ABIDE_fs-6.0.0/0050352/scripts/recon-all.log

Sat Oct  7 23:40:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050352 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050352
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-928 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    10240 kbytes
coredumpsize 0 kbytes
memoryuse    10485760 kbytes
vmemoryuse   unlimited
descriptors  65536 
memorylocked 64 kbytes
maxproc      1024 

             total       used       free     shared    buffers     cached
Mem:      66074808   63500996    2573812    1737676          0   56876712
-/+ buffers/cache:    6624284   59450524
Swap:            0          0          0

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $  User: ntraut  Machine: tars-928  Platform: Linux  PlatformVersion: 2.6.32-696.3.2.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/10/07-21:40:21-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $  User: ntraut  Machine: tars-928  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-6.0.0/0050352

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050352/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-6.0.0/0050352/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 23:40:23 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 23:40:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-928 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 23:40:32 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.775
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.775/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.775/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.775/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 23:40:34 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.775/nu0.mnc ./tmp.mri_nu_correct.mni.775/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.775/0/ -iterations 1000 -distance 50
[ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:40:34] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.775/0/ ./tmp.mri_nu_correct.mni.775/nu0.mnc ./tmp.mri_nu_correct.mni.775/nu1.imp

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Number of iterations: 38 
CV of field change: 0.00098934
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.775/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.775/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.775/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Sat Oct  7 23:41:50 CEST 2017
mri_nu_correct.mni done

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

talairach_avi log file is transforms/talairach_avi.log...
Started at Sat Oct 7 23:41:50 CEST 2017
Ended   at Sat Oct  7 23:42:58 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 23:43:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6900, 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-6.0.0/0050352/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach_avi.log 

TalAviQA: 0.97893
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 23:43:00 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-6.0.0/0050352/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-928 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Sat Oct  7 23:43:00 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.1549
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1549/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1549/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.1549/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 23:43:02 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.1549/nu0.mnc ./tmp.mri_nu_correct.mni.1549/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1549/0/
[ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:43:02] 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.1549/0/ ./tmp.mri_nu_correct.mni.1549/nu0.mnc ./tmp.mri_nu_correct.mni.1549/nu1.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 33 
CV of field change: 0.000999668
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 23:43:55 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.1549/nu1.mnc ./tmp.mri_nu_correct.mni.1549/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.1549/1/
[ntraut@tars-928:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/] [2017-10-07 23:43:55] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.1549/1/ ./tmp.mri_nu_correct.mni.1549/nu1.mnc ./tmp.mri_nu_correct.mni.1549/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 13 
CV of field change: 0.000984039
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1549/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-6.0.0/0050352/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.1549/ones.mgz 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.1549/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/input.mean.dat 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.1549/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.1549/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1549/ones.mgz --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/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.1549/ones.mgz --i ./tmp.mri_nu_correct.mni.1549/nu2.mnc --sum ./tmp.mri_nu_correct.mni.1549/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1549/output.mean.dat 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.1549/ones.mgz
Loading ./tmp.mri_nu_correct.mni.1549/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.1549/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.1549/nu2.mnc ./tmp.mri_nu_correct.mni.1549/nu2.mnc mul 1.02105105068371572756
Saving result to './tmp.mri_nu_correct.mni.1549/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.1549/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.1549/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.1549/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (10, 116) to ( 3, 110)
 
 
Sat Oct  7 23:45:18 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 23:45:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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
 1.00814  -0.09572  -0.06711  -112.88490;
 0.08598   1.00471   0.13264  -170.62601;
 0.05585  -0.04674   1.10461  -74.57378;
 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 = 14
Starting OpenSpline(): npoints = 14
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 76 (76), valley at 42 (42)
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 72 (72), valley at 18 (18)
csf peak at 37, setting threshold to 60
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 1 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 23:47:20 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = (40, 55, 31) --> (216, 198, 230)
using (99, 103, 131) as brain centroid...
mean wm in atlas = 108, using box (77,85,106) --> (120, 120,155) to find MRI wm
before smoothing, mri peak at 103
robust fit to distribution - 102 +- 7.2
after smoothing, mri peak at 102, scaling input intensities by 1.059
scaling channel 0 by 1.05882
initial log_p = -4.484
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.515277 @ (-9.091, -9.091, -27.273)
max log p =    -4.385285 @ (4.545, 4.545, 4.545)
max log p =    -4.283016 @ (6.818, -2.273, 2.273)
max log p =    -4.283016 @ (0.000, 0.000, 0.000)
max log p =    -4.283016 @ (0.000, 0.000, 0.000)
max log p =    -4.283016 @ (0.000, 0.000, 0.000)
Found translation: (2.3, -6.8, -20.5): log p = -4.283
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.208, old_max_log_p =-4.283 (thresh=-4.3)
 1.05669  -0.15727   0.11961  -4.45861;
 0.13912   1.05429   0.15727  -52.62578;
-0.13053  -0.12941   0.98296   17.06762;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.194, old_max_log_p =-4.208 (thresh=-4.2)
 1.05669  -0.15727   0.11961  -4.45861;
 0.14955   1.13337   0.16907  -67.23579;
-0.13053  -0.12941   0.98296   17.06762;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.194 (thresh=-4.2)
 1.06717  -0.00799   0.14065  -30.68564;
 0.01112   1.23001   0.16341  -55.36808;
-0.13053  -0.12941   0.98296   17.06762;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.186 (thresh=-4.2)
 1.06717  -0.00799   0.14065  -30.68564;
 0.01112   1.23001   0.16341  -55.36808;
-0.13053  -0.12941   0.98296   17.06762;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.091, old_max_log_p =-4.186 (thresh=-4.2)
 1.01124  -0.00386   0.10478  -17.39266;
 0.01133   1.25308   0.16648  -59.07198;
-0.09649  -0.13446   1.02424   9.70394;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.091, old_max_log_p =-4.091 (thresh=-4.1)
 1.01124  -0.00386   0.10478  -17.39266;
 0.01133   1.25308   0.16648  -59.07198;
-0.09649  -0.13446   1.02424   9.70394;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.073, old_max_log_p =-4.091 (thresh=-4.1)
 1.01005  -0.00385   0.10466  -16.28694;
 0.00976   1.25217   0.18343  -61.40710;
-0.09655  -0.15476   1.02018   12.18664;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.070, old_max_log_p =-4.073 (thresh=-4.1)
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 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
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.070 (old=-4.484)
transform before final EM align:
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 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
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.5  tol 0.000000
final transform:
 1.01199  -0.00251   0.09643  -16.12133;
 0.00897   1.25086   0.19177  -61.73931;
-0.08846  -0.16522   1.02066   12.58875;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1546.076960
mri_em_register stimesec    1.354794
mri_em_register ru_maxrss   611716
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157535
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  32
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    246
mri_em_register ru_nivcsw   21665
registration took 13 minutes and 25 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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=128 y=121 z=127 r=70
      first estimation of the main basin volume: 1457595 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        17 found in the rest of the brain 
      global maximum in x=109, y=109, z=93, Imax=255
      CSF=17, 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=9237295665 voxels, voxel volume =1.000 
                     = 9237295665 mmm3 = 9237296.128 cm3
done.
PostAnalyze...Basin Prior
 8 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=127,y=126, z=123, r=9764 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 44432
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1097445714
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1123489156
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1124157906
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1072194438
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1076085098
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    4,      6,        35,   64
  after  analyzing :    4,      25,        35,   34
   RIGHT_CER   
  before analyzing :    4,      4,        24,   76
  after  analyzing :    4,      18,        25,   32
   LEFT_CER    
  before analyzing :    4,      5,        34,   73
  after  analyzing :    4,      24,        34,   36
  RIGHT_BRAIN  
  before analyzing :    5,      8,        37,   64
  after  analyzing :    5,      27,        37,   36
  LEFT_BRAIN   
  before analyzing :    4,      5,        32,   64
  after  analyzing :    4,      23,        32,   33
     OTHER     
  before analyzing :    4,      4,        12,   91
  after  analyzing :    4,      18,        25,   36
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...60 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.008
curvature mean = 74.943, std = 7.408

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.59, sigma = 5.15
      after  rotation: sse = 3.59, sigma = 5.15
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  3.87, its var is  4.93   
      before Erosion-Dilatation  0.74% 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...28 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1813268 voxels, voxel volume = 1.000 mm3
           = 1813268 mmm3 = 1813.268 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    27.649796
mri_watershed stimesec    0.458930
mri_watershed ru_maxrss   821328
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   212670
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2848
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    2251
mri_watershed ru_nivcsw   119
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct  8 00:01:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

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

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (57, 65, 43) --> (201, 181, 215)
using (105, 104, 129) as brain centroid...
mean wm in atlas = 107, using box (87,90,108) --> (122, 118,150) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 102 +- 5.9
after smoothing, mri peak at 102, scaling input intensities by 1.049
scaling channel 0 by 1.04902
initial log_p = -4.285
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.116086 @ (-9.091, -9.091, -9.091)
max log p =    -3.932616 @ (4.545, 4.545, -13.636)
max log p =    -3.848806 @ (2.273, -2.273, 2.273)
max log p =    -3.810682 @ (1.136, 1.136, 1.136)
max log p =    -3.810517 @ (0.568, 0.568, 0.568)
max log p =    -3.800771 @ (0.284, -0.284, 0.284)
Found translation: (-0.3, -5.4, -18.5): log p = -3.801
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.790, old_max_log_p =-3.801 (thresh=-3.8)
 0.91709   0.00000   0.12074  -4.71285;
 0.00000   1.07500   0.00000  -14.74931;
-0.13053   0.00000   0.99144  -0.82625;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.790, old_max_log_p =-3.790 (thresh=-3.8)
 0.91709   0.00000   0.12074  -4.71285;
 0.00000   1.07500   0.00000  -14.74931;
-0.13053   0.00000   0.99144  -0.82625;
 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=-3.674, old_max_log_p =-3.790 (thresh=-3.8)
 0.95367  -0.07410   0.08683   4.08018;
 0.05916   1.09140   0.03647  -28.82669;
-0.10077  -0.03716   0.97485   3.95822;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.674, old_max_log_p =-3.674 (thresh=-3.7)
 0.95367  -0.07410   0.08683   4.08018;
 0.05916   1.09140   0.03647  -28.82669;
-0.10077  -0.03716   0.97485   3.95822;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.637, old_max_log_p =-3.674 (thresh=-3.7)
 0.95525  -0.06528   0.08710   2.73941;
 0.05277   1.08859   0.01973  -26.09005;
-0.09990  -0.01932   0.97646   0.95923;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.629, old_max_log_p =-3.637 (thresh=-3.6)
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.629, old_max_log_p =-3.629 (thresh=-3.6)
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 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
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.629 (old=-4.285)
transform before final EM align:
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 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
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.0  tol 0.000000
final transform:
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1393.353178
mri_em_register stimesec    1.640750
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   163581
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    464
mri_em_register ru_nivcsw   19873
registration took 11 minutes and 57 seconds.
#--------------------------------------
#@# CA Normalize Sun Oct  8 00:13:08 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

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

writing control point volume to ctrl_pts.mgz
using MR volume brainmask.mgz to mask input volume...
reading 1 input volume
reading atlas from '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=25.0
skull bounding box = (57, 65, 43) --> (201, 181, 215)
using (105, 104, 129) as brain centroid...
mean wm in atlas = 107, using box (87,90,108) --> (122, 118,150) to find MRI wm
before smoothing, mri peak at 101
robust fit to distribution - 102 +- 5.9
after smoothing, mri peak at 102, scaling input intensities by 1.049
scaling channel 0 by 1.04902
using 246344 sample points...
INFO: compute sample coordinates transform
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 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 (123, 63, 43) --> (198, 171, 214)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
1 of 910 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (59, 64, 40) --> (129, 175, 212)
Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0
1 of 1455 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 143, 66) --> (184, 180, 122)
Left_Cerebellum_White_Matter: limiting intensities to 112.0 --> 132.0
3 of 10 (30.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 143, 61) --> (133, 182, 120)
Right_Cerebellum_White_Matter: limiting intensities to 117.0 --> 132.0
11 of 15 (73.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 135, 101) --> (148, 199, 133)
Brain_Stem: limiting intensities to 106.0 --> 132.0
0 of 12 (0.0%) samples deleted
using 2402 total control points for intensity normalization...
bias field = 0.954 +- 0.051
15 of 2386 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 63, 43) --> (198, 171, 214)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 1400 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (59, 64, 40) --> (129, 175, 212)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
3 of 2035 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 143, 66) --> (184, 180, 122)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
15 of 72 (20.8%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 143, 61) --> (133, 182, 120)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
11 of 75 (14.7%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 135, 101) --> (148, 199, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
16 of 90 (17.8%) samples deleted
using 3672 total control points for intensity normalization...
bias field = 1.039 +- 0.062
11 of 3595 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (123, 63, 43) --> (198, 171, 214)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
2 of 1492 (0.1%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (59, 64, 40) --> (129, 175, 212)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 2098 (0.2%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (132, 143, 66) --> (184, 180, 122)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
71 of 133 (53.4%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (87, 143, 61) --> (133, 182, 120)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
14 of 63 (22.2%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (111, 135, 101) --> (148, 199, 133)
Brain_Stem: limiting intensities to 88.0 --> 132.0
65 of 186 (34.9%) samples deleted
using 3972 total control points for intensity normalization...
bias field = 1.040 +- 0.058
14 of 3738 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 43 seconds.
#--------------------------------------
#@# CA Reg Sun Oct  8 00:14:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 7.8)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
enabling zero nodes
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.823, neg=0, invalid=762
0001: dt=296.742586, rms=0.760 (7.589%), neg=0, invalid=762
0002: dt=161.210811, rms=0.751 (1.242%), neg=0, invalid=762
0003: dt=517.888000, rms=0.741 (1.339%), neg=0, invalid=762
0004: dt=131.605634, rms=0.738 (0.357%), neg=0, invalid=762
0005: dt=1775.616000, rms=0.728 (1.452%), neg=0, invalid=762
0006: dt=129.472000, rms=0.725 (0.370%), neg=0, invalid=762
0007: dt=517.888000, rms=0.722 (0.459%), neg=0, invalid=762
0008: dt=221.952000, rms=0.720 (0.187%), neg=0, invalid=762
0009: dt=221.952000, rms=0.719 (0.134%), neg=0, invalid=762
0010: dt=221.952000, rms=0.718 (0.163%), neg=0, invalid=762
0011: dt=221.952000, rms=0.716 (0.233%), neg=0, invalid=762
0012: dt=221.952000, rms=0.714 (0.337%), neg=0, invalid=762
0013: dt=221.952000, rms=0.712 (0.294%), neg=0, invalid=762
0014: dt=221.952000, rms=0.710 (0.251%), neg=0, invalid=762
0015: dt=221.952000, rms=0.709 (0.213%), neg=0, invalid=762
0016: dt=221.952000, rms=0.707 (0.255%), neg=0, invalid=762
0017: dt=221.952000, rms=0.705 (0.211%), neg=0, invalid=762
0018: dt=221.952000, rms=0.704 (0.133%), neg=0, invalid=762
0019: dt=221.952000, rms=0.703 (0.127%), neg=0, invalid=762
0020: dt=221.952000, rms=0.702 (0.197%), neg=0, invalid=762
0021: dt=221.952000, rms=0.701 (0.173%), neg=0, invalid=762
0022: dt=221.952000, rms=0.700 (0.142%), neg=0, invalid=762
0023: dt=221.952000, rms=0.699 (0.142%), neg=0, invalid=762
0024: dt=221.952000, rms=0.697 (0.214%), neg=0, invalid=762
0025: dt=221.952000, rms=0.696 (0.172%), neg=0, invalid=762
0026: dt=221.952000, rms=0.695 (0.124%), neg=0, invalid=762
0027: dt=221.952000, rms=0.695 (0.116%), neg=0, invalid=762
0028: dt=517.888000, rms=0.694 (0.098%), neg=0, invalid=762
0029: dt=517.888000, rms=0.694 (-0.436%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.694, neg=0, invalid=762
0030: dt=129.472000, rms=0.693 (0.165%), neg=0, invalid=762
0031: dt=443.904000, rms=0.692 (0.105%), neg=0, invalid=762
0032: dt=443.904000, rms=0.692 (0.113%), neg=0, invalid=762
0033: dt=443.904000, rms=0.691 (0.120%), neg=0, invalid=762
0034: dt=443.904000, rms=0.690 (0.106%), neg=0, invalid=762
0035: dt=443.904000, rms=0.689 (0.146%), neg=0, invalid=762
0036: dt=443.904000, rms=0.688 (0.132%), neg=0, invalid=762
0037: dt=443.904000, rms=0.688 (0.037%), neg=0, invalid=762
0038: dt=443.904000, rms=0.687 (0.077%), neg=0, invalid=762
0039: dt=443.904000, rms=0.687 (0.098%), neg=0, invalid=762
0040: dt=443.904000, rms=0.686 (0.031%), neg=0, invalid=762
0041: dt=129.472000, rms=0.686 (0.063%), neg=0, invalid=762
0042: dt=887.808000, rms=0.686 (0.032%), neg=0, invalid=762
0043: dt=887.808000, rms=0.686 (-0.138%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.693, neg=0, invalid=762
0044: dt=81.190083, rms=0.689 (0.507%), neg=0, invalid=762
0045: dt=248.832000, rms=0.680 (1.327%), neg=0, invalid=762
0046: dt=36.288000, rms=0.678 (0.350%), neg=0, invalid=762
0047: dt=145.152000, rms=0.675 (0.412%), neg=0, invalid=762
0048: dt=103.680000, rms=0.671 (0.581%), neg=0, invalid=762
0049: dt=36.288000, rms=0.670 (0.157%), neg=0, invalid=762
0050: dt=36.288000, rms=0.669 (0.097%), neg=0, invalid=762
0051: dt=36.288000, rms=0.668 (0.182%), neg=0, invalid=762
0052: dt=36.288000, rms=0.666 (0.271%), neg=0, invalid=762
0053: dt=36.288000, rms=0.664 (0.339%), neg=0, invalid=762
0054: dt=36.288000, rms=0.661 (0.362%), neg=0, invalid=762
0055: dt=36.288000, rms=0.659 (0.359%), neg=0, invalid=762
0056: dt=36.288000, rms=0.657 (0.350%), neg=0, invalid=762
0057: dt=36.288000, rms=0.654 (0.342%), neg=0, invalid=762
0058: dt=36.288000, rms=0.652 (0.327%), neg=0, invalid=762
0059: dt=36.288000, rms=0.650 (0.307%), neg=0, invalid=762
0060: dt=36.288000, rms=0.649 (0.279%), neg=0, invalid=762
0061: dt=36.288000, rms=0.647 (0.237%), neg=0, invalid=762
0062: dt=36.288000, rms=0.646 (0.207%), neg=0, invalid=762
0063: dt=36.288000, rms=0.644 (0.195%), neg=0, invalid=762
0064: dt=36.288000, rms=0.643 (0.192%), neg=0, invalid=762
0065: dt=36.288000, rms=0.642 (0.176%), neg=0, invalid=762
0066: dt=36.288000, rms=0.641 (0.161%), neg=0, invalid=762
0067: dt=36.288000, rms=0.640 (0.145%), neg=0, invalid=762
0068: dt=36.288000, rms=0.639 (0.144%), neg=0, invalid=762
0069: dt=36.288000, rms=0.638 (0.138%), neg=0, invalid=762
0070: dt=36.288000, rms=0.637 (0.120%), neg=0, invalid=762
0071: dt=36.288000, rms=0.637 (0.100%), neg=0, invalid=762
0072: dt=145.152000, rms=0.637 (0.028%), neg=0, invalid=762
0073: dt=145.152000, rms=0.637 (0.018%), neg=0, invalid=762
0074: dt=145.152000, rms=0.637 (-0.236%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.637, neg=0, invalid=762
0075: dt=67.706564, rms=0.635 (0.292%), neg=0, invalid=762
0076: dt=124.416000, rms=0.635 (0.122%), neg=0, invalid=762
0077: dt=124.416000, rms=0.635 (-0.085%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.665, neg=0, invalid=762
0078: dt=11.200000, rms=0.662 (0.331%), neg=0, invalid=762
0079: dt=9.600000, rms=0.662 (0.058%), neg=0, invalid=762
0080: dt=9.600000, rms=0.662 (0.025%), neg=0, invalid=762
0081: dt=9.600000, rms=0.662 (-0.081%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.662, neg=0, invalid=762
0082: dt=0.037500, rms=0.662 (0.075%), neg=0, invalid=762
0083: dt=0.007812, rms=0.662 (0.000%), neg=0, invalid=762
0084: dt=0.007812, rms=0.662 (-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=0.725, neg=0, invalid=762
0085: dt=5.990338, rms=0.710 (2.032%), neg=0, invalid=762
0086: dt=5.333333, rms=0.708 (0.257%), neg=0, invalid=762
0087: dt=4.000000, rms=0.708 (0.033%), neg=0, invalid=762
0088: dt=4.000000, rms=0.708 (0.004%), neg=0, invalid=762
0089: dt=4.000000, rms=0.708 (-0.083%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.708, neg=0, invalid=762
0090: dt=0.000000, rms=0.708 (0.060%), neg=0, invalid=762
0091: dt=0.000000, rms=0.708 (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=0.756, neg=0, invalid=762
0092: dt=0.000000, rms=0.756 (0.053%), neg=0, invalid=762
0093: dt=0.000000, rms=0.756 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.756, neg=0, invalid=762
0094: dt=0.000000, rms=0.756 (0.053%), neg=0, invalid=762
0095: dt=0.000000, rms=0.756 (0.000%), 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=0.675, neg=0, invalid=762
0096: dt=0.764925, rms=0.659 (2.380%), neg=0, invalid=762
0097: dt=0.064000, rms=0.658 (0.093%), neg=0, invalid=762
0098: dt=0.064000, rms=0.658 (-0.056%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.659, neg=0, invalid=762
0099: dt=0.028000, rms=0.658 (0.087%), neg=0, invalid=762
0100: dt=0.005000, rms=0.658 (-0.001%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.06617 (27)
Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2270 voxels, overlap=0.772)
Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2270 voxels, peak = 26), gca=26.5
gca peak = 0.15565 (16)
mri peak = 0.07752 (28)
Right_Lateral_Ventricle (43): linear fit = 1.83 x + 0.0 (1912 voxels, overlap=0.177)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1912 voxels, peak = 29), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.09275 (96)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1215 voxels, overlap=0.744)
Right_Pallidum (52): linear fit = 0.95 x + 0.0 (1215 voxels, peak = 92), gca=91.7
gca peak = 0.20183 (93)
mri peak = 0.08561 (92)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (1110 voxels, overlap=1.005)
Left_Pallidum (13): linear fit = 0.95 x + 0.0 (1110 voxels, peak = 89), gca=88.8
gca peak = 0.21683 (55)
mri peak = 0.05678 (65)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1373 voxels, overlap=0.364)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1373 voxels, peak = 62), gca=62.4
gca peak = 0.30730 (58)
mri peak = 0.06620 (59)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1283 voxels, overlap=0.972)
Left_Hippocampus (17): linear fit = 1.10 x + 0.0 (1283 voxels, peak = 64), gca=63.5
gca peak = 0.11430 (101)
mri peak = 0.07921 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85912 voxels, overlap=0.858)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (85912 voxels, peak = 104), gca=103.5
gca peak = 0.12076 (102)
mri peak = 0.07317 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84816 voxels, overlap=0.828)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (84816 voxels, peak = 106), gca=105.6
gca peak = 0.14995 (59)
mri peak = 0.03216 (71)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34054 voxels, overlap=0.285)
Left_Cerebral_Cortex (3): linear fit = 1.14 x + 0.0 (34054 voxels, peak = 68), gca=67.6
gca peak = 0.15082 (58)
mri peak = 0.03328 (72)
Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (34337 voxels, overlap=0.050)
Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (34337 voxels, peak = 71), gca=71.1
gca peak = 0.14161 (67)
mri peak = 0.06435 (72)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (1320 voxels, overlap=0.881)
Right_Caudate (50): linear fit = 1.07 x + 0.0 (1320 voxels, peak = 71), gca=71.4
gca peak = 0.15243 (71)
mri peak = 0.06299 (83)
Left_Caudate (11): linear fit = 1.08 x + 0.0 (1342 voxels, overlap=0.951)
Left_Caudate (11): linear fit = 1.08 x + 0.0 (1342 voxels, peak = 76), gca=76.3
gca peak = 0.13336 (57)
mri peak = 0.04329 (64)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32035 voxels, overlap=0.745)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (32035 voxels, peak = 64), gca=63.6
gca peak = 0.13252 (56)
mri peak = 0.04187 (67)
Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (35082 voxels, overlap=0.310)
Right_Cerebellum_Cortex (47): linear fit = 1.21 x + 0.0 (35082 voxels, peak = 67), gca=67.5
gca peak = 0.18181 (84)
mri peak = 0.06090 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12496 voxels, overlap=0.929)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (12496 voxels, peak = 86), gca=86.1
gca peak = 0.20573 (83)
mri peak = 0.05121 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (10895 voxels, overlap=0.923)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (10895 voxels, peak = 86), gca=85.9
gca peak = 0.21969 (57)
mri peak = 0.05783 (78)
Left_Amygdala (18): linear fit = 1.33 x + 0.0 (513 voxels, overlap=0.052)
Left_Amygdala (18): linear fit = 1.33 x + 0.0 (513 voxels, peak = 76), gca=75.5
gca peak = 0.39313 (56)
mri peak = 0.09059 (70)
Right_Amygdala (54): linear fit = 1.23 x + 0.0 (707 voxels, overlap=0.028)
Right_Amygdala (54): linear fit = 1.23 x + 0.0 (707 voxels, peak = 69), gca=68.6
gca peak = 0.14181 (85)
mri peak = 0.06436 (88)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6351 voxels, overlap=0.967)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (6351 voxels, peak = 86), gca=86.3
gca peak = 0.11978 (83)
mri peak = 0.06183 (84)
Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5494 voxels, overlap=0.895)
Right_Thalamus_Proper (49): linear fit = 1.03 x + 0.0 (5494 voxels, peak = 86), gca=85.9
gca peak = 0.13399 (79)
mri peak = 0.06316 (84)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2998 voxels, overlap=0.986)
Left_Putamen (12): linear fit = 1.04 x + 0.0 (2998 voxels, peak = 83), gca=82.6
gca peak = 0.14159 (79)
mri peak = 0.06607 (82)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (3136 voxels, overlap=0.900)
Right_Putamen (51): linear fit = 1.04 x + 0.0 (3136 voxels, peak = 83), gca=82.6
gca peak = 0.10025 (80)
mri peak = 0.07802 (85)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (14832 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (14832 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.07388 (87)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2074 voxels, overlap=0.724)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (2074 voxels, peak = 89), gca=89.0
gca peak = 0.12801 (89)
mri peak = 0.06712 (86)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (2122 voxels, overlap=0.796)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (2122 voxels, peak = 92), gca=92.1
gca peak = 0.20494 (23)
mri peak = 0.10321 (18)
gca peak = 0.15061 (21)
mri peak = 0.07988 (13)
Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (416 voxels, overlap=0.685)
Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (416 voxels, peak = 17), gca=17.1
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.19 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.21 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=0.646, neg=0, invalid=762
0101: dt=99.618625, rms=0.636 (1.496%), neg=0, invalid=762
0102: dt=295.936000, rms=0.633 (0.508%), neg=0, invalid=762
0103: dt=295.936000, rms=0.631 (0.327%), neg=0, invalid=762
0104: dt=110.976000, rms=0.630 (0.119%), neg=0, invalid=762
0105: dt=517.888000, rms=0.629 (0.220%), neg=0, invalid=762
0106: dt=92.480000, rms=0.628 (0.130%), neg=0, invalid=762
0107: dt=1479.680000, rms=0.626 (0.357%), neg=0, invalid=762
0108: dt=129.472000, rms=0.625 (0.139%), neg=0, invalid=762
0109: dt=295.936000, rms=0.624 (0.067%), neg=0, invalid=762
0110: dt=92.480000, rms=0.624 (0.036%), neg=0, invalid=762
0111: dt=92.480000, rms=0.624 (0.018%), neg=0, invalid=762
0112: dt=92.480000, rms=0.624 (0.032%), neg=0, invalid=762
0113: dt=92.480000, rms=0.623 (0.042%), neg=0, invalid=762
0114: dt=92.480000, rms=0.623 (0.055%), neg=0, invalid=762
0115: dt=92.480000, rms=0.623 (0.060%), neg=0, invalid=762
0116: dt=92.480000, rms=0.622 (0.063%), neg=0, invalid=762
0117: dt=92.480000, rms=0.622 (0.067%), neg=0, invalid=762
0118: dt=92.480000, rms=0.622 (0.068%), neg=0, invalid=762
0119: dt=92.480000, rms=0.621 (0.062%), neg=0, invalid=762
0120: dt=92.480000, rms=0.621 (0.056%), neg=0, invalid=762
0121: dt=92.480000, rms=0.620 (0.053%), neg=0, invalid=762
0122: dt=92.480000, rms=0.620 (0.053%), neg=0, invalid=762
0123: dt=92.480000, rms=0.620 (0.054%), neg=0, invalid=762
0124: dt=92.480000, rms=0.619 (0.054%), neg=0, invalid=762
0125: dt=92.480000, rms=0.619 (0.051%), neg=0, invalid=762
0126: dt=92.480000, rms=0.619 (0.046%), neg=0, invalid=762
0127: dt=92.480000, rms=0.619 (0.044%), neg=0, invalid=762
0128: dt=92.480000, rms=0.618 (0.043%), neg=0, invalid=762
0129: dt=92.480000, rms=0.618 (0.042%), neg=0, invalid=762
0130: dt=92.480000, rms=0.618 (0.042%), neg=0, invalid=762
0131: dt=92.480000, rms=0.618 (0.041%), neg=0, invalid=762
0132: dt=92.480000, rms=0.617 (0.038%), neg=0, invalid=762
0133: dt=92.480000, rms=0.617 (0.039%), neg=0, invalid=762
0134: dt=92.480000, rms=0.617 (0.036%), neg=0, invalid=762
0135: dt=92.480000, rms=0.617 (0.035%), neg=0, invalid=762
0136: dt=92.480000, rms=0.616 (0.032%), neg=0, invalid=762
0137: dt=92.480000, rms=0.616 (0.032%), neg=0, invalid=762
0138: dt=92.480000, rms=0.616 (0.030%), neg=0, invalid=762
0139: dt=92.480000, rms=0.616 (0.031%), neg=0, invalid=762
0140: dt=92.480000, rms=0.616 (0.028%), neg=0, invalid=762
0141: dt=92.480000, rms=0.616 (0.031%), neg=0, invalid=762
0142: dt=92.480000, rms=0.615 (0.025%), neg=0, invalid=762
0143: dt=92.480000, rms=0.615 (0.024%), neg=0, invalid=762
0144: dt=92.480000, rms=0.615 (0.023%), neg=0, invalid=762
0145: dt=5918.720000, rms=0.614 (0.117%), neg=0, invalid=762
0146: dt=92.480000, rms=0.614 (0.034%), neg=0, invalid=762
0147: dt=92.480000, rms=0.614 (0.003%), neg=0, invalid=762
0148: dt=92.480000, rms=0.614 (0.000%), neg=0, invalid=762
0149: dt=92.480000, rms=0.614 (0.002%), neg=0, invalid=762
0150: dt=92.480000, rms=0.614 (0.014%), neg=0, invalid=762
0151: dt=92.480000, rms=0.614 (0.018%), neg=0, invalid=762
0152: dt=92.480000, rms=0.614 (0.016%), neg=0, invalid=762
0153: dt=0.000000, rms=0.614 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.614, neg=0, invalid=762
0154: dt=295.936000, rms=0.613 (0.186%), neg=0, invalid=762
0155: dt=129.472000, rms=0.613 (0.048%), neg=0, invalid=762
0156: dt=129.472000, rms=0.613 (0.016%), neg=0, invalid=762
0157: dt=129.472000, rms=0.612 (0.035%), neg=0, invalid=762
0158: dt=129.472000, rms=0.612 (0.042%), neg=0, invalid=762
0159: dt=129.472000, rms=0.612 (0.037%), neg=0, invalid=762
0160: dt=129.472000, rms=0.612 (0.032%), neg=0, invalid=762
0161: dt=129.472000, rms=0.612 (0.030%), neg=0, invalid=762
0162: dt=129.472000, rms=0.611 (0.025%), neg=0, invalid=762
0163: dt=129.472000, rms=0.611 (0.028%), neg=0, invalid=762
0164: dt=129.472000, rms=0.611 (0.025%), neg=0, invalid=762
0165: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762
0166: dt=129.472000, rms=0.611 (0.023%), neg=0, invalid=762
0167: dt=1479.680000, rms=0.611 (0.036%), neg=0, invalid=762
0168: dt=110.976000, rms=0.610 (0.011%), neg=0, invalid=762
0169: dt=110.976000, rms=0.610 (0.006%), neg=0, invalid=762
0170: dt=110.976000, rms=0.610 (0.002%), neg=0, invalid=762
0171: dt=110.976000, rms=0.610 (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=0.611, neg=0, invalid=762
0172: dt=161.635036, rms=0.608 (0.601%), neg=0, invalid=762
0173: dt=181.612565, rms=0.602 (0.954%), neg=0, invalid=762
0174: dt=36.288000, rms=0.600 (0.385%), neg=0, invalid=762
0175: dt=103.680000, rms=0.598 (0.181%), neg=0, invalid=762
0176: dt=145.152000, rms=0.596 (0.435%), neg=0, invalid=762
0177: dt=36.288000, rms=0.595 (0.184%), neg=0, invalid=762
0178: dt=248.832000, rms=0.593 (0.360%), neg=0, invalid=762
0179: dt=63.806647, rms=0.591 (0.270%), neg=0, invalid=762
0180: dt=103.680000, rms=0.590 (0.188%), neg=0, invalid=762
0181: dt=36.288000, rms=0.589 (0.102%), neg=0, invalid=762
0182: dt=580.608000, rms=0.585 (0.772%), neg=0, invalid=762
0183: dt=2.268000, rms=0.585 (0.010%), neg=0, invalid=762
0184: dt=0.567000, rms=0.585 (0.002%), neg=0, invalid=762
0185: dt=0.141750, rms=0.585 (0.001%), neg=0, invalid=762
0186: dt=0.070875, rms=0.585 (0.000%), neg=0, invalid=762
0187: dt=0.035437, rms=0.585 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.585, neg=0, invalid=762
0188: dt=0.035437, rms=0.585 (0.083%), neg=0, invalid=762
0189: dt=0.000000, rms=0.585 (0.000%), neg=0, invalid=762
0190: dt=0.000879, rms=0.585 (0.000%), neg=0, invalid=762
0191: dt=0.000110, rms=0.585 (0.000%), neg=0, invalid=762
0192: dt=0.000055, rms=0.585 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.589, neg=0, invalid=762
0193: dt=44.800000, rms=0.574 (2.528%), neg=0, invalid=762
0194: dt=44.800000, rms=0.565 (1.462%), neg=0, invalid=762
0195: dt=53.828571, rms=0.560 (0.989%), neg=0, invalid=762
0196: dt=24.251710, rms=0.556 (0.734%), neg=0, invalid=762
0197: dt=67.840000, rms=0.552 (0.652%), neg=0, invalid=762
0198: dt=21.136364, rms=0.549 (0.617%), neg=0, invalid=762
0199: dt=44.800000, rms=0.546 (0.427%), neg=0, invalid=762
0200: dt=44.800000, rms=0.545 (0.252%), neg=0, invalid=762
0201: dt=31.627907, rms=0.543 (0.315%), neg=0, invalid=762
0202: dt=11.200000, rms=0.543 (0.108%), neg=0, invalid=762
0203: dt=2.800000, rms=0.543 (0.029%), neg=0, invalid=762
0204: dt=1.400000, rms=0.542 (0.011%), neg=0, invalid=762
0205: dt=0.021875, rms=0.542 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.543, neg=0, invalid=762
0206: dt=91.954023, rms=0.538 (0.867%), neg=0, invalid=762
0207: dt=29.151335, rms=0.536 (0.360%), neg=0, invalid=762
0208: dt=44.800000, rms=0.535 (0.162%), neg=0, invalid=762
0209: dt=9.600000, rms=0.535 (0.094%), neg=0, invalid=762
0210: dt=0.700000, rms=0.535 (0.012%), neg=0, invalid=762
0211: dt=0.350000, rms=0.535 (0.001%), neg=0, invalid=762
0212: dt=0.175000, rms=0.535 (0.001%), neg=0, invalid=762
0213: dt=0.087500, rms=0.535 (0.001%), neg=0, invalid=762
0214: dt=0.010937, rms=0.535 (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=0.550, neg=0, invalid=762
0215: dt=6.333333, rms=0.548 (0.265%), neg=0, invalid=762
0216: dt=4.032000, rms=0.548 (0.068%), neg=0, invalid=762
0217: dt=0.864000, rms=0.548 (0.019%), neg=0, invalid=762
0218: dt=0.006750, rms=0.548 (0.001%), neg=0, invalid=762
0219: dt=0.003375, rms=0.548 (0.000%), neg=0, invalid=762
0220: dt=0.000422, rms=0.548 (0.000%), neg=0, invalid=762
0221: dt=0.000211, rms=0.548 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.548, neg=0, invalid=762
0222: dt=7.724138, rms=0.547 (0.197%), neg=0, invalid=762
0223: dt=11.200000, rms=0.547 (0.087%), neg=0, invalid=762
0224: dt=16.128000, rms=0.546 (0.178%), neg=0, invalid=762
0225: dt=4.032000, rms=0.545 (0.058%), neg=0, invalid=762
0226: dt=3.456000, rms=0.545 (0.049%), neg=0, invalid=762
0227: dt=0.108000, rms=0.545 (0.002%), neg=0, invalid=762
0228: dt=0.054000, rms=0.545 (0.001%), neg=0, invalid=762
0229: dt=0.027000, rms=0.545 (0.000%), neg=0, invalid=762
0230: dt=0.002813, rms=0.545 (0.000%), neg=0, invalid=762
0231: dt=0.000000, rms=0.545 (-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=0.561, neg=0, invalid=762
0232: dt=0.000000, rms=0.561 (0.078%), neg=0, invalid=762
0233: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762
0234: dt=0.100000, rms=0.561 (-0.049%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.561, neg=0, invalid=762
0235: dt=0.000000, rms=0.561 (0.078%), neg=0, invalid=762
0236: dt=0.000000, rms=0.561 (0.000%), neg=0, invalid=762
0237: dt=0.100000, rms=0.561 (-0.034%), 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=0.535, neg=0, invalid=762
0238: dt=0.384000, rms=0.523 (2.160%), neg=0, invalid=762
0239: dt=0.384000, rms=0.520 (0.692%), neg=0, invalid=762
0240: dt=0.384000, rms=0.518 (0.335%), neg=0, invalid=762
0241: dt=0.384000, rms=0.517 (0.208%), neg=0, invalid=762
0242: dt=0.384000, rms=0.516 (0.143%), neg=0, invalid=762
0243: dt=0.384000, rms=0.515 (0.112%), neg=0, invalid=762
0244: dt=0.384000, rms=0.515 (0.085%), neg=0, invalid=762
0245: dt=0.384000, rms=0.515 (0.070%), neg=0, invalid=762
0246: dt=0.384000, rms=0.514 (0.058%), neg=0, invalid=762
0247: dt=0.384000, rms=0.514 (0.045%), neg=0, invalid=762
0248: dt=0.384000, rms=0.514 (0.043%), neg=0, invalid=762
0249: dt=0.384000, rms=0.514 (0.071%), neg=0, invalid=762
0250: dt=0.192000, rms=0.513 (0.017%), neg=0, invalid=762
0251: dt=0.192000, rms=0.513 (0.028%), neg=0, invalid=762
0252: dt=0.192000, rms=0.513 (0.011%), neg=0, invalid=762
0253: dt=0.192000, rms=0.513 (0.021%), neg=0, invalid=762
0254: dt=0.192000, rms=0.513 (0.027%), neg=0, invalid=762
0255: dt=0.192000, rms=0.513 (0.032%), neg=0, invalid=762
0256: dt=0.192000, rms=0.513 (0.035%), neg=0, invalid=762
0257: dt=0.192000, rms=0.512 (0.034%), neg=0, invalid=762
0258: dt=0.192000, rms=0.512 (0.002%), neg=0, invalid=762
0259: dt=0.192000, rms=0.512 (0.008%), neg=0, invalid=762
0260: dt=0.192000, rms=0.512 (0.008%), neg=0, invalid=762
0261: dt=0.192000, rms=0.512 (0.006%), neg=0, invalid=762
0262: dt=0.320000, rms=0.512 (0.003%), neg=0, invalid=762
0263: dt=0.320000, rms=0.512 (0.005%), neg=0, invalid=762
0264: dt=0.320000, rms=0.512 (0.005%), neg=0, invalid=762
0265: dt=0.160000, rms=0.512 (0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.513, neg=0, invalid=762
0266: dt=0.320000, rms=0.509 (0.781%), neg=0, invalid=762
0267: dt=0.448000, rms=0.507 (0.352%), neg=0, invalid=762
0268: dt=0.448000, rms=0.507 (0.043%), neg=0, invalid=762
0269: dt=0.448000, rms=0.507 (0.006%), neg=0, invalid=762
0270: dt=0.448000, rms=0.507 (0.004%), neg=0, invalid=762
0271: dt=0.224000, rms=0.507 (-0.003%), 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=0.505, neg=0, invalid=762
0272: dt=0.000000, rms=0.504 (0.105%), neg=0, invalid=762
0273: dt=0.000000, rms=0.504 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.505, neg=0, invalid=762
0274: dt=32.368000, rms=0.504 (0.108%), neg=0, invalid=762
0275: dt=73.984000, rms=0.504 (0.001%), neg=0, invalid=762
0276: dt=73.984000, rms=0.504 (0.007%), neg=0, invalid=762
0277: dt=73.984000, rms=0.504 (0.009%), neg=0, invalid=762
0278: dt=73.984000, rms=0.504 (0.011%), neg=0, invalid=762
0279: dt=73.984000, rms=0.504 (0.017%), neg=0, invalid=762
0280: dt=73.984000, rms=0.504 (0.015%), neg=0, invalid=762
0281: dt=73.984000, rms=0.504 (0.011%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.505, neg=0, invalid=762
0282: dt=25.920000, rms=0.504 (0.131%), neg=0, invalid=762
0283: dt=25.920000, rms=0.504 (0.010%), neg=0, invalid=762
0284: dt=25.920000, rms=0.504 (0.009%), neg=0, invalid=762
0285: dt=25.920000, rms=0.504 (-0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.504, neg=0, invalid=762
0286: dt=103.680000, rms=0.502 (0.388%), neg=0, invalid=762
0287: dt=36.288000, rms=0.502 (0.087%), neg=0, invalid=762
0288: dt=36.288000, rms=0.502 (0.044%), neg=0, invalid=762
0289: dt=36.288000, rms=0.501 (0.075%), neg=0, invalid=762
0290: dt=36.288000, rms=0.501 (0.090%), neg=0, invalid=762
0291: dt=36.288000, rms=0.500 (0.107%), neg=0, invalid=762
0292: dt=36.288000, rms=0.500 (0.112%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 8 iterations, nbhd size=1, neg = 0
0293: dt=36.288000, rms=0.499 (0.097%), neg=0, invalid=762
0294: dt=36.288000, rms=0.499 (0.095%), neg=0, invalid=762
0295: dt=103.680000, rms=0.499 (0.018%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.500, neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0296: dt=32.000000, rms=0.497 (0.471%), neg=0, invalid=762
iter 0, gcam->neg = 9
after 11 iterations, nbhd size=1, neg = 0
0297: dt=73.513514, rms=0.495 (0.487%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0298: dt=32.000000, rms=0.494 (0.247%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0299: dt=32.000000, rms=0.492 (0.285%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 2 iterations, nbhd size=0, neg = 0
0300: dt=32.000000, rms=0.491 (0.246%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 8 iterations, nbhd size=1, neg = 0
0301: dt=32.000000, rms=0.490 (0.197%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0302: dt=32.000000, rms=0.489 (0.194%), neg=0, invalid=762
iter 0, gcam->neg = 21
after 12 iterations, nbhd size=1, neg = 0
0303: dt=32.000000, rms=0.488 (0.164%), neg=0, invalid=762
iter 0, gcam->neg = 18
after 12 iterations, nbhd size=1, neg = 0
0304: dt=32.000000, rms=0.488 (0.109%), neg=0, invalid=762
iter 0, gcam->neg = 12
after 13 iterations, nbhd size=1, neg = 0
0305: dt=32.000000, rms=0.487 (0.127%), neg=0, invalid=762
iter 0, gcam->neg = 16
after 12 iterations, nbhd size=1, neg = 0
0306: dt=32.000000, rms=0.486 (0.119%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 2 iterations, nbhd size=0, neg = 0
0307: dt=32.000000, rms=0.486 (0.143%), neg=0, invalid=762
iter 0, gcam->neg = 10
after 12 iterations, nbhd size=1, neg = 0
0308: dt=32.000000, rms=0.485 (0.120%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 10 iterations, nbhd size=1, neg = 0
0309: dt=32.000000, rms=0.485 (0.131%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 4 iterations, nbhd size=0, neg = 0
0310: dt=32.000000, rms=0.484 (0.093%), neg=0, invalid=762
iter 0, gcam->neg = 11
after 7 iterations, nbhd size=0, neg = 0
0311: dt=32.000000, rms=0.484 (0.088%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 1 iterations, nbhd size=0, neg = 0
0312: dt=38.400000, rms=0.483 (0.060%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0313: dt=38.400000, rms=0.483 (-0.003%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.484, neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0314: dt=53.937107, rms=0.480 (0.786%), neg=0, invalid=762
0315: dt=25.600000, rms=0.479 (0.262%), neg=0, invalid=762
0316: dt=44.800000, rms=0.478 (0.195%), neg=0, invalid=762
0317: dt=44.800000, rms=0.478 (0.011%), neg=0, invalid=762
0318: dt=44.800000, rms=0.476 (0.312%), neg=0, invalid=762
0319: dt=44.800000, rms=0.476 (0.013%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0320: dt=44.800000, rms=0.476 (0.183%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0321: dt=44.800000, rms=0.475 (-0.086%), neg=0, invalid=762
0322: dt=19.200000, rms=0.475 (0.081%), neg=0, invalid=762
0323: dt=44.800000, rms=0.475 (0.068%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0324: dt=2.880000, rms=0.482 (0.126%), neg=0, invalid=762
0325: dt=0.720000, rms=0.482 (0.005%), neg=0, invalid=762
0326: dt=0.720000, rms=0.482 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.482, neg=0, invalid=762
0327: dt=6.000000, rms=0.481 (0.189%), neg=0, invalid=762
0328: dt=4.032000, rms=0.481 (0.026%), neg=0, invalid=762
0329: dt=4.032000, rms=0.481 (0.012%), neg=0, invalid=762
0330: dt=4.032000, rms=0.481 (-0.022%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
0331: dt=0.000000, rms=0.489 (0.104%), neg=0, invalid=762
0332: dt=0.000000, rms=0.489 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.489, neg=0, invalid=762
0333: dt=1.280000, rms=0.488 (0.235%), neg=0, invalid=762
0334: dt=0.768000, rms=0.488 (0.029%), neg=0, invalid=762
0335: dt=0.768000, rms=0.488 (0.006%), neg=0, invalid=762
0336: dt=0.768000, rms=0.488 (-0.047%), 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=0.480, neg=0, invalid=762
iter 0, gcam->neg = 664
after 14 iterations, nbhd size=1, neg = 0
0337: dt=2.087838, rms=0.453 (5.751%), neg=0, invalid=762
0338: dt=0.064000, rms=0.453 (0.037%), neg=0, invalid=762
0339: dt=0.064000, rms=0.453 (-0.038%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.453, neg=0, invalid=762
0340: dt=0.080000, rms=0.452 (0.182%), neg=0, invalid=762
0341: dt=0.004000, rms=0.452 (0.000%), neg=0, invalid=762
0342: dt=0.004000, rms=0.452 (-0.000%), 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=0.438, neg=0, invalid=762
0343: dt=0.000000, rms=0.438 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.438, neg=0, invalid=762
0344: dt=6.936000, rms=0.438 (0.000%), neg=0, invalid=762
0345: dt=1.445000, rms=0.438 (0.000%), neg=0, invalid=762
0346: dt=1.445000, rms=0.438 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.439, neg=0, invalid=762
0347: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.439, neg=0, invalid=762
0348: dt=36.288000, rms=0.439 (0.024%), neg=0, invalid=762
0349: dt=103.680000, rms=0.438 (0.026%), neg=0, invalid=762
0350: dt=248.832000, rms=0.438 (0.099%), neg=0, invalid=762
0351: dt=20.736000, rms=0.438 (0.008%), neg=0, invalid=762
0352: dt=20.736000, rms=0.438 (0.001%), neg=0, invalid=762
0353: dt=20.736000, rms=0.438 (-0.003%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.439, neg=0, invalid=762
0354: dt=11.200000, rms=0.438 (0.075%), neg=0, invalid=762
0355: dt=9.600000, rms=0.438 (0.020%), neg=0, invalid=762
0356: dt=9.600000, rms=0.438 (0.005%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0357: dt=9.600000, rms=0.438 (-0.048%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.438, neg=0, invalid=762
0358: dt=61.440000, rms=0.436 (0.547%), neg=0, invalid=762
0359: dt=25.600000, rms=0.435 (0.235%), neg=0, invalid=762
0360: dt=25.600000, rms=0.434 (0.101%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0361: dt=25.600000, rms=0.434 (0.143%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 8 iterations, nbhd size=1, neg = 0
0362: dt=25.600000, rms=0.433 (0.192%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0363: dt=25.600000, rms=0.432 (0.179%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 6 iterations, nbhd size=1, neg = 0
0364: dt=25.600000, rms=0.431 (0.174%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 2 iterations, nbhd size=0, neg = 0
0365: dt=25.600000, rms=0.431 (0.153%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0366: dt=25.600000, rms=0.430 (0.130%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 0 iterations, nbhd size=0, neg = 0
0367: dt=25.600000, rms=0.430 (0.118%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 9 iterations, nbhd size=1, neg = 0
0368: dt=25.600000, rms=0.429 (0.068%), neg=0, invalid=762
0369: dt=38.400000, rms=0.429 (0.021%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0370: dt=38.400000, rms=0.429 (0.010%), neg=0, invalid=762
0371: dt=38.400000, rms=0.429 (0.021%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0372: dt=38.400000, rms=0.429 (0.012%), neg=0, invalid=762
0373: dt=38.400000, rms=0.429 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0374: dt=38.400000, rms=0.429 (0.013%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0375: dt=0.000422, rms=0.433 (0.000%), neg=0, invalid=762
0376: dt=0.000000, rms=0.433 (0.000%), neg=0, invalid=762
0377: dt=0.150000, rms=0.433 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.433, neg=0, invalid=762
0378: dt=4.800000, rms=0.433 (0.027%), neg=0, invalid=762
0379: dt=4.032000, rms=0.433 (0.011%), neg=0, invalid=762
0380: dt=4.032000, rms=0.433 (0.007%), neg=0, invalid=762
0381: dt=4.032000, rms=0.433 (-0.005%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.440, neg=0, invalid=762
0382: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.440, neg=0, invalid=762
0383: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=762
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.428, neg=0, invalid=762
iter 0, gcam->neg = 480
after 16 iterations, nbhd size=1, neg = 0
0384: dt=1.280000, rms=0.419 (2.022%), neg=0, invalid=762
0385: dt=0.000023, rms=0.419 (0.000%), neg=0, invalid=762
0386: dt=0.000023, rms=0.419 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=762
0387: dt=0.112000, rms=0.419 (0.082%), neg=0, invalid=762
0388: dt=0.112000, rms=0.419 (0.033%), neg=0, invalid=762
0389: dt=0.112000, rms=0.419 (0.023%), neg=0, invalid=762
0390: dt=0.112000, rms=0.419 (-0.021%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 2 hours, 28 minutes and 56 seconds.
mri_ca_register utimesec    10050.217134
mri_ca_register stimesec    9.829505
mri_ca_register ru_maxrss   1333540
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4480819
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  63336
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3340
mri_ca_register ru_nivcsw   43366
FSRUNTIME@ mri_ca_register  2.4823 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sun Oct  8 02:43:47 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-928
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-6.0.0/0050352/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 7.80
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 = 0.06742 (29)
Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2482 voxels, overlap=0.935)
Left_Lateral_Ventricle (4): linear fit = 1.33 x + 0.0 (2482 voxels, peak = 26), gca=26.5
gca peak = 0.17677 (13)
mri peak = 0.08856 (28)
Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (2048 voxels, overlap=0.177)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2048 voxels, peak = 27), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.14358 (96)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.823)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 95), gca=94.5
gca peak = 0.16930 (96)
mri peak = 0.12101 (93)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (593 voxels, overlap=1.011)
Left_Pallidum (13): linear fit = 0.98 x + 0.0 (593 voxels, peak = 94), gca=93.6
gca peak = 0.24553 (55)
mri peak = 0.07667 (65)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1352 voxels, overlap=0.367)
Right_Hippocampus (53): linear fit = 1.13 x + 0.0 (1352 voxels, peak = 62), gca=62.4
gca peak = 0.30264 (59)
mri peak = 0.06650 (64)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1207 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.04 x + 0.0 (1207 voxels, peak = 62), gca=61.7
gca peak = 0.07580 (103)
mri peak = 0.08078 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, overlap=0.784)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, peak = 104), gca=103.5
gca peak = 0.07714 (104)
mri peak = 0.07366 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61498 voxels, overlap=0.750)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (61498 voxels, peak = 107), gca=106.6
gca peak = 0.09712 (58)
mri peak = 0.03610 (66)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39627 voxels, overlap=0.641)
Left_Cerebral_Cortex (3): linear fit = 1.13 x + 0.0 (39627 voxels, peak = 66), gca=65.8
gca peak = 0.11620 (58)
mri peak = 0.04075 (68)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (40904 voxels, overlap=0.321)
Right_Cerebral_Cortex (42): linear fit = 1.20 x + 0.0 (40904 voxels, peak = 69), gca=69.3
gca peak = 0.30970 (66)
mri peak = 0.08816 (76)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (1185 voxels, overlap=0.379)
Right_Caudate (50): linear fit = 1.10 x + 0.0 (1185 voxels, peak = 72), gca=72.3
gca peak = 0.15280 (69)
mri peak = 0.07814 (76)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (1200 voxels, overlap=0.853)
Left_Caudate (11): linear fit = 1.07 x + 0.0 (1200 voxels, peak = 73), gca=73.5
gca peak = 0.13902 (56)
mri peak = 0.04564 (65)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31494 voxels, overlap=0.797)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (31494 voxels, peak = 64), gca=63.6
gca peak = 0.14777 (55)
mri peak = 0.05111 (64)
Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (32655 voxels, overlap=0.439)
Right_Cerebellum_Cortex (47): linear fit = 1.20 x + 0.0 (32655 voxels, peak = 66), gca=65.7
gca peak = 0.16765 (84)
mri peak = 0.09173 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7206 voxels, overlap=0.937)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (7206 voxels, peak = 85), gca=85.3
gca peak = 0.18739 (84)
mri peak = 0.08231 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6204 voxels, overlap=0.911)
Right_Cerebellum_White_Matter (46): linear fit = 1.03 x + 0.0 (6204 voxels, peak = 87), gca=86.9
gca peak = 0.29869 (57)
mri peak = 0.06845 (78)
Left_Amygdala (18): linear fit = 1.29 x + 0.0 (683 voxels, overlap=0.077)
Left_Amygdala (18): linear fit = 1.29 x + 0.0 (683 voxels, peak = 74), gca=73.8
gca peak = 0.33601 (57)
mri peak = 0.07428 (74)
Right_Amygdala (54): linear fit = 1.30 x + 0.0 (728 voxels, overlap=0.064)
Right_Amygdala (54): linear fit = 1.30 x + 0.0 (728 voxels, peak = 74), gca=74.4
gca peak = 0.11131 (90)
mri peak = 0.07421 (88)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, overlap=1.000)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, peak = 90), gca=89.6
gca peak = 0.11793 (83)
mri peak = 0.07008 (86)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4931 voxels, overlap=0.949)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4931 voxels, peak = 85), gca=85.1
gca peak = 0.08324 (81)
mri peak = 0.07627 (84)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2240 voxels, overlap=0.838)
Left_Putamen (12): linear fit = 1.02 x + 0.0 (2240 voxels, peak = 83), gca=83.0
gca peak = 0.10360 (77)
mri peak = 0.08326 (83)
Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, overlap=0.916)
Right_Putamen (51): linear fit = 1.03 x + 0.0 (2306 voxels, peak = 80), gca=79.7
gca peak = 0.08424 (78)
mri peak = 0.06986 (87)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (14679 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.11 x + 0.0 (14679 voxels, peak = 86), gca=86.2
gca peak = 0.12631 (89)
mri peak = 0.07740 (90)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1862 voxels, overlap=0.823)
Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1862 voxels, peak = 92), gca=92.1
gca peak = 0.14500 (87)
mri peak = 0.07510 (93)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1883 voxels, overlap=0.893)
Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1883 voxels, peak = 89), gca=89.2
gca peak = 0.14975 (24)
mri peak = 0.11509 (18)
gca peak = 0.19357 (14)
mri peak = 0.09064 (13)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (314 voxels, overlap=0.848)
Fourth_Ventricle (15): linear fit = 1.03 x + 0.0 (314 voxels, peak = 14), gca=14.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.19 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 1.29 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.14196 (24)
mri peak = 0.06742 (29)
Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2482 voxels, overlap=0.860)
Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2482 voxels, peak = 23), gca=23.4
gca peak = 0.14095 (19)
mri peak = 0.08856 (28)
Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2048 voxels, overlap=0.422)
Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (2048 voxels, peak = 27), gca=26.7
gca peak = 0.28191 (93)
mri peak = 0.14358 (96)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.825)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 93), gca=92.5
gca peak = 0.18416 (94)
mri peak = 0.12101 (93)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (593 voxels, overlap=1.009)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (593 voxels, peak = 95), gca=95.4
gca peak = 0.26749 (63)
mri peak = 0.07667 (65)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1352 voxels, overlap=0.999)
Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1352 voxels, peak = 64), gca=63.9
gca peak = 0.27972 (59)
mri peak = 0.06650 (64)
Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (1207 voxels, overlap=1.002)
Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (1207 voxels, peak = 61), gca=61.1
gca peak = 0.07875 (103)
mri peak = 0.08078 (103)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, overlap=0.802)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (61203 voxels, peak = 103), gca=103.0
gca peak = 0.07720 (107)
mri peak = 0.07366 (103)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61498 voxels, overlap=0.847)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (61498 voxels, peak = 106), gca=106.5
gca peak = 0.08624 (66)
mri peak = 0.03610 (66)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39627 voxels, overlap=0.971)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (39627 voxels, peak = 66), gca=66.0
gca peak = 0.09981 (69)
mri peak = 0.04075 (68)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40904 voxels, overlap=0.963)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (40904 voxels, peak = 68), gca=68.0
gca peak = 0.25613 (73)
mri peak = 0.08816 (76)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1185 voxels, overlap=1.007)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1185 voxels, peak = 73), gca=73.0
gca peak = 0.12839 (73)
mri peak = 0.07814 (76)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1200 voxels, overlap=1.003)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1200 voxels, peak = 73), gca=73.0
gca peak = 0.12384 (63)
mri peak = 0.04564 (65)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31494 voxels, overlap=0.999)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31494 voxels, peak = 63), gca=63.0
gca peak = 0.12172 (66)
mri peak = 0.05111 (64)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32655 voxels, overlap=0.993)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (32655 voxels, peak = 65), gca=65.0
gca peak = 0.16169 (86)
mri peak = 0.09173 (85)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7206 voxels, overlap=0.963)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7206 voxels, peak = 86), gca=85.6
gca peak = 0.18134 (87)
mri peak = 0.08231 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6204 voxels, overlap=0.979)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6204 voxels, peak = 87), gca=86.6
gca peak = 0.27803 (75)
mri peak = 0.06845 (78)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (683 voxels, overlap=0.997)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (683 voxels, peak = 74), gca=73.9
gca peak = 0.31967 (74)
mri peak = 0.07428 (74)
Right_Amygdala (54): linear fit = 1.03 x + 0.0 (728 voxels, overlap=1.004)
Right_Amygdala (54): linear fit = 1.03 x + 0.0 (728 voxels, peak = 77), gca=76.6
gca peak = 0.10636 (89)
mri peak = 0.07421 (88)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, overlap=0.998)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4999 voxels, peak = 89), gca=88.6
gca peak = 0.11628 (85)
mri peak = 0.07008 (86)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4931 voxels, overlap=0.976)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4931 voxels, peak = 85), gca=84.6
gca peak = 0.09217 (77)
mri peak = 0.07627 (84)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (2240 voxels, overlap=0.880)
Left_Putamen (12): linear fit = 1.01 x + 0.0 (2240 voxels, peak = 78), gca=78.2
gca peak = 0.10883 (78)
mri peak = 0.08326 (83)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2306 voxels, overlap=0.906)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (2306 voxels, peak = 78), gca=78.0
gca peak = 0.07147 (86)
mri peak = 0.06986 (87)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (14679 voxels, overlap=0.809)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (14679 voxels, peak = 86), gca=85.6
gca peak = 0.12083 (87)
mri peak = 0.07740 (90)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1862 voxels, overlap=0.868)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1862 voxels, peak = 87), gca=86.6
gca peak = 0.14063 (89)
mri peak = 0.07510 (93)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1883 voxels, overlap=0.933)
Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1883 voxels, peak = 88), gca=87.7
gca peak = 0.12335 (33)
mri peak = 0.11509 (18)
gca peak = 0.18343 (17)
mri peak = 0.09064 (13)
Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (314 voxels, overlap=0.843)
Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (314 voxels, peak = 14), gca=13.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16503 (28)
gca peak Left_Thalamus = 0.64095 (104)
gca peak Third_Ventricle = 0.12335 (33)
gca peak CSF = 0.20554 (47)
gca peak Left_Accumbens_area = 0.64163 (66)
gca peak Left_undetermined = 0.95280 (30)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.11914 (35)
gca peak Right_Inf_Lat_Vent = 0.21972 (26)
gca peak Right_Accumbens_area = 0.34807 (71)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14509 (37)
gca peak Fifth_Ventricle = 0.75707 (40)
gca peak WM_hypointensities = 0.07483 (78)
gca peak non_WM_hypointensities = 0.09744 (44)
gca peak Optic_Chiasm = 0.71121 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.06 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
89664 voxels changed in iteration 0 of unlikely voxel relabeling
444 voxels changed in iteration 1 of unlikely voxel relabeling
19 voxels changed in iteration 2 of unlikely voxel relabeling
11 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
76959 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
497 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 87748 changed. image ll: -2.152, PF=0.500
pass 2: 24203 changed. image ll: -2.150, PF=0.500
pass 3: 7330 changed.
pass 4: 2452 changed.
69360 voxels changed in iteration 0 of unlikely voxel relabeling
482 voxels changed in iteration 1 of unlikely voxel relabeling
11 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
9213 voxels changed in iteration 0 of unlikely voxel relabeling
203 voxels changed in iteration 1 of unlikely voxel relabeling
16 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6597 voxels changed in iteration 0 of unlikely voxel relabeling
105 voxels changed in iteration 1 of unlikely voxel relabeling
8 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
6776 voxels changed in iteration 0 of unlikely voxel relabeling
49 voxels changed in iteration 1 of unlikely voxel relabeling
0 voxels changed in iteration 2 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    4206.011589
mri_ca_label stimesec    1.858717
mri_ca_label ru_maxrss   2108192
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   640551
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  63328
mri_ca_label ru_oublock  504
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    352
mri_ca_label ru_nivcsw   6784
auto-labeling took 69 minutes and 22 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/transforms/cc_up.lta 0050352 

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-6.0.0/0050352/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/norm.mgz
80449 voxels in left wm, 111265 in right wm, xrange [116, 134]
searching rotation angles z=[-5  9], y=[-2 12]

searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.8  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.3  
searching scale 1 Z rot 6.6  
searching scale 1 Z rot 6.8  
searching scale 1 Z rot 7.1  
searching scale 1 Z rot 7.3  
searching scale 1 Z rot 7.6  
searching scale 1 Z rot 7.8  
searching scale 1 Z rot 8.1  
searching scale 1 Z rot 8.3  
searching scale 1 Z rot 8.6  
searching scale 1 Z rot 8.8  global minimum found at slice 126.0, rotations (4.70, 2.06)
final transformation (x=126.0, yr=4.704, zr=2.060):
 0.99599  -0.03595   0.08195  -3.95324;
 0.03583   0.99935   0.00295   20.18620;
-0.08200  -0.00000   0.99663   14.75014;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [127, 132] in xformed coordinates
best xformed slice 129
cc center is found at 129 103 124
eigenvectors:
 0.00183   0.00166   1.00000;
 0.01257  -0.99992   0.00164;
 0.99992   0.01257  -0.00185;
error in mid anterior detected - correcting...
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aseg.auto.mgz...
corpus callosum segmentation took 2.1 minutes
#--------------------------------------
#@# Merge ASeg Sun Oct  8 03:55:18 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sun Oct  8 03:55:18 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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...
1755 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 109
gm peak at 70 (70), valley at 36 (36)
csf peak at 36, setting threshold to 58
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 69 (69), valley at 35 (35)
csf peak at 35, setting threshold to 57
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 6 seconds.
#--------------------------------------------
#@# Mask BFS Sun Oct  8 03:58:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1774278 voxels in mask (pct= 10.58)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sun Oct  8 03:58:27 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (102.0): 102.3 +- 7.0 [79.0 --> 125.0]
GM (72.0) : 70.3 +- 9.3 [30.0 --> 95.0]
setting bottom of white matter range to 79.6
setting top of gray matter range to 88.8
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...
6346 sparsely connected voxels removed...
thickening thin strands....
20 segments, 3553 filled
1511 bright non-wm voxels segmented.
3366 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 0.54 minutes
reading wm segmentation from wm.seg.mgz...
232 voxels added to wm to prevent paths from MTL structures to cortex
3164 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 50721 voxels turned on, 45036 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 110   new 110
115,126,128 old 110   new 110
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  26 found -  26 modified     |    TOTAL:  26
pass   2 (xy+):   0 found -  26 modified     |    TOTAL:  26
pass   1 (xy-):  24 found -  24 modified     |    TOTAL:  50
pass   2 (xy-):   0 found -  24 modified     |    TOTAL:  50
pass   1 (yz+):  24 found -  24 modified     |    TOTAL:  74
pass   2 (yz+):   0 found -  24 modified     |    TOTAL:  74
pass   1 (yz-):  27 found -  27 modified     |    TOTAL: 101
pass   2 (yz-):   0 found -  27 modified     |    TOTAL: 101
pass   1 (xz+):  19 found -  19 modified     |    TOTAL: 120
pass   2 (xz+):   0 found -  19 modified     |    TOTAL: 120
pass   1 (xz-):  27 found -  27 modified     |    TOTAL: 147
pass   2 (xz-):   0 found -  27 modified     |    TOTAL: 147
Iteration Number : 1
pass   1 (+++):  61 found -  61 modified     |    TOTAL:  61
pass   2 (+++):   0 found -  61 modified     |    TOTAL:  61
pass   1 (+++):  37 found -  37 modified     |    TOTAL:  98
pass   2 (+++):   0 found -  37 modified     |    TOTAL:  98
pass   1 (+++):  45 found -  45 modified     |    TOTAL: 143
pass   2 (+++):   0 found -  45 modified     |    TOTAL: 143
pass   1 (+++):  33 found -  33 modified     |    TOTAL: 176
pass   2 (+++):   0 found -  33 modified     |    TOTAL: 176
Iteration Number : 1
pass   1 (++): 110 found - 110 modified     |    TOTAL: 110
pass   2 (++):   0 found - 110 modified     |    TOTAL: 110
pass   1 (+-):  67 found -  67 modified     |    TOTAL: 177
pass   2 (+-):   0 found -  67 modified     |    TOTAL: 177
pass   1 (--):  63 found -  63 modified     |    TOTAL: 240
pass   2 (--):   0 found -  63 modified     |    TOTAL: 240
pass   1 (-+):  79 found -  79 modified     |    TOTAL: 319
pass   2 (-+):   0 found -  79 modified     |    TOTAL: 319
Iteration Number : 2
pass   1 (xy+):  10 found -  10 modified     |    TOTAL:  10
pass   2 (xy+):   0 found -  10 modified     |    TOTAL:  10
pass   1 (xy-):   8 found -   8 modified     |    TOTAL:  18
pass   2 (xy-):   0 found -   8 modified     |    TOTAL:  18
pass   1 (yz+):   9 found -   9 modified     |    TOTAL:  27
pass   2 (yz+):   0 found -   9 modified     |    TOTAL:  27
pass   1 (yz-):   4 found -   4 modified     |    TOTAL:  31
pass   2 (yz-):   0 found -   4 modified     |    TOTAL:  31
pass   1 (xz+):  10 found -  10 modified     |    TOTAL:  41
pass   2 (xz+):   0 found -  10 modified     |    TOTAL:  41
pass   1 (xz-):  18 found -  18 modified     |    TOTAL:  59
pass   2 (xz-):   0 found -  18 modified     |    TOTAL:  59
Iteration Number : 2
pass   1 (+++):   5 found -   5 modified     |    TOTAL:   5
pass   2 (+++):   0 found -   5 modified     |    TOTAL:   5
pass   1 (+++):   4 found -   4 modified     |    TOTAL:   9
pass   2 (+++):   0 found -   4 modified     |    TOTAL:   9
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  11
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  11
pass   1 (+++):   0 found -   0 modified     |    TOTAL:  11
Iteration Number : 2
pass   1 (++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+-):   5 found -   5 modified     |    TOTAL:  11
pass   2 (+-):   0 found -   5 modified     |    TOTAL:  11
pass   1 (--):   5 found -   5 modified     |    TOTAL:  16
pass   2 (--):   0 found -   5 modified     |    TOTAL:  16
pass   1 (-+):   9 found -   9 modified     |    TOTAL:  25
pass   2 (-+):   0 found -   9 modified     |    TOTAL:  25
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   4
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   3
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 744 (out of 694527: 0.107123)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sun Oct  8 04:00:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 0.95413  -0.06520   0.08700   2.88472;
 0.05271   1.08731   0.01970  -25.91927;
-0.09979  -0.01929   0.97531   1.08168;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1320 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75)
no need to search
using seed (127, 121, 91), TAL = (1.0, -37.0, 7.0)
talairach voxel to voxel transform
 1.03496   0.06040  -0.09354  -1.31879;
-0.05207   0.91633  -0.01387   23.91576;
 0.10486   0.02431   1.01547  -0.77087;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  121,  91) --> (1.0, -37.0, 7.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (1.00, -37.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, -37.00, 7.00) SRC: (110.29, 127.85, 106.01)
search lh wm seed point around talairach space (-17.00, -37.00, 7.00), SRC: (147.55, 125.98, 109.78)
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 04:01:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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


Iteration Number : 1
pass   1 (xy+):   5 found -   5 modified     |    TOTAL:   5
pass   2 (xy+):   0 found -   5 modified     |    TOTAL:   5
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   9
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   9
pass   1 (yz+):   5 found -   5 modified     |    TOTAL:  14
pass   2 (yz+):   0 found -   5 modified     |    TOTAL:  14
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:  17
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:  17
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  20
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  20
pass   1 (xz-):   4 found -   4 modified     |    TOTAL:  24
pass   2 (xz-):   0 found -   4 modified     |    TOTAL:  24
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (--):   2 found -   2 modified     |    TOTAL:   4
pass   2 (--):   0 found -   2 modified     |    TOTAL:   4
pass   1 (-+):   2 found -   2 modified     |    TOTAL:   6
pass   2 (-+):   0 found -   2 modified     |    TOTAL:   6
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 = 30 (out of 327785: 0.009152)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 908 vertices, 1007 faces
slice 60: 6411 vertices, 6668 faces
slice 70: 15533 vertices, 15901 faces
slice 80: 25661 vertices, 26084 faces
slice 90: 37638 vertices, 38060 faces
slice 100: 49324 vertices, 49776 faces
slice 110: 61767 vertices, 62287 faces
slice 120: 75034 vertices, 75611 faces
slice 130: 88695 vertices, 89288 faces
slice 140: 102788 vertices, 103442 faces
slice 150: 117164 vertices, 117866 faces
slice 160: 131053 vertices, 131690 faces
slice 170: 141710 vertices, 142296 faces
slice 180: 151516 vertices, 152084 faces
slice 190: 159921 vertices, 160464 faces
slice 200: 166966 vertices, 167489 faces
slice 210: 171723 vertices, 172108 faces
slice 220: 172174 vertices, 172468 faces
slice 230: 172174 vertices, 172468 faces
slice 240: 172174 vertices, 172468 faces
slice 250: 172174 vertices, 172468 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...
   172174 voxel in cpt #1: X=-294 [v=172174,e=517404,f=344936] located at (-28.166349, -1.312951, 9.485765)
For the whole surface: X=-294 [v=172174,e=517404,f=344936]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sun Oct  8 04:01:42 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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


Iteration Number : 1
pass   1 (xy+):   9 found -   9 modified     |    TOTAL:   9
pass   2 (xy+):   0 found -   9 modified     |    TOTAL:   9
pass   1 (xy-):   2 found -   2 modified     |    TOTAL:  11
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:  11
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:  13
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:  13
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  15
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  15
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:  17
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:  17
pass   1 (xz-):   7 found -   7 modified     |    TOTAL:  24
pass   2 (xz-):   0 found -   7 modified     |    TOTAL:  24
Iteration Number : 1
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (--):   2 found -   2 modified     |    TOTAL:   5
pass   2 (--):   0 found -   2 modified     |    TOTAL:   5
pass   1 (-+):   5 found -   5 modified     |    TOTAL:  10
pass   2 (-+):   0 found -   5 modified     |    TOTAL:  10
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 = 36 (out of 342713: 0.010504)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 50: 1463 vertices, 1596 faces
slice 60: 8749 vertices, 9066 faces
slice 70: 19184 vertices, 19639 faces
slice 80: 32377 vertices, 32963 faces
slice 90: 47305 vertices, 47862 faces
slice 100: 60944 vertices, 61505 faces
slice 110: 75515 vertices, 76169 faces
slice 120: 90167 vertices, 90778 faces
slice 130: 104430 vertices, 105108 faces
slice 140: 119587 vertices, 120369 faces
slice 150: 133510 vertices, 134196 faces
slice 160: 146115 vertices, 146852 faces
slice 170: 156195 vertices, 156838 faces
slice 180: 165046 vertices, 165653 faces
slice 190: 172950 vertices, 173534 faces
slice 200: 179473 vertices, 180009 faces
slice 210: 183407 vertices, 183819 faces
slice 220: 183780 vertices, 184134 faces
slice 230: 183780 vertices, 184134 faces
slice 240: 183780 vertices, 184134 faces
slice 250: 183780 vertices, 184134 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...
   183780 voxel in cpt #1: X=-354 [v=183780,e=552402,f=368268] located at (30.536516, -6.303988, 8.369474)
For the whole surface: X=-354 [v=183780,e=552402,f=368268]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sun Oct  8 04:01:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sun Oct  8 04:01:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

Waiting for PID 16188 of (16188 16191) to complete...
Waiting for PID 16191 of (16188 16191) 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 (16188 16191) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sun Oct  8 04:01:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sun Oct  8 04:01:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

Waiting for PID 16253 of (16253 16256) to complete...
Waiting for PID 16256 of (16253 16256) to complete...

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

Not saving sulc
Reading ../surf/lh.smoothwm.nofix
avg radius = 49.1 mm, total surface area = 88904 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.173 (target=0.015)   
step 005: RMS=0.136 (target=0.015)   
step 010: RMS=0.111 (target=0.015)   
step 015: RMS=0.099 (target=0.015)   
step 020: RMS=0.092 (target=0.015)   
step 025: RMS=0.085 (target=0.015)   
step 030: RMS=0.080 (target=0.015)   
step 035: RMS=0.077 (target=0.015)   
step 040: RMS=0.074 (target=0.015)   
step 045: RMS=0.072 (target=0.015)   
step 050: RMS=0.071 (target=0.015)   
step 055: RMS=0.070 (target=0.015)   
step 060: RMS=0.070 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    53.210910
mris_inflate stimesec    0.133979
mris_inflate ru_maxrss   252252
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   36435
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  12144
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2043
mris_inflate ru_nivcsw   5301

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 49.6 mm, total surface area = 94197 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.9 minutes

step 000: RMS=0.177 (target=0.015)   
step 005: RMS=0.139 (target=0.015)   
step 010: RMS=0.113 (target=0.015)   
step 015: RMS=0.103 (target=0.015)   
step 020: RMS=0.094 (target=0.015)   
step 025: RMS=0.088 (target=0.015)   
step 030: RMS=0.085 (target=0.015)   
step 035: RMS=0.081 (target=0.015)   
step 040: RMS=0.079 (target=0.015)   
step 045: RMS=0.077 (target=0.015)   
step 050: RMS=0.075 (target=0.015)   
step 055: RMS=0.075 (target=0.015)   
step 060: RMS=0.074 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    55.976490
mris_inflate stimesec    0.143978
mris_inflate ru_maxrss   269028
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   38579
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  12944
mris_inflate ru_oublock  12960
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    4920
mris_inflate ru_nivcsw   4102
PIDs (16253 16256) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sun Oct  8 04:02:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

#--------------------------------------------
#@# QSphere rh Sun Oct  8 04:02:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

Waiting for PID 16310 of (16310 16314) to complete...
Waiting for PID 16314 of (16310 16314) to complete...

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.89 +- 0.55 (0.00-->6.93) (max @ vno 57444 --> 57445)
face area 0.02 +- 0.03 (-0.21-->0.70)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.292...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.350, avgs=0
005/300: dt: 0.9000, rms radial error=176.091, avgs=0
010/300: dt: 0.9000, rms radial error=175.535, avgs=0
015/300: dt: 0.9000, rms radial error=174.806, avgs=0
020/300: dt: 0.9000, rms radial error=173.977, avgs=0
025/300: dt: 0.9000, rms radial error=173.090, avgs=0
030/300: dt: 0.9000, rms radial error=172.171, avgs=0
035/300: dt: 0.9000, rms radial error=171.235, avgs=0
040/300: dt: 0.9000, rms radial error=170.292, avgs=0
045/300: dt: 0.9000, rms radial error=169.345, avgs=0
050/300: dt: 0.9000, rms radial error=168.399, avgs=0
055/300: dt: 0.9000, rms radial error=167.455, avgs=0
060/300: dt: 0.9000, rms radial error=166.515, avgs=0
065/300: dt: 0.9000, rms radial error=165.580, avgs=0
070/300: dt: 0.9000, rms radial error=164.649, avgs=0
075/300: dt: 0.9000, rms radial error=163.723, avgs=0
080/300: dt: 0.9000, rms radial error=162.802, avgs=0
085/300: dt: 0.9000, rms radial error=161.886, avgs=0
090/300: dt: 0.9000, rms radial error=160.975, avgs=0
095/300: dt: 0.9000, rms radial error=160.069, avgs=0
100/300: dt: 0.9000, rms radial error=159.168, avgs=0
105/300: dt: 0.9000, rms radial error=158.271, avgs=0
110/300: dt: 0.9000, rms radial error=157.380, avgs=0
115/300: dt: 0.9000, rms radial error=156.493, avgs=0
120/300: dt: 0.9000, rms radial error=155.612, avgs=0
125/300: dt: 0.9000, rms radial error=154.735, avgs=0
130/300: dt: 0.9000, rms radial error=153.863, avgs=0
135/300: dt: 0.9000, rms radial error=152.995, avgs=0
140/300: dt: 0.9000, rms radial error=152.133, avgs=0
145/300: dt: 0.9000, rms radial error=151.275, avgs=0
150/300: dt: 0.9000, rms radial error=150.422, avgs=0
155/300: dt: 0.9000, rms radial error=149.574, avgs=0
160/300: dt: 0.9000, rms radial error=148.730, avgs=0
165/300: dt: 0.9000, rms radial error=147.891, avgs=0
170/300: dt: 0.9000, rms radial error=147.057, avgs=0
175/300: dt: 0.9000, rms radial error=146.227, avgs=0
180/300: dt: 0.9000, rms radial error=145.402, avgs=0
185/300: dt: 0.9000, rms radial error=144.582, avgs=0
190/300: dt: 0.9000, rms radial error=143.766, avgs=0
195/300: dt: 0.9000, rms radial error=142.955, avgs=0
200/300: dt: 0.9000, rms radial error=142.148, avgs=0
205/300: dt: 0.9000, rms radial error=141.346, avgs=0
210/300: dt: 0.9000, rms radial error=140.548, avgs=0
215/300: dt: 0.9000, rms radial error=139.755, avgs=0
220/300: dt: 0.9000, rms radial error=138.966, avgs=0
225/300: dt: 0.9000, rms radial error=138.181, avgs=0
230/300: dt: 0.9000, rms radial error=137.401, avgs=0
235/300: dt: 0.9000, rms radial error=136.625, avgs=0
240/300: dt: 0.9000, rms radial error=135.853, avgs=0
245/300: dt: 0.9000, rms radial error=135.085, avgs=0
250/300: dt: 0.9000, rms radial error=134.322, avgs=0
255/300: dt: 0.9000, rms radial error=133.563, avgs=0
260/300: dt: 0.9000, rms radial error=132.809, avgs=0
265/300: dt: 0.9000, rms radial error=132.059, avgs=0
270/300: dt: 0.9000, rms radial error=131.312, avgs=0
275/300: dt: 0.9000, rms radial error=130.571, avgs=0
280/300: dt: 0.9000, rms radial error=129.833, avgs=0
285/300: dt: 0.9000, rms radial error=129.100, avgs=0
290/300: dt: 0.9000, rms radial error=128.371, avgs=0
295/300: dt: 0.9000, rms radial error=127.646, avgs=0
300/300: dt: 0.9000, rms radial error=126.925, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20645.08
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 3646.27
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 3 (K=160.0), pass 1, starting sse = 452.69
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00421
epoch 4 (K=640.0), pass 1, starting sse = 54.66
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/12 = 0.00671
final distance error %26.88
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    307.246291
mris_sphere stimesec    0.179972
mris_sphere ru_maxrss   252452
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   36475
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  12128
mris_sphere ru_oublock  12168
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8235
mris_sphere ru_nivcsw   23619
FSRUNTIME@ mris_sphere  0.0855 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 0.87 +- 0.55 (0.00-->7.78) (max @ vno 70471 --> 70472)
face area 0.02 +- 0.03 (-0.20-->0.56)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.287...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.280, avgs=0
005/300: dt: 0.9000, rms radial error=176.020, avgs=0
010/300: dt: 0.9000, rms radial error=175.463, avgs=0
015/300: dt: 0.9000, rms radial error=174.731, avgs=0
020/300: dt: 0.9000, rms radial error=173.899, avgs=0
025/300: dt: 0.9000, rms radial error=173.009, avgs=0
030/300: dt: 0.9000, rms radial error=172.087, avgs=0
035/300: dt: 0.9000, rms radial error=171.149, avgs=0
040/300: dt: 0.9000, rms radial error=170.203, avgs=0
045/300: dt: 0.9000, rms radial error=169.256, avgs=0
050/300: dt: 0.9000, rms radial error=168.310, avgs=0
055/300: dt: 0.9000, rms radial error=167.368, avgs=0
060/300: dt: 0.9000, rms radial error=166.429, avgs=0
065/300: dt: 0.9000, rms radial error=165.495, avgs=0
070/300: dt: 0.9000, rms radial error=164.566, avgs=0
075/300: dt: 0.9000, rms radial error=163.642, avgs=0
080/300: dt: 0.9000, rms radial error=162.723, avgs=0
085/300: dt: 0.9000, rms radial error=161.808, avgs=0
090/300: dt: 0.9000, rms radial error=160.899, avgs=0
095/300: dt: 0.9000, rms radial error=159.994, avgs=0
100/300: dt: 0.9000, rms radial error=159.094, avgs=0
105/300: dt: 0.9000, rms radial error=158.199, avgs=0
110/300: dt: 0.9000, rms radial error=157.309, avgs=0
115/300: dt: 0.9000, rms radial error=156.423, avgs=0
120/300: dt: 0.9000, rms radial error=155.542, avgs=0
125/300: dt: 0.9000, rms radial error=154.667, avgs=0
130/300: dt: 0.9000, rms radial error=153.795, avgs=0
135/300: dt: 0.9000, rms radial error=152.929, avgs=0
140/300: dt: 0.9000, rms radial error=152.067, avgs=0
145/300: dt: 0.9000, rms radial error=151.211, avgs=0
150/300: dt: 0.9000, rms radial error=150.359, avgs=0
155/300: dt: 0.9000, rms radial error=149.512, avgs=0
160/300: dt: 0.9000, rms radial error=148.669, avgs=0
165/300: dt: 0.9000, rms radial error=147.831, avgs=0
170/300: dt: 0.9000, rms radial error=146.998, avgs=0
175/300: dt: 0.9000, rms radial error=146.170, avgs=0
180/300: dt: 0.9000, rms radial error=145.346, avgs=0
185/300: dt: 0.9000, rms radial error=144.527, avgs=0
190/300: dt: 0.9000, rms radial error=143.713, avgs=0
195/300: dt: 0.9000, rms radial error=142.903, avgs=0
200/300: dt: 0.9000, rms radial error=142.098, avgs=0
205/300: dt: 0.9000, rms radial error=141.297, avgs=0
210/300: dt: 0.9000, rms radial error=140.501, avgs=0
215/300: dt: 0.9000, rms radial error=139.709, avgs=0
220/300: dt: 0.9000, rms radial error=138.921, avgs=0
225/300: dt: 0.9000, rms radial error=138.138, avgs=0
230/300: dt: 0.9000, rms radial error=137.359, avgs=0
235/300: dt: 0.9000, rms radial error=136.585, avgs=0
240/300: dt: 0.9000, rms radial error=135.815, avgs=0
245/300: dt: 0.9000, rms radial error=135.049, avgs=0
250/300: dt: 0.9000, rms radial error=134.288, avgs=0
255/300: dt: 0.9000, rms radial error=133.531, avgs=0
260/300: dt: 0.9000, rms radial error=132.778, avgs=0
265/300: dt: 0.9000, rms radial error=132.030, avgs=0
270/300: dt: 0.9000, rms radial error=131.285, avgs=0
275/300: dt: 0.9000, rms radial error=130.545, avgs=0
280/300: dt: 0.9000, rms radial error=129.810, avgs=0
285/300: dt: 0.9000, rms radial error=129.078, avgs=0
290/300: dt: 0.9000, rms radial error=128.350, avgs=0
295/300: dt: 0.9000, rms radial error=127.626, avgs=0
300/300: dt: 0.9000, rms radial error=126.907, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 22174.97
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00009
epoch 2 (K=40.0), pass 1, starting sse = 4004.38
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 522.09
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00198
epoch 4 (K=640.0), pass 1, starting sse = 72.62
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00478
final distance error %26.73
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.09 hours
mris_sphere utimesec    313.009415
mris_sphere stimesec    0.192970
mris_sphere ru_maxrss   269252
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   38634
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  12984
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    10345
mris_sphere ru_nivcsw   22229
FSRUNTIME@ mris_sphere  0.0865 hours 1 threads
PIDs (16310 16314) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sun Oct  8 04:08:03 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sun Oct  8 04:08:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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


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

#@# Fix Topology lh Sun Oct  8 04:08:04 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 lh 

#@# Fix Topology rh Sun Oct  8 04:08:04 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 rh 

Waiting for PID 16546 of (16546 16549) to complete...
Waiting for PID 16549 of (16546 16549) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 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=-294 (nv=172174, nf=344936, ne=517404, g=148)
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 7 iterations
marking ambiguous vertices...
27566 ambiguous faces found in tessellation
segmenting defects...
116 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 35 into 32
      -merging segment 43 into 40
      -merging segment 48 into 40
      -merging segment 42 into 41
      -merging segment 63 into 61
      -merging segment 61 into 73
      -merging segment 88 into 90
      -merging segment 104 into 101
      -merging segment 115 into 114
107 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2572  (-4.6286)
      -vertex     loglikelihood: -6.0585  (-3.0292)
      -normal dot loglikelihood: -3.6004  (-3.6004)
      -quad curv  loglikelihood: -6.5483  (-3.2742)
      Total Loglikelihood : -25.4644

CORRECTING DEFECT 0 (vertices=29, convex hull=53, v0=2)
After retessellation of defect 0 (v0=2), euler #=-105 (156084,463153,306964) : difference with theory (-104) = 1 

CORRECTING DEFECT 1 (vertices=48, convex hull=55, v0=23)
After retessellation of defect 1 (v0=23), euler #=-104 (156089,463189,306996) : difference with theory (-103) = 1 

CORRECTING DEFECT 2 (vertices=42, convex hull=81, v0=229)
After retessellation of defect 2 (v0=229), euler #=-103 (156100,463254,307051) : difference with theory (-102) = 1 

CORRECTING DEFECT 3 (vertices=766, convex hull=362, v0=378)
After retessellation of defect 3 (v0=378), euler #=-103 (156287,464017,307627) : difference with theory (-101) = 2 

CORRECTING DEFECT 4 (vertices=6, convex hull=25, v0=668)
After retessellation of defect 4 (v0=668), euler #=-102 (156288,464026,307636) : difference with theory (-100) = 2 

CORRECTING DEFECT 5 (vertices=118, convex hull=27, v0=848)
After retessellation of defect 5 (v0=848), euler #=-101 (156292,464044,307651) : difference with theory (-99) = 2 

CORRECTING DEFECT 6 (vertices=50, convex hull=57, v0=1702)
After retessellation of defect 6 (v0=1702), euler #=-100 (156303,464100,307697) : difference with theory (-98) = 2 

CORRECTING DEFECT 7 (vertices=10, convex hull=26, v0=1939)
After retessellation of defect 7 (v0=1939), euler #=-99 (156304,464112,307709) : difference with theory (-97) = 2 

CORRECTING DEFECT 8 (vertices=21, convex hull=37, v0=2126)
After retessellation of defect 8 (v0=2126), euler #=-98 (156309,464142,307735) : difference with theory (-96) = 2 

CORRECTING DEFECT 9 (vertices=530, convex hull=427, v0=2918)
After retessellation of defect 9 (v0=2918), euler #=-98 (156481,464883,308304) : difference with theory (-95) = 3 

CORRECTING DEFECT 10 (vertices=13, convex hull=20, v0=3106)
After retessellation of defect 10 (v0=3106), euler #=-97 (156482,464893,308314) : difference with theory (-94) = 3 

CORRECTING DEFECT 11 (vertices=33, convex hull=81, v0=3766)
After retessellation of defect 11 (v0=3766), euler #=-96 (156499,464980,308385) : difference with theory (-93) = 3 

CORRECTING DEFECT 12 (vertices=62, convex hull=68, v0=5713)
After retessellation of defect 12 (v0=5713), euler #=-95 (156522,465076,308459) : difference with theory (-92) = 3 

CORRECTING DEFECT 13 (vertices=20, convex hull=55, v0=6929)
After retessellation of defect 13 (v0=6929), euler #=-94 (156534,465132,308504) : difference with theory (-91) = 3 

CORRECTING DEFECT 14 (vertices=10, convex hull=28, v0=7172)
After retessellation of defect 14 (v0=7172), euler #=-93 (156535,465144,308516) : difference with theory (-90) = 3 

CORRECTING DEFECT 15 (vertices=30, convex hull=47, v0=8715)
After retessellation of defect 15 (v0=8715), euler #=-92 (156540,465176,308544) : difference with theory (-89) = 3 

CORRECTING DEFECT 16 (vertices=33, convex hull=79, v0=8844)
After retessellation of defect 16 (v0=8844), euler #=-91 (156557,465254,308606) : difference with theory (-88) = 3 

CORRECTING DEFECT 17 (vertices=51, convex hull=43, v0=9644)
After retessellation of defect 17 (v0=9644), euler #=-90 (156566,465298,308642) : difference with theory (-87) = 3 

CORRECTING DEFECT 18 (vertices=157, convex hull=56, v0=13009)
After retessellation of defect 18 (v0=13009), euler #=-89 (156583,465374,308702) : difference with theory (-86) = 3 

CORRECTING DEFECT 19 (vertices=50, convex hull=90, v0=13928)
After retessellation of defect 19 (v0=13928), euler #=-88 (156608,465488,308792) : difference with theory (-85) = 3 

CORRECTING DEFECT 20 (vertices=6, convex hull=29, v0=14464)
After retessellation of defect 20 (v0=14464), euler #=-87 (156608,465496,308801) : difference with theory (-84) = 3 

CORRECTING DEFECT 21 (vertices=35, convex hull=59, v0=20239)
After retessellation of defect 21 (v0=20239), euler #=-86 (156625,465575,308864) : difference with theory (-83) = 3 

CORRECTING DEFECT 22 (vertices=74, convex hull=133, v0=20596)
After retessellation of defect 22 (v0=20596), euler #=-85 (156676,465789,309028) : difference with theory (-82) = 3 

CORRECTING DEFECT 23 (vertices=40, convex hull=21, v0=20599)
After retessellation of defect 23 (v0=20599), euler #=-84 (156678,465800,309038) : difference with theory (-81) = 3 

CORRECTING DEFECT 24 (vertices=33, convex hull=74, v0=22662)
After retessellation of defect 24 (v0=22662), euler #=-83 (156696,465884,309105) : difference with theory (-80) = 3 

CORRECTING DEFECT 25 (vertices=50, convex hull=84, v0=26818)
After retessellation of defect 25 (v0=26818), euler #=-82 (156729,466019,309208) : difference with theory (-79) = 3 

CORRECTING DEFECT 26 (vertices=26, convex hull=58, v0=27815)
After retessellation of defect 26 (v0=27815), euler #=-81 (156741,466079,309257) : difference with theory (-78) = 3 

CORRECTING DEFECT 27 (vertices=6, convex hull=17, v0=29119)
After retessellation of defect 27 (v0=29119), euler #=-80 (156742,466085,309263) : difference with theory (-77) = 3 

CORRECTING DEFECT 28 (vertices=50, convex hull=102, v0=35491)
After retessellation of defect 28 (v0=35491), euler #=-79 (156769,466210,309362) : difference with theory (-76) = 3 

CORRECTING DEFECT 29 (vertices=85, convex hull=118, v0=36517)
After retessellation of defect 29 (v0=36517), euler #=-78 (156818,466409,309513) : difference with theory (-75) = 3 

CORRECTING DEFECT 30 (vertices=40, convex hull=83, v0=39096)
After retessellation of defect 30 (v0=39096), euler #=-77 (156843,466515,309595) : difference with theory (-74) = 3 

CORRECTING DEFECT 31 (vertices=137, convex hull=67, v0=40936)
After retessellation of defect 31 (v0=40936), euler #=-76 (156868,466616,309672) : difference with theory (-73) = 3 

CORRECTING DEFECT 32 (vertices=881, convex hull=309, v0=42366)
After retessellation of defect 32 (v0=42366), euler #=-75 (156978,467093,310040) : difference with theory (-72) = 3 

CORRECTING DEFECT 33 (vertices=32, convex hull=64, v0=44298)
After retessellation of defect 33 (v0=44298), euler #=-74 (156993,467161,310094) : difference with theory (-71) = 3 

CORRECTING DEFECT 34 (vertices=26, convex hull=66, v0=44592)
After retessellation of defect 34 (v0=44592), euler #=-73 (157007,467231,310151) : difference with theory (-70) = 3 

CORRECTING DEFECT 35 (vertices=66, convex hull=83, v0=48182)
After retessellation of defect 35 (v0=48182), euler #=-72 (157035,467346,310239) : difference with theory (-69) = 3 

CORRECTING DEFECT 36 (vertices=91, convex hull=90, v0=50023)
After retessellation of defect 36 (v0=50023), euler #=-71 (157077,467509,310361) : difference with theory (-68) = 3 

CORRECTING DEFECT 37 (vertices=91, convex hull=120, v0=51833)
After retessellation of defect 37 (v0=51833), euler #=-70 (157127,467714,310517) : difference with theory (-67) = 3 

CORRECTING DEFECT 38 (vertices=27, convex hull=57, v0=52332)
After retessellation of defect 38 (v0=52332), euler #=-69 (157139,467772,310564) : difference with theory (-66) = 3 

CORRECTING DEFECT 39 (vertices=530, convex hull=303, v0=52876)
After retessellation of defect 39 (v0=52876), euler #=-66 (157304,468431,311061) : difference with theory (-65) = 1 

CORRECTING DEFECT 40 (vertices=527, convex hull=246, v0=55061)
After retessellation of defect 40 (v0=55061), euler #=-64 (157332,468638,311242) : difference with theory (-64) = 0 

CORRECTING DEFECT 41 (vertices=74, convex hull=133, v0=63103)
After retessellation of defect 41 (v0=63103), euler #=-63 (157365,468797,311369) : difference with theory (-63) = 0 

CORRECTING DEFECT 42 (vertices=18, convex hull=25, v0=63370)
After retessellation of defect 42 (v0=63370), euler #=-62 (157368,468814,311384) : difference with theory (-62) = 0 

CORRECTING DEFECT 43 (vertices=26, convex hull=52, v0=64436)
After retessellation of defect 43 (v0=64436), euler #=-61 (157378,468861,311422) : difference with theory (-61) = 0 

CORRECTING DEFECT 44 (vertices=118, convex hull=124, v0=68002)
After retessellation of defect 44 (v0=68002), euler #=-60 (157437,469097,311600) : difference with theory (-60) = 0 

CORRECTING DEFECT 45 (vertices=72, convex hull=71, v0=69339)
After retessellation of defect 45 (v0=69339), euler #=-59 (157471,469228,311698) : difference with theory (-59) = 0 

CORRECTING DEFECT 46 (vertices=245, convex hull=237, v0=70700)
After retessellation of defect 46 (v0=70700), euler #=-58 (157523,469504,311923) : difference with theory (-58) = 0 

CORRECTING DEFECT 47 (vertices=76, convex hull=113, v0=70911)
After retessellation of defect 47 (v0=70911), euler #=-57 (157565,469676,312054) : difference with theory (-57) = 0 

CORRECTING DEFECT 48 (vertices=16, convex hull=26, v0=73542)
After retessellation of defect 48 (v0=73542), euler #=-56 (157567,469690,312067) : difference with theory (-56) = 0 

CORRECTING DEFECT 49 (vertices=41, convex hull=65, v0=74200)
After retessellation of defect 49 (v0=74200), euler #=-55 (157590,469784,312139) : difference with theory (-55) = 0 

CORRECTING DEFECT 50 (vertices=27, convex hull=78, v0=82043)
After retessellation of defect 50 (v0=82043), euler #=-54 (157605,469860,312201) : difference with theory (-54) = 0 

CORRECTING DEFECT 51 (vertices=21, convex hull=12, v0=84998)
After retessellation of defect 51 (v0=84998), euler #=-53 (157606,469866,312207) : difference with theory (-53) = 0 

CORRECTING DEFECT 52 (vertices=661, convex hull=249, v0=85827)
After retessellation of defect 52 (v0=85827), euler #=-54 (157640,470101,312407) : difference with theory (-52) = 2 

CORRECTING DEFECT 53 (vertices=28, convex hull=42, v0=86243)
After retessellation of defect 53 (v0=86243), euler #=-53 (157652,470152,312447) : difference with theory (-51) = 2 

CORRECTING DEFECT 54 (vertices=248, convex hull=218, v0=87211)
After retessellation of defect 54 (v0=87211), euler #=-52 (157724,470473,312697) : difference with theory (-50) = 2 

CORRECTING DEFECT 55 (vertices=71, convex hull=64, v0=89208)
After retessellation of defect 55 (v0=89208), euler #=-51 (157743,470557,312763) : difference with theory (-49) = 2 

CORRECTING DEFECT 56 (vertices=49, convex hull=30, v0=89444)
After retessellation of defect 56 (v0=89444), euler #=-50 (157750,470586,312786) : difference with theory (-48) = 2 

CORRECTING DEFECT 57 (vertices=56, convex hull=81, v0=92147)
After retessellation of defect 57 (v0=92147), euler #=-49 (157766,470667,312852) : difference with theory (-47) = 2 

CORRECTING DEFECT 58 (vertices=40, convex hull=75, v0=95424)
After retessellation of defect 58 (v0=95424), euler #=-48 (157787,470760,312925) : difference with theory (-46) = 2 

CORRECTING DEFECT 59 (vertices=306, convex hull=111, v0=96898)
After retessellation of defect 59 (v0=96898), euler #=-48 (157823,470929,313058) : difference with theory (-45) = 3 

CORRECTING DEFECT 60 (vertices=37, convex hull=68, v0=97736)
After retessellation of defect 60 (v0=97736), euler #=-47 (157848,471030,313135) : difference with theory (-44) = 3 

CORRECTING DEFECT 61 (vertices=48, convex hull=38, v0=98345)
After retessellation of defect 61 (v0=98345), euler #=-46 (157856,471068,313166) : difference with theory (-43) = 3 

CORRECTING DEFECT 62 (vertices=9, convex hull=16, v0=101032)
After retessellation of defect 62 (v0=101032), euler #=-45 (157856,471071,313170) : difference with theory (-42) = 3 

CORRECTING DEFECT 63 (vertices=1511, convex hull=649, v0=102420)
XL defect detected...
After retessellation of defect 63 (v0=102420), euler #=-44 (158282,472737,314411) : difference with theory (-41) = 3 

CORRECTING DEFECT 64 (vertices=803, convex hull=286, v0=102689)
After retessellation of defect 64 (v0=102689), euler #=-44 (158501,473547,315002) : difference with theory (-40) = 4 

CORRECTING DEFECT 65 (vertices=132, convex hull=138, v0=102717)
After retessellation of defect 65 (v0=102717), euler #=-43 (158542,473733,315148) : difference with theory (-39) = 4 

CORRECTING DEFECT 66 (vertices=8, convex hull=13, v0=106833)
After retessellation of defect 66 (v0=106833), euler #=-42 (158542,473736,315152) : difference with theory (-38) = 4 

CORRECTING DEFECT 67 (vertices=237, convex hull=268, v0=107060)
After retessellation of defect 67 (v0=107060), euler #=-39 (158656,474227,315532) : difference with theory (-37) = 2 

CORRECTING DEFECT 68 (vertices=31, convex hull=73, v0=111625)
After retessellation of defect 68 (v0=111625), euler #=-38 (158667,474286,315581) : difference with theory (-36) = 2 

CORRECTING DEFECT 69 (vertices=504, convex hull=110, v0=114254)
After retessellation of defect 69 (v0=114254), euler #=-37 (158683,474389,315669) : difference with theory (-35) = 2 

CORRECTING DEFECT 70 (vertices=1970, convex hull=583, v0=115182)
XL defect detected...
After retessellation of defect 70 (v0=115182), euler #=-36 (159002,475659,316621) : difference with theory (-34) = 2 

CORRECTING DEFECT 71 (vertices=48, convex hull=68, v0=115744)
After retessellation of defect 71 (v0=115744), euler #=-35 (159029,475766,316702) : difference with theory (-33) = 2 

CORRECTING DEFECT 72 (vertices=48, convex hull=71, v0=116475)
After retessellation of defect 72 (v0=116475), euler #=-34 (159038,475821,316749) : difference with theory (-32) = 2 

CORRECTING DEFECT 73 (vertices=135, convex hull=144, v0=121405)
After retessellation of defect 73 (v0=121405), euler #=-33 (159112,476106,316961) : difference with theory (-31) = 2 

CORRECTING DEFECT 74 (vertices=35, convex hull=55, v0=123879)
After retessellation of defect 74 (v0=123879), euler #=-32 (159130,476188,317026) : difference with theory (-30) = 2 

CORRECTING DEFECT 75 (vertices=38, convex hull=19, v0=123938)
After retessellation of defect 75 (v0=123938), euler #=-31 (159134,476205,317040) : difference with theory (-29) = 2 

CORRECTING DEFECT 76 (vertices=352, convex hull=240, v0=123992)
After retessellation of defect 76 (v0=123992), euler #=-30 (159168,476420,317222) : difference with theory (-28) = 2 

CORRECTING DEFECT 77 (vertices=54, convex hull=42, v0=124126)
After retessellation of defect 77 (v0=124126), euler #=-29 (159177,476460,317254) : difference with theory (-27) = 2 

CORRECTING DEFECT 78 (vertices=319, convex hull=116, v0=124391)
After retessellation of defect 78 (v0=124391), euler #=-28 (159198,476574,317348) : difference with theory (-26) = 2 

CORRECTING DEFECT 79 (vertices=40, convex hull=50, v0=124436)
After retessellation of defect 79 (v0=124436), euler #=-27 (159210,476629,317392) : difference with theory (-25) = 2 

CORRECTING DEFECT 80 (vertices=353, convex hull=178, v0=128349)
After retessellation of defect 80 (v0=128349), euler #=-26 (159310,477011,317675) : difference with theory (-24) = 2 

CORRECTING DEFECT 81 (vertices=192, convex hull=146, v0=129529)
After retessellation of defect 81 (v0=129529), euler #=-25 (159385,477313,317903) : difference with theory (-23) = 2 

CORRECTING DEFECT 82 (vertices=24, convex hull=70, v0=133422)
After retessellation of defect 82 (v0=133422), euler #=-24 (159401,477387,317962) : difference with theory (-22) = 2 

CORRECTING DEFECT 83 (vertices=121, convex hull=140, v0=134413)
After retessellation of defect 83 (v0=134413), euler #=-22 (159451,477601,318128) : difference with theory (-21) = 1 

CORRECTING DEFECT 84 (vertices=189, convex hull=124, v0=137416)
After retessellation of defect 84 (v0=137416), euler #=-21 (159469,477712,318222) : difference with theory (-20) = 1 

CORRECTING DEFECT 85 (vertices=59, convex hull=54, v0=140396)
After retessellation of defect 85 (v0=140396), euler #=-20 (159484,477778,318274) : difference with theory (-19) = 1 

CORRECTING DEFECT 86 (vertices=412, convex hull=179, v0=143337)
After retessellation of defect 86 (v0=143337), euler #=-19 (159581,478150,318550) : difference with theory (-18) = 1 

CORRECTING DEFECT 87 (vertices=81, convex hull=101, v0=149604)
After retessellation of defect 87 (v0=149604), euler #=-18 (159611,478279,318650) : difference with theory (-17) = 1 

CORRECTING DEFECT 88 (vertices=72, convex hull=29, v0=152300)
After retessellation of defect 88 (v0=152300), euler #=-17 (159613,478296,318666) : difference with theory (-16) = 1 

CORRECTING DEFECT 89 (vertices=89, convex hull=127, v0=153501)
After retessellation of defect 89 (v0=153501), euler #=-16 (159653,478474,318805) : difference with theory (-15) = 1 

CORRECTING DEFECT 90 (vertices=49, convex hull=43, v0=154167)
After retessellation of defect 90 (v0=154167), euler #=-15 (159661,478514,318838) : difference with theory (-14) = 1 

CORRECTING DEFECT 91 (vertices=58, convex hull=96, v0=158119)
After retessellation of defect 91 (v0=158119), euler #=-15 (159684,478628,318929) : difference with theory (-13) = 2 

CORRECTING DEFECT 92 (vertices=40, convex hull=24, v0=158640)
After retessellation of defect 92 (v0=158640), euler #=-14 (159687,478644,318943) : difference with theory (-12) = 2 

CORRECTING DEFECT 93 (vertices=47, convex hull=81, v0=158691)
After retessellation of defect 93 (v0=158691), euler #=-13 (159711,478754,319030) : difference with theory (-11) = 2 

CORRECTING DEFECT 94 (vertices=31, convex hull=52, v0=159895)
After retessellation of defect 94 (v0=159895), euler #=-11 (159712,478785,319062) : difference with theory (-10) = 1 

CORRECTING DEFECT 95 (vertices=54, convex hull=76, v0=160084)
After retessellation of defect 95 (v0=160084), euler #=-10 (159730,478873,319133) : difference with theory (-9) = 1 

CORRECTING DEFECT 96 (vertices=48, convex hull=47, v0=161185)
After retessellation of defect 96 (v0=161185), euler #=-9 (159736,478914,319169) : difference with theory (-8) = 1 

CORRECTING DEFECT 97 (vertices=233, convex hull=147, v0=162026)
After retessellation of defect 97 (v0=162026), euler #=-8 (159799,479173,319366) : difference with theory (-7) = 1 

CORRECTING DEFECT 98 (vertices=69, convex hull=95, v0=165824)
After retessellation of defect 98 (v0=165824), euler #=-7 (159834,479321,319480) : difference with theory (-6) = 1 

CORRECTING DEFECT 99 (vertices=39, convex hull=62, v0=165959)
After retessellation of defect 99 (v0=165959), euler #=-6 (159854,479403,319543) : difference with theory (-5) = 1 

CORRECTING DEFECT 100 (vertices=52, convex hull=32, v0=166977)
After retessellation of defect 100 (v0=166977), euler #=-5 (159856,479418,319557) : difference with theory (-4) = 1 

CORRECTING DEFECT 101 (vertices=30, convex hull=37, v0=168434)
After retessellation of defect 101 (v0=168434), euler #=-4 (159857,479435,319574) : difference with theory (-3) = 1 

CORRECTING DEFECT 102 (vertices=36, convex hull=70, v0=168683)
After retessellation of defect 102 (v0=168683), euler #=-3 (159868,479495,319624) : difference with theory (-2) = 1 

CORRECTING DEFECT 103 (vertices=58, convex hull=80, v0=169808)
After retessellation of defect 103 (v0=169808), euler #=-2 (159889,479589,319698) : difference with theory (-1) = 1 

CORRECTING DEFECT 104 (vertices=14, convex hull=30, v0=169900)
After retessellation of defect 104 (v0=169900), euler #=-1 (159890,479602,319711) : difference with theory (0) = 1 

CORRECTING DEFECT 105 (vertices=59, convex hull=65, v0=169953)
After retessellation of defect 105 (v0=169953), euler #=0 (159909,479688,319779) : difference with theory (1) = 1 

CORRECTING DEFECT 106 (vertices=92, convex hull=77, v0=171367)
After retessellation of defect 106 (v0=171367), euler #=2 (159921,479757,319838) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.29 (0.03-->16.29) (max @ vno 105861 --> 122187)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.29 (0.03-->16.29) (max @ vno 105861 --> 122187)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
290 mutations (32.2%), 611 crossovers (67.8%), 816 vertices were eliminated
building final representation...
12253 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=159921, nf=319838, ne=479757, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 86.6 minutes
0 defective edges
removing intersecting faces
000: 1135 intersecting
001: 27 intersecting
mris_fix_topology utimesec    5196.526007
mris_fix_topology stimesec    0.649901
mris_fix_topology ru_maxrss   550368
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   65897
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  12128
mris_fix_topology ru_oublock  15896
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   14443
FSRUNTIME@ mris_fix_topology lh  1.4436 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050352 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=-354 (nv=183780, nf=368268, ne=552402, g=178)
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...
41797 ambiguous faces found in tessellation
segmenting defects...
106 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 39 into 18
      -merging segment 27 into 26
      -merging segment 38 into 37
      -merging segment 44 into 37
102 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1383  (-4.5692)
      -vertex     loglikelihood: -5.8863  (-2.9432)
      -normal dot loglikelihood: -3.5515  (-3.5515)
      -quad curv  loglikelihood: -6.0103  (-3.0052)
      Total Loglikelihood : -24.5865

CORRECTING DEFECT 0 (vertices=37, convex hull=52, v0=0)
After retessellation of defect 0 (v0=0), euler #=-90 (160015,473730,313625) : difference with theory (-99) = -9 

CORRECTING DEFECT 1 (vertices=39, convex hull=27, v0=49)
After retessellation of defect 1 (v0=49), euler #=-89 (160018,473747,313640) : difference with theory (-98) = -9 

CORRECTING DEFECT 2 (vertices=126, convex hull=78, v0=54)
After retessellation of defect 2 (v0=54), euler #=-88 (160030,473818,313700) : difference with theory (-97) = -9 

CORRECTING DEFECT 3 (vertices=72, convex hull=99, v0=312)
After retessellation of defect 3 (v0=312), euler #=-87 (160063,473960,313810) : difference with theory (-96) = -9 

CORRECTING DEFECT 4 (vertices=203, convex hull=230, v0=504)
After retessellation of defect 4 (v0=504), euler #=-86 (160144,474310,314080) : difference with theory (-95) = -9 

CORRECTING DEFECT 5 (vertices=34, convex hull=89, v0=550)
After retessellation of defect 5 (v0=550), euler #=-85 (160161,474395,314149) : difference with theory (-94) = -9 

CORRECTING DEFECT 6 (vertices=124, convex hull=128, v0=658)
After retessellation of defect 6 (v0=658), euler #=-84 (160208,474596,314304) : difference with theory (-93) = -9 

CORRECTING DEFECT 7 (vertices=43, convex hull=74, v0=924)
After retessellation of defect 7 (v0=924), euler #=-83 (160221,474665,314361) : difference with theory (-92) = -9 

CORRECTING DEFECT 8 (vertices=723, convex hull=226, v0=1463)
After retessellation of defect 8 (v0=1463), euler #=-82 (160329,475101,314690) : difference with theory (-91) = -9 

CORRECTING DEFECT 9 (vertices=74, convex hull=88, v0=1785)
After retessellation of defect 9 (v0=1785), euler #=-81 (160357,475225,314787) : difference with theory (-90) = -9 

CORRECTING DEFECT 10 (vertices=25, convex hull=62, v0=2082)
After retessellation of defect 10 (v0=2082), euler #=-80 (160369,475283,314834) : difference with theory (-89) = -9 

CORRECTING DEFECT 11 (vertices=153, convex hull=143, v0=2328)
After retessellation of defect 11 (v0=2328), euler #=-79 (160429,475529,315021) : difference with theory (-88) = -9 

CORRECTING DEFECT 12 (vertices=274, convex hull=62, v0=2657)
After retessellation of defect 12 (v0=2657), euler #=-78 (160445,475605,315082) : difference with theory (-87) = -9 

CORRECTING DEFECT 13 (vertices=220, convex hull=177, v0=3059)
After retessellation of defect 13 (v0=3059), euler #=-77 (160526,475921,315318) : difference with theory (-86) = -9 

CORRECTING DEFECT 14 (vertices=58, convex hull=132, v0=3566)
After retessellation of defect 14 (v0=3566), euler #=-76 (160558,476071,315437) : difference with theory (-85) = -9 

CORRECTING DEFECT 15 (vertices=39, convex hull=75, v0=4530)
After retessellation of defect 15 (v0=4530), euler #=-75 (160579,476167,315513) : difference with theory (-84) = -9 

CORRECTING DEFECT 16 (vertices=14, convex hull=13, v0=6123)
After retessellation of defect 16 (v0=6123), euler #=-74 (160579,476170,315517) : difference with theory (-83) = -9 

CORRECTING DEFECT 17 (vertices=329, convex hull=50, v0=6143)
After retessellation of defect 17 (v0=6143), euler #=-73 (160604,476265,315588) : difference with theory (-82) = -9 

CORRECTING DEFECT 18 (vertices=5818, convex hull=1520, v0=6178)
XL defect detected...
After retessellation of defect 18 (v0=6178), euler #=-78 (161095,478550,317377) : difference with theory (-81) = -3 

CORRECTING DEFECT 19 (vertices=75, convex hull=87, v0=6510)
After retessellation of defect 19 (v0=6510), euler #=-77 (161111,478632,317444) : difference with theory (-80) = -3 

CORRECTING DEFECT 20 (vertices=215, convex hull=222, v0=7492)
After retessellation of defect 20 (v0=7492), euler #=-77 (161208,479032,317747) : difference with theory (-79) = -2 

CORRECTING DEFECT 21 (vertices=35, convex hull=67, v0=10145)
After retessellation of defect 21 (v0=10145), euler #=-76 (161217,479087,317794) : difference with theory (-78) = -2 

CORRECTING DEFECT 22 (vertices=67, convex hull=80, v0=11171)
After retessellation of defect 22 (v0=11171), euler #=-75 (161239,479184,317870) : difference with theory (-77) = -2 

CORRECTING DEFECT 23 (vertices=47, convex hull=87, v0=13678)
After retessellation of defect 23 (v0=13678), euler #=-74 (161259,479284,317951) : difference with theory (-76) = -2 

CORRECTING DEFECT 24 (vertices=64, convex hull=33, v0=14984)
After retessellation of defect 24 (v0=14984), euler #=-73 (161270,479327,317984) : difference with theory (-75) = -2 

CORRECTING DEFECT 25 (vertices=43, convex hull=107, v0=18331)
After retessellation of defect 25 (v0=18331), euler #=-72 (161297,479458,318089) : difference with theory (-74) = -2 

CORRECTING DEFECT 26 (vertices=147, convex hull=232, v0=18468)
After retessellation of defect 26 (v0=18468), euler #=-70 (161373,479799,318356) : difference with theory (-73) = -3 

CORRECTING DEFECT 27 (vertices=232, convex hull=306, v0=25636)
After retessellation of defect 27 (v0=25636), euler #=-69 (161481,480278,318728) : difference with theory (-72) = -3 

CORRECTING DEFECT 28 (vertices=199, convex hull=163, v0=27626)
After retessellation of defect 28 (v0=27626), euler #=-68 (161542,480537,318927) : difference with theory (-71) = -3 

CORRECTING DEFECT 29 (vertices=85, convex hull=103, v0=30710)
After retessellation of defect 29 (v0=30710), euler #=-67 (161587,480721,319067) : difference with theory (-70) = -3 

CORRECTING DEFECT 30 (vertices=64, convex hull=76, v0=30737)
After retessellation of defect 30 (v0=30737), euler #=-66 (161611,480827,319150) : difference with theory (-69) = -3 

CORRECTING DEFECT 31 (vertices=34, convex hull=75, v0=37888)
After retessellation of defect 31 (v0=37888), euler #=-65 (161629,480908,319214) : difference with theory (-68) = -3 

CORRECTING DEFECT 32 (vertices=6, convex hull=22, v0=38071)
After retessellation of defect 32 (v0=38071), euler #=-64 (161629,480913,319220) : difference with theory (-67) = -3 

CORRECTING DEFECT 33 (vertices=6, convex hull=17, v0=38220)
After retessellation of defect 33 (v0=38220), euler #=-63 (161630,480920,319227) : difference with theory (-66) = -3 

CORRECTING DEFECT 34 (vertices=20, convex hull=22, v0=38369)
After retessellation of defect 34 (v0=38369), euler #=-62 (161631,480931,319238) : difference with theory (-65) = -3 

CORRECTING DEFECT 35 (vertices=12, convex hull=21, v0=41147)
After retessellation of defect 35 (v0=41147), euler #=-61 (161634,480946,319251) : difference with theory (-64) = -3 

CORRECTING DEFECT 36 (vertices=556, convex hull=392, v0=46035)
After retessellation of defect 36 (v0=46035), euler #=-58 (161754,481512,319700) : difference with theory (-63) = -5 

CORRECTING DEFECT 37 (vertices=774, convex hull=205, v0=66120)
After retessellation of defect 37 (v0=66120), euler #=-57 (161798,481738,319883) : difference with theory (-62) = -5 

CORRECTING DEFECT 38 (vertices=34, convex hull=50, v0=70793)
After retessellation of defect 38 (v0=70793), euler #=-56 (161813,481801,319932) : difference with theory (-61) = -5 

CORRECTING DEFECT 39 (vertices=165, convex hull=168, v0=70889)
After retessellation of defect 39 (v0=70889), euler #=-55 (161907,482165,320203) : difference with theory (-60) = -5 

CORRECTING DEFECT 40 (vertices=197, convex hull=199, v0=73834)
After retessellation of defect 40 (v0=73834), euler #=-54 (161989,482506,320463) : difference with theory (-59) = -5 

CORRECTING DEFECT 41 (vertices=31, convex hull=57, v0=74122)
After retessellation of defect 41 (v0=74122), euler #=-53 (162002,482574,320519) : difference with theory (-58) = -5 

CORRECTING DEFECT 42 (vertices=230, convex hull=309, v0=74758)
After retessellation of defect 42 (v0=74758), euler #=-52 (162169,483227,321006) : difference with theory (-57) = -5 

CORRECTING DEFECT 43 (vertices=76, convex hull=94, v0=80822)
After retessellation of defect 43 (v0=80822), euler #=-51 (162187,483326,321088) : difference with theory (-56) = -5 

CORRECTING DEFECT 44 (vertices=191, convex hull=233, v0=81364)
After retessellation of defect 44 (v0=81364), euler #=-50 (162322,483840,321468) : difference with theory (-55) = -5 

CORRECTING DEFECT 45 (vertices=45, convex hull=69, v0=83573)
After retessellation of defect 45 (v0=83573), euler #=-49 (162347,483943,321547) : difference with theory (-54) = -5 

CORRECTING DEFECT 46 (vertices=298, convex hull=332, v0=84908)
After retessellation of defect 46 (v0=84908), euler #=-48 (162528,484636,322060) : difference with theory (-53) = -5 

CORRECTING DEFECT 47 (vertices=65, convex hull=31, v0=86766)
After retessellation of defect 47 (v0=86766), euler #=-47 (162533,484666,322086) : difference with theory (-52) = -5 

CORRECTING DEFECT 48 (vertices=49, convex hull=71, v0=90673)
After retessellation of defect 48 (v0=90673), euler #=-46 (162557,484771,322168) : difference with theory (-51) = -5 

CORRECTING DEFECT 49 (vertices=158, convex hull=142, v0=90691)
After retessellation of defect 49 (v0=90691), euler #=-46 (162614,485014,322354) : difference with theory (-50) = -4 

CORRECTING DEFECT 50 (vertices=36, convex hull=66, v0=93452)
After retessellation of defect 50 (v0=93452), euler #=-45 (162632,485090,322413) : difference with theory (-49) = -4 

CORRECTING DEFECT 51 (vertices=114, convex hull=105, v0=94033)
After retessellation of defect 51 (v0=94033), euler #=-44 (162672,485256,322540) : difference with theory (-48) = -4 

CORRECTING DEFECT 52 (vertices=123, convex hull=91, v0=94392)
After retessellation of defect 52 (v0=94392), euler #=-43 (162715,485426,322668) : difference with theory (-47) = -4 

CORRECTING DEFECT 53 (vertices=895, convex hull=146, v0=101437)
After retessellation of defect 53 (v0=101437), euler #=-42 (162769,485657,322846) : difference with theory (-46) = -4 

CORRECTING DEFECT 54 (vertices=32, convex hull=38, v0=101458)
After retessellation of defect 54 (v0=101458), euler #=-41 (162772,485684,322871) : difference with theory (-45) = -4 

CORRECTING DEFECT 55 (vertices=19, convex hull=29, v0=102378)
After retessellation of defect 55 (v0=102378), euler #=-40 (162775,485700,322885) : difference with theory (-44) = -4 

CORRECTING DEFECT 56 (vertices=43, convex hull=37, v0=104074)
After retessellation of defect 56 (v0=104074), euler #=-39 (162779,485726,322908) : difference with theory (-43) = -4 

CORRECTING DEFECT 57 (vertices=1255, convex hull=311, v0=104364)
After retessellation of defect 57 (v0=104364), euler #=-38 (163005,486562,323519) : difference with theory (-42) = -4 

CORRECTING DEFECT 58 (vertices=32, convex hull=44, v0=105703)
After retessellation of defect 58 (v0=105703), euler #=-37 (163021,486623,323565) : difference with theory (-41) = -4 

CORRECTING DEFECT 59 (vertices=55, convex hull=61, v0=106032)
After retessellation of defect 59 (v0=106032), euler #=-36 (163055,486750,323659) : difference with theory (-40) = -4 

CORRECTING DEFECT 60 (vertices=35, convex hull=82, v0=106699)
After retessellation of defect 60 (v0=106699), euler #=-35 (163070,486824,323719) : difference with theory (-39) = -4 

CORRECTING DEFECT 61 (vertices=91, convex hull=126, v0=106766)
After retessellation of defect 61 (v0=106766), euler #=-34 (163093,486947,323820) : difference with theory (-38) = -4 

CORRECTING DEFECT 62 (vertices=10, convex hull=15, v0=108216)
After retessellation of defect 62 (v0=108216), euler #=-33 (163094,486956,323829) : difference with theory (-37) = -4 

CORRECTING DEFECT 63 (vertices=130, convex hull=37, v0=108784)
After retessellation of defect 63 (v0=108784), euler #=-32 (163104,486997,323861) : difference with theory (-36) = -4 

CORRECTING DEFECT 64 (vertices=25, convex hull=72, v0=109094)
After retessellation of defect 64 (v0=109094), euler #=-31 (163118,487066,323917) : difference with theory (-35) = -4 

CORRECTING DEFECT 65 (vertices=119, convex hull=154, v0=109223)
After retessellation of defect 65 (v0=109223), euler #=-30 (163156,487254,324068) : difference with theory (-34) = -4 

CORRECTING DEFECT 66 (vertices=1473, convex hull=583, v0=109735)
XL defect detected...
After retessellation of defect 66 (v0=109735), euler #=-31 (163364,488194,324799) : difference with theory (-33) = -2 

CORRECTING DEFECT 67 (vertices=20, convex hull=52, v0=115296)
After retessellation of defect 67 (v0=115296), euler #=-30 (163374,488243,324839) : difference with theory (-32) = -2 

CORRECTING DEFECT 68 (vertices=41, convex hull=70, v0=116131)
After retessellation of defect 68 (v0=116131), euler #=-29 (163397,488340,324914) : difference with theory (-31) = -2 

CORRECTING DEFECT 69 (vertices=82, convex hull=125, v0=121326)
After retessellation of defect 69 (v0=121326), euler #=-28 (163439,488523,325056) : difference with theory (-30) = -2 

CORRECTING DEFECT 70 (vertices=2129, convex hull=777, v0=122199)
XL defect detected...
After retessellation of defect 70 (v0=122199), euler #=-29 (164084,490895,326782) : difference with theory (-29) = 0 

CORRECTING DEFECT 71 (vertices=1604, convex hull=592, v0=126769)
XL defect detected...
After retessellation of defect 71 (v0=126769), euler #=-28 (164516,492512,327968) : difference with theory (-28) = 0 

CORRECTING DEFECT 72 (vertices=17, convex hull=29, v0=130383)
After retessellation of defect 72 (v0=130383), euler #=-27 (164519,492528,327982) : difference with theory (-27) = 0 

CORRECTING DEFECT 73 (vertices=649, convex hull=366, v0=130457)
After retessellation of defect 73 (v0=130457), euler #=-26 (164628,493041,328387) : difference with theory (-26) = 0 

CORRECTING DEFECT 74 (vertices=49, convex hull=76, v0=132923)
After retessellation of defect 74 (v0=132923), euler #=-25 (164637,493098,328436) : difference with theory (-25) = 0 

CORRECTING DEFECT 75 (vertices=48, convex hull=66, v0=134859)
After retessellation of defect 75 (v0=134859), euler #=-24 (164655,493178,328499) : difference with theory (-24) = 0 

CORRECTING DEFECT 76 (vertices=27, convex hull=47, v0=134880)
After retessellation of defect 76 (v0=134880), euler #=-23 (164669,493235,328543) : difference with theory (-23) = 0 

CORRECTING DEFECT 77 (vertices=46, convex hull=70, v0=141204)
After retessellation of defect 77 (v0=141204), euler #=-22 (164692,493333,328619) : difference with theory (-22) = 0 

CORRECTING DEFECT 78 (vertices=38, convex hull=69, v0=141828)
After retessellation of defect 78 (v0=141828), euler #=-21 (164711,493416,328684) : difference with theory (-21) = 0 

CORRECTING DEFECT 79 (vertices=37, convex hull=32, v0=144433)
After retessellation of defect 79 (v0=144433), euler #=-20 (164720,493453,328713) : difference with theory (-20) = 0 

CORRECTING DEFECT 80 (vertices=512, convex hull=161, v0=149124)
After retessellation of defect 80 (v0=149124), euler #=-19 (164767,493673,328887) : difference with theory (-19) = 0 

CORRECTING DEFECT 81 (vertices=54, convex hull=38, v0=149353)
After retessellation of defect 81 (v0=149353), euler #=-18 (164775,493711,328918) : difference with theory (-18) = 0 

CORRECTING DEFECT 82 (vertices=36, convex hull=66, v0=150090)
After retessellation of defect 82 (v0=150090), euler #=-17 (164785,493765,328963) : difference with theory (-17) = 0 

CORRECTING DEFECT 83 (vertices=31, convex hull=42, v0=151509)
After retessellation of defect 83 (v0=151509), euler #=-16 (164799,493824,329009) : difference with theory (-16) = 0 

CORRECTING DEFECT 84 (vertices=29, convex hull=80, v0=154273)
After retessellation of defect 84 (v0=154273), euler #=-15 (164817,493907,329075) : difference with theory (-15) = 0 

CORRECTING DEFECT 85 (vertices=35, convex hull=33, v0=157124)
After retessellation of defect 85 (v0=157124), euler #=-14 (164819,493926,329093) : difference with theory (-14) = 0 

CORRECTING DEFECT 86 (vertices=34, convex hull=62, v0=160182)
After retessellation of defect 86 (v0=160182), euler #=-13 (164832,493989,329144) : difference with theory (-13) = 0 

CORRECTING DEFECT 87 (vertices=46, convex hull=99, v0=161060)
After retessellation of defect 87 (v0=161060), euler #=-12 (164859,494114,329243) : difference with theory (-12) = 0 

CORRECTING DEFECT 88 (vertices=50, convex hull=87, v0=163969)
After retessellation of defect 88 (v0=163969), euler #=-11 (164894,494257,329352) : difference with theory (-11) = 0 

CORRECTING DEFECT 89 (vertices=48, convex hull=83, v0=165360)
After retessellation of defect 89 (v0=165360), euler #=-10 (164924,494385,329451) : difference with theory (-10) = 0 

CORRECTING DEFECT 90 (vertices=18, convex hull=20, v0=166231)
After retessellation of defect 90 (v0=166231), euler #=-9 (164924,494391,329458) : difference with theory (-9) = 0 

CORRECTING DEFECT 91 (vertices=48, convex hull=42, v0=168051)
After retessellation of defect 91 (v0=168051), euler #=-8 (164927,494418,329483) : difference with theory (-8) = 0 

CORRECTING DEFECT 92 (vertices=150, convex hull=85, v0=169012)
After retessellation of defect 92 (v0=169012), euler #=-7 (164943,494504,329554) : difference with theory (-7) = 0 

CORRECTING DEFECT 93 (vertices=58, convex hull=94, v0=171278)
After retessellation of defect 93 (v0=171278), euler #=-6 (164970,494623,329647) : difference with theory (-6) = 0 

CORRECTING DEFECT 94 (vertices=11, convex hull=19, v0=173430)
After retessellation of defect 94 (v0=173430), euler #=-5 (164971,494633,329657) : difference with theory (-5) = 0 

CORRECTING DEFECT 95 (vertices=42, convex hull=20, v0=174261)
After retessellation of defect 95 (v0=174261), euler #=-4 (164973,494646,329669) : difference with theory (-4) = 0 

CORRECTING DEFECT 96 (vertices=99, convex hull=100, v0=175048)
After retessellation of defect 96 (v0=175048), euler #=-3 (165006,494794,329785) : difference with theory (-3) = 0 

CORRECTING DEFECT 97 (vertices=104, convex hull=95, v0=176136)
After retessellation of defect 97 (v0=176136), euler #=-2 (165045,494956,329909) : difference with theory (-2) = 0 

CORRECTING DEFECT 98 (vertices=180, convex hull=150, v0=180352)
After retessellation of defect 98 (v0=180352), euler #=-1 (165109,495222,330112) : difference with theory (-1) = 0 

CORRECTING DEFECT 99 (vertices=172, convex hull=122, v0=180447)
After retessellation of defect 99 (v0=180447), euler #=0 (165155,495416,330261) : difference with theory (0) = 0 

CORRECTING DEFECT 100 (vertices=42, convex hull=24, v0=180967)
After retessellation of defect 100 (v0=180967), euler #=1 (165156,495426,330271) : difference with theory (1) = 0 

CORRECTING DEFECT 101 (vertices=52, convex hull=92, v0=183295)
After retessellation of defect 101 (v0=183295), euler #=2 (165183,495543,330362) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.32 (0.02-->28.62) (max @ vno 26853 --> 51271)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.32 (0.02-->28.62) (max @ vno 26853 --> 51271)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
263 mutations (32.5%), 545 crossovers (67.5%), 2111 vertices were eliminated
building final representation...
18597 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=165183, nf=330362, ne=495543, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 226.2 minutes
0 defective edges
removing intersecting faces
000: 1980 intersecting
001: 60 intersecting
002: 2 intersecting
mris_fix_topology utimesec    13573.626495
mris_fix_topology stimesec    0.542917
mris_fix_topology ru_maxrss   682248
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   71948
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  35984
mris_fix_topology ru_oublock  16536
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    479
mris_fix_topology ru_nivcsw   21178
FSRUNTIME@ mris_fix_topology rh  3.7701 hours 1 threads
PIDs (16546 16549) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 159921 - 479757 + 319838 = 2 --> 0 holes
      F =2V-4:          319838 = 319842-4 (0)
      2E=3F:            959514 = 959514 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 165183 - 495543 + 330362 = 2 --> 0 holes
      F =2V-4:          330362 = 330366-4 (0)
      2E=3F:            991086 = 991086 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 265 intersecting
001: 15 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 670 intersecting
001: 75 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sun Oct  8 07:54:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 lh 

#--------------------------------------------
#@# Make White Surf rh Sun Oct  8 07:54:29 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 rh 

Waiting for PID 25932 of (25932 25935) to complete...
Waiting for PID 25935 of (25932 25935) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
17660 bright wm thresholded.
2039 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig...
computing class statistics...
border white:    320647 voxels (1.91%)
border gray      377071 voxels (2.25%)
WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 58.4 (was 70)
setting MAX_BORDER_WHITE to 106.8 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 47.9 (was 40)
setting MAX_GRAY to 91.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 58.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.24 (0.02-->6.08) (max @ vno 56130 --> 60727)
face area 0.28 +- 0.14 (0.00-->9.12)
mean absolute distance = 0.68 +- 0.85
4499 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=99+-6.1,    GM=69+-7.0
mean inside = 91.5, mean outside = 75.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=81.2, 202 (202) missing vertices, mean dist 0.2 [0.6 (%40.1)->0.7 (%59.9))]
%71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.27 (0.09-->6.24) (max @ vno 54871 --> 60605)
face area 0.28 +- 0.14 (0.00-->9.51)
mean absolute distance = 0.37 +- 0.66
5058 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3082067.2, rms=8.847
001: dt: 0.5000, sse=1891597.5, rms=6.396 (27.704%)
002: dt: 0.5000, sse=1387078.4, rms=4.957 (22.502%)
003: dt: 0.5000, sse=1172859.1, rms=4.201 (15.248%)
004: dt: 0.5000, sse=1078760.6, rms=3.809 (9.326%)
005: dt: 0.5000, sse=1025619.2, rms=3.573 (6.198%)
006: dt: 0.5000, sse=981190.0, rms=3.375 (5.544%)
007: dt: 0.5000, sse=958772.1, rms=3.266 (3.236%)
008: dt: 0.5000, sse=943257.4, rms=3.177 (2.717%)
rms = 3.14, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=938490.4, rms=3.140 (1.182%)
010: dt: 0.2500, sse=795710.2, rms=2.180 (30.575%)
011: dt: 0.2500, sse=771011.6, rms=1.976 (9.335%)
012: dt: 0.2500, sse=764212.8, rms=1.923 (2.693%)
rms = 1.89, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=760691.6, rms=1.892 (1.598%)
rms = 1.86, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=756203.1, rms=1.862 (1.597%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
mean border=83.1, 248 (80) missing vertices, mean dist -0.2 [0.4 (%63.8)->0.3 (%36.2))]
%75 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.26 (0.05-->6.74) (max @ vno 54871 --> 60605)
face area 0.35 +- 0.18 (0.00-->13.17)
mean absolute distance = 0.32 +- 0.49
4911 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1228946.9, rms=3.734
015: dt: 0.5000, sse=1016613.8, rms=2.614 (29.984%)
016: dt: 0.5000, sse=985590.4, rms=2.483 (5.028%)
rms = 2.54, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=918147.9, rms=1.964 (20.909%)
018: dt: 0.2500, sse=888911.6, rms=1.686 (14.136%)
019: dt: 0.2500, sse=895696.8, rms=1.628 (3.465%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=889456.4, rms=1.603 (1.521%)
rms = 1.56, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=876294.9, rms=1.561 (2.600%)
positioning took 0.9 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
mean border=84.4, 272 (57) missing vertices, mean dist -0.1 [0.4 (%58.7)->0.2 (%41.3))]
%80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.26 (0.04-->6.92) (max @ vno 60727 --> 56130)
face area 0.34 +- 0.18 (0.00-->13.38)
mean absolute distance = 0.31 +- 0.43
4211 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=980696.7, rms=2.505
022: dt: 0.5000, sse=930464.1, rms=2.096 (16.345%)
rms = 2.17, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=877605.4, rms=1.683 (19.700%)
024: dt: 0.2500, sse=860596.7, rms=1.496 (11.082%)
rms = 1.45, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=856533.9, rms=1.453 (2.862%)
rms = 1.41, time step reduction 3 of 3 to 0.062...
026: dt: 0.1250, sse=850404.4, rms=1.412 (2.877%)
positioning took 0.7 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
mean border=85.0, 264 (47) missing vertices, mean dist -0.1 [0.3 (%52.7)->0.3 (%47.3))]
%84 local maxima, %11 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-6.0.0/0050352/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=878171.2, rms=1.765
027: dt: 0.5000, sse=865516.9, rms=1.611 (8.763%)
rms = 1.93, time step reduction 1 of 3 to 0.250...
028: dt: 0.2500, sse=831873.9, rms=1.282 (20.413%)
029: dt: 0.2500, sse=830962.7, rms=1.206 (5.948%)
rms = 1.17, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=832184.2, rms=1.172 (2.816%)
rms = 1.13, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=817161.9, rms=1.129 (3.681%)
positioning took 0.7 minutes
generating cortex label...
12 non-cortical segments detected
only using segment with 8687 vertices
erasing segment 1 (vno[0] = 75424)
erasing segment 2 (vno[0] = 93729)
erasing segment 3 (vno[0] = 97178)
erasing segment 4 (vno[0] = 97732)
erasing segment 5 (vno[0] = 102244)
erasing segment 6 (vno[0] = 104586)
erasing segment 7 (vno[0] = 110172)
erasing segment 8 (vno[0] = 111346)
erasing segment 9 (vno[0] = 112461)
erasing segment 10 (vno[0] = 112487)
erasing segment 11 (vno[0] = 157738)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area
vertex spacing 0.90 +- 0.27 (0.03-->7.14) (max @ vno 56130 --> 60727)
face area 0.34 +- 0.18 (0.00-->13.23)
refinement took 5.8 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
17660 bright wm thresholded.
2039 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig...
computing class statistics...
border white:    320647 voxels (1.91%)
border gray      377071 voxels (2.25%)
WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70)
setting MAX_BORDER_WHITE to 105.8 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 50.9 (was 40)
setting MAX_GRAY to 90.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.25 (0.01-->6.59) (max @ vno 78197 --> 162389)
face area 0.28 +- 0.14 (0.00-->5.58)
mean absolute distance = 0.67 +- 0.85
4694 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=98+-6.1,    GM=72+-6.1
mean inside = 91.3, mean outside = 76.8
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=83.3, 281 (281) missing vertices, mean dist 0.1 [0.7 (%45.7)->0.7 (%54.3))]
%75 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.27 (0.05-->6.73) (max @ vno 108009 --> 163207)
face area 0.28 +- 0.14 (0.00-->6.30)
mean absolute distance = 0.39 +- 0.67
5920 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2532878.8, rms=7.445
001: dt: 0.5000, sse=1471837.1, rms=5.038 (32.338%)
002: dt: 0.5000, sse=1075899.8, rms=3.608 (28.370%)
003: dt: 0.5000, sse=940748.9, rms=2.980 (17.415%)
004: dt: 0.5000, sse=900906.0, rms=2.756 (7.520%)
005: dt: 0.5000, sse=883643.8, rms=2.669 (3.137%)
rms = 2.64, time step reduction 1 of 3 to 0.250...
006: dt: 0.5000, sse=883764.4, rms=2.645 (0.931%)
007: dt: 0.2500, sse=773817.1, rms=1.790 (32.303%)
008: dt: 0.2500, sse=757897.6, rms=1.627 (9.133%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
009: dt: 0.2500, sse=757189.0, rms=1.599 (1.699%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
010: dt: 0.1250, sse=752244.0, rms=1.575 (1.491%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=85.1, 269 (73) missing vertices, mean dist -0.2 [0.5 (%63.5)->0.3 (%36.5))]
%79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.27 (0.07-->7.48) (max @ vno 108009 --> 163207)
face area 0.34 +- 0.17 (0.00-->8.98)
mean absolute distance = 0.33 +- 0.51
5228 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1178558.2, rms=3.371
011: dt: 0.5000, sse=982478.4, rms=2.257 (33.041%)
012: dt: 0.5000, sse=953683.6, rms=2.086 (7.596%)
rms = 2.13, time step reduction 1 of 3 to 0.250...
013: dt: 0.2500, sse=906935.5, rms=1.704 (18.306%)
014: dt: 0.2500, sse=889747.2, rms=1.505 (11.657%)
rms = 1.46, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=890636.4, rms=1.462 (2.872%)
rms = 1.43, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=884202.3, rms=1.434 (1.918%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=86.1, 277 (46) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.27 (0.05-->8.01) (max @ vno 108009 --> 163207)
face area 0.33 +- 0.17 (0.00-->9.26)
mean absolute distance = 0.32 +- 0.43
4522 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=974259.8, rms=2.280
017: dt: 0.5000, sse=921469.2, rms=1.811 (20.545%)
rms = 1.83, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=883277.1, rms=1.517 (16.252%)
019: dt: 0.2500, sse=872877.5, rms=1.368 (9.818%)
rms = 1.33, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=869855.9, rms=1.332 (2.640%)
rms = 1.31, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=863920.9, rms=1.307 (1.888%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=86.7, 328 (41) missing vertices, mean dist -0.0 [0.3 (%52.3)->0.3 (%47.7))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=883245.9, rms=1.585
022: dt: 0.5000, sse=878382.7, rms=1.314 (17.056%)
rms = 1.65, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=841154.0, rms=1.094 (16.745%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=855674.2, rms=1.082 (1.162%)
rms = 1.04, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=833807.8, rms=1.038 (4.021%)
positioning took 0.6 minutes
generating cortex label...
6 non-cortical segments detected
only using segment with 7856 vertices
erasing segment 1 (vno[0] = 115541)
erasing segment 2 (vno[0] = 116581)
erasing segment 3 (vno[0] = 116654)
erasing segment 4 (vno[0] = 117658)
erasing segment 5 (vno[0] = 164558)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area
vertex spacing 0.89 +- 0.27 (0.03-->8.41) (max @ vno 108009 --> 163207)
face area 0.33 +- 0.17 (0.00-->9.70)
refinement took 5.3 minutes
PIDs (25932 25935) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sun Oct  8 08:00:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sun Oct  8 08:00:19 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

Waiting for PID 26264 of (26264 26267) to complete...
Waiting for PID 26267 of (26264 26267) 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 (26264 26267) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sun Oct  8 08:00:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sun Oct  8 08:00:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 26313 of (26313 26316) to complete...
Waiting for PID 26316 of (26313 26316) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 48.6 mm, total surface area = 96635 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.185 (target=0.015)   
step 005: RMS=0.130 (target=0.015)   
step 010: RMS=0.100 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.071 (target=0.015)   
step 025: RMS=0.060 (target=0.015)   
step 030: RMS=0.052 (target=0.015)   
step 035: RMS=0.044 (target=0.015)   
step 040: RMS=0.040 (target=0.015)   
step 045: RMS=0.035 (target=0.015)   
step 050: RMS=0.030 (target=0.015)   
step 055: RMS=0.028 (target=0.015)   
step 060: RMS=0.026 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    49.088537
mris_inflate stimesec    0.105983
mris_inflate ru_maxrss   234812
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   34239
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11248
mris_inflate ru_oublock  12528
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2264
mris_inflate ru_nivcsw   3943

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.8 mm, total surface area = 97735 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.188 (target=0.015)   
step 005: RMS=0.133 (target=0.015)   
step 010: RMS=0.106 (target=0.015)   
step 015: RMS=0.089 (target=0.015)   
step 020: RMS=0.075 (target=0.015)   
step 025: RMS=0.064 (target=0.015)   
step 030: RMS=0.057 (target=0.015)   
step 035: RMS=0.049 (target=0.015)   
step 040: RMS=0.044 (target=0.015)   
step 045: RMS=0.039 (target=0.015)   
step 050: RMS=0.036 (target=0.015)   
step 055: RMS=0.033 (target=0.015)   
step 060: RMS=0.031 (target=0.015)   
inflation complete.
inflation took 0.8 minutes
mris_inflate utimesec    50.675296
mris_inflate stimesec    0.115982
mris_inflate ru_maxrss   242716
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   35192
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  11624
mris_inflate ru_oublock  12936
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2232
mris_inflate ru_nivcsw   3813
PIDs (26313 26316) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sun Oct  8 08:01:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 08:01:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 26427 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26430 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26433 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26436 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26439 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26442 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26445 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26448 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26451 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26454 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26457 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...
Waiting for PID 26460 of (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 18.035*4pi (226.639) --> -17 handles
ICI = 281.1, FI = 2023.5, variation=34940.246
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
202 vertices thresholded to be in k1 ~ [-0.34 0.79], k2 ~ [-0.12 0.08]
total integrated curvature = 0.289*4pi (3.628) --> 1 handles
ICI = 1.5, FI = 11.0, variation=183.930
139 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
165 vertices thresholded to be in [-0.17 0.36]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.015, std = 0.025
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 26.619*4pi (334.505) --> -26 handles
ICI = 326.0, FI = 2252.8, variation=39306.423
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
228 vertices thresholded to be in k1 ~ [-0.47 0.96], k2 ~ [-0.15 0.08]
total integrated curvature = 0.252*4pi (3.169) --> 1 handles
ICI = 1.5, FI = 12.1, variation=198.815
178 vertices thresholded to be in [-0.04 0.02]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
162 vertices thresholded to be in [-0.21 0.40]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.027
done.
PIDs (26427 26430 26433 26436 26439 26442 26445 26448 26451 26454 26457 26460) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sun Oct  8 08:02:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050352 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      [ 0050352/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                      [ 285 ]
Gb_filter = 0

#-----------------------------------------
#@# Curvature Stats rh Sun Oct  8 08:03:02 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050352 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      [ 0050352/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                      [ 326 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.429441
WARN:    S explicit min:                          0.000000	vertex = 384
#--------------------------------------------
#@# Sphere lh Sun Oct  8 08:03:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sun Oct  8 08:03:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 26628 of (26628 26631) to complete...
Waiting for PID 26631 of (26628 26631) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.275...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.03
pass 1: epoch 2 of 3 starting distance error %19.95
unfolding complete - removing small folds...
starting distance error %19.82
removing remaining folds...
final distance error %19.85
MRISunfold() return, current seed 1234
-01: dt=0.0000, 191 negative triangles
265: dt=0.9900, 191 negative triangles
266: dt=0.9900, 111 negative triangles
267: dt=0.9900, 91 negative triangles
268: dt=0.9900, 64 negative triangles
269: dt=0.9900, 65 negative triangles
270: dt=0.9900, 62 negative triangles
271: dt=0.9900, 44 negative triangles
272: dt=0.9900, 39 negative triangles
273: dt=0.9900, 35 negative triangles
274: dt=0.9900, 22 negative triangles
275: dt=0.9900, 19 negative triangles
276: dt=0.9900, 20 negative triangles
277: dt=0.9900, 22 negative triangles
278: dt=0.9900, 16 negative triangles
279: dt=0.9900, 16 negative triangles
280: dt=0.9900, 16 negative triangles
281: dt=0.9900, 13 negative triangles
282: dt=0.9900, 14 negative triangles
283: dt=0.9900, 8 negative triangles
284: dt=0.9900, 6 negative triangles
285: dt=0.9900, 10 negative triangles
286: dt=0.9900, 5 negative triangles
287: dt=0.9900, 3 negative triangles
288: dt=0.9900, 2 negative triangles
289: dt=0.9900, 2 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.31 hours
mris_sphere utimesec    4711.910680
mris_sphere stimesec    1.819723
mris_sphere ru_maxrss   328888
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   57908
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11296
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    171646
mris_sphere ru_nivcsw   378217
FSRUNTIME@ mris_sphere  1.3070 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0.274...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=tars-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.19
pass 1: epoch 2 of 3 starting distance error %20.07
unfolding complete - removing small folds...
starting distance error %19.89
removing remaining folds...
final distance error %19.92
MRISunfold() return, current seed 1234
-01: dt=0.0000, 389 negative triangles
249: dt=0.9900, 389 negative triangles
250: dt=0.9900, 203 negative triangles
251: dt=0.9900, 157 negative triangles
252: dt=0.9900, 145 negative triangles
253: dt=0.9900, 141 negative triangles
254: dt=0.9900, 128 negative triangles
255: dt=0.9900, 133 negative triangles
256: dt=0.9900, 116 negative triangles
257: dt=0.9900, 112 negative triangles
258: dt=0.9900, 104 negative triangles
259: dt=0.9900, 105 negative triangles
260: dt=0.9900, 100 negative triangles
261: dt=0.9900, 97 negative triangles
262: dt=0.9900, 89 negative triangles
263: dt=0.9900, 82 negative triangles
264: dt=0.9900, 70 negative triangles
265: dt=0.9900, 74 negative triangles
266: dt=0.9900, 67 negative triangles
267: dt=0.9900, 62 negative triangles
268: dt=0.9900, 53 negative triangles
269: dt=0.9900, 57 negative triangles
270: dt=0.9900, 45 negative triangles
271: dt=0.9900, 40 negative triangles
272: dt=0.9900, 42 negative triangles
273: dt=0.9900, 35 negative triangles
274: dt=0.9900, 28 negative triangles
275: dt=0.9900, 23 negative triangles
276: dt=0.9900, 19 negative triangles
277: dt=0.9900, 18 negative triangles
278: dt=0.9900, 11 negative triangles
279: dt=0.9900, 8 negative triangles
280: dt=0.9900, 9 negative triangles
281: dt=0.9900, 7 negative triangles
282: dt=0.9900, 6 negative triangles
283: dt=0.9900, 3 negative triangles
284: dt=0.9900, 3 negative triangles
285: dt=0.9900, 7 negative triangles
286: dt=0.9900, 7 negative triangles
287: dt=0.9900, 1 negative triangles
288: dt=0.9900, 2 negative triangles
289: dt=0.9900, 5 negative triangles
290: dt=0.9900, 2 negative triangles
291: dt=0.9900, 1 negative triangles
292: dt=0.9900, 2 negative triangles
293: dt=0.9900, 1 negative triangles
294: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.30 hours
mris_sphere utimesec    4694.641306
mris_sphere stimesec    1.756732
mris_sphere ru_maxrss   339468
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   59532
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  11680
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    166518
mris_sphere ru_nivcsw   377580
FSRUNTIME@ mris_sphere  1.3044 hours 1 threads
PIDs (26628 26631) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sun Oct  8 09:21:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 09:21:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 29352 of (29352 29355) to complete...
Waiting for PID 29355 of (29352 29355) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 5.778
curvature mean = 0.029, std = 0.820
curvature mean = 0.017, std = 0.856
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, 0.00, 8.00) sse = 345354.8, tmin=2.4124
  d=16.00 min @ (-4.00, -4.00, 0.00) sse = 325031.6, tmin=3.6389
  d=8.00 min @ (2.00, 0.00, -2.00) sse = 319974.4, tmin=4.8967
  d=4.00 min @ (-1.00, 0.00, 0.00) sse = 319718.5, tmin=6.1683
  d=2.00 min @ (0.50, 0.50, 0.50) sse = 319282.7, tmin=7.4417
  d=1.00 min @ (0.00, -0.25, 0.00) sse = 319194.3, tmin=8.6926
tol=1.0e+00, sigma=0.5, host=tars-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.93 min
curvature mean = -0.013, std = 0.823
curvature mean = 0.005, std = 0.942
curvature mean = -0.021, std = 0.831
curvature mean = 0.002, std = 0.976
curvature mean = -0.025, std = 0.831
curvature mean = 0.000, std = 0.989
2 Reading smoothwm
curvature mean = -0.035, std = 0.298
curvature mean = 0.034, std = 0.244
curvature mean = 0.069, std = 0.325
curvature mean = 0.031, std = 0.301
curvature mean = 0.053, std = 0.493
curvature mean = 0.030, std = 0.325
curvature mean = 0.032, std = 0.636
curvature mean = 0.030, std = 0.336
curvature mean = 0.013, std = 0.751
MRISregister() return, current seed 0
-01: dt=0.0000, 162 negative triangles
139: dt=0.9900, 162 negative triangles
140: dt=0.9405, 207 negative triangles
expanding nbhd size to 1
141: dt=0.9900, 179 negative triangles
142: dt=0.9900, 145 negative triangles
143: dt=0.9900, 142 negative triangles
144: dt=0.9900, 143 negative triangles
145: dt=0.9900, 133 negative triangles
146: dt=0.9900, 130 negative triangles
147: dt=0.9900, 116 negative triangles
148: dt=0.9900, 127 negative triangles
149: dt=0.9900, 116 negative triangles
150: dt=0.9900, 108 negative triangles
151: dt=0.9900, 106 negative triangles
152: dt=0.9900, 102 negative triangles
153: dt=0.9900, 100 negative triangles
154: dt=0.9900, 95 negative triangles
155: dt=0.9900, 88 negative triangles
156: dt=0.9900, 83 negative triangles
157: dt=0.9900, 85 negative triangles
158: dt=0.9900, 74 negative triangles
159: dt=0.9900, 72 negative triangles
160: dt=0.9900, 75 negative triangles
161: dt=0.9900, 69 negative triangles
162: dt=0.9900, 62 negative triangles
163: dt=0.9900, 53 negative triangles
164: dt=0.9900, 57 negative triangles
165: dt=0.9900, 52 negative triangles
166: dt=0.9900, 47 negative triangles
167: dt=0.9900, 47 negative triangles
168: dt=0.9900, 44 negative triangles
169: dt=0.9900, 47 negative triangles
170: dt=0.9900, 43 negative triangles
171: dt=0.9900, 41 negative triangles
172: dt=0.9900, 40 negative triangles
173: dt=0.9900, 38 negative triangles
174: dt=0.9900, 35 negative triangles
175: dt=0.9900, 35 negative triangles
176: dt=0.9900, 28 negative triangles
177: dt=0.9900, 26 negative triangles
178: dt=0.9900, 17 negative triangles
179: dt=0.9900, 22 negative triangles
180: dt=0.9900, 22 negative triangles
181: dt=0.9900, 19 negative triangles
182: dt=0.9900, 16 negative triangles
183: dt=0.9900, 15 negative triangles
184: dt=0.9900, 13 negative triangles
185: dt=0.9900, 14 negative triangles
186: dt=0.9900, 12 negative triangles
187: dt=0.9900, 13 negative triangles
188: dt=0.9900, 9 negative triangles
189: dt=0.9900, 14 negative triangles
190: dt=0.9900, 11 negative triangles
191: dt=0.9900, 10 negative triangles
192: dt=0.9900, 10 negative triangles
193: dt=0.9900, 13 negative triangles
194: dt=0.9900, 8 negative triangles
195: dt=0.9900, 7 negative triangles
196: dt=0.9900, 6 negative triangles
197: dt=0.9900, 2 negative triangles
198: dt=0.9900, 5 negative triangles
199: dt=0.9900, 4 negative triangles
200: dt=0.9900, 1 negative triangles
201: dt=0.9900, 3 negative triangles
202: dt=0.9900, 2 negative triangles
203: dt=0.9900, 1 negative triangles
204: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.77 hours
mris_register utimesec    6351.960355
mris_register stimesec    5.284196
mris_register ru_maxrss   289340
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   41427
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  11344
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    459768
mris_register ru_nivcsw   292004
FSRUNTIME@ mris_register  1.7656 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 5.765
curvature mean = 0.022, std = 0.803
curvature mean = 0.020, std = 0.854
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, 0.00, 16.00) sse = 377729.0, tmin=1.2466
  d=16.00 min @ (0.00, -4.00, 0.00) sse = 355968.7, tmin=3.7840
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 355588.5, tmin=5.0671
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 354644.7, tmin=6.3627
  d=2.00 min @ (0.00, 0.50, -0.50) sse = 354321.5, tmin=7.6612
  d=1.00 min @ (0.00, 0.00, 0.25) sse = 354289.4, tmin=8.9429
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 354264.6, tmin=10.2319
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  10.23 min
curvature mean = -0.014, std = 0.806
curvature mean = 0.005, std = 0.942
curvature mean = -0.021, std = 0.813
curvature mean = 0.002, std = 0.975
curvature mean = -0.024, std = 0.813
curvature mean = 0.000, std = 0.989
2 Reading smoothwm
curvature mean = -0.041, std = 0.359
curvature mean = 0.029, std = 0.239
curvature mean = 0.068, std = 0.269
curvature mean = 0.021, std = 0.297
curvature mean = 0.053, std = 0.406
curvature mean = 0.020, std = 0.324
curvature mean = 0.035, std = 0.525
curvature mean = 0.019, std = 0.335
curvature mean = 0.016, std = 0.632
MRISregister() return, current seed 0
-01: dt=0.0000, 362 negative triangles
137: dt=0.9900, 362 negative triangles
expanding nbhd size to 1
138: dt=0.9900, 391 negative triangles
139: dt=0.9900, 351 negative triangles
140: dt=0.9900, 323 negative triangles
141: dt=0.9900, 325 negative triangles
142: dt=0.9900, 323 negative triangles
143: dt=0.9900, 301 negative triangles
144: dt=0.9900, 287 negative triangles
145: dt=0.9900, 275 negative triangles
146: dt=0.9900, 254 negative triangles
147: dt=0.9900, 243 negative triangles
148: dt=0.9900, 224 negative triangles
149: dt=0.9900, 218 negative triangles
150: dt=0.9900, 208 negative triangles
151: dt=0.9900, 200 negative triangles
152: dt=0.9900, 182 negative triangles
153: dt=0.9900, 184 negative triangles
154: dt=0.9900, 172 negative triangles
155: dt=0.9900, 168 negative triangles
156: dt=0.9900, 157 negative triangles
157: dt=0.9900, 142 negative triangles
158: dt=0.9900, 142 negative triangles
159: dt=0.9900, 142 negative triangles
160: dt=0.9900, 122 negative triangles
161: dt=0.9900, 114 negative triangles
162: dt=0.9900, 106 negative triangles
163: dt=0.9900, 101 negative triangles
164: dt=0.9900, 98 negative triangles
165: dt=0.9900, 91 negative triangles
166: dt=0.9900, 86 negative triangles
167: dt=0.9900, 78 negative triangles
168: dt=0.9900, 78 negative triangles
169: dt=0.9900, 71 negative triangles
170: dt=0.9900, 73 negative triangles
171: dt=0.9900, 61 negative triangles
172: dt=0.9900, 67 negative triangles
173: dt=0.9900, 64 negative triangles
174: dt=0.9900, 57 negative triangles
175: dt=0.9900, 54 negative triangles
176: dt=0.9900, 57 negative triangles
177: dt=0.9900, 51 negative triangles
178: dt=0.9900, 55 negative triangles
179: dt=0.9900, 49 negative triangles
180: dt=0.9900, 51 negative triangles
181: dt=0.9900, 46 negative triangles
182: dt=0.9900, 42 negative triangles
183: dt=0.9900, 46 negative triangles
184: dt=0.9900, 45 negative triangles
185: dt=0.9900, 46 negative triangles
186: dt=0.9900, 42 negative triangles
187: dt=0.9900, 39 negative triangles
188: dt=0.9900, 38 negative triangles
189: dt=0.9900, 38 negative triangles
190: dt=0.9900, 36 negative triangles
191: dt=0.9900, 35 negative triangles
192: dt=0.9900, 34 negative triangles
193: dt=0.9900, 32 negative triangles
194: dt=0.9900, 33 negative triangles
195: dt=0.9900, 32 negative triangles
196: dt=0.9900, 31 negative triangles
197: dt=0.9900, 31 negative triangles
198: dt=0.9900, 34 negative triangles
199: dt=0.9900, 33 negative triangles
200: dt=0.9900, 31 negative triangles
201: dt=0.9900, 30 negative triangles
202: dt=0.9900, 30 negative triangles
203: dt=0.9900, 30 negative triangles
204: dt=0.9900, 30 negative triangles
205: dt=0.9900, 29 negative triangles
206: dt=0.9900, 28 negative triangles
207: dt=0.9900, 27 negative triangles
208: dt=0.9900, 28 negative triangles
209: dt=0.9900, 28 negative triangles
210: dt=0.9900, 28 negative triangles
211: dt=0.9900, 26 negative triangles
212: dt=0.9900, 26 negative triangles
213: dt=0.9900, 26 negative triangles
214: dt=0.9900, 25 negative triangles
215: dt=0.9900, 25 negative triangles
216: dt=0.9900, 25 negative triangles
217: dt=0.9900, 27 negative triangles
218: dt=0.9900, 27 negative triangles
219: dt=0.9900, 26 negative triangles
220: dt=0.9900, 25 negative triangles
221: dt=0.9900, 25 negative triangles
222: dt=0.9900, 26 negative triangles
223: dt=0.9900, 26 negative triangles
224: dt=0.9405, 27 negative triangles
225: dt=0.9405, 24 negative triangles
226: dt=0.9405, 24 negative triangles
227: dt=0.9405, 25 negative triangles
228: dt=0.9405, 23 negative triangles
229: dt=0.9405, 23 negative triangles
230: dt=0.9405, 23 negative triangles
231: dt=0.9405, 21 negative triangles
232: dt=0.9405, 21 negative triangles
233: dt=0.9405, 21 negative triangles
234: dt=0.9405, 23 negative triangles
235: dt=0.9405, 21 negative triangles
236: dt=0.9405, 21 negative triangles
237: dt=0.9405, 22 negative triangles
238: dt=0.9405, 21 negative triangles
239: dt=0.9405, 21 negative triangles
240: dt=0.9405, 19 negative triangles
241: dt=0.9405, 20 negative triangles
242: dt=0.9405, 21 negative triangles
243: dt=0.9405, 21 negative triangles
244: dt=0.9405, 20 negative triangles
245: dt=0.9405, 19 negative triangles
246: dt=0.9405, 19 negative triangles
247: dt=0.9405, 20 negative triangles
248: dt=0.9405, 22 negative triangles
249: dt=0.9405, 19 negative triangles
250: dt=0.8935, 19 negative triangles
251: dt=0.8935, 21 negative triangles
252: dt=0.8935, 22 negative triangles
253: dt=0.8935, 19 negative triangles
254: dt=0.8935, 19 negative triangles
255: dt=0.8935, 17 negative triangles
256: dt=0.8935, 21 negative triangles
257: dt=0.8935, 20 negative triangles
258: dt=0.8935, 20 negative triangles
259: dt=0.8935, 17 negative triangles
260: dt=0.8935, 15 negative triangles
261: dt=0.8935, 15 negative triangles
262: dt=0.8935, 15 negative triangles
263: dt=0.8935, 16 negative triangles
264: dt=0.8935, 16 negative triangles
265: dt=0.8935, 16 negative triangles
266: dt=0.8935, 15 negative triangles
267: dt=0.8935, 16 negative triangles
268: dt=0.8935, 15 negative triangles
269: dt=0.8935, 15 negative triangles
270: dt=0.8488, 15 negative triangles
271: dt=0.8488, 16 negative triangles
272: dt=0.8488, 15 negative triangles
273: dt=0.8488, 15 negative triangles
274: dt=0.8488, 15 negative triangles
275: dt=0.8488, 15 negative triangles
276: dt=0.8488, 14 negative triangles
277: dt=0.8488, 14 negative triangles
278: dt=0.8488, 14 negative triangles
279: dt=0.8488, 15 negative triangles
280: dt=0.8488, 14 negative triangles
281: dt=0.8488, 13 negative triangles
282: dt=0.8488, 13 negative triangles
283: dt=0.8488, 14 negative triangles
284: dt=0.8488, 14 negative triangles
285: dt=0.8488, 13 negative triangles
286: dt=0.8488, 12 negative triangles
287: dt=0.8488, 13 negative triangles
288: dt=0.8488, 13 negative triangles
289: dt=0.8488, 12 negative triangles
290: dt=0.8488, 10 negative triangles
291: dt=0.8488, 10 negative triangles
292: dt=0.8488, 12 negative triangles
293: dt=0.8488, 10 negative triangles
294: dt=0.8488, 10 negative triangles
295: dt=0.8488, 9 negative triangles
296: dt=0.8488, 10 negative triangles
297: dt=0.8488, 10 negative triangles
298: dt=0.8488, 9 negative triangles
299: dt=0.8488, 10 negative triangles
300: dt=0.8488, 9 negative triangles
301: dt=0.8488, 9 negative triangles
302: dt=0.8488, 9 negative triangles
303: dt=0.8488, 9 negative triangles
304: dt=0.8488, 8 negative triangles
305: dt=0.8488, 8 negative triangles
306: dt=0.8488, 6 negative triangles
307: dt=0.8488, 6 negative triangles
308: dt=0.8488, 8 negative triangles
309: dt=0.8488, 5 negative triangles
310: dt=0.8488, 5 negative triangles
311: dt=0.8488, 5 negative triangles
312: dt=0.8488, 5 negative triangles
313: dt=0.8488, 6 negative triangles
314: dt=0.8488, 6 negative triangles
315: dt=0.8488, 5 negative triangles
316: dt=0.8488, 3 negative triangles
317: dt=0.8488, 3 negative triangles
318: dt=0.8488, 3 negative triangles
319: dt=0.8488, 2 negative triangles
320: dt=0.8488, 2 negative triangles
321: dt=0.8488, 2 negative triangles
322: dt=0.8488, 1 negative triangles
323: dt=0.8488, 1 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.85 hours
mris_register utimesec    6859.043266
mris_register stimesec    5.310192
mris_register ru_maxrss   296560
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   41995
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  11736
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    470326
mris_register ru_nivcsw   283907
FSRUNTIME@ mris_register  1.8520 hours 1 threads
PIDs (29352 29355) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sun Oct  8 11:12:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sun Oct  8 11:12:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

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

Waiting for PID 1039 of (1039 1042) to complete...
Waiting for PID 1042 of (1039 1042) 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 (1039 1042) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sun Oct  8 11:12:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 11:12:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 1084 of (1084 1087) to complete...
Waiting for PID 1087 of (1084 1087) 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 (1084 1087) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sun Oct  8 11:12:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:12:45 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 1131 of (1131 1134) to complete...
Waiting for PID 1134 of (1131 1134) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
1134 labels changed using aseg
relabeling using gibbs priors...
000:   3637 changed, 159921 examined...
001:    846 changed, 14944 examined...
002:    206 changed, 4666 examined...
003:     66 changed, 1266 examined...
004:     26 changed, 377 examined...
005:     14 changed, 160 examined...
006:      4 changed, 68 examined...
007:      4 changed, 28 examined...
008:      2 changed, 17 examined...
009:      5 changed, 14 examined...
010:      0 changed, 16 examined...
254 labels changed using aseg
000: 136 total segments, 88 labels (376 vertices) changed
001: 48 total segments, 3 labels (6 vertices) changed
002: 45 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2165 vertices marked for relabeling...
2165 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 16 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
1295 labels changed using aseg
relabeling using gibbs priors...
000:   3003 changed, 165183 examined...
001:    719 changed, 12988 examined...
002:    183 changed, 4005 examined...
003:     58 changed, 1085 examined...
004:     27 changed, 371 examined...
005:      6 changed, 160 examined...
006:      2 changed, 35 examined...
007:      1 changed, 14 examined...
008:      1 changed, 7 examined...
009:      1 changed, 7 examined...
010:      1 changed, 7 examined...
011:      1 changed, 7 examined...
012:      0 changed, 7 examined...
169 labels changed using aseg
000: 104 total segments, 66 labels (298 vertices) changed
001: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2155 vertices marked for relabeling...
2155 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 16 seconds.
PIDs (1131 1134) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sun Oct  8 11:13:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sun Oct  8 11:13:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 rh 

Waiting for PID 1182 of (1182 1185) to complete...
Waiting for PID 1185 of (1182 1185) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
17660 bright wm thresholded.
2039 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.orig...
computing class statistics...
border white:    320647 voxels (1.91%)
border gray      377071 voxels (2.25%)
WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 58.4 (was 70)
setting MAX_BORDER_WHITE to 106.8 (was 105)
setting MIN_BORDER_WHITE to 69.0 (was 85)
setting MAX_CSF to 47.9 (was 40)
setting MAX_GRAY to 91.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 58.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 37.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=99+-6.1,    GM=69+-7.0
mean inside = 91.5, mean outside = 75.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.90 +- 0.27 (0.03-->7.14) (max @ vno 56130 --> 60727)
face area 0.34 +- 0.18 (0.00-->13.14)
mean absolute distance = 0.53 +- 0.83
4140 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 120 points - only 0.00% unknown
deleting segment 4 with 90 points - only 0.00% unknown
deleting segment 6 with 225 points - only 0.00% unknown
deleting segment 8 with 35 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 10 with 1 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 5 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 13 with 1 points - only 0.00% unknown
deleting segment 14 with 123 points - only 0.00% unknown
removing 3 vertex label from ripped group
mean border=81.0, 275 (275) missing vertices, mean dist 0.3 [0.6 (%22.9)->0.5 (%77.1))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.27 (0.07-->6.86) (max @ vno 54871 --> 65504)
face area 0.34 +- 0.18 (0.00-->12.46)
mean absolute distance = 0.37 +- 0.65
4881 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1860433.5, rms=5.948
001: dt: 0.5000, sse=1218953.2, rms=3.797 (36.168%)
002: dt: 0.5000, sse=1052613.9, rms=3.018 (20.523%)
003: dt: 0.5000, sse=1023272.9, rms=2.873 (4.800%)
004: dt: 0.5000, sse=1011710.2, rms=2.778 (3.287%)
rms = 2.85, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=915516.4, rms=2.138 (23.035%)
006: dt: 0.2500, sse=882689.1, rms=1.827 (14.571%)
007: dt: 0.2500, sse=874442.1, rms=1.755 (3.953%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=872185.0, rms=1.732 (1.310%)
rms = 1.70, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=868741.6, rms=1.696 (2.044%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 112 points - only 0.00% unknown
deleting segment 3 with 72 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 74 points - only 0.00% unknown
deleting segment 7 with 35 points - only 0.00% unknown
deleting segment 8 with 37 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 107 points - only 0.00% unknown
mean border=83.1, 215 (105) missing vertices, mean dist -0.2 [0.4 (%63.9)->0.3 (%36.1))]
%76 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.27 (0.05-->7.03) (max @ vno 54871 --> 65504)
face area 0.35 +- 0.19 (0.00-->13.62)
mean absolute distance = 0.32 +- 0.49
5031 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1197210.9, rms=3.535
010: dt: 0.5000, sse=1002927.2, rms=2.429 (31.283%)
011: dt: 0.5000, sse=980718.8, rms=2.327 (4.183%)
rms = 2.44, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=913009.9, rms=1.804 (22.480%)
013: dt: 0.2500, sse=891020.9, rms=1.545 (14.373%)
rms = 1.51, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=888721.8, rms=1.513 (2.045%)
rms = 1.48, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=882428.0, rms=1.483 (2.027%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 115 points - only 0.00% unknown
deleting segment 3 with 73 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 166 points - only 0.00% unknown
deleting segment 6 with 43 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 40 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 13 with 105 points - only 0.00% unknown
mean border=84.4, 236 (77) missing vertices, mean dist -0.1 [0.4 (%59.0)->0.2 (%41.0))]
%81 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.27 (0.04-->7.03) (max @ vno 54871 --> 65504)
face area 0.34 +- 0.18 (0.00-->13.46)
mean absolute distance = 0.31 +- 0.43
4151 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=983497.1, rms=2.471
016: dt: 0.5000, sse=943433.1, rms=2.062 (16.528%)
rms = 2.14, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=885016.3, rms=1.647 (20.141%)
018: dt: 0.2500, sse=890783.4, rms=1.461 (11.320%)
rms = 1.41, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=860965.7, rms=1.412 (3.306%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=854889.4, rms=1.375 (2.666%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 17 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 119 points - only 0.00% unknown
deleting segment 3 with 74 points - only 0.00% unknown
deleting segment 4 with 9 points - only 0.00% unknown
deleting segment 5 with 172 points - only 0.00% unknown
deleting segment 6 with 43 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 40 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 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
deleting segment 13 with 108 points - only 0.00% unknown
mean border=85.0, 247 (64) missing vertices, mean dist -0.1 [0.3 (%52.7)->0.3 (%47.3))]
%84 local maxima, %11 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-6.0.0/0050352/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=882570.6, rms=1.744
021: dt: 0.5000, sse=875049.6, rms=1.582 (9.302%)
rms = 1.90, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=836627.6, rms=1.242 (21.473%)
023: dt: 0.2500, sse=837364.1, rms=1.192 (4.035%)
rms = 1.15, time step reduction 2 of 3 to 0.125...
024: dt: 0.2500, sse=827933.8, rms=1.146 (3.908%)
rms = 1.10, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=823017.5, rms=1.099 (4.073%)
positioning took 0.7 minutes
generating cortex label...
9 non-cortical segments detected
only using segment with 8702 vertices
erasing segment 1 (vno[0] = 97732)
erasing segment 2 (vno[0] = 102244)
erasing segment 3 (vno[0] = 104586)
erasing segment 4 (vno[0] = 107961)
erasing segment 5 (vno[0] = 110172)
erasing segment 6 (vno[0] = 111346)
erasing segment 7 (vno[0] = 112461)
erasing segment 8 (vno[0] = 112487)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area
vertex spacing 0.90 +- 0.27 (0.05-->6.97) (max @ vno 98357 --> 157869)
face area 0.34 +- 0.18 (0.00-->13.04)
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 80 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 3 with 36 points - only 0.00% unknown
deleting segment 5 with 20 points - only 0.00% unknown
deleting segment 6 with 22 points - only 0.00% unknown
deleting segment 7 with 25 points - only 0.00% unknown
deleting segment 8 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 50.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=57.5, 264 (264) missing vertices, mean dist 1.6 [1.1 (%0.0)->2.9 (%100.0))]
%13 local maxima, %37 large gradients and %45 min vals, 692 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=25308272.0, rms=28.348
001: dt: 0.0500, sse=22638340.0, rms=26.761 (5.598%)
002: dt: 0.0500, sse=20707266.0, rms=25.552 (4.519%)
003: dt: 0.0500, sse=19205946.0, rms=24.570 (3.841%)
004: dt: 0.0500, sse=17974636.0, rms=23.735 (3.400%)
005: dt: 0.0500, sse=16924140.0, rms=22.998 (3.104%)
006: dt: 0.0500, sse=16002985.0, rms=22.332 (2.897%)
007: dt: 0.0500, sse=15178845.0, rms=21.719 (2.747%)
008: dt: 0.0500, sse=14430951.0, rms=21.146 (2.634%)
009: dt: 0.0500, sse=13743778.0, rms=20.607 (2.552%)
010: dt: 0.0500, sse=13108337.0, rms=20.095 (2.485%)
positioning took 1.1 minutes
mean border=57.3, 235 (154) missing vertices, mean dist 1.3 [0.5 (%0.0)->2.4 (%100.0))]
%14 local maxima, %38 large gradients and %44 min vals, 633 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=14032075.0, rms=20.834
011: dt: 0.0500, sse=13433637.0, rms=20.358 (2.286%)
012: dt: 0.0500, sse=12874301.0, rms=19.902 (2.237%)
013: dt: 0.0500, sse=12349945.0, rms=19.465 (2.194%)
014: dt: 0.0500, sse=11857777.0, rms=19.046 (2.153%)
015: dt: 0.0500, sse=11395210.0, rms=18.644 (2.114%)
016: dt: 0.0500, sse=10960952.0, rms=18.258 (2.071%)
017: dt: 0.0500, sse=10553168.0, rms=17.887 (2.028%)
018: dt: 0.0500, sse=10170341.0, rms=17.533 (1.983%)
019: dt: 0.0500, sse=9810546.0, rms=17.192 (1.940%)
020: dt: 0.0500, sse=9472828.0, rms=16.867 (1.894%)
positioning took 1.1 minutes
mean border=57.2, 268 (119) missing vertices, mean dist 1.1 [0.1 (%1.4)->2.1 (%98.6))]
%14 local maxima, %37 large gradients and %44 min vals, 602 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=9571632.0, rms=16.968
021: dt: 0.0500, sse=9245767.0, rms=16.649 (1.876%)
022: dt: 0.0500, sse=8940497.0, rms=16.345 (1.825%)
023: dt: 0.0500, sse=8652347.0, rms=16.053 (1.788%)
024: dt: 0.0500, sse=8382553.0, rms=15.775 (1.736%)
025: dt: 0.0500, sse=8129841.0, rms=15.509 (1.684%)
026: dt: 0.0500, sse=7892888.5, rms=15.256 (1.634%)
027: dt: 0.0500, sse=7669313.0, rms=15.012 (1.593%)
028: dt: 0.0500, sse=7456474.5, rms=14.777 (1.567%)
029: dt: 0.0500, sse=7253870.0, rms=14.550 (1.540%)
030: dt: 0.0500, sse=7061353.5, rms=14.330 (1.510%)
positioning took 1.1 minutes
mean border=57.2, 321 (99) missing vertices, mean dist 0.9 [0.1 (%11.0)->2.0 (%89.0))]
%14 local maxima, %38 large gradients and %43 min vals, 601 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=7135658.5, rms=14.414
031: dt: 0.5000, sse=5781775.5, rms=12.777 (11.363%)
032: dt: 0.5000, sse=4890548.0, rms=11.564 (9.492%)
033: dt: 0.5000, sse=4245457.0, rms=10.601 (8.326%)
034: dt: 0.5000, sse=3765931.5, rms=9.817 (7.399%)
035: dt: 0.5000, sse=3374981.5, rms=9.130 (6.990%)
036: dt: 0.5000, sse=3036233.5, rms=8.488 (7.037%)
037: dt: 0.5000, sse=2733787.8, rms=7.875 (7.215%)
038: dt: 0.5000, sse=2472625.8, rms=7.302 (7.282%)
039: dt: 0.5000, sse=2252052.8, rms=6.785 (7.081%)
040: dt: 0.5000, sse=2083718.1, rms=6.357 (6.304%)
041: dt: 0.5000, sse=1957419.4, rms=6.021 (5.295%)
042: dt: 0.5000, sse=1878639.0, rms=5.796 (3.725%)
043: dt: 0.5000, sse=1823120.5, rms=5.637 (2.754%)
044: dt: 0.5000, sse=1789904.5, rms=5.535 (1.812%)
045: dt: 0.5000, sse=1765039.5, rms=5.461 (1.326%)
rms = 5.42, time step reduction 1 of 3 to 0.250...
046: dt: 0.5000, sse=1753900.0, rms=5.424 (0.681%)
047: dt: 0.2500, sse=1666929.5, rms=5.114 (5.721%)
048: dt: 0.2500, sse=1642357.4, rms=5.032 (1.600%)
rms = 5.03, time step reduction 2 of 3 to 0.125...
049: dt: 0.2500, sse=1641327.5, rms=5.026 (0.112%)
050: dt: 0.1250, sse=1623718.8, rms=4.963 (1.264%)
rms = 4.95, time step reduction 3 of 3 to 0.062...
051: dt: 0.1250, sse=1620277.9, rms=4.951 (0.233%)
positioning took 3.2 minutes
mean border=56.3, 3115 (28) missing vertices, mean dist 0.2 [0.2 (%47.8)->0.7 (%52.2))]
%22 local maxima, %32 large gradients and %39 min vals, 322 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=1840226.4, rms=5.043
052: dt: 0.5000, sse=1730001.0, rms=4.685 (7.089%)
053: dt: 0.5000, sse=1655061.0, rms=4.441 (5.209%)
rms = 4.51, time step reduction 1 of 3 to 0.250...
054: dt: 0.2500, sse=1571264.8, rms=4.080 (8.130%)
055: dt: 0.2500, sse=1546017.9, rms=3.962 (2.905%)
rms = 3.94, time step reduction 2 of 3 to 0.125...
056: dt: 0.2500, sse=1540530.9, rms=3.939 (0.586%)
057: dt: 0.1250, sse=1518452.0, rms=3.836 (2.611%)
rms = 3.81, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1513212.5, rms=3.814 (0.564%)
positioning took 1.4 minutes
mean border=55.9, 3568 (21) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.5 (%50.8))]
%29 local maxima, %27 large gradients and %38 min vals, 403 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=1559771.0, rms=3.996
rms = 4.20, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1533505.9, rms=3.882 (2.835%)
rms = 3.84, time step reduction 2 of 3 to 0.125...
060: dt: 0.2500, sse=1520918.6, rms=3.835 (1.212%)
061: dt: 0.1250, sse=1509364.4, rms=3.781 (1.413%)
rms = 3.76, time step reduction 3 of 3 to 0.062...
062: dt: 0.1250, sse=1502854.0, rms=3.755 (0.677%)
positioning took 0.9 minutes
mean border=55.4, 7211 (21) missing vertices, mean dist 0.1 [0.2 (%48.6)->0.4 (%51.4))]
%33 local maxima, %22 large gradients and %36 min vals, 439 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-6.0.0/0050352/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1530470.5, rms=3.858
rms = 3.93, time step reduction 1 of 3 to 0.250...
063: dt: 0.2500, sse=1508682.0, rms=3.765 (2.412%)
064: dt: 0.2500, sse=1484530.5, rms=3.677 (2.330%)
rms = 3.63, time step reduction 2 of 3 to 0.125...
065: dt: 0.2500, sse=1471231.2, rms=3.627 (1.356%)
066: dt: 0.1250, sse=1453012.9, rms=3.539 (2.421%)
rms = 3.51, time step reduction 3 of 3 to 0.062...
067: dt: 0.1250, sse=1445074.5, rms=3.507 (0.911%)
positioning took 1.2 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.area.pial
vertex spacing 1.01 +- 0.46 (0.05-->8.40) (max @ vno 157872 --> 98357)
face area 0.40 +- 0.34 (0.00-->9.18)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 159921 vertices processed
25000 of 159921 vertices processed
50000 of 159921 vertices processed
75000 of 159921 vertices processed
100000 of 159921 vertices processed
125000 of 159921 vertices processed
150000 of 159921 vertices processed
0 of 159921 vertices processed
25000 of 159921 vertices processed
50000 of 159921 vertices processed
75000 of 159921 vertices processed
100000 of 159921 vertices processed
125000 of 159921 vertices processed
150000 of 159921 vertices processed
thickness calculation complete, 422:976 truncations.
33870 vertices at 0 distance
105995 vertices at 1 distance
96590 vertices at 2 distance
44343 vertices at 3 distance
15718 vertices at 4 distance
5428 vertices at 5 distance
2027 vertices at 6 distance
882 vertices at 7 distance
366 vertices at 8 distance
191 vertices at 9 distance
97 vertices at 10 distance
63 vertices at 11 distance
48 vertices at 12 distance
32 vertices at 13 distance
33 vertices at 14 distance
20 vertices at 15 distance
13 vertices at 16 distance
11 vertices at 17 distance
20 vertices at 18 distance
18 vertices at 19 distance
19 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.thickness
positioning took 17.7 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050352 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-6.0.0/0050352/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
17660 bright wm thresholded.
2039 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.orig...
computing class statistics...
border white:    320647 voxels (1.91%)
border gray      377071 voxels (2.25%)
WM (94.0): 95.4 +- 7.8 [70.0 --> 110.0]
GM (73.0) : 71.7 +- 10.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 61.4 (was 70)
setting MAX_BORDER_WHITE to 105.8 (was 105)
setting MIN_BORDER_WHITE to 72.0 (was 85)
setting MAX_CSF to 50.9 (was 40)
setting MAX_GRAY to 90.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 61.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 40.3 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=98+-6.1,    GM=72+-6.1
mean inside = 91.3, mean outside = 76.8
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.27 (0.03-->8.41) (max @ vno 108009 --> 163207)
face area 0.33 +- 0.17 (0.00-->9.65)
mean absolute distance = 0.54 +- 0.85
4536 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 1 with 69 points - only 0.00% unknown
deleting segment 2 with 14 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
deleting segment 4 with 245 points - only 0.00% unknown
deleting segment 5 with 68 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 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 8 with 1 points - only 0.00% unknown
deleting segment 9 with 48 points - only 0.00% unknown
mean border=83.2, 397 (395) missing vertices, mean dist 0.2 [0.6 (%24.2)->0.5 (%75.8))]
%74 local maxima, %22 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 0.90 +- 0.27 (0.02-->7.79) (max @ vno 108009 --> 163207)
face area 0.33 +- 0.17 (0.00-->9.26)
mean absolute distance = 0.39 +- 0.67
5808 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1698331.2, rms=5.326
001: dt: 0.5000, sse=1155934.9, rms=3.366 (36.794%)
002: dt: 0.5000, sse=1011278.4, rms=2.639 (21.618%)
003: dt: 0.5000, sse=984570.6, rms=2.483 (5.904%)
004: dt: 0.5000, sse=971679.3, rms=2.406 (3.094%)
rms = 2.46, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=909869.0, rms=1.915 (20.420%)
006: dt: 0.2500, sse=889970.2, rms=1.674 (12.600%)
007: dt: 0.2500, sse=884931.4, rms=1.621 (3.136%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
008: dt: 0.2500, sse=880575.8, rms=1.603 (1.136%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
009: dt: 0.1250, sse=877829.0, rms=1.577 (1.581%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 0.00% unknown
deleting segment 1 with 18 points - only 0.00% unknown
deleting segment 2 with 11 points - only 0.00% unknown
deleting segment 3 with 254 points - only 0.00% unknown
deleting segment 4 with 66 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 48 points - only 0.00% unknown
mean border=85.0, 324 (137) missing vertices, mean dist -0.2 [0.5 (%63.5)->0.3 (%36.5))]
%79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.27 (0.06-->8.06) (max @ vno 108009 --> 163207)
face area 0.34 +- 0.18 (0.00-->10.21)
mean absolute distance = 0.33 +- 0.50
5672 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1159586.9, rms=3.229
010: dt: 0.5000, sse=988661.1, rms=2.131 (34.020%)
011: dt: 0.5000, sse=959757.2, rms=1.974 (7.334%)
rms = 2.07, time step reduction 1 of 3 to 0.250...
012: dt: 0.2500, sse=916613.5, rms=1.607 (18.625%)
013: dt: 0.2500, sse=903480.8, rms=1.430 (10.968%)
rms = 1.40, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=893121.4, rms=1.405 (1.797%)
rms = 1.38, time step reduction 3 of 3 to 0.062...
015: dt: 0.1250, sse=893205.6, rms=1.385 (1.400%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 45 points - only 0.00% unknown
deleting segment 1 with 27 points - only 0.00% unknown
deleting segment 2 with 11 points - only 0.00% unknown
deleting segment 3 with 234 points - only 0.00% unknown
deleting segment 4 with 58 points - only 0.00% unknown
deleting segment 5 with 47 points - only 0.00% unknown
mean border=86.1, 369 (93) missing vertices, mean dist -0.1 [0.4 (%57.6)->0.3 (%42.4))]
%83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.27 (0.09-->8.28) (max @ vno 108009 --> 163207)
face area 0.34 +- 0.18 (0.00-->10.30)
mean absolute distance = 0.31 +- 0.42
4387 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=973929.6, rms=2.231
016: dt: 0.5000, sse=924500.6, rms=1.772 (20.595%)
rms = 1.79, time step reduction 1 of 3 to 0.250...
017: dt: 0.2500, sse=888262.7, rms=1.475 (16.730%)
018: dt: 0.2500, sse=876876.8, rms=1.334 (9.564%)
rms = 1.30, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=877732.0, rms=1.303 (2.335%)
rms = 1.28, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=874149.6, rms=1.282 (1.581%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 35 points - only 0.00% unknown
deleting segment 1 with 27 points - only 0.00% unknown
deleting segment 2 with 12 points - only 0.00% unknown
deleting segment 3 with 72 points - only 0.00% unknown
deleting segment 4 with 242 points - only 0.00% unknown
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
deleting segment 7 with 47 points - only 0.00% unknown
mean border=86.7, 439 (77) missing vertices, mean dist -0.0 [0.3 (%52.4)->0.3 (%47.6))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=894350.3, rms=1.576
021: dt: 0.5000, sse=875687.2, rms=1.303 (17.329%)
rms = 1.64, time step reduction 1 of 3 to 0.250...
022: dt: 0.2500, sse=846503.8, rms=1.085 (16.787%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=845152.2, rms=1.069 (1.432%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=845954.6, rms=1.031 (3.511%)
positioning took 0.6 minutes
generating cortex label...
7 non-cortical segments detected
only using segment with 7827 vertices
erasing segment 1 (vno[0] = 115541)
erasing segment 2 (vno[0] = 116581)
erasing segment 3 (vno[0] = 116654)
erasing segment 4 (vno[0] = 117658)
erasing segment 5 (vno[0] = 161798)
erasing segment 6 (vno[0] = 164558)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area
vertex spacing 0.89 +- 0.28 (0.05-->8.65) (max @ vno 108009 --> 163207)
face area 0.33 +- 0.18 (0.00-->10.30)
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 19 points - only 0.00% unknown
deleting segment 2 with 27 points - only 0.00% unknown
deleting segment 5 with 13 points - only 0.00% unknown
deleting segment 6 with 5 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 29 points - only 0.00% unknown
deleting segment 9 with 29 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=60.7, 386 (386) missing vertices, mean dist 1.5 [0.9 (%0.0)->3.2 (%100.0))]
%13 local maxima, %31 large gradients and %52 min vals, 708 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=23544016.0, rms=26.808
001: dt: 0.0500, sse=21158642.0, rms=25.364 (5.387%)
002: dt: 0.0500, sse=19439606.0, rms=24.269 (4.314%)
003: dt: 0.0500, sse=18106188.0, rms=23.385 (3.643%)
004: dt: 0.0500, sse=17012138.0, rms=22.634 (3.213%)
005: dt: 0.0500, sse=16080095.0, rms=21.974 (2.918%)
006: dt: 0.0500, sse=15263386.0, rms=21.378 (2.710%)
007: dt: 0.0500, sse=14532609.0, rms=20.831 (2.561%)
008: dt: 0.0500, sse=13868393.0, rms=20.320 (2.450%)
009: dt: 0.0500, sse=13257501.0, rms=19.839 (2.367%)
010: dt: 0.0500, sse=12691906.0, rms=19.383 (2.299%)
positioning took 1.1 minutes
mean border=60.6, 399 (223) missing vertices, mean dist 1.3 [0.3 (%0.1)->2.7 (%99.9))]
%13 local maxima, %31 large gradients and %51 min vals, 659 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=13666072.0, rms=20.157
011: dt: 0.0500, sse=13131304.0, rms=19.734 (2.102%)
012: dt: 0.0500, sse=12630489.0, rms=19.328 (2.053%)
013: dt: 0.0500, sse=12159891.0, rms=18.940 (2.011%)
014: dt: 0.0500, sse=11716678.0, rms=18.566 (1.973%)
015: dt: 0.0500, sse=11299747.0, rms=18.207 (1.931%)
016: dt: 0.0500, sse=10906847.0, rms=17.863 (1.892%)
017: dt: 0.0500, sse=10535416.0, rms=17.531 (1.859%)
018: dt: 0.0500, sse=10185154.0, rms=17.212 (1.820%)
019: dt: 0.0500, sse=9854004.0, rms=16.905 (1.785%)
020: dt: 0.0500, sse=9540912.0, rms=16.609 (1.750%)
positioning took 1.1 minutes
mean border=60.5, 449 (186) missing vertices, mean dist 1.1 [0.1 (%1.1)->2.4 (%98.9))]
%14 local maxima, %31 large gradients and %51 min vals, 605 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=9662268.0, rms=16.729
021: dt: 0.0500, sse=9360278.0, rms=16.440 (1.723%)
022: dt: 0.0500, sse=9075914.0, rms=16.164 (1.680%)
023: dt: 0.0500, sse=8806216.0, rms=15.898 (1.649%)
024: dt: 0.0500, sse=8552253.0, rms=15.643 (1.605%)
025: dt: 0.0500, sse=8312879.0, rms=15.398 (1.563%)
026: dt: 0.0500, sse=8087369.5, rms=15.164 (1.520%)
027: dt: 0.0500, sse=7873863.0, rms=14.939 (1.484%)
028: dt: 0.0500, sse=7670987.0, rms=14.722 (1.453%)
029: dt: 0.0500, sse=7477895.0, rms=14.512 (1.425%)
030: dt: 0.0500, sse=7294061.0, rms=14.309 (1.396%)
positioning took 1.1 minutes
mean border=60.5, 495 (166) missing vertices, mean dist 1.0 [0.1 (%8.1)->2.2 (%91.9))]
%14 local maxima, %32 large gradients and %50 min vals, 594 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=7372661.5, rms=14.396
031: dt: 0.5000, sse=6077852.5, rms=12.890 (10.461%)
032: dt: 0.5000, sse=5201354.5, rms=11.754 (8.816%)
033: dt: 0.5000, sse=4577101.5, rms=10.872 (7.502%)
034: dt: 0.5000, sse=4091796.0, rms=10.128 (6.847%)
035: dt: 0.5000, sse=3686014.2, rms=9.463 (6.568%)
036: dt: 0.5000, sse=3328144.2, rms=8.834 (6.648%)
037: dt: 0.5000, sse=3000743.5, rms=8.219 (6.961%)
038: dt: 0.5000, sse=2703600.8, rms=7.617 (7.317%)
039: dt: 0.5000, sse=2457405.8, rms=7.083 (7.015%)
040: dt: 0.5000, sse=2257831.5, rms=6.616 (6.591%)
041: dt: 0.5000, sse=2112330.2, rms=6.255 (5.456%)
042: dt: 0.5000, sse=2011447.5, rms=5.989 (4.248%)
043: dt: 0.5000, sse=1941394.0, rms=5.800 (3.165%)
044: dt: 0.5000, sse=1897147.0, rms=5.673 (2.190%)
045: dt: 0.5000, sse=1862829.9, rms=5.576 (1.704%)
046: dt: 0.5000, sse=1840550.9, rms=5.509 (1.209%)
rms = 5.48, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1829233.5, rms=5.476 (0.590%)
048: dt: 0.2500, sse=1758783.9, rms=5.228 (4.527%)
049: dt: 0.2500, sse=1734882.9, rms=5.155 (1.405%)
rms = 5.16, time step reduction 2 of 3 to 0.125...
rms = 5.13, time step reduction 3 of 3 to 0.062...
050: dt: 0.1250, sse=1728468.1, rms=5.133 (0.433%)
positioning took 3.3 minutes
mean border=59.9, 3726 (80) missing vertices, mean dist 0.2 [0.2 (%46.7)->0.8 (%53.3))]
%22 local maxima, %27 large gradients and %45 min vals, 326 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=1890522.4, rms=5.077
051: dt: 0.5000, sse=1769510.8, rms=4.696 (7.507%)
052: dt: 0.5000, sse=1702250.6, rms=4.490 (4.378%)
rms = 4.54, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1630112.0, rms=4.191 (6.678%)
054: dt: 0.2500, sse=1608542.9, rms=4.094 (2.305%)
rms = 4.08, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1604928.6, rms=4.081 (0.321%)
056: dt: 0.1250, sse=1582783.6, rms=3.984 (2.363%)
rms = 3.96, time step reduction 3 of 3 to 0.062...
057: dt: 0.1250, sse=1576792.2, rms=3.961 (0.585%)
positioning took 1.6 minutes
mean border=59.7, 4608 (59) missing vertices, mean dist 0.1 [0.2 (%49.2)->0.6 (%50.8))]
%27 local maxima, %22 large gradients and %44 min vals, 416 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=1617004.6, rms=4.125
rms = 4.30, time step reduction 1 of 3 to 0.250...
058: dt: 0.2500, sse=1588824.6, rms=4.013 (2.723%)
rms = 3.96, time step reduction 2 of 3 to 0.125...
059: dt: 0.2500, sse=1574283.1, rms=3.963 (1.241%)
rms = 3.92, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1564297.1, rms=3.919 (1.116%)
positioning took 0.8 minutes
mean border=59.3, 8959 (57) missing vertices, mean dist 0.1 [0.2 (%47.8)->0.5 (%52.2))]
%30 local maxima, %18 large gradients and %42 min vals, 488 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-6.0.0/0050352/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1581459.5, rms=3.981
rms = 4.02, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1556718.1, rms=3.883 (2.439%)
062: dt: 0.2500, sse=1528161.5, rms=3.787 (2.481%)
rms = 3.75, time step reduction 2 of 3 to 0.125...
063: dt: 0.2500, sse=1515412.2, rms=3.746 (1.099%)
064: dt: 0.1250, sse=1496270.0, rms=3.660 (2.292%)
rms = 3.63, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1487238.0, rms=3.626 (0.930%)
positioning took 1.3 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.area.pial
vertex spacing 0.99 +- 0.45 (0.07-->8.25) (max @ vno 111440 --> 109158)
face area 0.39 +- 0.34 (0.00-->18.90)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 165183 vertices processed
25000 of 165183 vertices processed
50000 of 165183 vertices processed
75000 of 165183 vertices processed
100000 of 165183 vertices processed
125000 of 165183 vertices processed
150000 of 165183 vertices processed
0 of 165183 vertices processed
25000 of 165183 vertices processed
50000 of 165183 vertices processed
75000 of 165183 vertices processed
100000 of 165183 vertices processed
125000 of 165183 vertices processed
150000 of 165183 vertices processed
thickness calculation complete, 583:1261 truncations.
32117 vertices at 0 distance
105552 vertices at 1 distance
99434 vertices at 2 distance
48548 vertices at 3 distance
18979 vertices at 4 distance
7284 vertices at 5 distance
2823 vertices at 6 distance
1178 vertices at 7 distance
547 vertices at 8 distance
268 vertices at 9 distance
165 vertices at 10 distance
91 vertices at 11 distance
60 vertices at 12 distance
57 vertices at 13 distance
43 vertices at 14 distance
28 vertices at 15 distance
27 vertices at 16 distance
16 vertices at 17 distance
28 vertices at 18 distance
24 vertices at 19 distance
43 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.thickness
positioning took 18.4 minutes
PIDs (1182 1185) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 11:31:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
Total face volume 282813
Total vertex volume 279572 (mask=0)
#@# 0050352 lh 279572
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 11:31:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
Total face volume 289365
Total vertex volume 286560 (mask=0)
#@# 0050352 rh 286560
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 11:31:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 

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 = 466
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/ribbon.mgz
mris_volmask took 14.24 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 11:45:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 0050352 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 11:45:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 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 0050352 rh pial 

Waiting for PID 2294 of (2294 2297 2300 2303) to complete...
Waiting for PID 2297 of (2294 2297 2300 2303) to complete...
Waiting for PID 2300 of (2294 2297 2300 2303) to complete...
Waiting for PID 2303 of (2294 2297 2300 2303) 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 0050352 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
Total vertex volume 279572 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1461    999   2374  2.693 0.525     0.112     0.026       10     1.5  bankssts
 1379    902   2794  2.736 0.810     0.147     0.031       21     1.7  caudalanteriorcingulate
 4942   3281   9181  2.583 0.617     0.119     0.030       45     5.8  caudalmiddlefrontal
 2515   1686   3664  1.999 0.541     0.151     0.051       38     5.2  cuneus
 1146    725   2011  2.411 0.784     0.172     0.085       23     4.7  entorhinal
 5233   3572   9651  2.386 0.655     0.141     0.050       74    10.8  fusiform
 6776   4505  12637  2.390 0.634     0.131     0.035       79     9.7  inferiorparietal
 5852   4013  13137  2.571 0.869     0.147     0.055      121    14.8  inferiortemporal
 1456    988   2560  2.474 0.896     0.122     0.029       18     1.5  isthmuscingulate
 8453   5658  14533  2.213 0.722     0.149     0.050      132    17.9  lateraloccipital
 4767   3149   9526  2.723 0.789     0.138     0.047       66     9.7  lateralorbitofrontal
 4558   3049   6686  1.961 0.591     0.151     0.055       74    10.2  lingual
 3190   2294   6544  2.507 0.822     0.143     0.044       49     5.8  medialorbitofrontal
 5018   3452  11876  2.704 0.758     0.125     0.033       54     6.6  middletemporal
 1164    708   1885  2.307 0.669     0.101     0.038       14     2.0  parahippocampal
 2615   1677   4592  2.493 0.652     0.141     0.045       34     5.2  paracentral
 2389   1616   4528  2.498 0.589     0.112     0.026       21     2.5  parsopercularis
 1186    795   2454  2.524 0.911     0.151     0.057       23     2.5  parsorbitalis
 2251   1469   4891  2.765 0.761     0.122     0.032       23     2.8  parstriangularis
 1781   1299   2094  1.848 0.493     0.163     0.053       24     4.0  pericalcarine
 7057   4571  10110  2.028 0.622     0.125     0.036       73    10.5  postcentral
 2305   1584   3732  2.310 0.639     0.145     0.040       31     3.7  posteriorcingulate
 9679   6401  16271  2.425 0.686     0.124     0.038       96    15.4  precentral
 6234   4227  11289  2.491 0.679     0.131     0.038       73     9.4  precuneus
 1208    848   2799  2.941 0.771     0.136     0.037       16     1.9  rostralanteriorcingulate
10933   7514  21687  2.588 0.656     0.149     0.049      164    21.6  rostralmiddlefrontal
15000   9996  29561  2.700 0.748     0.143     0.049      187    30.7  superiorfrontal
10890   7134  16511  2.136 0.573     0.135     0.044      133    18.9  superiorparietal
 6865   4721  14836  2.569 0.768     0.116     0.030       67     8.5  superiortemporal
 6047   4181  12041  2.500 0.666     0.133     0.038       85     9.4  supramarginal
  486    316   1377  3.076 0.787     0.196     0.084       13     1.9  frontalpole
  947    700   2618  2.783 0.919     0.172     0.066       16     2.7  temporalpole
  939    572   1268  2.143 0.548     0.141     0.051       10     1.9  transversetemporal
 4161   2808   7835  2.926 0.814     0.128     0.042       49     6.9  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 0050352 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
Total vertex volume 279572 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1461    817   2374  2.693 0.525     0.119     0.036       19     2.1  bankssts
 1379   1136   2794  2.736 0.810     0.154     0.041       36     2.3  caudalanteriorcingulate
 4942   3763   9181  2.583 0.617     0.130     0.031       63     6.9  caudalmiddlefrontal
 2515   2035   3664  1.999 0.541     0.138     0.037       31     4.1  cuneus
 1146    986   2011  2.411 0.784     0.200     0.127       60     8.8  entorhinal
 5233   4387   9651  2.386 0.655     0.165     0.047       96    11.6  fusiform
 6776   5935  12637  2.390 0.634     0.166     0.043       99    14.1  inferiorparietal
 5852   5758  13137  2.571 0.869     0.191     0.053       97    14.9  inferiortemporal
 1456   1189   2560  2.474 0.896     0.154     0.045       23     2.6  isthmuscingulate
 8453   7182  14533  2.213 0.722     0.157     0.043      155    17.0  lateraloccipital
 4767   3775   9526  2.723 0.789     0.152     0.044       77     9.3  lateralorbitofrontal
 4558   3821   6686  1.961 0.591     0.154     0.042       77     8.7  lingual
 3190   2917   6544  2.507 0.822     0.174     0.048       54     7.0  medialorbitofrontal
 5018   5135  11876  2.704 0.758     0.185     0.048       65    11.5  middletemporal
 1164    937   1885  2.307 0.669     0.146     0.039       12     2.0  parahippocampal
 2615   2029   4592  2.493 0.652     0.143     0.039       42     4.8  paracentral
 2389   1973   4528  2.498 0.589     0.146     0.036       35     4.0  parsopercularis
 1186   1088   2454  2.524 0.911     0.168     0.052      200     2.8  parsorbitalis
 2251   1966   4891  2.765 0.761     0.169     0.045       36     4.8  parstriangularis
 1781   1088   2094  1.848 0.493     0.134     0.041       29     3.1  pericalcarine
 7057   5457  10110  2.028 0.622     0.132     0.033       67    10.3  postcentral
 2305   1751   3732  2.310 0.639     0.152     0.040       53     4.4  posteriorcingulate
 9679   7020  16271  2.425 0.686     0.120     0.030      123    12.8  precentral
 6234   4854  11289  2.491 0.679     0.147     0.044      149    12.7  precuneus
 1208   1119   2799  2.941 0.771     0.178     0.055       54     2.7  rostralanteriorcingulate
10933   9038  21687  2.588 0.656     0.161     0.043      184    21.9  rostralmiddlefrontal
15000  11635  29561  2.700 0.748     0.143     0.042      264    27.5  superiorfrontal
10890   8251  16511  2.136 0.573     0.139     0.038      154    18.3  superiorparietal
 6865   6014  14836  2.569 0.768     0.141     0.033       75    10.2  superiortemporal
 6047   5265  12041  2.500 0.666     0.155     0.037       77    10.2  supramarginal
  486    513   1377  3.076 0.787     0.164     0.029        6     0.8  frontalpole
  947   1258   2618  2.783 0.919     0.218     0.051       13     2.3  temporalpole
  939    685   1268  2.143 0.548     0.137     0.041        9     1.7  transversetemporal
 4161   2542   7835  2.926 0.814     0.126     0.037       78     6.3  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050352 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
Total vertex volume 286560 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1205    865   2413  2.854 0.528     0.093     0.019        6     0.9  bankssts
 1393    920   2496  2.550 0.562     0.125     0.026       16     1.5  caudalanteriorcingulate
 5034   3350   8709  2.558 0.589     0.128     0.049       64    10.2  caudalmiddlefrontal
 2458   1590   3415  1.950 0.515     0.138     0.041       33     4.2  cuneus
  862    533   1945  2.824 0.900     0.167     0.080       22     3.1  entorhinal
 5294   3494  10625  2.667 0.776     0.134     0.046       68    10.4  fusiform
 8832   5726  17049  2.619 0.694     0.133     0.045      115    15.7  inferiorparietal
 6653   4352  14290  2.687 0.802     0.141     0.065      135    18.8  inferiortemporal
 1431    944   2648  2.495 0.799     0.136     0.038       18     2.0  isthmuscingulate
 7989   5151  12465  2.186 0.698     0.147     0.054      130    17.4  lateraloccipital
 4793   3124   8219  2.466 0.774     0.139     0.054       75    10.9  lateralorbitofrontal
 4841   3286   7356  2.069 0.556     0.148     0.047       68     8.8  lingual
 3427   2254   6376  2.509 0.912     0.137     0.054       56     7.9  medialorbitofrontal
 6429   4370  15378  2.950 0.717     0.139     0.048       87    12.5  middletemporal
 1127    705   1893  2.400 0.727     0.105     0.026        9     1.1  parahippocampal
 2737   1772   4181  2.259 0.624     0.130     0.053       36     6.2  paracentral
 2415   1656   4667  2.576 0.564     0.118     0.034       25     3.2  parsopercularis
 1903   1207   3932  2.669 0.822     0.160     0.066       40     5.1  parsorbitalis
 2887   1940   6035  2.683 0.632     0.126     0.034       34     3.6  parstriangularis
 2276   1563   2810  1.900 0.549     0.131     0.044       31     3.9  pericalcarine
 6805   4389   9915  2.093 0.714     0.122     0.046      136    13.4  postcentral
 2445   1663   4566  2.490 0.869     0.146     0.039       37     3.6  posteriorcingulate
 9868   6484  15157  2.361 0.674     0.132     0.043      104    18.2  precentral
 6542   4390  11989  2.512 0.668     0.131     0.037       74     9.8  precuneus
 1058    712   2550  3.139 0.837     0.131     0.034       16     1.5  rostralanteriorcingulate
13658   9095  25754  2.496 0.674     0.145     0.053      201    29.4  rostralmiddlefrontal
14491   9415  28835  2.781 0.785     0.141     0.056      238    35.3  superiorfrontal
 9451   6352  15822  2.289 0.659     0.137     0.046      137    19.6  superiorparietal
 6563   4296  12078  2.546 0.692     0.130     0.054       88    15.2  superiortemporal
 6067   3988  11430  2.673 0.619     0.131     0.042      106    11.1  supramarginal
  507    305   1225  2.626 0.798     0.157     0.074       12     1.4  frontalpole
  824    489   1611  2.528 0.816     0.167     0.076       17     2.8  temporalpole
  675    420    839  2.156 0.710     0.145     0.050       11     1.4  transversetemporal
 4096   2822   7843  3.060 0.722     0.136     0.043       50     6.7  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 0050352 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
Total vertex volume 286560 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1205    789   2413  2.854 0.528     0.108     0.026       14     1.4  bankssts
 1393   1089   2496  2.550 0.562     0.152     0.035       41     2.4  caudalanteriorcingulate
 5034   3475   8709  2.558 0.589     0.113     0.030       65     7.0  caudalmiddlefrontal
 2458   2000   3415  1.950 0.515     0.146     0.038       28     4.2  cuneus
  862    815   1945  2.824 0.900     0.164     0.046       12     1.9  entorhinal
 5294   4360  10625  2.667 0.776     0.160     0.049      112    12.7  fusiform
 8832   7175  17049  2.619 0.694     0.155     0.046      141    19.8  inferiorparietal
 6653   5838  14290  2.687 0.802     0.162     0.049      350    14.7  inferiortemporal
 1431   1139   2648  2.495 0.799     0.167     0.043       26     2.7  isthmuscingulate
 7989   6247  12465  2.186 0.698     0.142     0.041      135    14.7  lateraloccipital
 4793   3628   8219  2.466 0.774     0.162     0.048       81    10.8  lateralorbitofrontal
 4841   4029   7356  2.069 0.556     0.155     0.041       68     9.0  lingual
 3427   2939   6376  2.509 0.912     0.175     0.054       66     8.4  medialorbitofrontal
 6429   6024  15378  2.950 0.717     0.163     0.043      114    12.5  middletemporal
 1127    848   1893  2.400 0.727     0.135     0.034       15     1.7  parahippocampal
 2737   1927   4181  2.259 0.624     0.129     0.033       37     4.1  paracentral
 2415   2037   4667  2.576 0.564     0.144     0.035       27     3.7  parsopercularis
 1903   1689   3932  2.669 0.822     0.156     0.041       25     3.4  parsorbitalis
 2887   2570   6035  2.683 0.632     0.158     0.034       34     4.6  parstriangularis
 2276   1479   2810  1.900 0.549     0.138     0.044       44     4.2  pericalcarine
 6805   5214   9915  2.093 0.714     0.130     0.034       84    10.3  postcentral
 2445   1995   4566  2.490 0.869     0.159     0.042       50     4.7  posteriorcingulate
 9868   6535  15157  2.361 0.674     0.113     0.034      155    14.1  precentral
 6542   5038  11989  2.512 0.668     0.147     0.039      109    11.5  precuneus
 1058    971   2550  3.139 0.837     0.155     0.041       32     1.9  rostralanteriorcingulate
13658  11057  25754  2.496 0.674     0.152     0.041      267    26.1  rostralmiddlefrontal
14491  10927  28835  2.781 0.785     0.146     0.044      243    29.2  superiorfrontal
 9451   7516  15822  2.289 0.659     0.144     0.040      168    17.0  superiorparietal
 6563   5168  12078  2.546 0.692     0.145     0.039      109    11.8  superiortemporal
 6067   4561  11430  2.673 0.619     0.143     0.039      115    11.1  supramarginal
  507    568   1225  2.626 0.798     0.190     0.044        7     1.1  frontalpole
  824    706   1611  2.528 0.816     0.180     0.068       34     2.3  temporalpole
  675    410    839  2.156 0.710     0.128     0.041       10     1.1  transversetemporal
 4096   2400   7843  3.060 0.722     0.134     0.047       87     8.6  insula
PIDs (2294 2297 2300 2303) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 11:47:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:47:25 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 2403 of (2403 2406) to complete...
Waiting for PID 2406 of (2403 2406) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
57 labels changed using aseg
relabeling using gibbs priors...
000:  10261 changed, 159921 examined...
001:   2506 changed, 39819 examined...
002:    781 changed, 12993 examined...
003:    351 changed, 4484 examined...
004:    173 changed, 2002 examined...
005:     88 changed, 1017 examined...
006:     38 changed, 502 examined...
007:     11 changed, 212 examined...
008:      3 changed, 76 examined...
009:      2 changed, 16 examined...
010:      1 changed, 10 examined...
011:      0 changed, 8 examined...
33 labels changed using aseg
000: 295 total segments, 211 labels (2644 vertices) changed
001: 95 total segments, 12 labels (89 vertices) changed
002: 83 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 36 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1434 vertices marked for relabeling...
1434 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 21 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
1 labels changed using aseg
relabeling using gibbs priors...
000:  10278 changed, 165183 examined...
001:   2413 changed, 40284 examined...
002:    705 changed, 12705 examined...
003:    297 changed, 3968 examined...
004:    130 changed, 1665 examined...
005:     63 changed, 781 examined...
006:     37 changed, 350 examined...
007:     20 changed, 208 examined...
008:      7 changed, 107 examined...
009:      5 changed, 41 examined...
010:      4 changed, 25 examined...
011:      1 changed, 20 examined...
012:      0 changed, 4 examined...
0 labels changed using aseg
000: 300 total segments, 216 labels (2581 vertices) changed
001: 95 total segments, 11 labels (45 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 49 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1584 vertices marked for relabeling...
1584 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 22 seconds.
PIDs (2403 2406) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 11:47:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 11:47:48 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white 

Waiting for PID 2452 of (2452 2455) to complete...
Waiting for PID 2455 of (2452 2455) 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 0050352 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
Total vertex volume 279572 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1596   1066   3379  2.812 0.774     0.148     0.057       25     4.0  G&S_frontomargin
 1680   1138   3104  2.186 0.759     0.151     0.056       26     3.9  G&S_occipital_inf
 1818   1187   3333  2.351 0.823     0.148     0.049       26     3.9  G&S_paracentral
 1983   1282   4103  2.573 0.623     0.130     0.035       25     2.6  G&S_subcentral
 1011    702   3008  3.239 0.657     0.183     0.072       23     2.9  G&S_transv_frontopol
 2810   1980   5844  2.704 0.690     0.132     0.035       31     4.3  G&S_cingul-Ant
 1636   1110   3195  2.801 0.593     0.135     0.035       17     2.1  G&S_cingul-Mid-Ant
 1722   1188   2617  2.264 0.582     0.131     0.035       17     2.5  G&S_cingul-Mid-Post
  695    483   1605  2.703 0.761     0.166     0.051       14     1.4  G_cingul-Post-dorsal
  253    180    596  2.723 0.948     0.139     0.041        3     0.3  G_cingul-Post-ventral
 2168   1487   3545  2.049 0.642     0.158     0.059       36     5.3  G_cuneus
 1177    782   2716  2.576 0.611     0.129     0.040       15     2.1  G_front_inf-Opercular
  540    346   1289  2.601 0.807     0.159     0.054       10     1.3  G_front_inf-Orbital
 1527    948   3768  2.866 0.725     0.132     0.037       20     2.1  G_front_inf-Triangul
 6227   4146  14649  2.723 0.680     0.154     0.050      107    12.7  G_front_middle
10050   6575  21349  2.694 0.810     0.156     0.059      155    25.0  G_front_sup
  794    550   1704  2.964 0.944     0.149     0.053       15     1.4  G_Ins_lg&S_cent_ins
  827    546   2272  3.262 0.701     0.141     0.057       12     2.0  G_insular_short
 2203   1480   5619  2.684 0.732     0.164     0.058       46     5.3  G_occipital_middle
 1835   1137   3025  2.157 0.699     0.148     0.048       29     3.4  G_occipital_sup
 2108   1436   4247  2.344 0.660     0.160     0.072       43     6.6  G_oc-temp_lat-fusifor
 3455   2306   5361  1.932 0.620     0.165     0.066       67     9.5  G_oc-temp_med-Lingual
 1984   1237   3381  2.302 0.758     0.153     0.071       38     6.7  G_oc-temp_med-Parahip
 2893   1844   6447  2.580 0.835     0.155     0.067       61     7.8  G_orbital
 2899   1884   6121  2.423 0.738     0.150     0.042       51     5.0  G_pariet_inf-Angular
 3248   2190   7358  2.591 0.674     0.150     0.052       59     6.8  G_pariet_inf-Supramar
 4691   3024   7612  2.075 0.553     0.141     0.054       68    10.2  G_parietal_sup
 2660   1605   3913  2.072 0.633     0.132     0.045       31     4.9  G_postcentral
 3976   2556   7278  2.423 0.731     0.133     0.048       44     8.1  G_precentral
 3154   2136   7032  2.558 0.657     0.150     0.054       50     6.6  G_precuneus
 1078    834   2743  2.539 0.800     0.174     0.053       29     2.3  G_rectus
 1051    677   1598  2.399 0.968     0.129     0.052       15     2.0  G_subcallosal
  701    414    970  2.048 0.445     0.150     0.058       10     1.5  G_temp_sup-G_T_transv
 2223   1536   7197  3.025 0.836     0.146     0.044       34     4.0  G_temp_sup-Lateral
 1103    802   2723  2.895 0.860     0.115     0.039        9     1.8  G_temp_sup-Plan_polar
 1015    668   1679  2.307 0.510     0.078     0.019        5     0.8  G_temp_sup-Plan_tempo
 3226   2202   9087  2.857 0.932     0.176     0.079      102    11.7  G_temporal_inf
 2650   1752   7688  2.959 0.737     0.138     0.040       38     4.2  G_temporal_middle
  292    193    354  2.150 0.544     0.112     0.023        2     0.2  Lat_Fis-ant-Horizont
  361    266    534  2.451 0.673     0.094     0.013        2     0.2  Lat_Fis-ant-Vertical
 1120    760   1417  2.427 0.616     0.106     0.022        6     0.9  Lat_Fis-post
 2480   1676   4179  2.110 0.761     0.165     0.063       49     6.6  Pole_occipital
 1767   1282   4730  2.685 0.882     0.168     0.063       30     4.9  Pole_temporal
 2121   1497   2613  2.037 0.668     0.139     0.041       23     3.5  S_calcarine
 3498   2419   3933  1.854 0.524     0.122     0.030       28     4.5  S_central
 1302    899   1870  2.260 0.498     0.133     0.032       12     1.7  S_cingul-Marginalis
  524    367    988  3.260 0.502     0.100     0.018        2     0.4  S_circular_insula_ant
 1687   1150   2514  2.734 0.807     0.098     0.022        8     1.5  S_circular_insula_inf
 1983   1361   3005  2.827 0.509     0.103     0.020        9     1.8  S_circular_insula_sup
 1232    862   1899  2.469 0.618     0.117     0.028        9     1.4  S_collat_transv_ant
  617    409    661  1.973 0.468     0.120     0.027        4     0.7  S_collat_transv_post
 2499   1730   3547  2.206 0.489     0.119     0.033       22     3.2  S_front_inf
 1936   1358   2894  2.425 0.590     0.131     0.033       17     2.5  S_front_middle
 4859   3292   7788  2.588 0.528     0.113     0.030       34     5.8  S_front_sup
  413    293    590  2.107 0.464     0.099     0.020        2     0.4  S_interm_prim-Jensen
 3759   2525   4876  2.187 0.500     0.117     0.025       30     3.7  S_intrapariet&P_trans
 1150    766   1371  2.011 0.405     0.119     0.028        9     1.3  S_oc_middle&Lunatus
 1354    910   1803  2.203 0.483     0.116     0.032        9     1.7  S_oc_sup&transversal
  805    562   1203  2.350 0.616     0.129     0.031        6     1.0  S_occipital_ant
 1130    785   1563  2.104 0.525     0.092     0.016        5     0.7  S_oc-temp_lat
 2117   1406   3216  2.312 0.523     0.101     0.020       13     1.5  S_oc-temp_med&Lingual
  490    365   1202  3.246 0.770     0.165     0.047        8     1.0  S_orbital_lateral
  726    528    908  2.022 0.605     0.119     0.027        5     0.8  S_orbital_med-olfact
 1929   1315   3658  2.807 0.713     0.129     0.033       18     2.9  S_orbital-H_Shaped
 2541   1703   3376  2.345 0.707     0.123     0.030       22     3.1  S_parieto_occipital
 1415    910   1550  2.116 0.704     0.131     0.025       22     1.2  S_pericallosal
 2719   1924   3637  2.123 0.509     0.123     0.029       23     3.2  S_postcentral
 2570   1717   4205  2.517 0.525     0.101     0.025       22     2.8  S_precentral-inf-part
 2005   1336   3030  2.640 0.566     0.117     0.031       15     2.8  S_precentral-sup-part
  669    465   1198  2.656 1.044     0.124     0.026        4     0.8  S_suborbital
 1173    802   1714  2.297 0.555     0.120     0.024       10     1.1  S_subparietal
 2004   1377   3123  2.186 0.583     0.112     0.026       14     2.2  S_temporal_inf
 6392   4403  10512  2.422 0.576     0.112     0.025       49     6.6  S_temporal_sup
  519    342    758  2.390 0.467     0.130     0.031        4     0.7  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 0050352 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
Total vertex volume 286560 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1308    877   2462  2.458 0.631     0.152     0.051       19     2.8  G&S_frontomargin
 1180    763   1992  2.235 0.611     0.151     0.053       19     2.3  G&S_occipital_inf
 1721   1107   2685  2.099 0.657     0.136     0.056       25     3.8  G&S_paracentral
 1787   1096   3382  2.613 0.623     0.125     0.064       86     5.3  G&S_subcentral
 1739   1112   3380  2.349 0.660     0.175     0.083       34     6.2  G&S_transv_frontopol
 3648   2463   7363  2.828 0.807     0.129     0.039       45     5.8  G&S_cingul-Ant
 1622   1120   3267  2.838 0.692     0.110     0.024       12     1.5  G&S_cingul-Mid-Ant
 1898   1271   3234  2.606 0.717     0.139     0.041       21     3.1  G&S_cingul-Mid-Post
  605    416   1788  3.016 0.993     0.170     0.059       10     1.4  G_cingul-Post-dorsal
  316    215    682  2.512 0.878     0.137     0.055        4     0.6  G_cingul-Post-ventral
 2328   1480   3302  1.968 0.532     0.145     0.047       41     4.5  G_cuneus
 1417    934   3140  2.574 0.530     0.128     0.043       21     2.2  G_front_inf-Opercular
  611    365   1262  2.501 0.562     0.152     0.066       13     1.7  G_front_inf-Orbital
 1304    848   3441  2.891 0.662     0.144     0.044       20     2.1  G_front_inf-Triangul
 7343   4626  15602  2.582 0.765     0.159     0.073      154    22.0  G_front_middle
 9699   6046  20898  2.764 0.863     0.153     0.073      214    31.5  G_front_sup
  780    542   1737  3.237 0.860     0.150     0.051       12     1.5  G_Ins_lg&S_cent_ins
  870    560   1877  3.107 0.726     0.149     0.056       15     1.9  G_insular_short
 2713   1750   6675  2.753 0.881     0.160     0.071       58     7.7  G_occipital_middle
 1767   1107   3761  2.593 0.834     0.135     0.052       26     4.0  G_occipital_sup
 2420   1518   5911  2.871 0.896     0.151     0.056       40     5.3  G_oc-temp_lat-fusifor
 3240   2150   5426  2.088 0.577     0.152     0.052       53     6.6  G_oc-temp_med-Lingual
 1669   1031   3592  2.753 0.840     0.148     0.069       35     4.8  G_oc-temp_med-Parahip
 4011   2569   8341  2.495 0.819     0.164     0.075       94    12.6  G_orbital
 3676   2289   7628  2.580 0.702     0.147     0.059       63     8.3  G_pariet_inf-Angular
 2967   1898   6463  2.646 0.701     0.150     0.065       84     8.7  G_pariet_inf-Supramar
 2823   1952   5095  2.124 0.618     0.156     0.067       69     8.8  G_parietal_sup
 2396   1493   3820  2.046 0.769     0.136     0.052       32     5.2  G_postcentral
 4059   2479   6383  2.227 0.754     0.148     0.061       62    10.9  G_precentral
 2829   1810   6587  2.683 0.668     0.147     0.054       48     6.4  G_precuneus
 1038    670   1995  2.189 0.822     0.148     0.061       18     2.9  G_rectus
  616    425   1021  2.687 1.024     0.156     0.079       15     1.7  G_subcallosal
  589    338    817  2.316 0.765     0.144     0.057       10     1.3  G_temp_sup-G_T_transv
 2449   1525   5508  2.672 0.802     0.148     0.072       45     7.2  G_temp_sup-Lateral
 1332    883   2304  2.457 0.681     0.157     0.071       22     4.5  G_temp_sup-Plan_polar
 1246    843   2102  2.393 0.567     0.120     0.050       12     3.0  G_temp_sup-Plan_tempo
 3988   2556   9713  2.704 0.872     0.162     0.086      110    15.7  G_temporal_inf
 3794   2574  10354  2.951 0.753     0.150     0.058       64     8.5  G_temporal_middle
  328    247    471  2.307 0.509     0.105     0.021        2     0.2  Lat_Fis-ant-Horizont
  305    230    482  2.332 0.468     0.107     0.018        2     0.2  Lat_Fis-ant-Vertical
 1629   1108   2401  2.663 0.600     0.120     0.026       14     1.6  Lat_Fis-post
 3700   2373   4853  1.924 0.569     0.149     0.055       61     8.3  Pole_occipital
 1520    981   4203  2.897 0.926     0.181     0.096       41     6.7  Pole_temporal
 2200   1554   2806  2.015 0.618     0.129     0.036       21     3.3  S_calcarine
 3671   2507   4165  1.987 0.600     0.118     0.031       27     4.5  S_central
 1315    912   1855  2.131 0.522     0.097     0.021        6     1.0  S_cingul-Marginalis
  817    548   1416  3.396 0.595     0.113     0.023        5     0.8  S_circular_insula_ant
 1315    878   1977  2.749 0.711     0.102     0.026        9     1.5  S_circular_insula_inf
 1657   1147   2712  2.864 0.481     0.105     0.020        8     1.4  S_circular_insula_sup
 1265    877   2008  2.544 0.597     0.105     0.026        8     1.3  S_collat_transv_ant
  542    389    693  2.001 0.485     0.130     0.029        5     0.7  S_collat_transv_post
 2684   1896   4269  2.509 0.485     0.115     0.025       19     2.7  S_front_inf
 3756   2603   5734  2.350 0.555     0.124     0.036       30     5.0  S_front_middle
 3932   2779   6641  2.772 0.539     0.116     0.028       25     4.5  S_front_sup
  506    342    739  2.721 0.530     0.109     0.027        3     0.5  S_interm_prim-Jensen
 4193   2817   6009  2.407 0.629     0.121     0.029       33     5.1  S_intrapariet&P_trans
 1117    776   1372  1.973 0.393     0.137     0.029       12     1.4  S_oc_middle&Lunatus
 1502   1023   2088  2.271 0.451     0.118     0.027       11     1.7  S_oc_sup&transversal
  805    555   1109  2.320 0.449     0.126     0.031        6     1.1  S_occipital_ant
 1557   1067   2246  2.532 0.563     0.107     0.023        9     1.4  S_oc-temp_lat
 2262   1544   2887  2.149 0.525     0.105     0.019       13     1.7  S_oc-temp_med&Lingual
  638    447    943  2.436 0.530     0.119     0.025        4     0.6  S_orbital_lateral
  736    512    901  1.959 0.474     0.112     0.025        5     0.7  S_orbital_med-olfact
 1805   1198   3094  2.566 0.721     0.122     0.036       16     2.4  S_orbital-H_Shaped
 2984   2015   4143  2.246 0.596     0.124     0.030       26     3.6  S_parieto_occipital
 1878   1221   2192  2.290 0.777     0.135     0.022       29     1.5  S_pericallosal
 2505   1722   3434  2.314 0.572     0.132     0.034       25     3.5  S_postcentral
 2465   1710   4096  2.656 0.549     0.109     0.024       17     2.3  S_precentral-inf-part
 1966   1386   2932  2.478 0.511     0.113     0.024       12     2.1  S_precentral-sup-part
  263    176    482  2.394 0.522     0.117     0.028        2     0.4  S_suborbital
 1288    885   2318  2.737 0.689     0.127     0.032       12     1.5  S_subparietal
 1650   1119   2577  2.733 0.544     0.115     0.025       11     1.6  S_temporal_inf
 6233   4213  10930  2.809 0.561     0.102     0.022       38     5.5  S_temporal_sup
  257    184    389  2.378 0.497     0.106     0.025        1     0.3  S_temporal_transverse
PIDs (2452 2455) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 11:48:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 11:48:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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 2525 of (2525 2528) to complete...
Waiting for PID 2528 of (2525 2528) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
1377 labels changed using aseg
relabeling using gibbs priors...
000:   2293 changed, 159921 examined...
001:    537 changed, 10466 examined...
002:    180 changed, 3010 examined...
003:     82 changed, 1028 examined...
004:     48 changed, 464 examined...
005:     38 changed, 256 examined...
006:     25 changed, 194 examined...
007:     21 changed, 124 examined...
008:     12 changed, 109 examined...
009:     11 changed, 70 examined...
010:     10 changed, 65 examined...
011:      9 changed, 63 examined...
012:      7 changed, 56 examined...
013:      2 changed, 35 examined...
014:      1 changed, 14 examined...
015:      1 changed, 7 examined...
016:      1 changed, 7 examined...
017:      1 changed, 6 examined...
018:      1 changed, 7 examined...
019:      2 changed, 6 examined...
020:      3 changed, 9 examined...
021:      2 changed, 17 examined...
022:      0 changed, 11 examined...
350 labels changed using aseg
000: 75 total segments, 42 labels (402 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...
1017 vertices marked for relabeling...
1017 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050352 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...
1236 labels changed using aseg
relabeling using gibbs priors...
000:   2187 changed, 165183 examined...
001:    546 changed, 10201 examined...
002:    164 changed, 3073 examined...
003:     66 changed, 1002 examined...
004:     32 changed, 365 examined...
005:     18 changed, 177 examined...
006:     16 changed, 99 examined...
007:      7 changed, 69 examined...
008:      2 changed, 33 examined...
009:      3 changed, 14 examined...
010:      1 changed, 20 examined...
011:      0 changed, 7 examined...
199 labels changed using aseg
000: 53 total segments, 20 labels (169 vertices) changed
001: 34 total segments, 1 labels (2 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 9 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1285 vertices marked for relabeling...
1285 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 17 seconds.
PIDs (2525 2528) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 11:48:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 11:48:53 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white 

Waiting for PID 2576 of (2576 2579) to complete...
Waiting for PID 2579 of (2576 2579) 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 0050352 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 282813
Total vertex volume 279572 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1984   1295   3801  2.718 0.739     0.145     0.034       27     2.6  caudalanteriorcingulate
 5259   3525   9733  2.591 0.605     0.120     0.029       47     6.2  caudalmiddlefrontal
 3483   2330   5258  2.074 0.615     0.141     0.048       46     6.5  cuneus
 1061    677   1823  2.324 0.738     0.177     0.087       24     4.2  entorhinal
 4864   3321   8796  2.374 0.631     0.137     0.048       65     9.7  fusiform
 7016   4674  13325  2.378 0.658     0.134     0.036       89    10.3  inferiorparietal
 5846   3973  13327  2.616 0.887     0.146     0.057      120    15.1  inferiortemporal
 1407    954   2554  2.540 0.879     0.124     0.029       18     1.4  isthmuscingulate
 8406   5619  14308  2.194 0.722     0.150     0.050      130    17.7  lateraloccipital
 5351   3524  10861  2.710 0.821     0.147     0.054       86    12.5  lateralorbitofrontal
 4672   3130   6916  1.966 0.589     0.150     0.055       78    10.5  lingual
 2639   1905   5501  2.473 0.873     0.144     0.044       44     4.5  medialorbitofrontal
 6508   4486  14276  2.627 0.705     0.125     0.033       71     8.7  middletemporal
 1229    754   1992  2.295 0.668     0.100     0.037       13     2.0  parahippocampal
 3140   2030   5537  2.457 0.658     0.141     0.046       40     6.3  paracentral
 2046   1397   3939  2.523 0.589     0.114     0.027       18     2.2  parsopercularis
 1104    721   1907  2.359 0.722     0.132     0.046       16     2.0  parsorbitalis
 2927   1916   6047  2.689 0.744     0.123     0.032       30     3.7  parstriangularis
 1790   1289   2059  1.840 0.494     0.162     0.054       24     4.1  pericalcarine
 8053   5247  11744  2.064 0.630     0.127     0.037       86    11.9  postcentral
 2430   1688   3879  2.271 0.634     0.145     0.041       32     3.9  posteriorcingulate
 9482   6253  15899  2.428 0.680     0.123     0.038       92    15.1  precentral
 6054   4090  11174  2.500 0.678     0.134     0.040       75     9.6  precuneus
 1909   1320   3904  2.850 0.751     0.137     0.038       24     3.0  rostralanteriorcingulate
 8092   5512  15743  2.569 0.666     0.148     0.049      122    15.7  rostralmiddlefrontal
16665  11194  33950  2.701 0.747     0.145     0.050      223    35.1  superiorfrontal
 8937   5877  13322  2.121 0.543     0.134     0.044      105    15.7  superiorparietal
 9036   6227  19576  2.626 0.784     0.123     0.035       95    13.1  superiortemporal
 5420   3738  10524  2.511 0.632     0.131     0.038       73     8.3  supramarginal
  910    552   1236  2.145 0.555     0.141     0.051       10     1.8  transversetemporal
 3105   2153   6661  3.190 0.682     0.123     0.035       31     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 0050352 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 289365
Total vertex volume 286560 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1542   1014   2786  2.549 0.572     0.125     0.026       18     1.6  caudalanteriorcingulate
 5126   3420   8908  2.552 0.593     0.129     0.049       65    10.4  caudalmiddlefrontal
 3021   1961   4084  1.971 0.522     0.138     0.041       42     4.9  cuneus
  701    435   1756  3.006 0.836     0.162     0.076       19     2.2  entorhinal
 4849   3201   9621  2.674 0.781     0.130     0.043       58     8.2  fusiform
 8875   5746  17133  2.614 0.696     0.133     0.046      115    16.0  inferiorparietal
 7063   4640  15203  2.663 0.803     0.143     0.067      143    21.1  inferiortemporal
 1450    956   2652  2.481 0.792     0.135     0.039       18     2.1  isthmuscingulate
 8041   5170  12610  2.195 0.705     0.149     0.056      134    18.4  lateraloccipital
 5995   3862  10502  2.429 0.747     0.145     0.059      102    14.8  lateralorbitofrontal
 4755   3235   7255  2.071 0.555     0.149     0.047       68     8.7  lingual
 2512   1678   4773  2.448 0.939     0.138     0.054       40     5.5  medialorbitofrontal
 7430   5066  17004  2.927 0.686     0.133     0.044       93    13.3  middletemporal
 1239    770   2018  2.378 0.739     0.111     0.032       12     1.6  parahippocampal
 2979   1920   4703  2.274 0.638     0.137     0.061       43     8.4  paracentral
 2907   2000   5650  2.566 0.544     0.118     0.035       30     3.8  parsopercularis
 1435    916   2556  2.655 0.766     0.147     0.059       27     3.5  parsorbitalis
 2812   1882   5636  2.662 0.640     0.132     0.034       34     3.5  parstriangularis
 2241   1554   2803  1.911 0.546     0.130     0.041       27     3.8  pericalcarine
 7477   4868  10805  2.094 0.701     0.124     0.044      140    14.3  postcentral
 2486   1700   4588  2.495 0.866     0.149     0.040       38     3.8  posteriorcingulate
 9396   6125  14482  2.384 0.675     0.132     0.045      103    17.9  precentral
 6753   4500  12606  2.505 0.681     0.131     0.039       80    10.4  precuneus
 1525   1028   3561  3.105 0.885     0.131     0.040       21     2.5  rostralanteriorcingulate
 9844   6566  19487  2.597 0.700     0.143     0.050      146    19.7  rostralmiddlefrontal
18652  12191  35936  2.671 0.777     0.141     0.056      299    44.0  superiorfrontal
 7905   5343  13406  2.298 0.650     0.137     0.046      116    16.1  superiorparietal
 8248   5407  15580  2.577 0.718     0.134     0.055      115    19.6  superiortemporal
 5691   3740  10782  2.687 0.621     0.129     0.042      101    10.4  supramarginal
  703    428    857  2.158 0.707     0.146     0.050       11     1.4  transversetemporal
 3391   2322   6818  3.180 0.678     0.130     0.036       36     4.6  insula
PIDs (2576 2579) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 11:49:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 pctsurfcon --s 0050352 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 11:49:40 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts

 pctsurfcon --s 0050352 --rh-only 

Waiting for PID 2645 of (2645 2656) to complete...
Waiting for PID 2656 of (2645 2656) to complete...

 pctsurfcon --s 0050352 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts/pctsurfcon.log
Sun Oct  8 11:49:40 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-6.0.0/0050352/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-928 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-6.0.0/0050352/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh --regheader 0050352 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 76153
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh
Dim: 159921 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh --projfrac 0.3 --regheader 0050352 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 88661
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh
Dim: 159921 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2645/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.w-g.pct.mgh --annot 0050352 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh --annot 0050352 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/lh.w-g.pct.mgh
Vertex Area is 0.673795 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 0050352 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/scripts/pctsurfcon.log
Sun Oct  8 11:49:40 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-6.0.0/0050352/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-928 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-6.0.0/0050352/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh --regheader 0050352 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 76979
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh
Dim: 165183 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh --projfrac 0.3 --regheader 0050352 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000  -0.00002;
 0.00000   0.00000   1.00000  -0.00001;
 0.00000  -1.00000   0.00000   0.00003;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 90051
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh
Dim: 165183 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/tmp.pctsurfcon.2656/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.w-g.pct.mgh --annot 0050352 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh --annot 0050352 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.w-g.pct.mgh
Vertex Area is 0.661551 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 (2645 2656) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 11:49:47 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
3168 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
4008 voxels changed to hypointensity...
7379 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 11:50:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352

 mri_aparc2aseg --s 0050352 --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 11:50:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352

 mri_aparc2aseg --s 0050352 --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 11:50:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352

 mri_aparc2aseg --s 0050352 --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 2839 of (2839 2842 2845) to complete...
Waiting for PID 2842 of (2839 2842 2845) to complete...
Waiting for PID 2845 of (2839 2842 2845) to complete...

 mri_aparc2aseg --s 0050352 --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 0050352
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/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 7.80
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 63
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 89
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 35
rescaling Fourth_Ventricle from 22 --> 14
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 74
rescaling CSF from 32 --> 50
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 88
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 27
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 65
rescaling Right_Thalamus_Proper from 85 --> 85
rescaling Right_Caudate from 62 --> 73
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 64
rescaling Right_Amygdala from 55 --> 77
rescaling Right_Accumbens_area from 65 --> 71
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 42
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 558621
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 159 changed.
pass 2: 14 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050352 --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 0050352
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/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 7.80
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 63
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 89
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 35
rescaling Fourth_Ventricle from 22 --> 14
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 74
rescaling CSF from 32 --> 50
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 88
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 27
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 65
rescaling Right_Thalamus_Proper from 85 --> 85
rescaling Right_Caudate from 62 --> 73
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 64
rescaling Right_Amygdala from 55 --> 77
rescaling Right_Accumbens_area from 65 --> 71
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 42
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 558598
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 159 changed.
pass 2: 14 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050352 --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 0050352
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/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-6.0.0/0050352/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 7.80
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 106
rescaling Left_Cerebral_Cortex from 61 --> 66
rescaling Left_Lateral_Ventricle from 13 --> 23
rescaling Left_Inf_Lat_Vent from 34 --> 29
rescaling Left_Cerebellum_White_Matter from 86 --> 86
rescaling Left_Cerebellum_Cortex from 60 --> 63
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 89
rescaling Left_Caudate from 75 --> 73
rescaling Left_Putamen from 80 --> 78
rescaling Left_Pallidum from 98 --> 95
rescaling Third_Ventricle from 25 --> 35
rescaling Fourth_Ventricle from 22 --> 14
rescaling Brain_Stem from 81 --> 86
rescaling Left_Hippocampus from 57 --> 61
rescaling Left_Amygdala from 56 --> 74
rescaling CSF from 32 --> 50
rescaling Left_Accumbens_area from 62 --> 66
rescaling Left_VentralDC from 87 --> 88
rescaling Right_Cerebral_White_Matter from 105 --> 103
rescaling Right_Cerebral_Cortex from 58 --> 68
rescaling Right_Lateral_Ventricle from 13 --> 27
rescaling Right_Inf_Lat_Vent from 25 --> 26
rescaling Right_Cerebellum_White_Matter from 87 --> 87
rescaling Right_Cerebellum_Cortex from 59 --> 65
rescaling Right_Thalamus_Proper from 85 --> 85
rescaling Right_Caudate from 62 --> 73
rescaling Right_Putamen from 80 --> 78
rescaling Right_Pallidum from 97 --> 93
rescaling Right_Hippocampus from 53 --> 64
rescaling Right_Amygdala from 55 --> 77
rescaling Right_Accumbens_area from 65 --> 71
rescaling Right_VentralDC from 86 --> 87
rescaling Fifth_Ventricle from 40 --> 42
rescaling WM_hypointensities from 78 --> 78
rescaling non_WM_hypointensities from 40 --> 44
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 558598
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 159 changed.
pass 2: 14 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (2839 2842 2845) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 11:57:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri

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

Sun Oct  8 11:57:31 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-6.0.0/0050352/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-928 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-6.0.0/0050352/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-928
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 11:57:31 CEST 2017 
Ended   at Sun Oct  8 11:57:38 CEST 2017
Apas2aseg-Run-Time-Sec 7
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 11:57:38 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352

 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 0050352 


$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 0050352 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1712602 mm^3    (det: 1.137512 )
Computing euler number
orig.nofix lheno = -294, rheno = -354
orig.nofix lhholes =  148, rhholes = 178
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
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 11:59:27 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352

 mri_aparc2aseg --s 0050352 --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 0050352
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-6.0.0/0050352/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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-6.0.0/0050352/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 9038 vertices from left hemi
Ripped 8147 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-6.0.0/0050352/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 = 1119622
Used brute-force search on 711 voxels
Fixing Parahip LH WM
  Found 6 clusters
     0 k 2.000000
     1 k 4.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1561.000000
Fixing Parahip RH WM
  Found 8 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 2.000000
     3 k 2.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1734.000000
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 0050352 --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 0050352 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-928
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1712602 mm^3    (det: 1.137512 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
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-6.0.0/0050352/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 12:08:55 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 3670 of (3670 3675 3682 3687 3694) to complete...
Waiting for PID 3675 of (3670 3675 3682 3687 3694) to complete...
Waiting for PID 3682 of (3670 3675 3682 3687 3694) to complete...
Waiting for PID 3687 of (3670 3675 3682 3687 3694) to complete...
Waiting for PID 3694 of (3670 3675 3682 3687 3694) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 429
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4558
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 632
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8541
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 263
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4340
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 450
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6433
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 1000
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6784
mri_label2label: Done

PIDs (3670 3675 3682 3687 3694) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 3755 of (3755 3761 3767 3772) to complete...
Waiting for PID 3761 of (3755 3761 3767 3772) to complete...
Waiting for PID 3767 of (3755 3761 3767 3772) to complete...
Waiting for PID 3772 of (3755 3761 3767 3772) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 465
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4535
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 4184
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 17773
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 609
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4790
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 1134
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4556
mri_label2label: Done

PIDs (3755 3761 3767 3772) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 3814 of (3814 3820 3826 3832 3838) to complete...
Waiting for PID 3820 of (3814 3820 3826 3832 3838) to complete...
Waiting for PID 3826 of (3814 3820 3826 3832 3838) to complete...
Waiting for PID 3832 of (3814 3820 3826 3832 3838) to complete...
Waiting for PID 3838 of (3814 3820 3826 3832 3838) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 1579
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6220
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 3361
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11475
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 565
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2583
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 603
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1893
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 549
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1748
mri_label2label: Done

PIDs (3814 3820 3826 3832 3838) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 3919 of (3919 3925 3931 3937 3943) to complete...
Waiting for PID 3925 of (3919 3925 3931 3937 3943) to complete...
Waiting for PID 3931 of (3919 3925 3931 3937 3943) to complete...
Waiting for PID 3937 of (3919 3925 3931 3937 3943) to complete...
Waiting for PID 3943 of (3919 3925 3931 3937 3943) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1118
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 179
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2271
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 112
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1616
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 188
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2184
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 365
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2684
mri_label2label: Done

PIDs (3919 3925 3931 3937 3943) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 3988 of (3988 3994 4000 4005) to complete...
Waiting for PID 3994 of (3988 3994 4000 4005) to complete...
Waiting for PID 4000 of (3988 3994 4000 4005) to complete...
Waiting for PID 4005 of (3988 3994 4000 4005) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 90
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1639
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 1882
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 8917
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 163
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2075
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 527
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1678
mri_label2label: Done

PIDs (3988 3994 4000 4005) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 4052 of (4052 4058 4064 4069 4074) to complete...
Waiting for PID 4058 of (4052 4058 4064 4069 4074) to complete...
Waiting for PID 4064 of (4052 4058 4064 4069 4074) to complete...
Waiting for PID 4069 of (4052 4058 4064 4069 4074) to complete...
Waiting for PID 4074 of (4052 4058 4064 4069 4074) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 1170
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4575
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 1483
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4817
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 131
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 644
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 262
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 732
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 159921
Number of reverse mapping hits = 264
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 714
mri_label2label: Done

PIDs (4052 4058 4064 4069 4074) completed and logs appended.

 mris_label2annot --s 0050352 --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-6.0.0/0050352/label
cmdline mris_label2annot --s 0050352 --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-928
machine  x86_64
user     ntraut

subject 0050352
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-6.0.0/0050352/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 110687 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050352 --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-6.0.0/0050352/label
cmdline mris_label2annot --s 0050352 --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-928
machine  x86_64
user     ntraut

subject 0050352
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-6.0.0/0050352/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 131466 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 282813
Total vertex volume 279572 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1264    762   2039  2.137 0.690     0.140     0.046       16     2.2  BA1_exvivo
 4066   2764   6269  2.202 0.598     0.133     0.038       46     6.5  BA2_exvivo
 1185    811   1341  1.896 0.575     0.141     0.038       13     1.8  BA3a_exvivo
 2625   1746   3897  1.899 0.706     0.125     0.036       28     3.8  BA3b_exvivo
 2093   1292   3153  2.281 0.709     0.137     0.045       26     4.3  BA4a_exvivo
 1515   1056   2241  2.232 0.677     0.132     0.038       12     2.5  BA4p_exvivo
13908   9155  24122  2.471 0.692     0.136     0.048      169    28.3  BA6_exvivo
 2336   1562   4233  2.432 0.586     0.111     0.027       20     2.7  BA44_exvivo
 3687   2465   7665  2.579 0.732     0.132     0.038       45     6.0  BA45_exvivo
 3460   2497   4797  1.865 0.568     0.170     0.063       62     9.3  V1_exvivo
 8815   5767  13023  2.027 0.647     0.149     0.053      138    19.1  V2_exvivo
 2297   1555   4609  2.492 0.767     0.144     0.042       34     4.0  MT_exvivo
  929    549   1365  2.249 0.681     0.153     0.073       18     3.3  perirhinal_exvivo
 1054    744   2325  2.670 0.821     0.164     0.073       21     3.6  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050352 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 282813
Total vertex volume 279572 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
  803    454   1195  2.064 0.669     0.143     0.048       11     1.6  BA1_exvivo
 1570   1039   2454  2.229 0.559     0.124     0.039       17     2.6  BA2_exvivo
 1036    703   1028  1.855 0.510     0.146     0.040       12     1.7  BA3a_exvivo
 1640   1114   1795  1.578 0.348     0.110     0.028       11     1.9  BA3b_exvivo
 2004   1270   2973  2.227 0.720     0.138     0.049       24     4.4  BA4a_exvivo
 1150    835   1635  2.193 0.658     0.136     0.037        9     1.9  BA4p_exvivo
 7478   4950  12444  2.388 0.692     0.140     0.050       85    16.6  BA6_exvivo
 1403    947   2439  2.326 0.543     0.123     0.035       15     2.1  BA44_exvivo
 1584   1014   3841  2.812 0.739     0.126     0.037       19     2.2  BA45_exvivo
 3740   2654   5176  1.882 0.575     0.168     0.064       66    10.2  V1_exvivo
 4349   2917   6614  2.028 0.654     0.159     0.056       78     9.8  V2_exvivo
  577    389   1083  2.470 0.700     0.133     0.038        8     0.9  MT_exvivo
  485    307    711  2.241 0.701     0.158     0.083        9     1.9  perirhinal_exvivo
  636    410   1250  2.459 0.742     0.179     0.092       16     2.9  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 12:12:21 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 4207 of (4207 4213 4219 4225 4231) to complete...
Waiting for PID 4213 of (4207 4213 4219 4225 4231) to complete...
Waiting for PID 4219 of (4207 4213 4219 4225 4231) to complete...
Waiting for PID 4225 of (4207 4213 4219 4225 4231) to complete...
Waiting for PID 4231 of (4207 4213 4219 4225 4231) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 501
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4463
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 690
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7377
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 326
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4306
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 585
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5107
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 1317
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 7064
mri_label2label: Done

PIDs (4207 4213 4219 4225 4231) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 4284 of (4284 4290 4296 4302) to complete...
Waiting for PID 4290 of (4284 4290 4296 4302) to complete...
Waiting for PID 4296 of (4284 4290 4296 4302) to complete...
Waiting for PID 4302 of (4284 4290 4296 4302) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 588
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 5061
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 3560
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 15816
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 1684
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 8596
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 1882
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 7237
mri_label2label: Done

PIDs (4284 4290 4296 4302) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 4358 of (4358 4364 4370 4375 4382) to complete...
Waiting for PID 4364 of (4358 4364 4370 4375 4382) to complete...
Waiting for PID 4370 of (4358 4364 4370 4375 4382) to complete...
Waiting for PID 4375 of (4358 4364 4370 4375 4382) to complete...
Waiting for PID 4382 of (4358 4364 4370 4375 4382) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 1904
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6631
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 3270
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 11286
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 615
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2547
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 295
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1333
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 190
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 942
mri_label2label: Done

PIDs (4358 4364 4370 4375 4382) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 4434 of (4434 4440 4446 4452 4458) to complete...
Waiting for PID 4440 of (4434 4440 4446 4452 4458) to complete...
Waiting for PID 4446 of (4434 4440 4446 4452 4458) to complete...
Waiting for PID 4452 of (4434 4440 4446 4452 4458) to complete...
Waiting for PID 4458 of (4434 4440 4446 4452 4458) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 126
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1002
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 147
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 2835
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 99
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1797
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 282
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2465
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 271
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1659
mri_label2label: Done

PIDs (4434 4440 4446 4452 4458) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 4504 of (4504 4510 4516 4521) to complete...
Waiting for PID 4510 of (4504 4510 4516 4521) to complete...
Waiting for PID 4516 of (4504 4510 4516 4521) to complete...
Waiting for PID 4521 of (4504 4510 4516 4521) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 279
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1768
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 2018
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8977
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 251
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1263
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 396
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1574
mri_label2label: Done

PIDs (4504 4510 4516 4521) 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 0050352 --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 0050352 --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 0050352 --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 0050352 --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 0050352 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 4579 of (4579 4585 4591 4596 4602) to complete...
Waiting for PID 4585 of (4579 4585 4591 4596 4602) to complete...
Waiting for PID 4591 of (4579 4585 4591 4596 4602) to complete...
Waiting for PID 4596 of (4579 4585 4591 4596 4602) to complete...
Waiting for PID 4602 of (4579 4585 4591 4596 4602) 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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 1188
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4420
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 1581
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 5018
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 95
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 363
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 195
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 889
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 0050352 --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 = 0050352
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-6.0.0/0050352/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 165183
Number of reverse mapping hits = 79
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 370
mri_label2label: Done

PIDs (4579 4585 4591 4596 4602) completed and logs appended.

 mris_label2annot --s 0050352 --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-6.0.0/0050352/label
cmdline mris_label2annot --s 0050352 --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-928
machine  x86_64
user     ntraut

subject 0050352
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-6.0.0/0050352/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 115506 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050352 --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-6.0.0/0050352/label
cmdline mris_label2annot --s 0050352 --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-928
machine  x86_64
user     ntraut

subject 0050352
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-6.0.0/0050352/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 137244 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/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 0050352 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 289365
Total vertex volume 286560 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
 1113    655   1936  2.206 0.833     0.149     0.062       17     2.7  BA1_exvivo
 3341   2188   5246  2.300 0.605     0.135     0.044       40     6.5  BA2_exvivo
 1215    867   1244  1.971 0.495     0.142     0.037       12     1.7  BA3a_exvivo
 2286   1513   2760  1.659 0.569     0.112     0.051       82     5.7  BA3b_exvivo
 2018   1228   3158  2.363 0.654     0.127     0.059       25     5.1  BA4a_exvivo
 1587   1070   2117  2.243 0.660     0.132     0.046       15     2.8  BA4p_exvivo
12072   7760  20645  2.501 0.779     0.138     0.052      158    28.2  BA6_exvivo
 4478   2988   8571  2.621 0.572     0.118     0.034       46     5.8  BA44_exvivo
 5432   3676  10839  2.634 0.653     0.139     0.041       76     8.3  BA45_exvivo
 4068   2739   5413  1.875 0.549     0.141     0.049       61     8.0  V1_exvivo
 8541   5588  12255  2.060 0.615     0.150     0.050      134    17.7  V2_exvivo
 2316   1556   4345  2.513 0.723     0.141     0.042       32     3.4  MT_exvivo
  789    485   1866  2.910 0.952     0.159     0.070       15     2.8  perirhinal_exvivo
  421    279    808  2.436 0.677     0.157     0.073        9     1.4  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050352 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050352/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 289365
Total vertex volume 286560 (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) = 1712602 mm^3    (det: 1.137512 )
lhCtxGM: 276583.918 275557.000  diff= 1026.9  pctdiff= 0.371
rhCtxGM: 282762.460 281806.000  diff=  956.5  pctdiff= 0.338
lhCtxWM: 279774.026 280096.000  diff= -322.0  pctdiff=-0.115
rhCtxWM: 281871.829 283851.000  diff=-1979.2  pctdiff=-0.702
SubCortGMVol  65474.000
SupraTentVol  1211716.233 (1206791.000) diff=4925.233 pctdiff=0.406
SupraTentVolNotVent  1191724.233 (1186799.000) diff=4925.233 pctdiff=0.413
BrainSegVol  1372132.000 (1369028.000) diff=3104.000 pctdiff=0.226
BrainSegVolNotVent  1346802.000 (1346232.233) diff=569.767 pctdiff=0.042
BrainSegVolNotVent  1346802.000
CerebellumVol 159751.000
VentChorVol   19992.000
3rd4th5thCSF   5338.000
CSFVol  2234.000, OptChiasmVol   252.000
MaskVol 1787646.000
  747    464   1190  1.948 0.739     0.152     0.058       11     1.8  BA1_exvivo
 1766   1123   2907  2.394 0.631     0.116     0.038       16     2.6  BA2_exvivo
 1101    778   1048  1.941 0.489     0.143     0.036       11     1.6  BA3a_exvivo
 1768   1211   1826  1.522 0.386     0.096     0.022       10     1.5  BA3b_exvivo
 1256    782   2056  2.289 0.710     0.140     0.070       20     3.9  BA4a_exvivo
 1395    937   1948  2.362 0.654     0.132     0.049       13     2.7  BA4p_exvivo
 7774   4988  12516  2.373 0.769     0.143     0.054      105    19.3  BA6_exvivo
 1094    750   2301  2.670 0.552     0.114     0.034       11     1.4  BA44_exvivo
 1445    956   3617  2.784 0.654     0.151     0.049       24     2.7  BA45_exvivo
 3840   2590   5064  1.874 0.546     0.139     0.049       57     7.5  V1_exvivo
 4616   3027   6524  1.985 0.594     0.151     0.050       69     9.2  V2_exvivo
  340    225    783  2.675 0.725     0.156     0.047        6     0.6  MT_exvivo
  486    294   1063  2.891 0.950     0.161     0.075       10     1.8  perirhinal_exvivo
  311    198    629  2.409 0.929     0.188     0.095       10     1.4  entorhinal_exvivo

Started at Sat Oct 7 23:40:21 CEST 2017 
Ended   at Sun Oct 8 12:15:48 CEST 2017
#@#%# recon-all-run-time-hours 12.591
recon-all -s 0050352 finished without error at Sun Oct  8 12:15:48 CEST 2017