f=343856] located at (-28.985769, -23.873447, 23.407436)
For the whole surface: X=-56 [v=171872,e=515784,f=343856]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 00:11:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   5
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   5
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   7
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   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
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 = 8 (out of 308775: 0.002591)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 30: 1515 vertices, 1661 faces
slice 40: 8075 vertices, 8391 faces
slice 50: 19384 vertices, 19839 faces
slice 60: 32523 vertices, 32970 faces
slice 70: 47419 vertices, 47918 faces
slice 80: 60751 vertices, 61210 faces
slice 90: 73809 vertices, 74253 faces
slice 100: 86705 vertices, 87139 faces
slice 110: 99135 vertices, 99573 faces
slice 120: 110937 vertices, 111355 faces
slice 130: 122282 vertices, 122694 faces
slice 140: 133425 vertices, 133840 faces
slice 150: 143439 vertices, 143821 faces
slice 160: 152405 vertices, 152708 faces
slice 170: 159313 vertices, 159610 faces
slice 180: 166294 vertices, 166558 faces
slice 190: 170859 vertices, 171020 faces
slice 200: 172771 vertices, 172830 faces
slice 210: 172780 vertices, 172834 faces
slice 220: 172780 vertices, 172834 faces
slice 230: 172780 vertices, 172834 faces
slice 240: 172780 vertices, 172834 faces
slice 250: 172780 vertices, 172834 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...
   172780 voxel in cpt #1: X=-54 [v=172780,e=518502,f=345668] located at (26.971107, -25.925825, 25.859035)
For the whole surface: X=-54 [v=172780,e=518502,f=345668]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 00:11:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 00:11:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

Waiting for PID 1974 of (1974 1977) to complete...
Waiting for PID 1977 of (1974 1977) 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 (1974 1977) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 00:11:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 00:11:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

Waiting for PID 2020 of (2020 2023) to complete...
Waiting for PID 2023 of (2020 2023) 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 = 50.2 mm, total surface area = 89258 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.157 (target=0.015)   
step 005: RMS=0.117 (target=0.015)   
step 010: RMS=0.087 (target=0.015)   
step 015: RMS=0.073 (target=0.015)   
step 020: RMS=0.063 (target=0.015)   
step 025: RMS=0.055 (target=0.015)   
step 030: RMS=0.050 (target=0.015)   
step 035: RMS=0.046 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.041 (target=0.015)   
step 050: RMS=0.039 (target=0.015)   
step 055: RMS=0.039 (target=0.015)   
step 060: RMS=0.039 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    55.190609
mris_inflate stimesec    0.155976
mris_inflate ru_maxrss   250120
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35894
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12096
mris_inflate ru_oublock  12112
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2262
mris_inflate ru_nivcsw   4187

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 50.2 mm, total surface area = 89813 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.156 (target=0.015)   
step 005: RMS=0.116 (target=0.015)   
step 010: RMS=0.085 (target=0.015)   
step 015: RMS=0.072 (target=0.015)   
step 020: RMS=0.061 (target=0.015)   
step 025: RMS=0.054 (target=0.015)   
step 030: RMS=0.047 (target=0.015)   
step 035: RMS=0.043 (target=0.015)   
step 040: RMS=0.040 (target=0.015)   
step 045: RMS=0.037 (target=0.015)   
step 050: RMS=0.036 (target=0.015)   
step 055: RMS=0.035 (target=0.015)   
step 060: RMS=0.035 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    55.636541
mris_inflate stimesec    0.149977
mris_inflate ru_maxrss   251724
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35783
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12160
mris_inflate ru_oublock  12176
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2284
mris_inflate ru_nivcsw   4648
PIDs (2020 2023) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 00:12:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 00:12:23 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

Waiting for PID 2093 of (2093 2096) to complete...
Waiting for PID 2096 of (2093 2096) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.88 +- 0.55 (0.00-->6.99) (max @ vno 78745 --> 80037)
face area 0.02 +- 0.03 (-0.30-->0.45)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.280...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.792, avgs=0
005/300: dt: 0.9000, rms radial error=176.531, avgs=0
010/300: dt: 0.9000, rms radial error=175.971, avgs=0
015/300: dt: 0.9000, rms radial error=175.234, avgs=0
020/300: dt: 0.9000, rms radial error=174.393, avgs=0
025/300: dt: 0.9000, rms radial error=173.492, avgs=0
030/300: dt: 0.9000, rms radial error=172.558, avgs=0
035/300: dt: 0.9000, rms radial error=171.605, avgs=0
040/300: dt: 0.9000, rms radial error=170.644, avgs=0
045/300: dt: 0.9000, rms radial error=169.686, avgs=0
050/300: dt: 0.9000, rms radial error=168.736, avgs=0
055/300: dt: 0.9000, rms radial error=167.788, avgs=0
060/300: dt: 0.9000, rms radial error=166.844, avgs=0
065/300: dt: 0.9000, rms radial error=165.903, avgs=0
070/300: dt: 0.9000, rms radial error=164.968, avgs=0
075/300: dt: 0.9000, rms radial error=164.040, avgs=0
080/300: dt: 0.9000, rms radial error=163.120, avgs=0
085/300: dt: 0.9000, rms radial error=162.204, avgs=0
090/300: dt: 0.9000, rms radial error=161.294, avgs=0
095/300: dt: 0.9000, rms radial error=160.389, avgs=0
100/300: dt: 0.9000, rms radial error=159.488, avgs=0
105/300: dt: 0.9000, rms radial error=158.592, avgs=0
110/300: dt: 0.9000, rms radial error=157.702, avgs=0
115/300: dt: 0.9000, rms radial error=156.815, avgs=0
120/300: dt: 0.9000, rms radial error=155.934, avgs=0
125/300: dt: 0.9000, rms radial error=155.057, avgs=0
130/300: dt: 0.9000, rms radial error=154.185, avgs=0
135/300: dt: 0.9000, rms radial error=153.318, avgs=0
140/300: dt: 0.9000, rms radial error=152.455, avgs=0
145/300: dt: 0.9000, rms radial error=151.597, avgs=0
150/300: dt: 0.9000, rms radial error=150.744, avgs=0
155/300: dt: 0.9000, rms radial error=149.896, avgs=0
160/300: dt: 0.9000, rms radial error=149.052, avgs=0
165/300: dt: 0.9000, rms radial error=148.213, avgs=0
170/300: dt: 0.9000, rms radial error=147.378, avgs=0
175/300: dt: 0.9000, rms radial error=146.549, avgs=0
180/300: dt: 0.9000, rms radial error=145.724, avgs=0
185/300: dt: 0.9000, rms radial error=144.903, avgs=0
190/300: dt: 0.9000, rms radial error=144.087, avgs=0
195/300: dt: 0.9000, rms radial error=143.275, avgs=0
200/300: dt: 0.9000, rms radial error=142.468, avgs=0
205/300: dt: 0.9000, rms radial error=141.666, avgs=0
210/300: dt: 0.9000, rms radial error=140.868, avgs=0
215/300: dt: 0.9000, rms radial error=140.074, avgs=0
220/300: dt: 0.9000, rms radial error=139.284, avgs=0
225/300: dt: 0.9000, rms radial error=138.499, avgs=0
230/300: dt: 0.9000, rms radial error=137.719, avgs=0
235/300: dt: 0.9000, rms radial error=136.943, avgs=0
240/300: dt: 0.9000, rms radial error=136.171, avgs=0
245/300: dt: 0.9000, rms radial error=135.403, avgs=0
250/300: dt: 0.9000, rms radial error=134.640, avgs=0
255/300: dt: 0.9000, rms radial error=133.881, avgs=0
260/300: dt: 0.9000, rms radial error=133.126, avgs=0
265/300: dt: 0.9000, rms radial error=132.375, avgs=0
270/300: dt: 0.9000, rms radial error=131.629, avgs=0
275/300: dt: 0.9000, rms radial error=130.887, avgs=0
280/300: dt: 0.9000, rms radial error=130.149, avgs=0
285/300: dt: 0.9000, rms radial error=129.415, avgs=0
290/300: dt: 0.9000, rms radial error=128.685, avgs=0
295/300: dt: 0.9000, rms radial error=127.959, avgs=0
300/300: dt: 0.9000, rms radial error=127.237, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20820.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00018
epoch 2 (K=40.0), pass 1, starting sse = 3775.72
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 = 464.26
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/10 = 0.00551
epoch 4 (K=640.0), pass 1, starting sse = 37.80
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.15/14 = 0.01037
final distance error %31.10
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    326.640343
mris_sphere stimesec    0.243962
mris_sphere ru_maxrss   250324
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   35946
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12136
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    11849
mris_sphere ru_nivcsw   23256
FSRUNTIME@ mris_sphere  0.0900 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 0.89 +- 0.55 (0.00-->7.18) (max @ vno 80073 --> 81373)
face area 0.02 +- 0.03 (-0.36-->0.65)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.277...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.885, avgs=0
005/300: dt: 0.9000, rms radial error=176.624, avgs=0
010/300: dt: 0.9000, rms radial error=176.062, avgs=0
015/300: dt: 0.9000, rms radial error=175.323, avgs=0
020/300: dt: 0.9000, rms radial error=174.480, avgs=0
025/300: dt: 0.9000, rms radial error=173.578, avgs=0
030/300: dt: 0.9000, rms radial error=172.643, avgs=0
035/300: dt: 0.9000, rms radial error=171.696, avgs=0
040/300: dt: 0.9000, rms radial error=170.747, avgs=0
045/300: dt: 0.9000, rms radial error=169.795, avgs=0
050/300: dt: 0.9000, rms radial error=168.844, avgs=0
055/300: dt: 0.9000, rms radial error=167.895, avgs=0
060/300: dt: 0.9000, rms radial error=166.951, avgs=0
065/300: dt: 0.9000, rms radial error=166.014, avgs=0
070/300: dt: 0.9000, rms radial error=165.085, avgs=0
075/300: dt: 0.9000, rms radial error=164.161, avgs=0
080/300: dt: 0.9000, rms radial error=163.242, avgs=0
085/300: dt: 0.9000, rms radial error=162.328, avgs=0
090/300: dt: 0.9000, rms radial error=161.418, avgs=0
095/300: dt: 0.9000, rms radial error=160.514, avgs=0
100/300: dt: 0.9000, rms radial error=159.614, avgs=0
105/300: dt: 0.9000, rms radial error=158.719, avgs=0
110/300: dt: 0.9000, rms radial error=157.829, avgs=0
115/300: dt: 0.9000, rms radial error=156.944, avgs=0
120/300: dt: 0.9000, rms radial error=156.064, avgs=0
125/300: dt: 0.9000, rms radial error=155.188, avgs=0
130/300: dt: 0.9000, rms radial error=154.317, avgs=0
135/300: dt: 0.9000, rms radial error=153.451, avgs=0
140/300: dt: 0.9000, rms radial error=152.589, avgs=0
145/300: dt: 0.9000, rms radial error=151.732, avgs=0
150/300: dt: 0.9000, rms radial error=150.880, avgs=0
155/300: dt: 0.9000, rms radial error=150.033, avgs=0
160/300: dt: 0.9000, rms radial error=149.190, avgs=0
165/300: dt: 0.9000, rms radial error=148.352, avgs=0
170/300: dt: 0.9000, rms radial error=147.518, avgs=0
175/300: dt: 0.9000, rms radial error=146.689, avgs=0
180/300: dt: 0.9000, rms radial error=145.864, avgs=0
185/300: dt: 0.9000, rms radial error=145.044, avgs=0
190/300: dt: 0.9000, rms radial error=144.229, avgs=0
195/300: dt: 0.9000, rms radial error=143.418, avgs=0
200/300: dt: 0.9000, rms radial error=142.611, avgs=0
205/300: dt: 0.9000, rms radial error=141.809, avgs=0
210/300: dt: 0.9000, rms radial error=141.011, avgs=0
215/300: dt: 0.9000, rms radial error=140.218, avgs=0
220/300: dt: 0.9000, rms radial error=139.429, avgs=0
225/300: dt: 0.9000, rms radial error=138.644, avgs=0
230/300: dt: 0.9000, rms radial error=137.863, avgs=0
235/300: dt: 0.9000, rms radial error=137.087, avgs=0
240/300: dt: 0.9000, rms radial error=136.315, avgs=0
245/300: dt: 0.9000, rms radial error=135.548, avgs=0
250/300: dt: 0.9000, rms radial error=134.784, avgs=0
255/300: dt: 0.9000, rms radial error=134.025, avgs=0
260/300: dt: 0.9000, rms radial error=133.271, avgs=0
265/300: dt: 0.9000, rms radial error=132.520, avgs=0
270/300: dt: 0.9000, rms radial error=131.774, avgs=0
275/300: dt: 0.9000, rms radial error=131.032, avgs=0
280/300: dt: 0.9000, rms radial error=130.294, avgs=0
285/300: dt: 0.9000, rms radial error=129.560, avgs=0
290/300: dt: 0.9000, rms radial error=128.830, avgs=0
295/300: dt: 0.9000, rms radial error=128.105, avgs=0
300/300: dt: 0.9000, rms radial error=127.383, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20982.97
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 3824.27
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 465.59
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00522
epoch 4 (K=640.0), pass 1, starting sse = 36.55
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/12 = 0.00553
final distance error %30.49
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    318.886521
mris_sphere stimesec    0.245962
mris_sphere ru_maxrss   251928
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   35835
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12200
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8225
mris_sphere ru_nivcsw   25102
FSRUNTIME@ mris_sphere  0.0887 hours 1 threads
PIDs (2093 2096) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 00:17:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 00:17:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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


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

#@# Fix Topology lh Sun Oct  8 00:17:47 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050270 lh 

#@# Fix Topology rh Sun Oct  8 00:17:47 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050270 rh 

Waiting for PID 2319 of (2319 2322) to complete...
Waiting for PID 2322 of (2319 2322) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050270 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=-56 (nv=171872, nf=343856, ne=515784, g=29)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
6479 ambiguous faces found in tessellation
segmenting defects...
31 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 7 into 5
      -merging segment 20 into 5
      -merging segment 13 into 11
      -merging segment 25 into 22
27 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.4636  (-4.7318)
      -vertex     loglikelihood: -6.0761  (-3.0381)
      -normal dot loglikelihood: -3.6280  (-3.6280)
      -quad curv  loglikelihood: -6.5773  (-3.2886)
      Total Loglikelihood : -25.7449

CORRECTING DEFECT 0 (vertices=23, convex hull=43, v0=41825)
After retessellation of defect 0 (v0=41825), euler #=-24 (168045,502988,334919) : difference with theory (-24) = 0 

CORRECTING DEFECT 1 (vertices=272, convex hull=217, v0=63191)
After retessellation of defect 1 (v0=63191), euler #=-23 (168073,503176,335080) : difference with theory (-23) = 0 

CORRECTING DEFECT 2 (vertices=32, convex hull=68, v0=65483)
After retessellation of defect 2 (v0=65483), euler #=-22 (168087,503246,335137) : difference with theory (-22) = 0 

CORRECTING DEFECT 3 (vertices=74, convex hull=51, v0=70880)
After retessellation of defect 3 (v0=70880), euler #=-21 (168099,503299,335179) : difference with theory (-21) = 0 

CORRECTING DEFECT 4 (vertices=5, convex hull=20, v0=83721)
After retessellation of defect 4 (v0=83721), euler #=-20 (168100,503306,335186) : difference with theory (-20) = 0 

CORRECTING DEFECT 5 (vertices=888, convex hull=502, v0=88456)
L defect detected...
After retessellation of defect 5 (v0=88456), euler #=-18 (168219,503924,335687) : difference with theory (-19) = -1 

CORRECTING DEFECT 6 (vertices=25, convex hull=47, v0=89955)
After retessellation of defect 6 (v0=89955), euler #=-17 (168227,503965,335721) : difference with theory (-18) = -1 

CORRECTING DEFECT 7 (vertices=116, convex hull=41, v0=109916)
After retessellation of defect 7 (v0=109916), euler #=-16 (168239,504016,335761) : difference with theory (-17) = -1 

CORRECTING DEFECT 8 (vertices=127, convex hull=42, v0=110913)
After retessellation of defect 8 (v0=110913), euler #=-15 (168248,504056,335793) : difference with theory (-16) = -1 

CORRECTING DEFECT 9 (vertices=7, convex hull=17, v0=116114)
After retessellation of defect 9 (v0=116114), euler #=-14 (168248,504062,335800) : difference with theory (-15) = -1 

CORRECTING DEFECT 10 (vertices=127, convex hull=107, v0=116786)
After retessellation of defect 10 (v0=116786), euler #=-12 (168285,504233,335936) : difference with theory (-14) = -2 

CORRECTING DEFECT 11 (vertices=84, convex hull=34, v0=117834)
After retessellation of defect 11 (v0=117834), euler #=-11 (168296,504276,335969) : difference with theory (-13) = -2 

CORRECTING DEFECT 12 (vertices=954, convex hull=335, v0=121558)
After retessellation of defect 12 (v0=121558), euler #=-13 (168463,505001,336525) : difference with theory (-12) = 1 

CORRECTING DEFECT 13 (vertices=10, convex hull=31, v0=121735)
After retessellation of defect 13 (v0=121735), euler #=-12 (168466,505021,336543) : difference with theory (-11) = 1 

CORRECTING DEFECT 14 (vertices=16, convex hull=21, v0=122785)
After retessellation of defect 14 (v0=122785), euler #=-11 (168468,505033,336554) : difference with theory (-10) = 1 

CORRECTING DEFECT 15 (vertices=306, convex hull=150, v0=123912)
After retessellation of defect 15 (v0=123912), euler #=-10 (168517,505246,336719) : difference with theory (-9) = 1 

CORRECTING DEFECT 16 (vertices=49, convex hull=35, v0=123928)
After retessellation of defect 16 (v0=123928), euler #=-9 (168526,505284,336749) : difference with theory (-8) = 1 

CORRECTING DEFECT 17 (vertices=11, convex hull=12, v0=125223)
After retessellation of defect 17 (v0=125223), euler #=-8 (168528,505293,336757) : difference with theory (-7) = 1 

CORRECTING DEFECT 18 (vertices=214, convex hull=114, v0=130396)
After retessellation of defect 18 (v0=130396), euler #=-7 (168577,505492,336908) : difference with theory (-6) = 1 

CORRECTING DEFECT 19 (vertices=45, convex hull=83, v0=141385)
After retessellation of defect 19 (v0=141385), euler #=-5 (168589,505558,336964) : difference with theory (-5) = 0 

CORRECTING DEFECT 20 (vertices=18, convex hull=53, v0=141633)
After retessellation of defect 20 (v0=141633), euler #=-4 (168598,505601,336999) : difference with theory (-4) = 0 

CORRECTING DEFECT 21 (vertices=7, convex hull=34, v0=144492)
After retessellation of defect 21 (v0=144492), euler #=-3 (168600,505619,337016) : difference with theory (-3) = 0 

CORRECTING DEFECT 22 (vertices=124, convex hull=155, v0=146156)
After retessellation of defect 22 (v0=146156), euler #=-2 (168673,505911,337236) : difference with theory (-2) = 0 

CORRECTING DEFECT 23 (vertices=100, convex hull=106, v0=161502)
After retessellation of defect 23 (v0=161502), euler #=-1 (168688,505998,337309) : difference with theory (-1) = 0 

CORRECTING DEFECT 24 (vertices=27, convex hull=77, v0=170254)
After retessellation of defect 24 (v0=170254), euler #=0 (168700,506059,337359) : difference with theory (0) = 0 

CORRECTING DEFECT 25 (vertices=74, convex hull=64, v0=171459)
After retessellation of defect 25 (v0=171459), euler #=1 (168716,506130,337415) : difference with theory (1) = 0 

CORRECTING DEFECT 26 (vertices=89, convex hull=26, v0=171663)
After retessellation of defect 26 (v0=171663), euler #=2 (168718,506148,337432) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.07-->9.88) (max @ vno 65737 --> 66915)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.07-->9.88) (max @ vno 65737 --> 66915)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
100 mutations (35.0%), 186 crossovers (65.0%), 423 vertices were eliminated
building final representation...
3154 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=168718, nf=337432, ne=506148, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 29.6 minutes
0 defective edges
removing intersecting faces
000: 292 intersecting
001: 2 intersecting
expanding nbhd size to 2
002: 2 intersecting
mris_fix_topology utimesec    1776.824881
mris_fix_topology stimesec    0.242963
mris_fix_topology ru_maxrss   538552
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   59876
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  12096
mris_fix_topology ru_oublock  16056
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    630
mris_fix_topology ru_nivcsw   5110
FSRUNTIME@ mris_fix_topology lh  0.4936 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050270 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=-54 (nv=172780, nf=345668, ne=518502, g=28)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
7550 ambiguous faces found in tessellation
segmenting defects...
32 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 20 into 19
31 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.3897  (-4.6948)
      -vertex     loglikelihood: -6.0233  (-3.0117)
      -normal dot loglikelihood: -3.6351  (-3.6351)
      -quad curv  loglikelihood: -6.5717  (-3.2859)
      Total Loglikelihood : -25.6198

CORRECTING DEFECT 0 (vertices=26, convex hull=56, v0=724)
After retessellation of defect 0 (v0=724), euler #=-28 (168421,504065,335616) : difference with theory (-28) = 0 

CORRECTING DEFECT 1 (vertices=52, convex hull=57, v0=12901)
After retessellation of defect 1 (v0=12901), euler #=-27 (168429,504110,335654) : difference with theory (-27) = 0 

CORRECTING DEFECT 2 (vertices=1048, convex hull=434, v0=16458)
After retessellation of defect 2 (v0=16458), euler #=-26 (168661,505024,336337) : difference with theory (-26) = 0 

CORRECTING DEFECT 3 (vertices=19, convex hull=41, v0=20057)
After retessellation of defect 3 (v0=20057), euler #=-25 (168665,505050,336360) : difference with theory (-25) = 0 

CORRECTING DEFECT 4 (vertices=305, convex hull=149, v0=24135)
After retessellation of defect 4 (v0=24135), euler #=-24 (168716,505281,336541) : difference with theory (-24) = 0 

CORRECTING DEFECT 5 (vertices=6, convex hull=24, v0=33564)
After retessellation of defect 5 (v0=33564), euler #=-23 (168717,505291,336551) : difference with theory (-23) = 0 

CORRECTING DEFECT 6 (vertices=6, convex hull=27, v0=36180)
After retessellation of defect 6 (v0=36180), euler #=-22 (168718,505301,336561) : difference with theory (-22) = 0 

CORRECTING DEFECT 7 (vertices=13, convex hull=33, v0=39182)
After retessellation of defect 7 (v0=39182), euler #=-21 (168721,505320,336578) : difference with theory (-21) = 0 

CORRECTING DEFECT 8 (vertices=673, convex hull=243, v0=68091)
normal vector of length zero at vertex 170487 with 4 faces
normal vector of length zero at vertex 170487 with 4 faces
After retessellation of defect 8 (v0=68091), euler #=-20 (168756,505551,336775) : difference with theory (-20) = 0 

CORRECTING DEFECT 9 (vertices=34, convex hull=29, v0=79068)
After retessellation of defect 9 (v0=79068), euler #=-19 (168759,505572,336794) : difference with theory (-19) = 0 

CORRECTING DEFECT 10 (vertices=32, convex hull=37, v0=85154)
After retessellation of defect 10 (v0=85154), euler #=-18 (168763,505595,336814) : difference with theory (-18) = 0 

CORRECTING DEFECT 11 (vertices=33, convex hull=43, v0=98663)
After retessellation of defect 11 (v0=98663), euler #=-17 (168771,505638,336850) : difference with theory (-17) = 0 

CORRECTING DEFECT 12 (vertices=397, convex hull=160, v0=98821)
normal vector of length zero at vertex 170773 with 3 faces
normal vector of length zero at vertex 170773 with 4 faces
normal vector of length zero at vertex 170772 with 3 faces
normal vector of length zero at vertex 170772 with 3 faces
normal vector of length zero at vertex 170772 with 3 faces
normal vector of length zero at vertex 170772 with 3 faces
normal vector of length zero at vertex 170735 with 3 faces
After retessellation of defect 12 (v0=98821), euler #=-16 (168786,505761,336959) : difference with theory (-16) = 0 

CORRECTING DEFECT 13 (vertices=45, convex hull=30, v0=99249)
After retessellation of defect 13 (v0=99249), euler #=-15 (168789,505781,336977) : difference with theory (-15) = 0 

CORRECTING DEFECT 14 (vertices=24, convex hull=39, v0=104667)
After retessellation of defect 14 (v0=104667), euler #=-14 (168798,505823,337011) : difference with theory (-14) = 0 

CORRECTING DEFECT 15 (vertices=60, convex hull=80, v0=115621)
After retessellation of defect 15 (v0=115621), euler #=-13 (168833,505963,337117) : difference with theory (-13) = 0 

CORRECTING DEFECT 16 (vertices=16, convex hull=32, v0=118713)
After retessellation of defect 16 (v0=118713), euler #=-12 (168837,505986,337137) : difference with theory (-12) = 0 

CORRECTING DEFECT 17 (vertices=25, convex hull=39, v0=119841)
After retessellation of defect 17 (v0=119841), euler #=-11 (168844,506026,337171) : difference with theory (-11) = 0 

CORRECTING DEFECT 18 (vertices=38, convex hull=42, v0=119884)
After retessellation of defect 18 (v0=119884), euler #=-10 (168853,506068,337205) : difference with theory (-10) = 0 

CORRECTING DEFECT 19 (vertices=32, convex hull=60, v0=120838)
After retessellation of defect 19 (v0=120838), euler #=-8 (168865,506131,337258) : difference with theory (-9) = -1 

CORRECTING DEFECT 20 (vertices=144, convex hull=148, v0=125147)
After retessellation of defect 20 (v0=125147), euler #=-7 (168945,506436,337484) : difference with theory (-8) = -1 

CORRECTING DEFECT 21 (vertices=863, convex hull=340, v0=127387)
L defect detected...
After retessellation of defect 21 (v0=127387), euler #=-7 (169238,507496,338251) : difference with theory (-7) = 0 

CORRECTING DEFECT 22 (vertices=61, convex hull=78, v0=128512)
After retessellation of defect 22 (v0=128512), euler #=-6 (169267,507613,338340) : difference with theory (-6) = 0 

CORRECTING DEFECT 23 (vertices=20, convex hull=23, v0=128978)
After retessellation of defect 23 (v0=128978), euler #=-5 (169270,507630,338355) : difference with theory (-5) = 0 

CORRECTING DEFECT 24 (vertices=7, convex hull=16, v0=131974)
After retessellation of defect 24 (v0=131974), euler #=-4 (169272,507639,338363) : difference with theory (-4) = 0 

CORRECTING DEFECT 25 (vertices=12, convex hull=42, v0=132319)
After retessellation of defect 25 (v0=132319), euler #=-3 (169274,507661,338384) : difference with theory (-3) = 0 

CORRECTING DEFECT 26 (vertices=29, convex hull=78, v0=136347)
After retessellation of defect 26 (v0=136347), euler #=-2 (169292,507749,338455) : difference with theory (-2) = 0 

CORRECTING DEFECT 27 (vertices=71, convex hull=92, v0=137591)
After retessellation of defect 27 (v0=137591), euler #=-1 (169310,507840,338529) : difference with theory (-1) = 0 

CORRECTING DEFECT 28 (vertices=85, convex hull=69, v0=141433)
After retessellation of defect 28 (v0=141433), euler #=0 (169333,507936,338603) : difference with theory (0) = 0 

CORRECTING DEFECT 29 (vertices=136, convex hull=68, v0=171346)
After retessellation of defect 29 (v0=171346), euler #=1 (169356,508035,338680) : difference with theory (1) = 0 

CORRECTING DEFECT 30 (vertices=54, convex hull=62, v0=172210)
After retessellation of defect 30 (v0=172210), euler #=2 (169365,508089,338726) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.24 (0.03-->15.87) (max @ vno 74300 --> 75602)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.24 (0.03-->15.87) (max @ vno 74300 --> 75602)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
132 mutations (35.7%), 238 crossovers (64.3%), 241 vertices were eliminated
building final representation...
3415 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=169365, nf=338726, ne=508089, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 33.0 minutes
0 defective edges
removing intersecting faces
000: 441 intersecting
001: 38 intersecting
002: 10 intersecting
expanding nbhd size to 2
003: 12 intersecting
expanding nbhd size to 3
004: 12 intersecting
005: 11 intersecting
006: 10 intersecting
007: 6 intersecting
expanding nbhd size to 4
008: 6 intersecting
009: 5 intersecting
expanding nbhd size to 5
010: 5 intersecting
expanding nbhd size to 6
011: 13 intersecting
012: 9 intersecting
expanding nbhd size to 7
013: 9 intersecting
014: 8 intersecting
015: 6 intersecting
016: 4 intersecting
mris_fix_topology utimesec    1977.893314
mris_fix_topology stimesec    0.226965
mris_fix_topology ru_maxrss   538508
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   59616
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  23680
mris_fix_topology ru_oublock  16184
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    612
mris_fix_topology ru_nivcsw   3654
FSRUNTIME@ mris_fix_topology rh  0.5492 hours 1 threads
PIDs (2319 2322) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 168718 - 506148 + 337432 = 2 --> 0 holes
      F =2V-4:          337432 = 337436-4 (0)
      2E=3F:            1012296 = 1012296 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 169365 - 508089 + 338726 = 2 --> 0 holes
      F =2V-4:          338726 = 338730-4 (0)
      2E=3F:            1016178 = 1016178 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 43 intersecting
001: 3 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 107 intersecting
001: 10 intersecting
expanding nbhd size to 2
002: 10 intersecting
expanding nbhd size to 3
003: 10 intersecting
expanding nbhd size to 4
004: 13 intersecting
005: 11 intersecting
expanding nbhd size to 5
006: 12 intersecting
007: 9 intersecting
expanding nbhd size to 6
008: 10 intersecting
expanding nbhd size to 7
009: 10 intersecting
expanding nbhd size to 8
010: 12 intersecting
011: 10 intersecting
012: 9 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 00:51:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050270 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 00:51:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050270 rh 

Waiting for PID 4151 of (4151 4154) to complete...
Waiting for PID 4154 of (4151 4154) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050270 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-6.0.0/0050270/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
37890 bright wm thresholded.
1716 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.orig...
computing class statistics...
border white:    313918 voxels (1.87%)
border gray      354793 voxels (2.11%)
WM (101.0): 100.8 +- 7.7 [70.0 --> 110.0]
GM (77.0) : 76.0 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 64.1 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 54.2 (was 40)
setting MAX_GRAY to 98.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->4.97) (max @ vno 137208 --> 168368)
face area 0.28 +- 0.12 (0.00-->2.77)
mean absolute distance = 0.72 +- 0.93
3838 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=106+-5.2,    GM=74+-7.0
mean inside = 96.7, mean outside = 79.4
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=84.1, 48 (48) missing vertices, mean dist 0.2 [0.6 (%38.8)->0.8 (%61.2))]
%65 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.09-->5.72) (max @ vno 168368 --> 168374)
face area 0.28 +- 0.13 (0.00-->4.10)
mean absolute distance = 0.35 +- 0.55
3778 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3557301.2, rms=9.375
001: dt: 0.5000, sse=2047815.9, rms=6.511 (30.554%)
002: dt: 0.5000, sse=1404221.6, rms=4.776 (26.645%)
003: dt: 0.5000, sse=1130251.9, rms=3.801 (20.405%)
004: dt: 0.5000, sse=1004434.6, rms=3.255 (14.386%)
005: dt: 0.5000, sse=962282.8, rms=3.048 (6.353%)
006: dt: 0.5000, sse=940433.4, rms=2.927 (3.954%)
rms = 2.91, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=937543.4, rms=2.912 (0.510%)
008: dt: 0.2500, sse=782379.3, rms=1.797 (38.310%)
009: dt: 0.2500, sse=754369.9, rms=1.534 (14.604%)
010: dt: 0.2500, sse=748160.5, rms=1.472 (4.027%)
rms = 1.44, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=745900.5, rms=1.439 (2.275%)
rms = 1.41, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=744116.4, rms=1.408 (2.178%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=87.2, 108 (21) missing vertices, mean dist -0.2 [0.4 (%74.9)->0.2 (%25.1))]
%78 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.06-->5.85) (max @ vno 168368 --> 168374)
face area 0.35 +- 0.16 (0.00-->5.30)
mean absolute distance = 0.24 +- 0.35
4530 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1453895.6, rms=4.319
013: dt: 0.5000, sse=1081026.5, rms=2.688 (37.750%)
014: dt: 0.5000, sse=1068909.2, rms=2.628 (2.250%)
rms = 2.60, time step reduction 1 of 3 to 0.250...
015: dt: 0.5000, sse=1058864.6, rms=2.598 (1.138%)
016: dt: 0.2500, sse=920657.8, rms=1.517 (41.604%)
017: dt: 0.2500, sse=898266.6, rms=1.270 (16.300%)
rms = 1.23, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=898068.6, rms=1.226 (3.410%)
rms = 1.18, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=892099.6, rms=1.183 (3.511%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=89.5, 112 (13) missing vertices, mean dist -0.1 [0.3 (%75.0)->0.2 (%25.0))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.24 (0.09-->6.05) (max @ vno 168368 --> 168374)
face area 0.33 +- 0.16 (0.00-->5.35)
mean absolute distance = 0.18 +- 0.28
4212 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1124792.6, rms=3.075
020: dt: 0.5000, sse=986980.0, rms=2.237 (27.248%)
rms = 2.49, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=899329.7, rms=1.539 (31.224%)
022: dt: 0.2500, sse=867170.2, rms=1.187 (22.839%)
023: dt: 0.2500, sse=860644.9, rms=1.099 (7.465%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=861044.9, rms=1.094 (0.468%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=858489.2, rms=1.065 (2.603%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=90.2, 117 (11) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=868116.4, rms=1.389
rms = 1.36, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=869623.4, rms=1.364 (1.784%)
027: dt: 0.2500, sse=839628.7, rms=1.024 (24.908%)
028: dt: 0.2500, sse=827296.8, rms=0.856 (16.464%)
rms = 0.90, time step reduction 2 of 3 to 0.125...
rms = 0.84, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=824700.1, rms=0.837 (2.208%)
positioning took 0.6 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 7604 vertices
erasing segment 1 (vno[0] = 101546)
erasing segment 2 (vno[0] = 111829)
erasing segment 3 (vno[0] = 123117)
erasing segment 4 (vno[0] = 124344)
erasing segment 5 (vno[0] = 125542)
erasing segment 6 (vno[0] = 126775)
erasing segment 7 (vno[0] = 128778)
erasing segment 8 (vno[0] = 128801)
erasing segment 9 (vno[0] = 129818)
erasing segment 10 (vno[0] = 142409)
erasing segment 11 (vno[0] = 148070)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.area
vertex spacing 0.88 +- 0.25 (0.02-->6.24) (max @ vno 168368 --> 168374)
face area 0.33 +- 0.15 (0.00-->5.72)
refinement took 6.0 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050270 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-6.0.0/0050270/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
37890 bright wm thresholded.
1716 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.orig...
computing class statistics...
border white:    313918 voxels (1.87%)
border gray      354793 voxels (2.11%)
WM (101.0): 100.8 +- 7.7 [70.0 --> 110.0]
GM (77.0) : 76.0 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 65.1 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 75.0 (was 85)
setting MAX_CSF to 55.2 (was 40)
setting MAX_GRAY to 98.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 65.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.4 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.22 (0.03-->6.63) (max @ vno 74300 --> 74301)
face area 0.28 +- 0.13 (0.00-->6.92)
mean absolute distance = 0.70 +- 0.90
4308 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=106+-5.2,    GM=75+-6.1
mean inside = 96.9, mean outside = 79.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=84.7, 115 (115) missing vertices, mean dist 0.2 [0.6 (%39.4)->0.7 (%60.6))]
%66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.09-->7.25) (max @ vno 76800 --> 74319)
face area 0.28 +- 0.13 (0.00-->8.21)
mean absolute distance = 0.34 +- 0.53
3985 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3480857.8, rms=9.189
001: dt: 0.5000, sse=1979844.2, rms=6.306 (31.368%)
002: dt: 0.5000, sse=1357614.0, rms=4.596 (27.114%)
003: dt: 0.5000, sse=1104602.6, rms=3.669 (20.177%)
004: dt: 0.5000, sse=993434.6, rms=3.181 (13.300%)
005: dt: 0.5000, sse=970130.9, rms=2.999 (5.720%)
006: dt: 0.5000, sse=939506.8, rms=2.898 (3.359%)
rms = 2.89, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=938965.8, rms=2.887 (0.379%)
008: dt: 0.2500, sse=790830.4, rms=1.784 (38.198%)
009: dt: 0.2500, sse=757778.6, rms=1.536 (13.932%)
010: dt: 0.2500, sse=752286.2, rms=1.476 (3.897%)
rms = 1.45, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=750278.3, rms=1.448 (1.905%)
rms = 1.42, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=746835.8, rms=1.418 (2.063%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=87.7, 95 (21) missing vertices, mean dist -0.2 [0.4 (%75.3)->0.2 (%24.7))]
%78 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 0.89 +- 0.24 (0.04-->7.45) (max @ vno 76800 --> 74319)
face area 0.34 +- 0.16 (0.00-->11.30)
mean absolute distance = 0.23 +- 0.33
4159 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1445115.2, rms=4.276
013: dt: 0.5000, sse=1077296.2, rms=2.648 (38.063%)
014: dt: 0.5000, sse=1064515.4, rms=2.572 (2.885%)
rms = 2.55, time step reduction 1 of 3 to 0.250...
015: dt: 0.5000, sse=1055312.0, rms=2.548 (0.931%)
016: dt: 0.2500, sse=923555.7, rms=1.524 (40.193%)
017: dt: 0.2500, sse=904074.8, rms=1.296 (14.960%)
rms = 1.26, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=901692.2, rms=1.261 (2.721%)
rms = 1.22, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=899555.1, rms=1.218 (3.349%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=90.0, 107 (12) missing vertices, mean dist -0.1 [0.2 (%75.1)->0.2 (%24.9))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.24 (0.11-->7.54) (max @ vno 76800 --> 74319)
face area 0.33 +- 0.16 (0.00-->11.51)
mean absolute distance = 0.17 +- 0.26
3792 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1117380.5, rms=3.007
020: dt: 0.5000, sse=987744.5, rms=2.217 (26.282%)
rms = 2.43, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=903393.6, rms=1.560 (29.621%)
022: dt: 0.2500, sse=874648.9, rms=1.226 (21.429%)
023: dt: 0.2500, sse=869562.8, rms=1.134 (7.514%)
rms = 1.13, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=865396.6, rms=1.126 (0.675%)
rms = 1.10, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=860838.0, rms=1.095 (2.712%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 1 vertex label from ripped group
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=90.7, 106 (11) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=869073.9, rms=1.390
rms = 1.35, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=869148.2, rms=1.350 (2.824%)
027: dt: 0.2500, sse=841637.9, rms=1.035 (23.351%)
028: dt: 0.2500, sse=834881.9, rms=0.881 (14.894%)
rms = 0.93, time step reduction 2 of 3 to 0.125...
rms = 0.86, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=832501.6, rms=0.862 (2.143%)
positioning took 0.6 minutes
generating cortex label...
11 non-cortical segments detected
only using segment with 7267 vertices
erasing segment 1 (vno[0] = 97355)
erasing segment 2 (vno[0] = 100889)
erasing segment 3 (vno[0] = 109193)
erasing segment 4 (vno[0] = 120065)
erasing segment 5 (vno[0] = 123341)
erasing segment 6 (vno[0] = 125573)
erasing segment 7 (vno[0] = 126701)
erasing segment 8 (vno[0] = 127639)
erasing segment 9 (vno[0] = 128657)
erasing segment 10 (vno[0] = 129424)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.area
vertex spacing 0.88 +- 0.25 (0.06-->7.62) (max @ vno 74319 --> 76800)
face area 0.33 +- 0.16 (0.00-->11.60)
refinement took 6.0 minutes
PIDs (4151 4154) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 00:57:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 00:57:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

Waiting for PID 4554 of (4554 4557) to complete...
Waiting for PID 4557 of (4554 4557) 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 (4554 4557) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 00:57:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 00:57:15 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 4603 of (4603 4606) to complete...
Waiting for PID 4606 of (4603 4606) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 50.3 mm, total surface area = 99772 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.178 (target=0.015)   
step 005: RMS=0.123 (target=0.015)   
step 010: RMS=0.090 (target=0.015)   
step 015: RMS=0.074 (target=0.015)   
step 020: RMS=0.061 (target=0.015)   
step 025: RMS=0.051 (target=0.015)   
step 030: RMS=0.042 (target=0.015)   
step 035: RMS=0.037 (target=0.015)   
step 040: RMS=0.032 (target=0.015)   
step 045: RMS=0.027 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.023 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    50.736286
mris_inflate stimesec    0.165974
mris_inflate ru_maxrss   245700
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35434
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  13208
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2106
mris_inflate ru_nivcsw   3560

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 50.3 mm, total surface area = 99910 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.177 (target=0.015)   
step 005: RMS=0.122 (target=0.015)   
step 010: RMS=0.090 (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=0.041 (target=0.015)   
step 035: RMS=0.035 (target=0.015)   
step 040: RMS=0.030 (target=0.015)   
step 045: RMS=0.026 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.020 (target=0.015)   
inflation complete.
inflation took 0.9 minutes
mris_inflate utimesec    51.154223
mris_inflate stimesec    0.143978
mris_inflate ru_maxrss   246996
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35751
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  13264
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2352
mris_inflate ru_nivcsw   3645
PIDs (4603 4606) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 00:58:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf

 mris_curvature -w lh.white.preaparc 

rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
rm -f lh.white.K
ln -s lh.white.preaparc.K lh.white.K

 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated 

#--------------------------------------------
#@# Curv .H and .K rh Sun Oct  8 00:58:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 4705 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4708 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4711 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4714 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4717 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4722 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4725 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4728 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4731 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4734 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4737 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...
Waiting for PID 4741 of (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 5.265*4pi (66.165) --> -4 handles
ICI = 191.4, FI = 2282.9, variation=34957.809
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
241 vertices thresholded to be in k1 ~ [-0.21 0.34], k2 ~ [-0.10 0.05]
total integrated curvature = 0.518*4pi (6.514) --> 0 handles
ICI = 1.6, FI = 11.3, variation=189.146
170 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
177 vertices thresholded to be in [-0.13 0.15]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 6.199*4pi (77.905) --> -5 handles
ICI = 194.8, FI = 2319.6, variation=35512.062
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
288 vertices thresholded to be in k1 ~ [-0.19 0.31], k2 ~ [-0.10 0.07]
total integrated curvature = 0.534*4pi (6.706) --> 0 handles
ICI = 1.6, FI = 11.3, variation=187.825
163 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
165 vertices thresholded to be in [-0.11 0.16]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.015, std = 0.022
done.
PIDs (4705 4708 4711 4714 4717 4722 4725 4728 4731 4734 4737 4741) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 00:59:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050270 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      [ 0050270/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                      [ 327 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.447377
WARN:    S explicit min:                          0.000000	vertex = 574

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 00:59:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050270 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      [ 0050270/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                      [ 329 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.436443
WARN:    S explicit min:                          0.000000	vertex = 141
#--------------------------------------------
#@# Sphere lh Sun Oct  8 00:59:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 00:59:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 4896 of (4896 4899) to complete...
Waiting for PID 4899 of (4896 4899) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0.263...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.67
pass 1: epoch 2 of 3 starting distance error %20.59
unfolding complete - removing small folds...
starting distance error %20.51
removing remaining folds...
final distance error %20.52
MRISunfold() return, current seed 1234
-01: dt=0.0000, 225 negative triangles
169: dt=0.9900, 225 negative triangles
170: dt=0.9900, 120 negative triangles
171: dt=0.9900, 88 negative triangles
172: dt=0.9900, 81 negative triangles
173: dt=0.9900, 62 negative triangles
174: dt=0.9900, 50 negative triangles
175: dt=0.9900, 55 negative triangles
176: dt=0.9900, 49 negative triangles
177: dt=0.9900, 51 negative triangles
178: dt=0.9900, 48 negative triangles
179: dt=0.9900, 42 negative triangles
180: dt=0.9900, 42 negative triangles
181: dt=0.9900, 42 negative triangles
182: dt=0.9900, 47 negative triangles
183: dt=0.9900, 46 negative triangles
184: dt=0.9900, 46 negative triangles
185: dt=0.9900, 43 negative triangles
186: dt=0.9900, 53 negative triangles
187: dt=0.9900, 49 negative triangles
188: dt=0.9900, 51 negative triangles
189: dt=0.9405, 50 negative triangles
190: dt=0.9405, 51 negative triangles
191: dt=0.9405, 50 negative triangles
192: dt=0.9405, 52 negative triangles
193: dt=0.9405, 55 negative triangles
194: dt=0.9405, 48 negative triangles
195: dt=0.9405, 50 negative triangles
196: dt=0.9405, 45 negative triangles
197: dt=0.9405, 46 negative triangles
198: dt=0.9405, 47 negative triangles
199: dt=0.8935, 46 negative triangles
200: dt=0.8935, 49 negative triangles
201: dt=0.8935, 47 negative triangles
202: dt=0.8935, 48 negative triangles
203: dt=0.8935, 45 negative triangles
204: dt=0.8935, 45 negative triangles
205: dt=0.8935, 48 negative triangles
206: dt=0.8935, 53 negative triangles
207: dt=0.8935, 45 negative triangles
208: dt=0.8935, 40 negative triangles
209: dt=0.8935, 37 negative triangles
210: dt=0.8935, 43 negative triangles
211: dt=0.8935, 41 negative triangles
212: dt=0.8935, 36 negative triangles
213: dt=0.8935, 40 negative triangles
214: dt=0.8935, 34 negative triangles
215: dt=0.8935, 36 negative triangles
216: dt=0.8935, 31 negative triangles
217: dt=0.8935, 34 negative triangles
218: dt=0.8935, 31 negative triangles
219: dt=0.8935, 32 negative triangles
220: dt=0.8935, 28 negative triangles
221: dt=0.8935, 36 negative triangles
222: dt=0.8935, 28 negative triangles
223: dt=0.8935, 29 negative triangles
224: dt=0.8935, 31 negative triangles
225: dt=0.8935, 30 negative triangles
226: dt=0.8935, 28 negative triangles
227: dt=0.8935, 26 negative triangles
228: dt=0.8935, 26 negative triangles
229: dt=0.8935, 29 negative triangles
230: dt=0.8935, 26 negative triangles
231: dt=0.8935, 31 negative triangles
232: dt=0.8935, 24 negative triangles
233: dt=0.8935, 29 negative triangles
234: dt=0.8935, 23 negative triangles
235: dt=0.8935, 26 negative triangles
236: dt=0.8935, 25 negative triangles
237: dt=0.8935, 25 negative triangles
238: dt=0.8935, 24 negative triangles
239: dt=0.8935, 25 negative triangles
240: dt=0.8935, 25 negative triangles
241: dt=0.8935, 22 negative triangles
242: dt=0.8935, 21 negative triangles
243: dt=0.8935, 20 negative triangles
244: dt=0.8935, 20 negative triangles
245: dt=0.8935, 21 negative triangles
246: dt=0.8935, 21 negative triangles
247: dt=0.8935, 16 negative triangles
248: dt=0.8935, 15 negative triangles
249: dt=0.8935, 14 negative triangles
250: dt=0.8935, 14 negative triangles
251: dt=0.8935, 15 negative triangles
252: dt=0.8935, 14 negative triangles
253: dt=0.8935, 16 negative triangles
254: dt=0.8935, 11 negative triangles
255: dt=0.8935, 8 negative triangles
256: dt=0.8935, 9 negative triangles
257: dt=0.8935, 11 negative triangles
258: dt=0.8935, 8 negative triangles
259: dt=0.8935, 4 negative triangles
260: dt=0.8935, 9 negative triangles
261: dt=0.8935, 6 negative triangles
262: dt=0.8935, 1 negative triangles
263: dt=0.8935, 3 negative triangles
264: dt=0.8935, 6 negative triangles
265: dt=0.8935, 3 negative triangles
266: dt=0.8935, 2 negative triangles
267: dt=0.8935, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.15 hours
mris_sphere utimesec    4146.218678
mris_sphere stimesec    1.906710
mris_sphere ru_maxrss   342040
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   59647
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11984
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    146260
mris_sphere ru_nivcsw   336424
FSRUNTIME@ mris_sphere  1.1511 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0.260...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %21.03
pass 1: epoch 2 of 3 starting distance error %20.95
unfolding complete - removing small folds...
starting distance error %20.84
removing remaining folds...
final distance error %20.85
MRISunfold() return, current seed 1234
-01: dt=0.0000, 153 negative triangles
182: dt=0.9900, 153 negative triangles
183: dt=0.9900, 62 negative triangles
184: dt=0.9900, 56 negative triangles
185: dt=0.9900, 47 negative triangles
186: dt=0.9900, 38 negative triangles
187: dt=0.9900, 22 negative triangles
188: dt=0.9900, 26 negative triangles
189: dt=0.9900, 18 negative triangles
190: dt=0.9900, 14 negative triangles
191: dt=0.9900, 14 negative triangles
192: dt=0.9900, 10 negative triangles
193: dt=0.9900, 5 negative triangles
194: dt=0.9900, 6 negative triangles
195: dt=0.9900, 2 negative triangles
196: dt=0.9900, 4 negative triangles
197: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.19 hours
mris_sphere utimesec    4366.126247
mris_sphere stimesec    2.052687
mris_sphere ru_maxrss   343968
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   60143
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11944
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    153565
mris_sphere ru_nivcsw   335969
FSRUNTIME@ mris_sphere  1.1875 hours 1 threads
PIDs (4896 4899) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 02:11:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 

#--------------------------------------------
#@# Surf Reg rh Sun Oct  8 02:11:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 14093 of (14093 14096) to complete...
Waiting for PID 14096 of (14093 14096) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 5.543
curvature mean = 0.031, std = 0.821
curvature mean = 0.027, std = 0.847
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 383989.3, tmin=1.2675
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 294729.3, tmin=2.5469
  d=16.00 min @ (0.00, 0.00, -4.00) sse = 292404.6, tmin=3.8502
  d=8.00 min @ (-2.00, -2.00, 2.00) sse = 283110.1, tmin=5.1563
  d=4.00 min @ (1.00, 1.00, 0.00) sse = 280358.2, tmin=6.4835
  d=2.00 min @ (-0.50, 0.00, 0.50) sse = 280248.6, tmin=7.8081
  d=1.00 min @ (0.25, 0.00, -0.25) sse = 280138.8, tmin=9.1256
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 280123.6, tmin=10.4508
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  10.45 min
curvature mean = -0.002, std = 0.822
curvature mean = 0.011, std = 0.941
curvature mean = -0.008, std = 0.830
curvature mean = 0.005, std = 0.976
curvature mean = -0.013, std = 0.829
curvature mean = 0.001, std = 0.991
2 Reading smoothwm
curvature mean = -0.027, std = 0.302
curvature mean = 0.037, std = 0.242
curvature mean = 0.078, std = 0.312
curvature mean = 0.033, std = 0.299
curvature mean = 0.041, std = 0.500
curvature mean = 0.032, std = 0.326
curvature mean = 0.023, std = 0.651
curvature mean = 0.031, std = 0.337
curvature mean = 0.008, std = 0.768
MRISregister() return, current seed 0
-01: dt=0.0000, 42 negative triangles
121: dt=0.9900, 42 negative triangles
expanding nbhd size to 1
122: dt=0.9900, 44 negative triangles
123: dt=0.9900, 31 negative triangles
124: dt=0.9900, 28 negative triangles
125: dt=0.9900, 27 negative triangles
126: dt=0.9900, 24 negative triangles
127: dt=0.9900, 24 negative triangles
128: dt=0.9900, 23 negative triangles
129: dt=0.9900, 18 negative triangles
130: dt=0.9900, 15 negative triangles
131: dt=0.9900, 13 negative triangles
132: dt=0.9900, 10 negative triangles
133: dt=0.9900, 8 negative triangles
134: dt=0.9900, 5 negative triangles
135: dt=0.9900, 7 negative triangles
136: dt=0.9900, 5 negative triangles
137: dt=0.9900, 4 negative triangles
138: dt=0.9900, 2 negative triangles
139: dt=0.9900, 5 negative triangles
140: dt=0.9900, 2 negative triangles
141: dt=0.9900, 3 negative triangles
142: dt=0.9900, 1 negative triangles
143: dt=0.9900, 2 negative triangles
144: dt=0.9900, 2 negative triangles
145: dt=0.9900, 3 negative triangles
146: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.95 hours
mris_register utimesec    7053.110764
mris_register stimesec    6.157063
mris_register ru_maxrss   300272
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   42735
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  11968
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    489475
mris_register ru_nivcsw   311055
FSRUNTIME@ mris_register  1.9482 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 5.522
curvature mean = 0.006, std = 0.807
curvature mean = 0.026, std = 0.842
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 300970.4, tmin=2.5411
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 285925.0, tmin=3.8351
  d=8.00 min @ (0.00, 2.00, 0.00) sse = 269794.5, tmin=5.1428
  d=2.00 min @ (0.00, 0.00, 0.50) sse = 269689.9, tmin=7.7801
  d=1.00 min @ (0.00, 0.00, -0.25) sse = 269529.5, tmin=9.0822
  d=0.50 min @ (0.12, -0.12, 0.12) sse = 269468.5, tmin=10.3905
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  10.39 min
curvature mean = -0.014, std = 0.810
curvature mean = 0.011, std = 0.936
curvature mean = -0.021, std = 0.814
curvature mean = 0.005, std = 0.973
curvature mean = -0.023, std = 0.813
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.025, std = 0.304
curvature mean = 0.030, std = 0.235
curvature mean = 0.067, std = 0.310
curvature mean = 0.025, std = 0.293
curvature mean = 0.033, std = 0.492
curvature mean = 0.024, std = 0.320
curvature mean = 0.018, std = 0.640
curvature mean = 0.024, std = 0.331
curvature mean = 0.006, std = 0.757
MRISregister() return, current seed 0
-01: dt=0.0000, 57 negative triangles
124: dt=0.9900, 57 negative triangles
expanding nbhd size to 1
125: dt=0.9900, 77 negative triangles
126: dt=0.9900, 66 negative triangles
127: dt=0.9900, 52 negative triangles
128: dt=0.9900, 56 negative triangles
129: dt=0.9900, 46 negative triangles
130: dt=0.9900, 48 negative triangles
131: dt=0.9900, 42 negative triangles
132: dt=0.9900, 47 negative triangles
133: dt=0.9900, 41 negative triangles
134: dt=0.9900, 41 negative triangles
135: dt=0.9900, 35 negative triangles
136: dt=0.9900, 38 negative triangles
137: dt=0.9900, 35 negative triangles
138: dt=0.9900, 39 negative triangles
139: dt=0.9900, 36 negative triangles
140: dt=0.9900, 36 negative triangles
141: dt=0.9900, 35 negative triangles
142: dt=0.9900, 35 negative triangles
143: dt=0.9900, 31 negative triangles
144: dt=0.9900, 34 negative triangles
145: dt=0.9900, 27 negative triangles
146: dt=0.9900, 27 negative triangles
147: dt=0.9900, 24 negative triangles
148: dt=0.9900, 27 negative triangles
149: dt=0.9900, 22 negative triangles
150: dt=0.9900, 20 negative triangles
151: dt=0.9900, 23 negative triangles
152: dt=0.9900, 21 negative triangles
153: dt=0.9900, 20 negative triangles
154: dt=0.9900, 22 negative triangles
155: dt=0.9900, 22 negative triangles
156: dt=0.9900, 17 negative triangles
157: dt=0.9900, 15 negative triangles
158: dt=0.9900, 16 negative triangles
159: dt=0.9900, 16 negative triangles
160: dt=0.9900, 10 negative triangles
161: dt=0.9900, 12 negative triangles
162: dt=0.9900, 10 negative triangles
163: dt=0.9900, 8 negative triangles
164: dt=0.9900, 6 negative triangles
165: dt=0.9900, 6 negative triangles
166: dt=0.9900, 9 negative triangles
167: dt=0.9900, 5 negative triangles
168: dt=0.9900, 8 negative triangles
169: dt=0.9900, 6 negative triangles
170: dt=0.9900, 3 negative triangles
171: dt=0.9900, 4 negative triangles
172: dt=0.9900, 2 negative triangles
173: dt=0.9900, 1 negative triangles
174: dt=0.9900, 1 negative triangles
175: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.93 hours
mris_register utimesec    6928.507706
mris_register stimesec    6.060078
mris_register ru_maxrss   303524
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   43457
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  12008
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    475628
mris_register ru_nivcsw   313832
FSRUNTIME@ mris_register  1.9258 hours 1 threads
PIDs (14093 14096) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 04:08:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 04:08:06 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

Waiting for PID 18578 of (18578 18581) to complete...
Waiting for PID 18581 of (18578 18581) 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 (18578 18581) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 04:08:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

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

#--------------------------------------------
#@# AvgCurv rh Sun Oct  8 04:08:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 18624 of (18624 18627) to complete...
Waiting for PID 18627 of (18624 18627) 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 (18624 18627) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 04:08:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 

#-----------------------------------------
#@# Cortical Parc rh Sun Oct  8 04:08:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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 18671 of (18671 18674) to complete...
Waiting for PID 18674 of (18671 18674) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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...
2255 labels changed using aseg
relabeling using gibbs priors...
000:   3561 changed, 168718 examined...
001:    843 changed, 14833 examined...
002:    215 changed, 4529 examined...
003:     81 changed, 1269 examined...
004:     38 changed, 499 examined...
005:     10 changed, 215 examined...
006:      4 changed, 62 examined...
007:      1 changed, 27 examined...
008:      0 changed, 10 examined...
239 labels changed using aseg
000: 134 total segments, 89 labels (445 vertices) changed
001: 45 total segments, 6 labels (27 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 15 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2894 vertices marked for relabeling...
2894 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 18 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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...
1895 labels changed using aseg
relabeling using gibbs priors...
000:   3261 changed, 169365 examined...
001:    781 changed, 13898 examined...
002:    197 changed, 4392 examined...
003:     79 changed, 1178 examined...
004:     26 changed, 470 examined...
005:     14 changed, 163 examined...
006:      6 changed, 80 examined...
007:      3 changed, 31 examined...
008:      1 changed, 17 examined...
009:      0 changed, 7 examined...
172 labels changed using aseg
000: 108 total segments, 71 labels (454 vertices) changed
001: 38 total segments, 1 labels (1 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1977 vertices marked for relabeling...
1977 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 18 seconds.
PIDs (18671 18674) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 04:08:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050270 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 04:08:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050270 rh 

Waiting for PID 18731 of (18731 18734) to complete...
Waiting for PID 18734 of (18731 18734) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050270 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-6.0.0/0050270/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
37890 bright wm thresholded.
1716 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.orig...
computing class statistics...
border white:    313918 voxels (1.87%)
border gray      354793 voxels (2.11%)
WM (101.0): 100.8 +- 7.7 [70.0 --> 110.0]
GM (77.0) : 76.0 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 64.1 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 74.0 (was 85)
setting MAX_CSF to 54.2 (was 40)
setting MAX_GRAY to 98.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-5.2,    GM=74+-7.0
mean inside = 96.7, mean outside = 79.4
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.25 (0.02-->6.24) (max @ vno 168368 --> 168374)
face area 0.32 +- 0.15 (0.00-->5.68)
mean absolute distance = 0.65 +- 0.87
2995 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
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
deleting segment 5 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 15 points - only 0.00% unknown
deleting segment 11 with 9 points - only 0.00% unknown
deleting segment 12 with 50 points - only 0.00% unknown
deleting segment 13 with 29 points - only 0.00% unknown
deleting segment 14 with 107 points - only 0.00% unknown
deleting segment 15 with 5 points - only 0.00% unknown
deleting segment 16 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 17 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 18 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 19 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 20 with 1 points - only 0.00% unknown
mean border=84.0, 94 (94) missing vertices, mean dist 0.4 [1.1 (%12.0)->0.6 (%88.0))]
%63 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.03-->5.02) (max @ vno 168368 --> 168374)
face area 0.32 +- 0.15 (0.00-->5.69)
mean absolute distance = 0.34 +- 0.54
3491 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2677446.5, rms=7.605
001: dt: 0.5000, sse=1414190.4, rms=4.372 (42.512%)
002: dt: 0.5000, sse=1087089.5, rms=3.010 (31.142%)
003: dt: 0.5000, sse=1036161.6, rms=2.790 (7.318%)
004: dt: 0.5000, sse=1006913.1, rms=2.583 (7.433%)
rms = 2.74, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=902091.8, rms=1.859 (28.033%)
006: dt: 0.2500, sse=871774.9, rms=1.520 (18.231%)
007: dt: 0.2500, sse=860422.0, rms=1.431 (5.812%)
rms = 1.40, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=858461.2, rms=1.404 (1.902%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=856181.1, rms=1.375 (2.111%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 9 points - only 0.00% unknown
deleting segment 7 with 24 points - only 0.00% unknown
deleting segment 8 with 108 points - only 0.00% unknown
deleting segment 9 with 21 points - only 0.00% unknown
deleting segment 10 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
mean border=87.1, 91 (32) missing vertices, mean dist -0.2 [0.4 (%74.5)->0.2 (%25.5))]
%77 local maxima, %19 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.25 (0.07-->5.13) (max @ vno 168368 --> 168374)
face area 0.35 +- 0.16 (0.00-->6.61)
mean absolute distance = 0.24 +- 0.34
4477 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1437002.2, rms=4.241
010: dt: 0.5000, sse=1077011.4, rms=2.584 (39.073%)
011: dt: 0.5000, sse=1053223.9, rms=2.503 (3.115%)
rms = 2.52, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=957490.1, rms=1.774 (29.142%)
013: dt: 0.2500, sse=908178.6, rms=1.299 (26.759%)
014: dt: 0.2500, sse=899469.9, rms=1.192 (8.210%)
rms = 1.17, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=898227.5, rms=1.165 (2.283%)
rms = 1.14, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=895898.6, rms=1.135 (2.561%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 1 with 3 points - only 0.00% unknown
deleting segment 2 with 14 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 24 points - only 0.00% unknown
deleting segment 5 with 110 points - only 0.00% unknown
deleting segment 6 with 23 points - only 0.00% unknown
deleting segment 7 with 19 points - only 0.00% unknown
deleting segment 9 with 14 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
deleting segment 12 with 18 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=89.5, 109 (21) missing vertices, mean dist -0.1 [0.3 (%75.4)->0.2 (%24.6))]
%87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.25 (0.08-->5.24) (max @ vno 168368 --> 168374)
face area 0.33 +- 0.16 (0.00-->6.77)
mean absolute distance = 0.18 +- 0.28
4042 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1132454.2, rms=3.092
017: dt: 0.5000, sse=995596.3, rms=2.221 (28.182%)
rms = 2.45, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=902171.1, rms=1.516 (31.757%)
019: dt: 0.2500, sse=869467.2, rms=1.156 (23.719%)
020: dt: 0.2500, sse=861976.2, rms=1.064 (7.957%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=861858.9, rms=1.062 (0.234%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=859301.0, rms=1.034 (2.605%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 6 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
deleting segment 2 with 17 points - only 0.00% unknown
deleting segment 3 with 6 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 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 24 points - only 0.00% unknown
deleting segment 8 with 108 points - only 0.00% unknown
deleting segment 9 with 53 points - only 0.00% unknown
deleting segment 10 with 14 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=90.2, 116 (19) missing vertices, mean dist -0.0 [0.2 (%58.2)->0.2 (%41.8))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=870442.4, rms=1.388
rms = 1.35, time step reduction 1 of 3 to 0.250...
023: dt: 0.5000, sse=870164.9, rms=1.354 (2.447%)
024: dt: 0.2500, sse=840888.6, rms=1.000 (26.155%)
025: dt: 0.2500, sse=831447.5, rms=0.828 (17.213%)
rms = 0.88, time step reduction 2 of 3 to 0.125...
rms = 0.81, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=828321.1, rms=0.809 (2.282%)
positioning took 0.6 minutes
generating cortex label...
14 non-cortical segments detected
only using segment with 7607 vertices
erasing segment 0 (vno[0] = 51744)
erasing segment 2 (vno[0] = 101546)
erasing segment 3 (vno[0] = 111829)
erasing segment 4 (vno[0] = 114647)
erasing segment 5 (vno[0] = 122108)
erasing segment 6 (vno[0] = 123117)
erasing segment 7 (vno[0] = 124344)
erasing segment 8 (vno[0] = 125542)
erasing segment 9 (vno[0] = 126775)
erasing segment 10 (vno[0] = 128778)
erasing segment 11 (vno[0] = 128801)
erasing segment 12 (vno[0] = 129818)
erasing segment 13 (vno[0] = 142409)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.area
vertex spacing 0.88 +- 0.25 (0.02-->5.28) (max @ vno 168368 --> 168374)
face area 0.33 +- 0.16 (0.00-->6.82)
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 118 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=62.1, 98 (98) missing vertices, mean dist 1.7 [0.2 (%0.0)->2.7 (%100.0))]
%15 local maxima, %45 large gradients and %37 min vals, 276 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=27720954.0, rms=28.769
001: dt: 0.0500, sse=24474662.0, rms=26.980 (6.221%)
002: dt: 0.0500, sse=22169636.0, rms=25.633 (4.992%)
003: dt: 0.0500, sse=20424222.0, rms=24.564 (4.170%)
004: dt: 0.0500, sse=19027324.0, rms=23.673 (3.625%)
005: dt: 0.0500, sse=17864556.0, rms=22.906 (3.243%)
006: dt: 0.0500, sse=16868582.0, rms=22.227 (2.963%)
007: dt: 0.0500, sse=15997209.0, rms=21.616 (2.750%)
008: dt: 0.0500, sse=15221281.0, rms=21.057 (2.587%)
009: dt: 0.0500, sse=14522080.0, rms=20.540 (2.456%)
010: dt: 0.0500, sse=13885686.0, rms=20.057 (2.348%)
positioning took 1.2 minutes
mean border=61.9, 82 (45) missing vertices, mean dist 1.4 [0.2 (%0.1)->2.2 (%99.9))]
%16 local maxima, %45 large gradients and %36 min vals, 252 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=14673370.0, rms=20.655
011: dt: 0.0500, sse=14085994.0, rms=20.212 (2.141%)
012: dt: 0.0500, sse=13545319.0, rms=19.797 (2.057%)
013: dt: 0.0500, sse=13044991.0, rms=19.404 (1.984%)
014: dt: 0.0500, sse=12581279.0, rms=19.033 (1.914%)
015: dt: 0.0500, sse=12149715.0, rms=18.680 (1.851%)
016: dt: 0.0500, sse=11747376.0, rms=18.346 (1.791%)
017: dt: 0.0500, sse=11371865.0, rms=18.028 (1.733%)
018: dt: 0.0500, sse=11020867.0, rms=17.725 (1.678%)
019: dt: 0.0500, sse=10692029.0, rms=17.437 (1.626%)
020: dt: 0.0500, sse=10382860.0, rms=17.162 (1.580%)
positioning took 1.2 minutes
mean border=61.8, 98 (33) missing vertices, mean dist 1.2 [0.1 (%0.6)->1.8 (%99.4))]
%16 local maxima, %45 large gradients and %35 min vals, 249 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.05
000: dt: 0.0000, sse=10489315.0, rms=17.264
021: dt: 0.0500, sse=10192117.0, rms=16.996 (1.549%)
022: dt: 0.0500, sse=9911748.0, rms=16.740 (1.508%)
023: dt: 0.0500, sse=9645613.0, rms=16.493 (1.476%)
024: dt: 0.0500, sse=9393593.0, rms=16.256 (1.440%)
025: dt: 0.0500, sse=9154239.0, rms=16.027 (1.408%)
026: dt: 0.0500, sse=8926287.0, rms=15.806 (1.380%)
027: dt: 0.0500, sse=8707307.0, rms=15.590 (1.363%)
028: dt: 0.0500, sse=8495000.0, rms=15.378 (1.359%)
029: dt: 0.0500, sse=8288886.0, rms=15.170 (1.356%)
030: dt: 0.0500, sse=8088699.0, rms=14.964 (1.354%)
positioning took 1.2 minutes
mean border=61.7, 114 (27) missing vertices, mean dist 1.0 [0.1 (%5.9)->1.6 (%94.1))]
%16 local maxima, %45 large gradients and %35 min vals, 212 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=8187318.5, rms=15.066
031: dt: 0.5000, sse=6695270.0, rms=13.449 (10.735%)
032: dt: 0.5000, sse=5491757.0, rms=11.981 (10.914%)
033: dt: 0.5000, sse=4445505.5, rms=10.543 (12.007%)
034: dt: 0.5000, sse=3570336.5, rms=9.163 (13.086%)
035: dt: 0.5000, sse=2880254.2, rms=7.908 (13.696%)
036: dt: 0.5000, sse=2363039.5, rms=6.815 (13.825%)
037: dt: 0.5000, sse=1995728.6, rms=5.921 (13.110%)
038: dt: 0.5000, sse=1763234.6, rms=5.274 (10.931%)
039: dt: 0.5000, sse=1624085.8, rms=4.848 (8.073%)
040: dt: 0.5000, sse=1548849.6, rms=4.600 (5.128%)
041: dt: 0.5000, sse=1503822.0, rms=4.446 (3.343%)
042: dt: 0.5000, sse=1479987.9, rms=4.359 (1.960%)
043: dt: 0.5000, sse=1463305.2, rms=4.300 (1.339%)
rms = 4.27, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1456950.8, rms=4.275 (0.596%)
045: dt: 0.2500, sse=1303858.2, rms=3.615 (15.434%)
046: dt: 0.2500, sse=1263600.4, rms=3.435 (4.972%)
rms = 3.43, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1263523.4, rms=3.429 (0.176%)
048: dt: 0.1250, sse=1242607.6, rms=3.327 (2.983%)
rms = 3.31, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1239843.6, rms=3.314 (0.399%)
positioning took 2.9 minutes
mean border=60.5, 2197 (7) missing vertices, mean dist 0.1 [0.2 (%46.4)->0.4 (%53.6))]
%30 local maxima, %34 large gradients and %31 min vals, 137 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=1586794.9, rms=3.982
050: dt: 0.5000, sse=1533934.1, rms=3.784 (4.959%)
rms = 3.79, time step reduction 1 of 3 to 0.250...
051: dt: 0.2500, sse=1391046.9, rms=3.110 (17.831%)
052: dt: 0.2500, sse=1341306.0, rms=2.843 (8.580%)
053: dt: 0.2500, sse=1326315.4, rms=2.758 (2.998%)
rms = 2.73, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1320372.9, rms=2.727 (1.115%)
055: dt: 0.1250, sse=1299527.1, rms=2.595 (4.820%)
rms = 2.57, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1295360.0, rms=2.572 (0.907%)
positioning took 1.4 minutes
mean border=59.6, 2481 (6) missing vertices, mean dist 0.1 [0.1 (%44.2)->0.3 (%55.8))]
%45 local maxima, %20 large gradients and %30 min vals, 127 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=1365117.0, rms=2.988
rms = 3.43, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1319224.2, rms=2.730 (8.613%)
058: dt: 0.2500, sse=1304764.2, rms=2.650 (2.955%)
rms = 2.65, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1302876.5, rms=2.647 (0.084%)
060: dt: 0.1250, sse=1289086.2, rms=2.559 (3.328%)
rms = 2.55, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1286421.0, rms=2.545 (0.538%)
positioning took 1.1 minutes
mean border=59.0, 4675 (6) missing vertices, mean dist 0.0 [0.2 (%46.1)->0.2 (%53.9))]
%49 local maxima, %16 large gradients and %29 min vals, 108 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-6.0.0/0050270/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1309995.0, rms=2.680
rms = 3.08, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1291408.8, rms=2.564 (4.301%)
rms = 2.52, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1281146.0, rms=2.516 (1.893%)
064: dt: 0.1250, sse=1273529.8, rms=2.463 (2.082%)
rms = 2.43, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1268109.0, rms=2.434 (1.188%)
positioning took 1.0 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.area.pial
vertex spacing 0.98 +- 0.41 (0.05-->8.10) (max @ vno 115591 --> 114498)
face area 0.38 +- 0.29 (0.00-->8.24)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 168718 vertices processed
25000 of 168718 vertices processed
50000 of 168718 vertices processed
75000 of 168718 vertices processed
100000 of 168718 vertices processed
125000 of 168718 vertices processed
150000 of 168718 vertices processed
0 of 168718 vertices processed
25000 of 168718 vertices processed
50000 of 168718 vertices processed
75000 of 168718 vertices processed
100000 of 168718 vertices processed
125000 of 168718 vertices processed
150000 of 168718 vertices processed
thickness calculation complete, 306:343 truncations.
42375 vertices at 0 distance
125705 vertices at 1 distance
100326 vertices at 2 distance
39098 vertices at 3 distance
12039 vertices at 4 distance
3785 vertices at 5 distance
1245 vertices at 6 distance
457 vertices at 7 distance
185 vertices at 8 distance
65 vertices at 9 distance
49 vertices at 10 distance
23 vertices at 11 distance
39 vertices at 12 distance
20 vertices at 13 distance
19 vertices at 14 distance
18 vertices at 15 distance
19 vertices at 16 distance
5 vertices at 17 distance
3 vertices at 18 distance
4 vertices at 19 distance
3 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.thickness
positioning took 18.3 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050270 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-6.0.0/0050270/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
37890 bright wm thresholded.
1716 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.orig...
computing class statistics...
border white:    313918 voxels (1.87%)
border gray      354793 voxels (2.11%)
WM (101.0): 100.8 +- 7.7 [70.0 --> 110.0]
GM (77.0) : 76.0 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 65.1 (was 70)
setting MAX_BORDER_WHITE to 113.7 (was 105)
setting MIN_BORDER_WHITE to 75.0 (was 85)
setting MAX_CSF to 55.2 (was 40)
setting MAX_GRAY to 98.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 65.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.4 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106+-5.2,    GM=75+-6.1
mean inside = 96.9, mean outside = 79.9
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.25 (0.06-->7.62) (max @ vno 74319 --> 76800)
face area 0.32 +- 0.16 (0.00-->11.51)
mean absolute distance = 0.64 +- 0.86
2849 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 69 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
deleting segment 3 with 10 points - only 0.00% unknown
deleting segment 4 with 57 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 1 points - only 0.00% unknown
deleting segment 8 with 13 points - only 0.00% unknown
deleting segment 9 with 40 points - only 0.00% unknown
deleting segment 10 with 15 points - only 0.00% unknown
mean border=84.6, 125 (125) missing vertices, mean dist 0.4 [1.1 (%12.1)->0.6 (%87.9))]
%64 local maxima, %33 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.25 (0.12-->7.86) (max @ vno 76800 --> 74319)
face area 0.32 +- 0.16 (0.00-->10.90)
mean absolute distance = 0.33 +- 0.52
3144 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2599274.2, rms=7.413
001: dt: 0.5000, sse=1387995.9, rms=4.260 (42.541%)
002: dt: 0.5000, sse=1070078.4, rms=2.927 (31.292%)
003: dt: 0.5000, sse=1039492.9, rms=2.735 (6.555%)
004: dt: 0.5000, sse=994721.6, rms=2.538 (7.216%)
rms = 2.71, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=900961.2, rms=1.827 (28.000%)
006: dt: 0.2500, sse=869315.8, rms=1.501 (17.842%)
007: dt: 0.2500, sse=869876.6, rms=1.417 (5.586%)
rms = 1.40, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=860063.3, rms=1.396 (1.518%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=857533.2, rms=1.366 (2.125%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 61 points - only 0.00% unknown
deleting segment 1 with 12 points - only 0.00% unknown
deleting segment 2 with 28 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 3 with 4 points - only 0.00% unknown
deleting segment 4 with 8 points - only 0.00% unknown
deleting segment 6 with 14 points - only 0.00% unknown
deleting segment 7 with 5 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 19 points - only 0.00% unknown
mean border=87.6, 81 (17) missing vertices, mean dist -0.2 [0.4 (%74.6)->0.2 (%25.4))]
%78 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 0.89 +- 0.25 (0.08-->7.93) (max @ vno 76800 --> 74319)
face area 0.35 +- 0.17 (0.00-->12.58)
mean absolute distance = 0.23 +- 0.33
4226 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1423801.6, rms=4.178
010: dt: 0.5000, sse=1067323.5, rms=2.559 (38.756%)
011: dt: 0.5000, sse=1055834.4, rms=2.441 (4.615%)
rms = 2.46, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=955270.3, rms=1.741 (28.659%)
013: dt: 0.2500, sse=911390.4, rms=1.286 (26.150%)
014: dt: 0.2500, sse=905196.6, rms=1.192 (7.286%)
rms = 1.17, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=900249.3, rms=1.173 (1.655%)
rms = 1.15, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=900017.1, rms=1.145 (2.347%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 60 points - only 0.00% unknown
deleting segment 1 with 9 points - only 0.00% unknown
deleting segment 2 with 43 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 8 points - only 0.00% unknown
deleting segment 6 with 29 points - only 0.00% unknown
deleting segment 7 with 5 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 20 points - only 0.00% unknown
mean border=89.9, 80 (10) missing vertices, mean dist -0.1 [0.2 (%75.4)->0.2 (%24.6))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.25 (0.09-->8.02) (max @ vno 76800 --> 74319)
face area 0.33 +- 0.17 (0.00-->12.74)
mean absolute distance = 0.18 +- 0.26
3739 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1119131.4, rms=3.000
017: dt: 0.5000, sse=986250.4, rms=2.179 (27.367%)
rms = 2.38, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=903754.7, rms=1.515 (30.499%)
019: dt: 0.2500, sse=872481.6, rms=1.170 (22.760%)
020: dt: 0.2500, sse=870150.6, rms=1.081 (7.616%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=865703.4, rms=1.074 (0.590%)
rms = 1.05, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=862857.2, rms=1.048 (2.490%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 51 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 6 points - only 0.00% unknown
deleting segment 3 with 43 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 14 points - only 0.00% unknown
deleting segment 6 with 44 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 20 points - only 0.00% unknown
mean border=90.7, 84 (9) missing vertices, mean dist -0.0 [0.2 (%58.1)->0.2 (%41.9))]
%91 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=871540.3, rms=1.361
rms = 1.33, time step reduction 1 of 3 to 0.250...
023: dt: 0.5000, sse=873708.6, rms=1.326 (2.582%)
024: dt: 0.2500, sse=846895.1, rms=1.008 (23.987%)
025: dt: 0.2500, sse=832908.9, rms=0.848 (15.799%)
rms = 0.90, time step reduction 2 of 3 to 0.125...
rms = 0.83, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=830948.7, rms=0.829 (2.314%)
positioning took 0.6 minutes
generating cortex label...
13 non-cortical segments detected
only using segment with 7249 vertices
erasing segment 1 (vno[0] = 98586)
erasing segment 2 (vno[0] = 100882)
erasing segment 3 (vno[0] = 109193)
erasing segment 4 (vno[0] = 122344)
erasing segment 5 (vno[0] = 122362)
erasing segment 6 (vno[0] = 123443)
erasing segment 7 (vno[0] = 125573)
erasing segment 8 (vno[0] = 126701)
erasing segment 9 (vno[0] = 127639)
erasing segment 10 (vno[0] = 128657)
erasing segment 11 (vno[0] = 129424)
erasing segment 12 (vno[0] = 147048)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.area
vertex spacing 0.88 +- 0.25 (0.05-->8.06) (max @ vno 74319 --> 76800)
face area 0.33 +- 0.16 (0.00-->12.74)
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 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 17 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 1 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=63.2, 130 (130) missing vertices, mean dist 1.6 [0.7 (%0.0)->2.7 (%100.0))]
%15 local maxima, %43 large gradients and %39 min vals, 246 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=26639968.0, rms=28.111
001: dt: 0.0500, sse=23473988.0, rms=26.333 (6.325%)
002: dt: 0.0500, sse=21238360.0, rms=25.001 (5.057%)
003: dt: 0.0500, sse=19546484.0, rms=23.944 (4.228%)
004: dt: 0.0500, sse=18195156.0, rms=23.065 (3.672%)
005: dt: 0.0500, sse=17071674.0, rms=22.308 (3.284%)
006: dt: 0.0500, sse=16110721.0, rms=21.639 (2.999%)
007: dt: 0.0500, sse=15271087.0, rms=21.037 (2.782%)
008: dt: 0.0500, sse=14525589.0, rms=20.487 (2.611%)
009: dt: 0.0500, sse=13854695.0, rms=19.980 (2.476%)
010: dt: 0.0500, sse=13245184.0, rms=19.507 (2.365%)
positioning took 1.2 minutes
mean border=63.0, 68 (39) missing vertices, mean dist 1.3 [0.2 (%0.1)->2.2 (%99.9))]
%16 local maxima, %43 large gradients and %38 min vals, 216 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=14014188.0, rms=20.102
011: dt: 0.0500, sse=13453394.0, rms=19.670 (2.146%)
012: dt: 0.0500, sse=12937329.0, rms=19.265 (2.062%)
013: dt: 0.0500, sse=12460525.0, rms=18.882 (1.986%)
014: dt: 0.0500, sse=12018380.0, rms=18.521 (1.916%)
015: dt: 0.0500, sse=11608002.0, rms=18.178 (1.849%)
016: dt: 0.0500, sse=11225935.0, rms=17.853 (1.786%)
017: dt: 0.0500, sse=10869725.0, rms=17.545 (1.727%)
018: dt: 0.0500, sse=10537379.0, rms=17.253 (1.668%)
019: dt: 0.0500, sse=10226225.0, rms=16.974 (1.615%)
020: dt: 0.0500, sse=9934455.0, rms=16.708 (1.565%)
positioning took 1.2 minutes
mean border=62.9, 60 (26) missing vertices, mean dist 1.1 [0.1 (%0.6)->1.9 (%99.4))]
%16 local maxima, %43 large gradients and %38 min vals, 200 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=10056901.0, rms=16.827
021: dt: 0.0500, sse=9776317.0, rms=16.569 (1.531%)
022: dt: 0.0500, sse=9512487.0, rms=16.323 (1.485%)
023: dt: 0.0500, sse=9262526.0, rms=16.087 (1.450%)
024: dt: 0.0500, sse=9026396.0, rms=15.860 (1.410%)
025: dt: 0.0500, sse=8802888.0, rms=15.642 (1.374%)
026: dt: 0.0500, sse=8590342.0, rms=15.432 (1.343%)
027: dt: 0.0500, sse=8386701.5, rms=15.228 (1.323%)
028: dt: 0.0500, sse=8189950.5, rms=15.028 (1.313%)
029: dt: 0.0500, sse=7999224.5, rms=14.831 (1.307%)
030: dt: 0.0500, sse=7814125.5, rms=14.638 (1.303%)
positioning took 1.2 minutes
mean border=62.8, 75 (16) missing vertices, mean dist 0.9 [0.1 (%5.9)->1.6 (%94.1))]
%16 local maxima, %43 large gradients and %37 min vals, 192 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=7901313.0, rms=14.730
031: dt: 0.5000, sse=6512271.0, rms=13.200 (10.384%)
032: dt: 0.5000, sse=5389616.0, rms=11.814 (10.499%)
033: dt: 0.5000, sse=4418194.0, rms=10.470 (11.376%)
034: dt: 0.5000, sse=3598338.8, rms=9.180 (12.327%)
035: dt: 0.5000, sse=2915329.2, rms=7.948 (13.414%)
036: dt: 0.5000, sse=2387982.5, rms=6.845 (13.885%)
037: dt: 0.5000, sse=1995045.6, rms=5.894 (13.881%)
038: dt: 0.5000, sse=1753887.9, rms=5.223 (11.395%)
039: dt: 0.5000, sse=1612215.6, rms=4.788 (8.332%)
040: dt: 0.5000, sse=1545863.8, rms=4.565 (4.657%)
041: dt: 0.5000, sse=1502328.4, rms=4.417 (3.238%)
042: dt: 0.5000, sse=1485713.4, rms=4.353 (1.438%)
043: dt: 0.5000, sse=1470264.5, rms=4.300 (1.231%)
rms = 4.28, time step reduction 1 of 3 to 0.250...
044: dt: 0.5000, sse=1465486.4, rms=4.279 (0.487%)
045: dt: 0.2500, sse=1318934.9, rms=3.653 (14.631%)
046: dt: 0.2500, sse=1279344.4, rms=3.479 (4.758%)
rms = 3.48, time step reduction 2 of 3 to 0.125...
047: dt: 0.2500, sse=1280202.1, rms=3.478 (0.041%)
048: dt: 0.1250, sse=1258750.6, rms=3.374 (2.972%)
rms = 3.36, time step reduction 3 of 3 to 0.062...
049: dt: 0.1250, sse=1256650.1, rms=3.364 (0.304%)
positioning took 2.9 minutes
mean border=61.6, 2631 (6) missing vertices, mean dist 0.1 [0.2 (%45.9)->0.4 (%54.1))]
%30 local maxima, %32 large gradients and %33 min vals, 125 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=1611276.6, rms=4.052
050: dt: 0.5000, sse=1549398.6, rms=3.823 (5.642%)
rms = 3.81, time step reduction 1 of 3 to 0.250...
051: dt: 0.5000, sse=1536445.9, rms=3.809 (0.371%)
052: dt: 0.2500, sse=1378468.9, rms=3.022 (20.651%)
053: dt: 0.2500, sse=1340405.0, rms=2.821 (6.654%)
rms = 2.79, time step reduction 2 of 3 to 0.125...
054: dt: 0.2500, sse=1335614.2, rms=2.791 (1.058%)
055: dt: 0.1250, sse=1307829.5, rms=2.623 (6.034%)
rms = 2.60, time step reduction 3 of 3 to 0.062...
056: dt: 0.1250, sse=1303681.9, rms=2.599 (0.908%)
positioning took 1.4 minutes
mean border=60.7, 2859 (5) missing vertices, mean dist 0.1 [0.2 (%44.3)->0.3 (%55.7))]
%44 local maxima, %19 large gradients and %32 min vals, 128 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=1377324.9, rms=3.021
rms = 3.44, time step reduction 1 of 3 to 0.250...
057: dt: 0.2500, sse=1328668.1, rms=2.753 (8.884%)
058: dt: 0.2500, sse=1315560.1, rms=2.680 (2.665%)
rms = 2.67, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1311955.9, rms=2.668 (0.441%)
060: dt: 0.1250, sse=1297568.1, rms=2.577 (3.386%)
rms = 2.56, time step reduction 3 of 3 to 0.062...
061: dt: 0.1250, sse=1294300.2, rms=2.560 (0.661%)
positioning took 1.2 minutes
mean border=60.1, 5218 (5) missing vertices, mean dist 0.0 [0.2 (%46.0)->0.2 (%54.0))]
%48 local maxima, %15 large gradients and %31 min vals, 120 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-6.0.0/0050270/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1317417.9, rms=2.692
rms = 3.07, time step reduction 1 of 3 to 0.250...
062: dt: 0.2500, sse=1298582.4, rms=2.577 (4.273%)
rms = 2.54, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1290189.5, rms=2.540 (1.463%)
064: dt: 0.1250, sse=1281583.6, rms=2.483 (2.247%)
rms = 2.46, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1276800.4, rms=2.458 (0.989%)
positioning took 1.0 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.area.pial
vertex spacing 0.98 +- 0.41 (0.06-->9.19) (max @ vno 76800 --> 74319)
face area 0.38 +- 0.29 (0.00-->14.05)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 169365 vertices processed
25000 of 169365 vertices processed
50000 of 169365 vertices processed
75000 of 169365 vertices processed
100000 of 169365 vertices processed
125000 of 169365 vertices processed
150000 of 169365 vertices processed
0 of 169365 vertices processed
25000 of 169365 vertices processed
50000 of 169365 vertices processed
75000 of 169365 vertices processed
100000 of 169365 vertices processed
125000 of 169365 vertices processed
150000 of 169365 vertices processed
thickness calculation complete, 222:440 truncations.
40305 vertices at 0 distance
125099 vertices at 1 distance
102843 vertices at 2 distance
40167 vertices at 3 distance
12502 vertices at 4 distance
4069 vertices at 5 distance
1317 vertices at 6 distance
464 vertices at 7 distance
174 vertices at 8 distance
97 vertices at 9 distance
59 vertices at 10 distance
34 vertices at 11 distance
29 vertices at 12 distance
26 vertices at 13 distance
19 vertices at 14 distance
8 vertices at 15 distance
9 vertices at 16 distance
1 vertices at 17 distance
4 vertices at 18 distance
6 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.thickness
positioning took 18.4 minutes
PIDs (18731 18734) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 04:26:56 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/lh.cortex.label
Total face volume 293115
Total vertex volume 289540 (mask=0)
#@# 0050270 lh 289540
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 04:27:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/rh.cortex.label
Total face volume 295494
Total vertex volume 291646 (mask=0)
#@# 0050270 rh 291646
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 04:27:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 

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 = 144
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/ribbon.mgz
mris_volmask took 22.63 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 04:49:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 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 0050270 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 04:49:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 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 0050270 rh pial 

Waiting for PID 20791 of (20791 20794 20797 20800) to complete...
Waiting for PID 20794 of (20791 20794 20797 20800) to complete...
Waiting for PID 20797 of (20791 20794 20797 20800) to complete...
Waiting for PID 20800 of (20791 20794 20797 20800) 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 0050270 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 293115
Total vertex volume 289540 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1131    805   1728  2.314 0.306     0.073     0.008        4     0.4  bankssts
 1386    902   3046  2.762 0.806     0.133     0.026       23     1.4  caudalanteriorcingulate
 4987   3298   9891  2.699 0.491     0.119     0.023       51     4.7  caudalmiddlefrontal
 3107   1851   3687  1.869 0.444     0.140     0.033       48     4.2  cuneus
 1043    736   2500  2.795 0.847     0.134     0.061       18     2.9  entorhinal
 6098   4008  11965  2.605 0.642     0.141     0.034       96     8.2  fusiform
 7083   4658  12762  2.534 0.473     0.126     0.026       94     7.5  inferiorparietal
 6327   4179  12581  2.538 0.659     0.121     0.029       95     7.6  inferiortemporal
 2024   1246   3428  2.519 0.910     0.124     0.029       30     2.0  isthmuscingulate
 9549   6084  14086  2.094 0.509     0.143     0.033      140    12.8  lateraloccipital
 4921   3229   9177  2.695 0.551     0.136     0.035       73     7.3  lateralorbitofrontal
 5527   3517   7532  2.050 0.587     0.139     0.035       81     8.0  lingual
 3281   2150   5751  2.443 0.629     0.132     0.036       61     4.7  medialorbitofrontal
 4887   3320  10407  2.756 0.568     0.134     0.029       79     6.1  middletemporal
 1261    840   2882  3.125 0.757     0.105     0.024       12     1.1  parahippocampal
 2682   1571   4163  2.481 0.497     0.103     0.027       25     3.1  paracentral
 3600   2423   7393  2.760 0.448     0.116     0.021       41     3.1  parsopercularis
 1162    754   2722  2.661 0.590     0.139     0.033       20     1.5  parsorbitalis
 2710   1801   5008  2.523 0.443     0.119     0.023       34     2.6  parstriangularis
 2472   1616   2704  1.802 0.435     0.117     0.026       22     2.5  pericalcarine
 7450   4618  10722  2.091 0.573     0.112     0.022       76     6.9  postcentral
 2553   1671   4528  2.474 0.807     0.133     0.025       43     2.6  posteriorcingulate
 8467   5091  14718  2.713 0.515     0.103     0.022       71     7.5  precentral
 7347   4850  12478  2.480 0.435     0.128     0.025       99     7.3  precuneus
 1846   1227   3683  2.757 0.732     0.137     0.033       34     2.4  rostralanteriorcingulate
11323   7562  20196  2.397 0.488     0.136     0.030      177    13.8  rostralmiddlefrontal
14841   9826  30481  2.847 0.508     0.126     0.026      192    15.9  superiorfrontal
10455   6685  16363  2.234 0.432     0.128     0.024      139    10.3  superiorparietal
 6105   4059  13082  2.878 0.607     0.113     0.020       64     4.9  superiortemporal
 8381   5471  15222  2.609 0.401     0.129     0.024      120     7.8  supramarginal
  355    234    908  2.836 0.473     0.179     0.076       13     1.0  frontalpole
  768    538   2774  3.591 0.514     0.163     0.043       15     1.4  temporalpole
  990    529   1619  2.559 0.433     0.089     0.019        8     0.7  transversetemporal
 4762   3123   9322  3.058 0.792     0.133     0.052       82     7.2  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 0050270 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 293115
Total vertex volume 289540 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1131    706   1728  2.314 0.306     0.106     0.021       23     0.9  bankssts
 1386   1226   3046  2.762 0.806     0.145     0.031       24     1.9  caudalanteriorcingulate
 4987   3899   9891  2.699 0.491     0.130     0.029      222     6.5  caudalmiddlefrontal
 3107   2155   3687  1.869 0.444     0.132     0.031       38     4.2  cuneus
 1043    994   2500  2.795 0.847     0.167     0.043       18     1.9  entorhinal
 6098   4984  11965  2.605 0.642     0.144     0.035       88     9.8  fusiform
 7083   5408  12762  2.534 0.473     0.137     0.030       89     9.6  inferiorparietal
 6327   5530  12581  2.538 0.659     0.142     0.031       85     8.7  inferiortemporal
 2024   1480   3428  2.519 0.910     0.137     0.035       27     2.9  isthmuscingulate
 9549   7450  14086  2.094 0.509     0.145     0.034      115    14.4  lateraloccipital
 4921   3591   9177  2.695 0.551     0.142     0.036       86     7.6  lateralorbitofrontal
 5527   4086   7532  2.050 0.587     0.137     0.035       80     8.6  lingual
 3281   2590   5751  2.443 0.629     0.142     0.037       45     5.3  medialorbitofrontal
 4887   4150  10407  2.756 0.568     0.147     0.033       88     7.1  middletemporal
 1261   1074   2882  3.125 0.757     0.158     0.039       18     2.4  parahippocampal
 2682   1782   4163  2.481 0.497     0.106     0.022       30     2.7  paracentral
 3600   2953   7393  2.760 0.448     0.133     0.027       43     4.2  parsopercularis
 1162   1207   2722  2.661 0.590     0.184     0.039       18     2.2  parsorbitalis
 2710   2188   5008  2.523 0.443     0.142     0.028       31     3.6  parstriangularis
 2472   1446   2704  1.802 0.435     0.109     0.027       35     2.7  pericalcarine
 7450   5647  10722  2.091 0.573     0.126     0.025       70     8.6  postcentral
 2553   1936   4528  2.474 0.807     0.140     0.032       54     3.8  posteriorcingulate
 8467   5812  14718  2.713 0.515     0.106     0.024      100     8.4  precentral
 7347   5226  12478  2.480 0.435     0.129     0.030      109     9.5  precuneus
 1846   1438   3683  2.757 0.732     0.142     0.039       29     3.0  rostralanteriorcingulate
11323   9024  20196  2.397 0.488     0.146     0.031      149    15.7  rostralmiddlefrontal
14841  11395  30481  2.847 0.508     0.133     0.030      221    19.4  superiorfrontal
10455   7884  16363  2.234 0.432     0.133     0.027      134    11.9  superiorparietal
 6105   4894  13082  2.878 0.607     0.134     0.030       84     8.1  superiortemporal
 8381   6195  15222  2.609 0.401     0.132     0.031      111    11.0  supramarginal
  355    381    908  2.836 0.473     0.194     0.042        5     0.7  frontalpole
  768    977   2774  3.591 0.514     0.184     0.035        9     1.3  temporalpole
  990    780   1619  2.559 0.433     0.126     0.028        8     1.2  transversetemporal
 4762   2884   9322  3.058 0.792     0.140     0.049      136     9.6  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 0050270 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 295494
Total vertex volume 291646 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1145    784   1960  2.613 0.402     0.099     0.016        8     0.8  bankssts
 1898   1220   4042  2.908 0.474     0.112     0.017       24     1.2  caudalanteriorcingulate
 4096   2680   8122  2.772 0.449     0.113     0.022       41     3.5  caudalmiddlefrontal
 3136   2010   4250  1.933 0.405     0.147     0.034       48     4.5  cuneus
  800    553   2305  3.136 0.660     0.124     0.035        8     1.3  entorhinal
 5790   3871  11974  2.697 0.565     0.130     0.027       79     6.3  fusiform
 8549   5584  14992  2.488 0.449     0.127     0.025      118     8.5  inferiorparietal
 6527   4273  13699  2.786 0.617     0.125     0.030      102     7.8  inferiortemporal
 1770   1067   2960  2.451 0.793     0.125     0.032       30     2.0  isthmuscingulate
 8989   5774  12938  2.051 0.504     0.143     0.031      137    11.3  lateraloccipital
 5096   3317   9343  2.679 0.594     0.141     0.045       95     9.8  lateralorbitofrontal
 5578   3559   7980  2.074 0.564     0.142     0.035       82     8.4  lingual
 3727   2431   6356  2.364 0.702     0.135     0.040       72     6.0  medialorbitofrontal
 5577   3804  12411  2.864 0.560     0.124     0.024       79     5.6  middletemporal
 1076    704   2341  2.906 0.741     0.100     0.016        9     0.6  parahippocampal
 2977   1737   4623  2.483 0.532     0.106     0.022       25     2.6  paracentral
 2570   1681   5272  2.845 0.477     0.121     0.024       32     2.4  parsopercularis
 1687   1080   3532  2.748 0.515     0.148     0.035       31     2.0  parsorbitalis
 3158   2118   6122  2.637 0.450     0.137     0.030       52     3.9  parstriangularis
 2457   1639   2957  2.008 0.578     0.143     0.036       33     3.8  pericalcarine
 7193   4397  10186  2.092 0.620     0.105     0.020       75     5.9  postcentral
 2500   1623   4452  2.520 0.787     0.129     0.026       40     2.7  posteriorcingulate
 9381   5643  16398  2.695 0.521     0.107     0.022       80     8.8  precentral
 7584   4982  12386  2.395 0.480     0.135     0.029      118     8.3  precuneus
 1505    948   2919  2.794 0.456     0.125     0.028       22     1.9  rostralanteriorcingulate
12459   8302  22025  2.433 0.476     0.141     0.031      202    16.3  rostralmiddlefrontal
12971   8537  26911  2.838 0.508     0.128     0.029      167    15.4  superiorfrontal
10668   6856  16394  2.190 0.414     0.117     0.020      125     8.8  superiorparietal
 6043   3953  12837  2.941 0.538     0.108     0.020       61     5.0  superiortemporal
 8354   5482  15562  2.626 0.477     0.126     0.023      114     7.7  supramarginal
  705    418   1209  2.397 0.622     0.177     0.065       17     2.0  frontalpole
  748    564   2702  3.465 0.745     0.152     0.033       11     1.1  temporalpole
  671    401   1064  2.331 0.463     0.110     0.033        7     0.8  transversetemporal
 4213   2728   8254  3.030 0.712     0.132     0.040       66     6.9  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 0050270 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 295494
Total vertex volume 291646 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1145    671   1960  2.613 0.402     0.104     0.025       17     1.3  bankssts
 1898   1605   4042  2.908 0.474     0.149     0.036       77     2.3  caudalanteriorcingulate
 4096   3134   8122  2.772 0.449     0.120     0.025       50     4.5  caudalmiddlefrontal
 3136   2468   4250  1.933 0.405     0.146     0.034       46     4.7  cuneus
  800    852   2305  3.136 0.660     0.191     0.043       16     1.6  entorhinal
 5790   4898  11974  2.697 0.565     0.144     0.033       79     8.7  fusiform
 8549   6375  14992  2.488 0.449     0.138     0.031      110    11.8  inferiorparietal
 6527   5367  13699  2.786 0.617     0.139     0.036       81     9.8  inferiortemporal
 1770   1315   2960  2.451 0.793     0.152     0.041       50     3.2  isthmuscingulate
 8989   6885  12938  2.051 0.504     0.139     0.031      113    12.2  lateraloccipital
 5096   3686   9343  2.679 0.594     0.144     0.040      108     8.6  lateralorbitofrontal
 5578   4254   7980  2.074 0.564     0.139     0.034       84     8.8  lingual
 3727   2986   6356  2.364 0.702     0.155     0.040       69     6.5  medialorbitofrontal
 5577   4804  12411  2.864 0.560     0.133     0.028       53     7.0  middletemporal
 1076    906   2341  2.906 0.741     0.142     0.034       13     1.9  parahippocampal
 2977   1981   4623  2.483 0.532     0.115     0.027       32     3.4  paracentral
 2570   2010   5272  2.845 0.477     0.132     0.030       32     3.5  parsopercularis
 1687   1538   3532  2.748 0.515     0.162     0.038       22     2.7  parsorbitalis
 3158   2625   6122  2.637 0.450     0.156     0.032       44     4.8  parstriangularis
 2457   1460   2957  2.008 0.578     0.116     0.033       29     3.4  pericalcarine
 7193   5377  10186  2.092 0.620     0.119     0.022       59     7.3  postcentral
 2500   1818   4452  2.520 0.787     0.136     0.039       70     4.4  posteriorcingulate
 9381   6427  16398  2.695 0.521     0.105     0.022       92     9.3  precentral
 7584   5357  12386  2.395 0.480     0.134     0.033      112    10.3  precuneus
 1505   1193   2919  2.794 0.456     0.156     0.047       35     3.2  rostralanteriorcingulate
12459   9704  22025  2.433 0.476     0.147     0.034      167    18.6  rostralmiddlefrontal
12971  10175  26911  2.838 0.508     0.138     0.034      207    19.2  superiorfrontal
10668   7977  16394  2.190 0.414     0.123     0.024      123    10.1  superiorparietal
 6043   4762  12837  2.941 0.538     0.127     0.029       68     7.5  superiortemporal
 8354   6263  15562  2.626 0.477     0.131     0.029      116    10.4  supramarginal
  705    567   1209  2.397 0.622     0.171     0.047       11     1.5  frontalpole
  748    934   2702  3.465 0.745     0.196     0.041       14     1.4  temporalpole
  671    530   1064  2.331 0.463     0.136     0.035        5     1.1  transversetemporal
 4213   2610   8254  3.030 0.712     0.146     0.048      120     8.1  insula
PIDs (20791 20794 20797 20800) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 04:51:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 

#-----------------------------------------
#@# Cortical Parc 2 rh Sun Oct  8 04:51:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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 20913 of (20913 20916) to complete...
Waiting for PID 20916 of (20913 20916) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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...
8 labels changed using aseg
relabeling using gibbs priors...
000:  10953 changed, 168718 examined...
001:   2686 changed, 42257 examined...
002:    848 changed, 13868 examined...
003:    375 changed, 4776 examined...
004:    187 changed, 2121 examined...
005:     80 changed, 1054 examined...
006:     25 changed, 442 examined...
007:     14 changed, 155 examined...
008:     14 changed, 84 examined...
009:      3 changed, 77 examined...
010:      1 changed, 26 examined...
011:      1 changed, 8 examined...
012:      0 changed, 6 examined...
0 labels changed using aseg
000: 308 total segments, 219 labels (2543 vertices) changed
001: 98 total segments, 10 labels (57 vertices) changed
002: 88 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 48 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1902 vertices marked for relabeling...
1902 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 24 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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...
19 labels changed using aseg
relabeling using gibbs priors...
000:  11358 changed, 169365 examined...
001:   2694 changed, 44107 examined...
002:    820 changed, 13982 examined...
003:    322 changed, 4553 examined...
004:    168 changed, 1813 examined...
005:     93 changed, 932 examined...
006:     50 changed, 547 examined...
007:     27 changed, 298 examined...
008:     11 changed, 159 examined...
009:      8 changed, 64 examined...
010:      6 changed, 36 examined...
011:      6 changed, 30 examined...
012:      4 changed, 32 examined...
013:      2 changed, 21 examined...
014:      1 changed, 14 examined...
015:      0 changed, 6 examined...
8 labels changed using aseg
000: 335 total segments, 245 labels (3795 vertices) changed
001: 115 total segments, 25 labels (115 vertices) changed
002: 92 total segments, 2 labels (43 vertices) changed
003: 90 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 58 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1483 vertices marked for relabeling...
1483 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 25 seconds.
PIDs (20913 20916) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 04:51:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 04:51:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 rh white 

Waiting for PID 20968 of (20968 20971) to complete...
Waiting for PID 20971 of (20968 20971) 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 0050270 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 293115
Total vertex volume 289540 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1593   1026   2662  2.310 0.591     0.132     0.034       26     2.1  G&S_frontomargin
 2171   1431   3704  2.277 0.514     0.150     0.035       33     2.9  G&S_occipital_inf
 1863   1007   3207  2.557 0.531     0.106     0.022       19     1.6  G&S_paracentral
 1753   1188   3391  2.537 0.419     0.138     0.027       28     1.9  G&S_subcentral
 1153    764   2172  2.394 0.585     0.163     0.050       30     2.5  G&S_transv_frontopol
 3355   2278   6191  2.726 0.538     0.123     0.026       43     3.5  G&S_cingul-Ant
 1943   1332   4064  2.992 0.490     0.104     0.022       17     1.6  G&S_cingul-Mid-Ant
 1843   1237   3414  2.746 0.413     0.124     0.023       23     1.7  G&S_cingul-Mid-Post
  888    558   2353  3.150 0.446     0.159     0.038       19     1.2  G_cingul-Post-dorsal
  408    210    789  2.957 0.688     0.118     0.036        7     0.5  G_cingul-Post-ventral
 2837   1619   3364  1.826 0.432     0.144     0.036       48     4.4  G_cuneus
 1964   1240   4871  2.961 0.366     0.127     0.025       33     2.0  G_front_inf-Opercular
  654    401   1544  2.861 0.446     0.153     0.042       15     1.1  G_front_inf-Orbital
 1569   1007   3433  2.648 0.431     0.127     0.026       26     1.6  G_front_inf-Triangul
 6799   4389  15221  2.690 0.534     0.143     0.031      127     8.6  G_front_middle
10113   6424  22829  2.913 0.540     0.137     0.033      175    13.7  G_front_sup
 1133    701   2274  3.155 0.683     0.155     0.102       32     2.9  G_Ins_lg&S_cent_ins
 1023    635   2921  3.633 0.700     0.132     0.036       17     1.4  G_insular_short
 2853   1732   5613  2.495 0.512     0.139     0.029       54     3.3  G_occipital_middle
 1522    974   2327  2.078 0.475     0.143     0.035       23     1.9  G_occipital_sup
 2576   1627   5302  2.712 0.513     0.150     0.035       50     3.6  G_oc-temp_lat-fusifor
 3946   2379   5335  1.955 0.585     0.149     0.040       69     6.5  G_oc-temp_med-Lingual
 1943   1303   5036  3.014 0.821     0.133     0.048       33     4.1  G_oc-temp_med-Parahip
 3170   2034   7186  2.688 0.612     0.142     0.040       58     5.5  G_orbital
 2885   1825   5968  2.637 0.510     0.142     0.033       54     3.7  G_pariet_inf-Angular
 4399   2771   9104  2.681 0.408     0.135     0.026       83     4.5  G_pariet_inf-Supramar
 4395   2737   8037  2.364 0.422     0.135     0.026       73     4.7  G_parietal_sup
 2880   1594   4337  2.164 0.499     0.115     0.027       34     3.1  G_postcentral
 3263   1696   6460  2.939 0.464     0.095     0.022       28     2.9  G_precentral
 3647   2325   7285  2.524 0.411     0.136     0.027       65     3.8  G_precuneus
 1093    670   2219  2.419 0.642     0.141     0.041       24     2.0  G_rectus
 1093    729   1656  2.405 0.962     0.136     0.061       24     1.7  G_subcallosal
  975    505   1750  2.651 0.417     0.094     0.018       11     0.7  G_temp_sup-G_T_transv
 2073   1368   5662  3.021 0.631     0.148     0.030       36     2.4  G_temp_sup-Lateral
  738    516   2242  3.608 0.637     0.099     0.024        5     0.6  G_temp_sup-Plan_polar
 1022    697   2020  2.646 0.384     0.084     0.013        6     0.6  G_temp_sup-Plan_tempo
 3602   2333   8654  2.702 0.688     0.147     0.041       82     6.4  G_temporal_inf
 2577   1721   6794  2.947 0.498     0.145     0.034       57     3.9  G_temporal_middle
  363    263    494  2.243 0.479     0.134     0.018        4     0.3  Lat_Fis-ant-Horizont
  585    427    879  2.535 0.408     0.081     0.013        2     0.3  Lat_Fis-ant-Vertical
 1372    924   1872  2.577 0.364     0.115     0.022       10     1.2  Lat_Fis-post
 2679   1651   3558  1.906 0.481     0.156     0.041       47     4.5  Pole_occipital
 1858   1228   5481  3.243 0.798     0.148     0.049       32     3.7  Pole_temporal
 3149   2130   3760  2.035 0.648     0.120     0.023       32     2.9  S_calcarine
 3465   2337   3874  1.947 0.600     0.109     0.022       22     3.3  S_central
 1271    874   1891  2.358 0.409     0.103     0.017       10     0.9  S_cingul-Marginalis
  577    400    954  2.877 0.614     0.108     0.019        3     0.5  S_circular_insula_ant
 1662   1114   2702  2.903 0.492     0.089     0.012        9     0.8  S_circular_insula_inf
 2091   1391   3261  2.888 0.455     0.112     0.021       14     1.8  S_circular_insula_sup
 1623   1103   2393  2.299 0.439     0.092     0.013       11     0.9  S_collat_transv_ant
  757    508    791  1.817 0.361     0.140     0.030        7     1.1  S_collat_transv_post
 3281   2274   5118  2.366 0.413     0.113     0.021       27     2.8  S_front_inf
 1910   1317   2978  2.308 0.376     0.129     0.025       21     2.1  S_front_middle
 4106   2825   6458  2.481 0.386     0.109     0.020       31     3.3  S_front_sup
  208    149    312  2.469 0.504     0.142     0.023        2     0.2  S_interm_prim-Jensen
 4166   2760   5419  2.262 0.436     0.124     0.023       41     3.9  S_intrapariet&P_trans
 1162    791   1376  1.934 0.383     0.114     0.020        8     1.0  S_oc_middle&Lunatus
 1096    762   1381  2.007 0.326     0.114     0.019        7     0.9  S_oc_sup&transversal
  850    582   1149  2.289 0.348     0.121     0.024        7     0.8  S_occipital_ant
  955    649   1221  2.145 0.436     0.118     0.020        9     0.8  S_oc-temp_lat
 2390   1666   3936  2.552 0.580     0.115     0.022       19     2.0  S_oc-temp_med&Lingual
  679    473    914  2.320 0.385     0.136     0.027        5     0.9  S_orbital_lateral
  831    572   1096  2.394 0.560     0.106     0.017        5     0.5  S_orbital_med-olfact
 1678   1122   2879  2.655 0.476     0.131     0.031       22     1.9  S_orbital-H_Shaped
 3044   1987   4243  2.345 0.484     0.116     0.020       29     2.5  S_parieto_occipital
 1864   1157   1881  1.739 0.904     0.124     0.022       32     1.4  S_pericallosal
 3899   2613   5248  2.227 0.409     0.108     0.017       29     2.6  S_postcentral
 2364   1626   3759  2.574 0.420     0.104     0.017       17     1.6  S_precentral-inf-part
 1274    885   2096  2.653 0.389     0.103     0.018        7     0.9  S_precentral-sup-part
  597    428    820  2.352 0.619     0.138     0.020        6     0.6  S_suborbital
 1236    863   1785  2.411 0.366     0.121     0.024        8     1.3  S_subparietal
 2010   1408   2654  2.263 0.478     0.106     0.017       13     1.4  S_temporal_inf
 5664   3914   8876  2.463 0.428     0.102     0.017       41     4.2  S_temporal_sup
  463    333    641  2.470 0.404     0.109     0.014        3     0.3  S_temporal_transverse

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab 0050270 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 295494
Total vertex volume 291646 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1086    754   2016  2.408 0.587     0.156     0.036       22     1.7  G&S_frontomargin
 1527    980   2410  2.166 0.476     0.134     0.028       22     1.7  G&S_occipital_inf
 1847   1041   2959  2.343 0.501     0.109     0.021       18     1.6  G&S_paracentral
 1797   1148   3794  2.825 0.437     0.132     0.029       26     2.1  G&S_subcentral
 2017   1258   3648  2.379 0.601     0.162     0.048       47     4.3  G&S_transv_frontopol
 3835   2560   6908  2.650 0.524     0.125     0.026       49     4.2  G&S_cingul-Ant
 2258   1494   4495  2.836 0.464     0.106     0.017       20     1.6  G&S_cingul-Mid-Ant
 1903   1283   3678  2.784 0.468     0.114     0.022       19     1.7  G&S_cingul-Mid-Post
  773    439   1746  3.018 0.389     0.153     0.036       17     1.1  G_cingul-Post-dorsal
  414    228    963  2.881 0.618     0.141     0.051       11     0.7  G_cingul-Post-ventral
 3032   1874   3907  1.874 0.391     0.145     0.036       48     4.7  G_cuneus
 1816   1143   4680  3.043 0.394     0.119     0.025       29     1.7  G_front_inf-Opercular
  765    487   1745  2.757 0.502     0.153     0.034       19     1.1  G_front_inf-Orbital
 1181    761   2600  2.754 0.443     0.150     0.036       25     1.6  G_front_inf-Triangul
 6390   4018  14028  2.730 0.468     0.151     0.034      128     9.2  G_front_middle
 8724   5481  19934  2.930 0.522     0.135     0.033      137    11.7  G_front_sup
 1102    682   2222  3.037 0.997     0.145     0.054       24     2.3  G_Ins_lg&S_cent_ins
  911    560   2524  3.302 0.598     0.136     0.038       16     1.3  G_insular_short
 3032   1872   6003  2.533 0.465     0.152     0.032       62     3.9  G_occipital_middle
 1779   1034   2577  2.038 0.501     0.126     0.027       24     1.9  G_occipital_sup
 2528   1590   5706  2.766 0.479     0.147     0.033       51     3.2  G_oc-temp_lat-fusifor
 3807   2320   5668  2.068 0.576     0.151     0.042       69     6.8  G_oc-temp_med-Lingual
 1565   1032   4320  3.183 0.700     0.118     0.029       15     1.8  G_oc-temp_med-Parahip
 3668   2343   8031  2.687 0.557     0.149     0.046       83     6.5  G_orbital
 3130   1944   6238  2.624 0.430     0.140     0.030       59     3.7  G_pariet_inf-Angular
 4731   3029   9987  2.755 0.463     0.136     0.027       81     4.8  G_pariet_inf-Supramar
 3641   2266   7005  2.396 0.373     0.128     0.025       61     3.7  G_parietal_sup
 2491   1345   3563  2.087 0.510     0.107     0.023       33     2.3  G_postcentral
 3837   1935   7677  2.933 0.449     0.094     0.021       31     3.4  G_precentral
 3529   2247   6412  2.380 0.519     0.141     0.030       69     4.1  G_precuneus
 1077    626   2064  2.393 0.755     0.153     0.061       32     2.6  G_rectus
  689    437    987  2.207 1.007     0.139     0.063       13     1.8  G_subcallosal
  647    385   1114  2.370 0.493     0.114     0.035        9     1.0  G_temp_sup-G_T_transv
 1909   1194   4988  3.201 0.465     0.125     0.025       30     1.8  G_temp_sup-Lateral
 1226    804   2826  3.088 0.785     0.120     0.048       21     2.8  G_temp_sup-Plan_polar
  790    557   1517  2.516 0.393     0.077     0.012        3     0.4  G_temp_sup-Plan_tempo
 3488   2153   8264  2.871 0.626     0.137     0.036       78     5.0  G_temporal_inf
 3271   2178   8468  2.977 0.529     0.140     0.030       68     3.9  G_temporal_middle
  361    232    556  2.726 0.465     0.085     0.013        2     0.2  Lat_Fis-ant-Horizont
  469    351    691  2.410 0.443     0.128     0.019        3     0.4  Lat_Fis-ant-Vertical
 1731   1163   2414  2.539 0.402     0.121     0.023       15     1.8  Lat_Fis-post
 3783   2353   5013  1.891 0.491     0.142     0.033       56     5.2  Pole_occipital
 1940   1361   6474  3.262 0.688     0.146     0.045       33     3.5  Pole_temporal
 2588   1813   3487  2.214 0.586     0.140     0.032       34     3.4  S_calcarine
 3257   2252   3548  1.871 0.569     0.112     0.021       23     3.0  S_central
 1588   1048   2269  2.288 0.407     0.114     0.022       16     1.3  S_cingul-Marginalis
  822    563   1249  2.901 0.476     0.103     0.017        4     0.6  S_circular_insula_ant
 1342    901   2187  3.003 0.521     0.098     0.014        8     0.8  S_circular_insula_inf
 1610   1073   2498  2.888 0.387     0.110     0.020       10     1.3  S_circular_insula_sup
 1657   1192   2847  2.700 0.484     0.089     0.010        7     0.7  S_collat_transv_ant
  709    482    689  1.688 0.315     0.143     0.027        7     0.9  S_collat_transv_post
 2635   1824   3908  2.411 0.384     0.124     0.025       27     2.6  S_front_inf
 3131   2198   4634  2.312 0.394     0.121     0.024       27     3.1  S_front_middle
 2835   1955   4672  2.573 0.412     0.099     0.019       17     2.2  S_front_sup
  431    303    796  2.720 0.432     0.124     0.018        3     0.4  S_interm_prim-Jensen
 5294   3592   6817  2.146 0.394     0.114     0.018       48     3.9  S_intrapariet&P_trans
 1074    762   1277  1.938 0.373     0.137     0.027       11     1.1  S_oc_middle&Lunatus
 1130    760   1312  1.904 0.313     0.107     0.014        8     0.7  S_oc_sup&transversal
  751    538   1025  2.179 0.523     0.138     0.023        8     0.7  S_occipital_ant
 1624   1114   2413  2.425 0.481     0.118     0.022       13     1.5  S_oc-temp_lat
 2053   1455   3232  2.498 0.529     0.107     0.016       13     1.5  S_oc-temp_med&Lingual
  818    570   1249  2.435 0.602     0.155     0.039       10     1.4  S_orbital_lateral
  910    616   1225  2.373 0.636     0.137     0.047       16     2.0  S_orbital_med-olfact
 1778   1190   3076  2.733 0.471     0.137     0.031       25     2.3  S_orbital-H_Shaped
 3162   2086   4463  2.338 0.440     0.128     0.025       36     3.1  S_parieto_occipital
 2171   1364   2564  2.124 0.872     0.117     0.024       34     1.9  S_pericallosal
 3189   2172   4216  2.099 0.393     0.095     0.014       22     1.9  S_postcentral
 2640   1722   4185  2.603 0.394     0.106     0.018       21     1.9  S_precentral-inf-part
 1529   1076   2351  2.568 0.381     0.101     0.015        8     1.0  S_precentral-sup-part
  518    360    794  2.464 0.553     0.133     0.021        6     0.5  S_suborbital
 1522   1054   2404  2.391 0.434     0.133     0.024       18     1.6  S_subparietal
 1788   1259   2794  2.601 0.554     0.120     0.020       12     1.7  S_temporal_inf
 6229   4264  10108  2.571 0.445     0.101     0.016       40     4.2  S_temporal_sup
  397    268    535  2.278 0.270     0.121     0.015        5     0.2  S_temporal_transverse
PIDs (20968 20971) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 04:52:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 lh ../surf/lh.sphere.reg /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 

#-----------------------------------------
#@# Cortical Parc 3 rh Sun Oct  8 04:52:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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 21093 of (21093 21096) to complete...
Waiting for PID 21096 of (21093 21096) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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...
1404 labels changed using aseg
relabeling using gibbs priors...
000:   2294 changed, 168718 examined...
001:    515 changed, 10634 examined...
002:    124 changed, 3005 examined...
003:     46 changed, 741 examined...
004:     24 changed, 299 examined...
005:     19 changed, 133 examined...
006:      4 changed, 100 examined...
007:      1 changed, 27 examined...
008:      0 changed, 7 examined...
63 labels changed using aseg
000: 55 total segments, 22 labels (186 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1630 vertices marked for relabeling...
1630 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 18 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050270 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...
1431 labels changed using aseg
relabeling using gibbs priors...
000:   2241 changed, 169365 examined...
001:    534 changed, 10546 examined...
002:    148 changed, 3042 examined...
003:     65 changed, 879 examined...
004:     28 changed, 378 examined...
005:     10 changed, 158 examined...
006:      9 changed, 67 examined...
007:      6 changed, 44 examined...
008:      8 changed, 37 examined...
009:      8 changed, 41 examined...
010:     10 changed, 39 examined...
011:      9 changed, 49 examined...
012:      9 changed, 39 examined...
013:      4 changed, 36 examined...
014:      3 changed, 28 examined...
015:      2 changed, 17 examined...
016:      1 changed, 12 examined...
017:      0 changed, 8 examined...
152 labels changed using aseg
000: 51 total segments, 18 labels (122 vertices) changed
001: 34 total segments, 1 labels (1 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 8 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1117 vertices marked for relabeling...
1117 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 19 seconds.
PIDs (21093 21096) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 04:53:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 04:53:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 rh white 

Waiting for PID 21147 of (21147 21150) to complete...
Waiting for PID 21150 of (21147 21150) 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 0050270 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 293115
Total vertex volume 289540 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 2517   1642   4994  2.755 0.782     0.116     0.022       33     2.2  caudalanteriorcingulate
 5212   3451  10377  2.700 0.495     0.120     0.022       54     4.7  caudalmiddlefrontal
 4164   2502   5102  1.937 0.462     0.134     0.030       60     5.2  cuneus
  939    659   2260  2.775 0.864     0.139     0.062       17     2.7  entorhinal
 5575   3673  10379  2.532 0.555     0.138     0.029       85     6.5  fusiform
 7073   4651  12634  2.531 0.475     0.129     0.026       95     7.7  inferiorparietal
 6450   4237  13608  2.604 0.744     0.125     0.035      102     9.2  inferiortemporal
 1996   1235   3435  2.542 0.907     0.125     0.029       30     2.0  isthmuscingulate
 9486   6066  14222  2.104 0.511     0.142     0.033      139    12.4  lateraloccipital
 5568   3635  10342  2.601 0.615     0.139     0.041       93     9.5  lateralorbitofrontal
 5691   3621   7626  2.024 0.579     0.142     0.036       84     8.5  lingual
 3032   2028   5222  2.321 0.708     0.140     0.047       69     4.9  medialorbitofrontal
 6455   4419  13100  2.681 0.543     0.125     0.025       91     7.2  middletemporal
 1300    865   2936  3.111 0.748     0.104     0.024       12     1.1  parahippocampal
 3142   1854   5100  2.556 0.513     0.106     0.027       31     3.5  paracentral
 3363   2260   6880  2.778 0.438     0.115     0.021       38     2.8  parsopercularis
 1157    765   2509  2.753 0.537     0.135     0.028       17     1.3  parsorbitalis
 3300   2214   6049  2.481 0.440     0.119     0.024       40     3.2  parstriangularis
 2457   1598   2686  1.805 0.432     0.118     0.026       22     2.6  pericalcarine
 8402   5246  12170  2.127 0.569     0.114     0.023       86     7.6  postcentral
 2554   1687   4670  2.567 0.721     0.137     0.027       44     2.7  posteriorcingulate
 8385   5037  14501  2.717 0.512     0.104     0.022       70     7.5  precentral
 7100   4693  12228  2.482 0.427     0.130     0.025       98     7.0  precuneus
 2568   1678   4677  2.730 0.695     0.134     0.031       41     3.0  rostralanteriorcingulate
 8119   5374  14858  2.441 0.481     0.134     0.027      119     9.3  rostralmiddlefrontal
15961  10629  32597  2.758 0.539     0.131     0.029      234    18.9  superiorfrontal
 8620   5513  13619  2.247 0.429     0.126     0.024      115     8.5  superiorparietal
 7847   5253  17251  2.904 0.652     0.115     0.028       92     7.2  superiortemporal
 7864   5116  14248  2.617 0.399     0.130     0.024      115     7.4  supramarginal
  971    514   1600  2.566 0.436     0.089     0.019        9     0.6  transversetemporal
 3625   2369   7660  3.258 0.634     0.126     0.030       48     4.4  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 0050270 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 295494
Total vertex volume 291646 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 2161   1397   4583  2.880 0.542     0.114     0.017       29     1.4  caudalanteriorcingulate
 4317   2840   8559  2.768 0.450     0.114     0.022       45     3.7  caudalmiddlefrontal
 3855   2443   5179  1.963 0.407     0.140     0.031       55     5.1  cuneus
  749    514   2114  3.134 0.665     0.120     0.031        7     1.0  entorhinal
 5189   3489  10373  2.653 0.535     0.129     0.024       70     5.1  fusiform
 8309   5438  14469  2.474 0.450     0.127     0.025      115     8.1  inferiorparietal
 7150   4669  15253  2.795 0.630     0.126     0.032      110     9.1  inferiortemporal
 1773   1065   2950  2.452 0.783     0.124     0.032       30     2.0  isthmuscingulate
 9157   5831  13075  2.039 0.501     0.143     0.031      140    11.3  lateraloccipital
 5642   3688  10626  2.638 0.613     0.147     0.048      117    11.3  lateralorbitofrontal
 5418   3492   7807  2.074 0.563     0.142     0.035       80     8.2  lingual
 2579   1650   4391  2.350 0.750     0.142     0.046       53     4.6  medialorbitofrontal
 6621   4534  14299  2.843 0.549     0.124     0.024       90     6.5  middletemporal
 1146    753   2483  2.896 0.748     0.100     0.016        9     0.7  parahippocampal
 3185   1855   5081  2.521 0.549     0.106     0.022       27     2.9  paracentral
 2944   1938   5957  2.806 0.470     0.123     0.025       37     2.7  parsopercularis
 1330    869   2578  2.609 0.520     0.129     0.026       21     1.4  parsorbitalis
 3148   2117   5971  2.652 0.482     0.136     0.031       47     3.9  parstriangularis
 2467   1606   2934  2.017 0.581     0.140     0.035       32     3.8  pericalcarine
 8002   4969  11557  2.121 0.621     0.108     0.020       84     6.7  postcentral
 2521   1648   4498  2.539 0.774     0.129     0.026       40     2.7  posteriorcingulate
 8968   5373  15821  2.714 0.514     0.107     0.022       77     8.3  precentral
 7721   5078  12789  2.397 0.474     0.136     0.029      122     8.5  precuneus
 1816   1170   3561  2.775 0.514     0.121     0.027       26     2.1  rostralanteriorcingulate
 9076   5976  16089  2.465 0.450     0.142     0.031      146    11.9  rostralmiddlefrontal
17282  11358  33939  2.697 0.558     0.132     0.031      247    22.4  superiorfrontal
 9007   5812  13947  2.203 0.413     0.118     0.021      107     7.7  superiorparietal
 7709   5116  17034  2.943 0.621     0.114     0.025       89     8.5  superiortemporal
 8043   5264  15056  2.629 0.472     0.125     0.023      110     7.4  supramarginal
  649    388   1041  2.359 0.472     0.112     0.033        7     0.8  transversetemporal
 3745   2435   7631  3.152 0.599     0.125     0.029       44     4.4  insula
PIDs (21147 21150) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 04:53:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 pctsurfcon --s 0050270 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 04:53:54 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts

 pctsurfcon --s 0050270 --rh-only 

Waiting for PID 21212 of (21212 21224) to complete...
Waiting for PID 21224 of (21212 21224) to complete...

 pctsurfcon --s 0050270 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts/pctsurfcon.log
Sun Oct  8 04:53:54 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-6.0.0/0050270/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-388 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-6.0.0/0050270/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21212/lh.wm.mgh --regheader 0050270 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 89455
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21212/lh.wm.mgh
Dim: 168718 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21212/lh.gm.mgh --projfrac 0.3 --regheader 0050270 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 110974
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21212/lh.gm.mgh
Dim: 168718 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21212/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21212/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.w-g.pct.mgh --annot 0050270 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/lh.w-g.pct.mgh --annot 0050270 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/lh.w-g.pct.mgh
Vertex Area is 0.650388 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 0050270 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/scripts/pctsurfcon.log
Sun Oct  8 04:53:54 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-6.0.0/0050270/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-388 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-6.0.0/0050270/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21224/rh.wm.mgh --regheader 0050270 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 89200
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21224/rh.wm.mgh
Dim: 169365 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21224/rh.gm.mgh --projfrac 0.3 --regheader 0050270 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 111583
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21224/rh.gm.mgh
Dim: 169365 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21224/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/tmp.pctsurfcon.21224/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.w-g.pct.mgh --annot 0050270 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.w-g.pct.mgh --annot 0050270 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.w-g.pct.mgh
Vertex Area is 0.649683 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 (21212 21224) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 04:54:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2361 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
2411 voxels changed to hypointensity...
4518 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 04:54:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270

 mri_aparc2aseg --s 0050270 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 

#-----------------------------------------
#@# AParc-to-ASeg a2009s Sun Oct  8 04:54:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270

 mri_aparc2aseg --s 0050270 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 

#-----------------------------------------
#@# AParc-to-ASeg DKTatlas Sun Oct  8 04:54:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270

 mri_aparc2aseg --s 0050270 --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 21394 of (21394 21397 21400) to complete...
Waiting for PID 21397 of (21394 21397 21400) to complete...
Waiting for PID 21400 of (21394 21397 21400) to complete...

 mri_aparc2aseg --s 0050270 --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 0050270
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/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-6.0.0/0050270/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 7.73
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 66
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 94
rescaling Left_Caudate from 75 --> 79
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 42
rescaling Fourth_Ventricle from 22 --> 27
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 66
rescaling Left_Amygdala from 56 --> 70
rescaling CSF from 32 --> 60
rescaling Left_Accumbens_area from 62 --> 72
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 81
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 92
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 79
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 51
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 576801
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 196 changed.
pass 2: 20 changed.
pass 3: 7 changed.
pass 4: 2 changed.
pass 5: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050270 --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 0050270
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/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-6.0.0/0050270/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 7.73
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 66
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 94
rescaling Left_Caudate from 75 --> 79
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 42
rescaling Fourth_Ventricle from 22 --> 27
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 66
rescaling Left_Amygdala from 56 --> 70
rescaling CSF from 32 --> 60
rescaling Left_Accumbens_area from 62 --> 72
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 81
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 92
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 79
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 51
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 576933
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 196 changed.
pass 2: 20 changed.
pass 3: 7 changed.
pass 4: 2 changed.
pass 5: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050270 --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 0050270
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/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-6.0.0/0050270/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 7.73
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 104
rescaling Left_Cerebral_Cortex from 61 --> 68
rescaling Left_Lateral_Ventricle from 13 --> 25
rescaling Left_Inf_Lat_Vent from 34 --> 32
rescaling Left_Cerebellum_White_Matter from 86 --> 90
rescaling Left_Cerebellum_Cortex from 60 --> 66
rescaling Left_Thalamus from 94 --> 101
rescaling Left_Thalamus_Proper from 84 --> 94
rescaling Left_Caudate from 75 --> 79
rescaling Left_Putamen from 80 --> 87
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 42
rescaling Fourth_Ventricle from 22 --> 27
rescaling Brain_Stem from 81 --> 85
rescaling Left_Hippocampus from 57 --> 66
rescaling Left_Amygdala from 56 --> 70
rescaling CSF from 32 --> 60
rescaling Left_Accumbens_area from 62 --> 72
rescaling Left_VentralDC from 87 --> 89
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 23
rescaling Right_Inf_Lat_Vent from 25 --> 28
rescaling Right_Cerebellum_White_Matter from 87 --> 91
rescaling Right_Cerebellum_Cortex from 59 --> 66
rescaling Right_Thalamus_Proper from 85 --> 89
rescaling Right_Caudate from 62 --> 81
rescaling Right_Putamen from 80 --> 81
rescaling Right_Pallidum from 97 --> 92
rescaling Right_Hippocampus from 53 --> 67
rescaling Right_Amygdala from 55 --> 67
rescaling Right_Accumbens_area from 65 --> 79
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 51
rescaling WM_hypointensities from 78 --> 76
rescaling non_WM_hypointensities from 40 --> 43
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 576933
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 196 changed.
pass 2: 20 changed.
pass 3: 7 changed.
pass 4: 2 changed.
pass 5: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (21394 21397 21400) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 05:03:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri

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

Sun Oct  8 05:03:32 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-6.0.0/0050270/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-388 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-6.0.0/0050270/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-388
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 05:03:32 CEST 2017 
Ended   at Sun Oct  8 05:03:39 CEST 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 05:03:39 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270

 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 0050270 


$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 0050270 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1778356 mm^3    (det: 1.095453 )
Computing euler number
orig.nofix lheno =  -56, rheno = -54
orig.nofix lhholes =   29, rhholes = 28
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
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 05:05:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270

 mri_aparc2aseg --s 0050270 --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 0050270
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-6.0.0/0050270/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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-6.0.0/0050270/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 7837 vertices from left hemi
Ripped 7767 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-6.0.0/0050270/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 = 1095453
Used brute-force search on 404 voxels
Fixing Parahip LH WM
  Found 11 clusters
     0 k 1.000000
     1 k 1844.000000
     2 k 1.000000
     3 k 1.000000
     4 k 2.000000
     5 k 2.000000
     6 k 2.000000
     7 k 7.000000
     8 k 4.000000
     9 k 1.000000
     10 k 1.000000
Fixing Parahip RH WM
  Found 11 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 2.000000
     3 k 1.000000
     4 k 6.000000
     5 k 1.000000
     6 k 2.000000
     7 k 1.000000
     8 k 3.000000
     9 k 18.000000
     10 k 1483.000000
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 0050270 --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 0050270 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-388
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1778356 mm^3    (det: 1.095453 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
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-6.0.0/0050270/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 05:16:02 CEST 2017

 mri_label2label --srcsubject fsaverage --srclabel /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/fsaverage/label/lh.BA1_exvivo.label --trgsubject 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22867 of (22867 22873 22879 22885 22891) to complete...
Waiting for PID 22873 of (22867 22873 22879 22885 22891) to complete...
Waiting for PID 22879 of (22867 22873 22879 22885 22891) to complete...
Waiting for PID 22885 of (22867 22873 22879 22885 22891) to complete...
Waiting for PID 22891 of (22867 22873 22879 22885 22891) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 610
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4739
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1093
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 9002
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 216
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4293
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 680
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6663
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 860
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6644
mri_label2label: Done

PIDs (22867 22873 22879 22885 22891) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 22942 of (22942 22948 22954 22959) to complete...
Waiting for PID 22948 of (22942 22948 22954 22959) to complete...
Waiting for PID 22954 of (22942 22948 22954 22959) to complete...
Waiting for PID 22959 of (22942 22948 22954 22959) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 370
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4440
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 2918
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 16507
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1118
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 5299
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1711
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 5133
mri_label2label: Done

PIDs (22942 22948 22954 22959) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 23011 of (23011 23017 23023 23029 23035) to complete...
Waiting for PID 23017 of (23011 23017 23023 23029 23035) to complete...
Waiting for PID 23023 of (23011 23017 23023 23029 23035) to complete...
Waiting for PID 23029 of (23011 23017 23023 23029 23035) to complete...
Waiting for PID 23035 of (23011 23017 23023 23029 23035) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 2250
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6891
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 4540
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 12654
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1034
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 3052
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 403
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1693
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 382
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1581
mri_label2label: Done

PIDs (23011 23017 23023 23029 23035) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 23137 of (23137 23143 23149 23155 23161) to complete...
Waiting for PID 23143 of (23137 23143 23149 23155 23161) to complete...
Waiting for PID 23149 of (23137 23143 23149 23155 23161) to complete...
Waiting for PID 23155 of (23137 23143 23149 23155 23161) to complete...
Waiting for PID 23161 of (23137 23143 23149 23155 23161) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 203
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1217
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 309
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2401
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 41
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1545
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 166
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2162
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 380
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2699
mri_label2label: Done

PIDs (23137 23143 23149 23155 23161) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 23216 of (23216 23222 23228 23233) to complete...
Waiting for PID 23222 of (23216 23222 23228 23233) to complete...
Waiting for PID 23228 of (23216 23222 23228 23233) to complete...
Waiting for PID 23233 of (23216 23222 23228 23233) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 144
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1693
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1133
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8168
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 483
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2395
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 630
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1781
mri_label2label: Done

PIDs (23216 23222 23228 23233) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 23281 of (23281 23287 23293 23299 23305) to complete...
Waiting for PID 23287 of (23281 23287 23293 23299 23305) to complete...
Waiting for PID 23293 of (23281 23287 23293 23299 23305) to complete...
Waiting for PID 23299 of (23281 23287 23293 23299 23305) to complete...
Waiting for PID 23305 of (23281 23287 23293 23299 23305) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1649
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 5054
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 1945
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 5279
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 262
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 775
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 140
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 610
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 168718
Number of reverse mapping hits = 184
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 634
mri_label2label: Done

PIDs (23281 23287 23293 23299 23305) completed and logs appended.

 mris_label2annot --s 0050270 --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-6.0.0/0050270/label
cmdline mris_label2annot --s 0050270 --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-388
machine  x86_64
user     ntraut

subject 0050270
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-6.0.0/0050270/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 115328 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050270 --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-6.0.0/0050270/label
cmdline mris_label2annot --s 0050270 --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-388
machine  x86_64
user     ntraut

subject 0050270
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-6.0.0/0050270/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 138284 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 293115
Total vertex volume 289540 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1412    747   2181  2.228 0.476     0.121     0.032       19     1.7  BA1_exvivo
 5066   3253   7876  2.308 0.450     0.112     0.020       51     3.9  BA2_exvivo
 1102    768   1040  1.780 0.376     0.146     0.031       11     1.3  BA3a_exvivo
 2715   1789   3857  1.893 0.623     0.115     0.021       28     2.5  BA3b_exvivo
 2025   1129   3358  2.711 0.543     0.104     0.029       18     2.6  BA4a_exvivo
 1464    886   2132  2.554 0.479     0.089     0.024        7     1.5  BA4p_exvivo
12335   7733  25941  2.906 0.494     0.113     0.023      132    11.8  BA6_exvivo
 3325   2196   6637  2.741 0.401     0.112     0.021       38     2.8  BA44_exvivo
 4326   2874   8219  2.531 0.489     0.119     0.025       52     4.4  BA45_exvivo
 4542   2840   5103  1.765 0.455     0.130     0.032       60     5.9  V1_exvivo
10236   6415  13538  1.977 0.523     0.146     0.036      154    15.1  V2_exvivo
 2846   1829   4610  2.351 0.443     0.130     0.026       38     3.0  MT_exvivo
  901    598   2144  2.800 0.785     0.127     0.062       18     2.7  perirhinal_exvivo
 1095    759   2763  3.075 0.863     0.131     0.031       16     1.3  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 0050270 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 293115
Total vertex volume 289540 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
  998    474   1447  2.224 0.379     0.114     0.032       13     1.3  BA1_exvivo
 1941   1201   2957  2.255 0.465     0.102     0.018       17     1.4  BA2_exvivo
  904    637    828  1.752 0.377     0.151     0.033       10     1.2  BA3a_exvivo
 1575   1029   1602  1.503 0.340     0.098     0.017       10     1.2  BA3b_exvivo
 2052   1105   3333  2.762 0.515     0.093     0.022       13     2.1  BA4a_exvivo
 1156    742   1672  2.476 0.462     0.101     0.026        7     1.3  BA4p_exvivo
 6332   3801  12961  2.940 0.443     0.108     0.023       57     5.6  BA6_exvivo
 2132   1410   4496  2.805 0.408     0.114     0.021       26     1.7  BA44_exvivo
 1723   1154   3738  2.614 0.470     0.120     0.025       24     1.7  BA45_exvivo
 4794   3006   5467  1.766 0.459     0.129     0.032       62     6.3  V1_exvivo
 5050   3148   5970  1.828 0.465     0.154     0.040       81     8.4  V2_exvivo
  750    489   1447  2.439 0.394     0.138     0.027       12     0.8  MT_exvivo
  429    300   1075  2.860 0.676     0.087     0.031        4     0.6  perirhinal_exvivo
  598    423   1436  3.156 0.877     0.125     0.025        6     0.6  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 05:19:41 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 23434 of (23434 23440 23446 23452 23456) to complete...
Waiting for PID 23440 of (23434 23440 23446 23452 23456) to complete...
Waiting for PID 23446 of (23434 23440 23446 23452 23456) to complete...
Waiting for PID 23452 of (23434 23440 23446 23452 23456) to complete...
Waiting for PID 23456 of (23434 23440 23446 23452 23456) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 491
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4453
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 724
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7411
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 136
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4116
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 380
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 4902
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 916
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6663
mri_label2label: Done

PIDs (23434 23440 23446 23452 23456) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 23522 of (23522 23528 23534 23540) to complete...
Waiting for PID 23528 of (23522 23528 23534 23540) to complete...
Waiting for PID 23534 of (23522 23528 23534 23540) to complete...
Waiting for PID 23540 of (23522 23528 23534 23540) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 344
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4817
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 2138
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14394
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 1786
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8698
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 2085
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7440
mri_label2label: Done

PIDs (23522 23528 23534 23540) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 23597 of (23597 23603 23609 23612 23619) to complete...
Waiting for PID 23603 of (23597 23603 23609 23612 23619) to complete...
Waiting for PID 23609 of (23597 23603 23609 23612 23619) to complete...
Waiting for PID 23612 of (23597 23603 23609 23612 23619) to complete...
Waiting for PID 23619 of (23597 23603 23609 23612 23619) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 2211
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6938
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 4507
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 12523
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 716
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2648
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 283
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1321
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 196
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 948
mri_label2label: Done

PIDs (23597 23603 23609 23612 23619) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 23691 of (23691 23697 23703 23709 23715) to complete...
Waiting for PID 23697 of (23691 23697 23703 23709 23715) to complete...
Waiting for PID 23703 of (23691 23697 23703 23709 23715) to complete...
Waiting for PID 23709 of (23691 23697 23703 23709 23715) to complete...
Waiting for PID 23715 of (23691 23697 23703 23709 23715) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 156
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1032
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 129
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2817
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 48
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1746
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 136
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2319
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 284
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1672
mri_label2label: Done

PIDs (23691 23697 23703 23709 23715) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 23767 of (23767 23773 23779 23784) to complete...
Waiting for PID 23773 of (23767 23773 23779 23784) to complete...
Waiting for PID 23779 of (23767 23773 23779 23784) to complete...
Waiting for PID 23784 of (23767 23773 23779 23784) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 79
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1568
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 985
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 7944
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 283
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1295
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 410
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1588
mri_label2label: Done

PIDs (23767 23773 23779 23784) 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 0050270 --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 0050270 --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 0050270 --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 0050270 --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 0050270 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 23833 of (23833 23839 23845 23851 23854) to complete...
Waiting for PID 23839 of (23833 23839 23845 23851 23854) to complete...
Waiting for PID 23845 of (23833 23839 23845 23851 23854) to complete...
Waiting for PID 23851 of (23833 23839 23845 23851 23854) to complete...
Waiting for PID 23854 of (23833 23839 23845 23851 23854) 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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 1429
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4661
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 2027
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5464
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 82
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 350
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 166
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 860
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 0050270 --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 = 0050270
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-6.0.0/0050270/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 169365
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 378
mri_label2label: Done

PIDs (23833 23839 23845 23851 23854) completed and logs appended.

 mris_label2annot --s 0050270 --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-6.0.0/0050270/label
cmdline mris_label2annot --s 0050270 --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-388
machine  x86_64
user     ntraut

subject 0050270
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-6.0.0/0050270/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 118428 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050270 --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-6.0.0/0050270/label
cmdline mris_label2annot --s 0050270 --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-388
machine  x86_64
user     ntraut

subject 0050270
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-6.0.0/0050270/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 142024 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/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 0050270 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 295494
Total vertex volume 291646 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
 1233    594   1965  2.314 0.513     0.119     0.029       17     1.4  BA1_exvivo
 3816   2471   5448  2.169 0.466     0.101     0.016       39     2.6  BA2_exvivo
 1168    806   1099  1.804 0.472     0.143     0.029       12     1.4  BA3a_exvivo
 2276   1424   2716  1.711 0.528     0.100     0.018       18     1.7  BA3b_exvivo
 2159   1123   3514  2.727 0.462     0.086     0.018       14     1.6  BA4a_exvivo
 1346    891   2004  2.387 0.432     0.108     0.026       10     1.4  BA4p_exvivo
10096   6152  20498  2.864 0.499     0.112     0.025       99    10.5  BA6_exvivo
 4732   3103   9426  2.808 0.449     0.116     0.023       52     4.2  BA44_exvivo
 5760   3821  11236  2.638 0.475     0.140     0.031       94     6.8  BA45_exvivo
 4422   2830   5933  2.019 0.576     0.138     0.035       61     6.8  V1_exvivo
10146   6452  13430  1.942 0.474     0.149     0.036      160    15.1  V2_exvivo
 2465   1639   3980  2.298 0.470     0.144     0.026       38     2.6  MT_exvivo
  784    524   2348  3.169 0.675     0.121     0.039        8     1.4  perirhinal_exvivo
  534    362   1282  3.060 0.648     0.119     0.027        5     0.7  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050270 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050270/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 295494
Total vertex volume 291646 (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) = 1778356 mm^3    (det: 1.095453 )
lhCtxGM: 288531.841 287519.000  diff= 1012.8  pctdiff= 0.351
rhCtxGM: 290406.847 289754.000  diff=  652.8  pctdiff= 0.225
lhCtxWM: 259161.159 260414.000  diff=-1252.8  pctdiff=-0.483
rhCtxWM: 260545.835 261259.000  diff= -713.2  pctdiff=-0.274
SubCortGMVol  68876.000
SupraTentVol  1181106.682 (1177976.000) diff=3130.682 pctdiff=0.265
SupraTentVolNotVent  1171014.682 (1167884.000) diff=3130.682 pctdiff=0.267
BrainSegVol  1342224.000 (1339771.000) diff=2453.000 pctdiff=0.183
BrainSegVolNotVent  1328841.000 (1328525.682) diff=315.318 pctdiff=0.024
BrainSegVolNotVent  1328841.000
CerebellumVol 160942.000
VentChorVol   10092.000
3rd4th5thCSF   3291.000
CSFVol   838.000, OptChiasmVol    15.000
MaskVol 1860133.000
  826    380   1138  2.120 0.468     0.106     0.024       10     0.8  BA1_exvivo
 1925   1230   2762  2.118 0.423     0.087     0.013       12     1.0  BA2_exvivo
 1031    710    881  1.806 0.438     0.148     0.031       11     1.3  BA3a_exvivo
 1706   1135   1708  1.497 0.349     0.091     0.015       10     1.1  BA3b_exvivo
 1344    667   2123  2.769 0.444     0.089     0.021        9     1.2  BA4a_exvivo
 1084    745   1637  2.408 0.465     0.105     0.024        7     1.2  BA4p_exvivo
 6229   3732  12549  2.880 0.510     0.109     0.026       58     6.8  BA6_exvivo
 1198    780   2799  2.975 0.450     0.119     0.025       15     1.2  BA44_exvivo
 1473    978   2967  2.662 0.463     0.152     0.033       31     1.8  BA45_exvivo
 4183   2681   5498  2.019 0.582     0.137     0.034       56     6.3  V1_exvivo
 5196   3329   6652  1.874 0.469     0.160     0.040       92     8.6  V2_exvivo
  318    225    674  2.363 0.524     0.129     0.022        5     0.3  MT_exvivo
  473    306   1435  3.172 0.713     0.085     0.016        2     0.3  perirhinal_exvivo
  355    271    682  2.958 0.616     0.127     0.025        2     0.4  entorhinal_exvivo

Started at Sat Oct 7 20:07:57 CEST 2017 
Ended   at Sun Oct 8 05:23:18 CEST 2017
#@#%# recon-all-run-time-hours 9.256
recon-all -s 0050270 finished without error at Sun Oct  8 05:23:18 CEST 2017