ABIDE_fs-6.0.0/0050660/scripts/recon-all.log

Sat Oct  7 16:10:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660
/pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/recon-all
-subjid 0050660 -sd fs-6.0.0 -i /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz -autorecon-all -parallel -openmp 2
subjid 0050660
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-542 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:      65993388   54952940   11040448    1752720          0   51971412
-/+ buffers/cache:    2981528   63011860
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: 2017/10/07-14:10:09-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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: 2017/10/07-14:10:10-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-542  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-6.0.0/0050660

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig/001.mgz 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/CMU_a_2/0050660/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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/CMU_a_2/0050660/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-6.0.0/0050660/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Sat Oct  7 16:10:13 CEST 2017
Found 1 runs
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz --conform 

mri_convert.bin /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/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-6.0.0/0050660/mri/orig.mgz...

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Sat Oct  7 16:10:21 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/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-542 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 16:10:21 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.1777
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1777/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1777/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.1777/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 16:10:23 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.1777/nu0.mnc ./tmp.mri_nu_correct.mni.1777/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1777/0/ -iterations 1000 -distance 50
[ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:10:24] running:
  /pasteur/homes/ntraut/bin/freesurfer-6.0.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 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.1777/0/ ./tmp.mri_nu_correct.mni.1777/nu0.mnc ./tmp.mri_nu_correct.mni.1777/nu1.imp

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Number of iterations: 39 
CV of field change: 0.00099166
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.1777/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.1777/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.1777/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 16:11:25 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 16:11:26 CEST 2017
Ended   at Sat Oct  7 16:11:58 CEST 2017
talairach_avi done

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

#--------------------------------------------
#@# Talairach Failure Detection Sat Oct  7 16:12:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3137, pval=0.0254 >= 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-6.0.0/0050660/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach_avi.log 

TalAviQA: 0.97325
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Sat Oct  7 16:12:00 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-6.0.0/0050660/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-542 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 16:12:00 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.2541
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2541/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.2541/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.2541/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Sat Oct  7 16:12:02 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.2541/nu0.mnc ./tmp.mri_nu_correct.mni.2541/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.2541/0/
[ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:12:02] 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.2541/0/ ./tmp.mri_nu_correct.mni.2541/nu0.mnc ./tmp.mri_nu_correct.mni.2541/nu1.imp

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Number of iterations: 39 
CV of field change: 0.000952228
 
 
--------------------------------------------------------
Iteration 2 Sat Oct  7 16:12:49 CEST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.2541/nu1.mnc ./tmp.mri_nu_correct.mni.2541/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.2541/1/
[ntraut@tars-542:/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/] [2017-10-07 16:12:49] 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.2541/1/ ./tmp.mri_nu_correct.mni.2541/nu1.mnc ./tmp.mri_nu_correct.mni.2541/nu2.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 8 
CV of field change: 0.00093359
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2541/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-6.0.0/0050660/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.2541/ones.mgz 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut

input      ./tmp.mri_nu_correct.mni.2541/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.2541/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.2541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/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.2541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/input.mean.dat 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.2541/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.2541/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.2541/ones.mgz --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/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.2541/ones.mgz --i ./tmp.mri_nu_correct.mni.2541/nu2.mnc --sum ./tmp.mri_nu_correct.mni.2541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.2541/output.mean.dat 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.2541/ones.mgz
Loading ./tmp.mri_nu_correct.mni.2541/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.2541/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.2541/nu2.mnc ./tmp.mri_nu_correct.mni.2541/nu2.mnc mul .97354204708638120492
Saving result to './tmp.mri_nu_correct.mni.2541/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.2541/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.2541/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.2541/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 7 seconds.
mapping ( 9, 129) to ( 3, 110)
 
 
Sat Oct  7 16:13:50 CEST 2017
mri_nu_correct.mni done

 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Sat Oct  7 16:13:51 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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
 1.03450   0.05910  -0.05801   6.31035;
-0.02976   0.83984   0.56017  -36.56604;
 0.09372  -0.60837   1.10812  -64.27377;
 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 = 18
Starting OpenSpline(): npoints = 18
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 81 (81), valley at 39 (39)
csf peak at 41, setting threshold to 67
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 81 (81), valley at 39 (39)
csf peak at 41, setting threshold to 67
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 0 seconds.
#--------------------------------------------
#@# Skull Stripping Sat Oct  7 16:15:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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=19.0
skull bounding box = (39, 27, 14) --> (207, 172, 214)
using (95, 75, 114) as brain centroid...
mean wm in atlas = 108, using box (74,57,89) --> (115, 92,138) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 5.1
after smoothing, mri peak at 106, scaling input intensities by 1.019
scaling channel 0 by 1.01887
initial log_p = -4.568
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.575286 @ (9.091, 27.273, -9.091)
max log p =    -4.504565 @ (-4.545, -13.636, 4.545)
max log p =    -4.485532 @ (-2.273, 2.273, -2.273)
max log p =    -4.466875 @ (1.136, -1.136, 1.136)
max log p =    -4.447379 @ (-0.568, 1.705, -0.568)
max log p =    -4.447379 @ (0.000, 0.000, 0.000)
Found translation: (2.8, 16.5, -6.3): log p = -4.447
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.272, old_max_log_p =-4.447 (thresh=-4.4)
 1.06375   0.00000   0.00000  -4.93878;
 0.00000   1.07062   0.61813  -53.42551;
 0.00000  -0.57500   0.99593   55.63156;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.186, old_max_log_p =-4.272 (thresh=-4.3)
 1.06375   0.00000   0.00000  -4.93878;
 0.00000   1.18814   0.54970  -58.44056;
 0.00000  -0.32386   0.93208   42.46684;
 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 =-4.186 (thresh=-4.2)
 1.06375   0.00000   0.00000  -4.93878;
 0.00000   1.18814   0.54970  -58.44056;
 0.00000  -0.32386   0.93208   42.46684;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.137, old_max_log_p =-4.186 (thresh=-4.2)
 1.06113  -0.01141  -0.07578   3.45823;
 0.04251   1.20165   0.69975  -80.27608;
 0.06471  -0.47812   0.84930   60.03991;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.135, old_max_log_p =-4.137 (thresh=-4.1)
 1.04325  -0.03931  -0.01826   2.25901;
 0.04113   1.23946   0.68418  -82.62960;
-0.00354  -0.44506   0.89123   59.91553;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.112, old_max_log_p =-4.135 (thresh=-4.1)
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47589   0.87520   64.93446;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.110, old_max_log_p =-4.112 (thresh=-4.1)
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 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
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3243
Quasinewton: input matrix
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -4.110 (old=-4.568)
transform before final EM align:
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 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
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 0.00000   0.00000   0.00000   1.00000;
nsamples 364799
Quasinewton: input matrix
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 011: -log(p) =    4.5  tol 0.000000
final transform:
 1.04532  -0.04954  -0.02397   4.29910;
 0.04962   1.22924   0.70650  -83.66947;
-0.00469  -0.47533   0.87417   64.98835;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach_with_skull.lta...
mri_em_register utimesec    1176.780102
mri_em_register stimesec    1.087834
mri_em_register ru_maxrss   609824
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   157601
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    174
mri_em_register ru_nivcsw   5745
registration took 10 minutes and 13 seconds.

 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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=123 y=95 z=106 r=69
      first estimation of the main basin volume: 1410028 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        14 found in the rest of the brain 
      global maximum in x=144, y=92, z=76, Imax=255
      CSF=18, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=7541118642 voxels, voxel volume =1.000 
                     = 7541118642 mmm3 = 7541118.464 cm3
done.
PostAnalyze...Basin Prior
 51 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=123,y=105, z=106, r=10367 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 39104
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1050308968
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1046739996
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = -1077193073
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=43 , nb = 1065464322
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1078504670
 Problem with the least square interpolation in GM_MIN calculation.
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    5,      10,        53,   76
  after  analyzing :    5,      38,        53,   47
   RIGHT_CER   
  before analyzing :    4,      9,        60,   79
  after  analyzing :    4,      43,        60,   52
   LEFT_CER    
  before analyzing :    4,      8,        56,   76
  after  analyzing :    4,      40,        56,   49
  RIGHT_BRAIN  
  before analyzing :    56,      53,        53,   77
  after  analyzing :    32,      53,        53,   59
  LEFT_BRAIN   
  before analyzing :    43,      48,        52,   76
  after  analyzing :    43,      50,        52,   56
     OTHER     
  before analyzing :    4,      12,        76,   91
  after  analyzing :    4,      54,        76,   63
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...66 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 70.412, std = 8.191

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 5.83, sigma = 10.94
      after  rotation: sse = 5.83, sigma = 10.94
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  8.95, its var is 16.76   
      before Erosion-Dilatation  9.16% of inacurate vertices
      after  Erosion-Dilatation 11.74% 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...43 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1688594 voxels, voxel volume = 1.000 mm3
           = 1688594 mmm3 = 1688.594 cm3


******************************
Saving brainmask.auto.mgz
done
mri_watershed utimesec    23.246466
mri_watershed stimesec    0.378942
mri_watershed ru_maxrss   819116
mri_watershed ru_ixrss    0
mri_watershed ru_idrss    0
mri_watershed ru_isrss    0
mri_watershed ru_minflt   212123
mri_watershed ru_majflt   0
mri_watershed ru_nswap    0
mri_watershed ru_inblock  0
mri_watershed ru_oublock  2672
mri_watershed ru_msgsnd   0
mri_watershed ru_msgrcv   0
mri_watershed ru_nsignals 0
mri_watershed ru_nvcsw    1299
mri_watershed ru_nivcsw   87
mri_watershed done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sat Oct  7 16:26:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

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

== Number of threads available to mri_em_register for OpenMP = 2 == 
reading 1 input volumes...
logging results to talairach.log
reading '/pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.8 (1011 zeros)
************************************************
spacing=8, using 2830 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2830, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=28.0
skull bounding box = (53, 41, 29) --> (192, 172, 191)
using (99, 85, 110) as brain centroid...
mean wm in atlas = 107, using box (82,69,90) --> (116, 101,129) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 4.7
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.223
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.234888 @ (0.000, 0.000, 0.000)
max log p =    -4.040623 @ (4.545, 13.636, -4.545)
max log p =    -4.013413 @ (-2.273, 2.273, -2.273)
max log p =    -3.997553 @ (1.136, 1.136, 1.136)
max log p =    -3.957727 @ (-0.568, 0.568, -1.705)
max log p =    -3.957727 @ (0.000, 0.000, 0.000)
Found translation: (2.8, 17.6, -7.4): log p = -3.958
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.684, old_max_log_p =-3.958 (thresh=-4.0)
 0.99144  -0.13262  -0.06526   24.74865;
 0.13053   1.00733   0.49572  -55.23638;
 0.00000  -0.53750   0.76973   80.74652;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.684, old_max_log_p =-3.684 (thresh=-3.7)
 0.99144  -0.13262  -0.06526   24.74865;
 0.13053   1.00733   0.49572  -55.23638;
 0.00000  -0.53750   0.76973   80.74652;
 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=-3.599, old_max_log_p =-3.684 (thresh=-3.7)
 1.05319  -0.05904  -0.06662   9.36601;
 0.06143   1.00903   0.46828  -42.19876;
 0.03837  -0.52483   0.81343   68.17387;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.599 (thresh=-3.6)
 1.03344  -0.05793  -0.06537   11.56671;
 0.06383   1.00991   0.50392  -46.38089;
 0.03634  -0.55756   0.79768   73.47760;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.590, old_max_log_p =-3.594 (thresh=-3.6)
 1.02903  -0.07435  -0.10754   18.29556;
 0.09633   1.02573   0.47428  -50.75941;
 0.07084  -0.51598   0.79595   63.22182;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.590, old_max_log_p =-3.590 (thresh=-3.6)
 1.02903  -0.07435  -0.10754   18.29556;
 0.09633   1.02573   0.47428  -50.75941;
 0.07084  -0.51598   0.79595   63.22182;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.564, old_max_log_p =-3.590 (thresh=-3.6)
 1.02854  -0.09137  -0.11521   20.95689;
 0.11237   1.03631   0.46099  -51.46078;
 0.07233  -0.49854   0.80266   60.49803;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.563, old_max_log_p =-3.564 (thresh=-3.6)
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2830 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2830
Quasinewton: input matrix
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;

pass 1, spacing 8: log(p) = -3.563 (old=-4.223)
transform before final EM align:
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 315557 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;
nsamples 315557
Quasinewton: input matrix
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;
outof QuasiNewtonEMA: 012: -log(p) =    4.0  tol 0.000000
final transform:
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 0.00000   0.00000   0.00000   1.00000;

writing output transformation to transforms/talairach.lta...
mri_em_register utimesec    1186.531619
mri_em_register stimesec    1.230812
mri_em_register ru_maxrss   599052
mri_em_register ru_ixrss    0
mri_em_register ru_idrss    0
mri_em_register ru_isrss    0
mri_em_register ru_minflt   158954
mri_em_register ru_majflt   0
mri_em_register ru_nswap    0
mri_em_register ru_inblock  0
mri_em_register ru_oublock  24
mri_em_register ru_msgsnd   0
mri_em_register ru_msgrcv   0
mri_em_register ru_nsignals 0
mri_em_register ru_nvcsw    189
mri_em_register ru_nivcsw   3631
registration took 10 minutes and 15 seconds.
#--------------------------------------
#@# CA Normalize Sat Oct  7 16:36:43 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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=24.0
skull bounding box = (53, 40, 28) --> (192, 172, 192)
using (99, 84, 110) as brain centroid...
mean wm in atlas = 107, using box (82,68,90) --> (116, 100,130) to find MRI wm
before smoothing, mri peak at 106
robust fit to distribution - 106 +- 4.7
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
using 246344 sample points...
INFO: compute sample coordinates transform
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36522;
 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 (118, 43, 29) --> (189, 159, 202)
Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0
0 of 228 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (60, 45, 34) --> (129, 154, 203)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0
0 of 124 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (125, 130, 69) --> (175, 168, 127)
Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 132.0
0 of 12 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 131, 70) --> (126, 169, 130)
Right_Cerebellum_White_Matter: limiting intensities to 105.0 --> 132.0
0 of 13 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 112, 101) --> (146, 170, 139)
Brain_Stem: limiting intensities to 92.0 --> 132.0
0 of 13 (0.0%) samples deleted
using 390 total control points for intensity normalization...
bias field = 0.935 +- 0.065
0 of 390 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (118, 43, 29) --> (189, 159, 202)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
0 of 383 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (60, 45, 34) --> (129, 154, 203)
Right_Cerebral_White_Matter: limiting intensities to 89.0 --> 132.0
18 of 229 (7.9%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (125, 130, 69) --> (175, 168, 127)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
9 of 91 (9.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 131, 70) --> (126, 169, 130)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
4 of 79 (5.1%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 112, 101) --> (146, 170, 139)
Brain_Stem: limiting intensities to 88.0 --> 132.0
19 of 93 (20.4%) samples deleted
using 875 total control points for intensity normalization...
bias field = 0.993 +- 0.073
1 of 811 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 39915 control points for structure...
bounding box (118, 43, 29) --> (189, 159, 202)
Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 390 (0.3%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 39557 control points for structure...
bounding box (60, 45, 34) --> (129, 154, 203)
Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0
1 of 292 (0.3%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3059 control points for structure...
bounding box (125, 130, 69) --> (175, 168, 127)
Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
56 of 117 (47.9%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2705 control points for structure...
bounding box (85, 131, 70) --> (126, 169, 130)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0
69 of 146 (47.3%) samples deleted
finding control points in Brain_Stem....
found 3518 control points for structure...
bounding box (110, 112, 101) --> (146, 170, 139)
Brain_Stem: limiting intensities to 88.0 --> 132.0
72 of 154 (46.8%) samples deleted
using 1099 total control points for intensity normalization...
bias field = 0.996 +- 0.060
4 of 893 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 46 seconds.
#--------------------------------------
#@# CA Reg Sat Oct  7 16:38:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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) = 1.11 (predicted orig area = 7.2)
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=0.899, neg=0, invalid=762
0001: dt=275.147192, rms=0.827 (7.999%), neg=0, invalid=762
0002: dt=242.955950, rms=0.802 (3.077%), neg=0, invalid=762
0003: dt=231.836735, rms=0.791 (1.282%), neg=0, invalid=762
0004: dt=140.698413, rms=0.786 (0.668%), neg=0, invalid=762
0005: dt=517.888000, rms=0.778 (1.067%), neg=0, invalid=762
0006: dt=129.472000, rms=0.776 (0.182%), neg=0, invalid=762
0007: dt=129.472000, rms=0.775 (0.147%), neg=0, invalid=762
0008: dt=129.472000, rms=0.773 (0.244%), neg=0, invalid=762
0009: dt=129.472000, rms=0.771 (0.325%), neg=0, invalid=762
0010: dt=129.472000, rms=0.768 (0.349%), neg=0, invalid=762
0011: dt=129.472000, rms=0.765 (0.351%), neg=0, invalid=762
0012: dt=129.472000, rms=0.763 (0.294%), neg=0, invalid=762
0013: dt=129.472000, rms=0.761 (0.231%), neg=0, invalid=762
0014: dt=129.472000, rms=0.760 (0.197%), neg=0, invalid=762
0015: dt=129.472000, rms=0.759 (0.172%), neg=0, invalid=762
0016: dt=129.472000, rms=0.758 (0.133%), neg=0, invalid=762
0017: dt=129.472000, rms=0.757 (0.090%), neg=0, invalid=762
0018: dt=129.472000, rms=0.756 (0.077%), neg=0, invalid=762
0019: dt=517.888000, rms=0.755 (0.113%), neg=0, invalid=762
0020: dt=129.472000, rms=0.755 (0.059%), neg=0, invalid=762
0021: dt=129.472000, rms=0.755 (0.041%), neg=0, invalid=762
0022: dt=129.472000, rms=0.754 (0.047%), neg=0, invalid=762
0023: dt=129.472000, rms=0.754 (0.054%), neg=0, invalid=762
0024: dt=129.472000, rms=0.753 (0.060%), neg=0, invalid=762
0025: dt=129.472000, rms=0.753 (0.052%), neg=0, invalid=762
0026: dt=129.472000, rms=0.753 (0.062%), neg=0, invalid=762
0027: dt=129.472000, rms=0.752 (0.056%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.753, neg=0, invalid=762
0028: dt=129.472000, rms=0.751 (0.265%), neg=0, invalid=762
0029: dt=32.368000, rms=0.751 (-0.002%), neg=0, invalid=762
0030: dt=32.368000, rms=0.751 (0.002%), neg=0, invalid=762
0031: dt=32.368000, rms=0.751 (0.003%), neg=0, invalid=762
0032: dt=32.368000, rms=0.751 (-0.005%), neg=0, invalid=762
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.758, neg=0, invalid=762
0033: dt=77.623762, rms=0.753 (0.689%), neg=0, invalid=762
0034: dt=248.163265, rms=0.737 (2.160%), neg=0, invalid=762
0035: dt=29.312336, rms=0.732 (0.623%), neg=0, invalid=762
0036: dt=9.072000, rms=0.732 (0.024%), neg=0, invalid=762
0037: dt=9.072000, rms=0.732 (0.017%), neg=0, invalid=762
0038: dt=9.072000, rms=0.732 (0.010%), neg=0, invalid=762
0039: dt=9.072000, rms=0.732 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.732, neg=0, invalid=762
0040: dt=62.208000, rms=0.729 (0.415%), neg=0, invalid=762
0041: dt=82.944000, rms=0.728 (0.097%), neg=0, invalid=762
0042: dt=82.944000, rms=0.726 (0.310%), neg=0, invalid=762
0043: dt=82.944000, rms=0.724 (0.357%), neg=0, invalid=762
0044: dt=82.944000, rms=0.721 (0.368%), neg=0, invalid=762
0045: dt=82.944000, rms=0.717 (0.548%), neg=0, invalid=762
0046: dt=82.944000, rms=0.712 (0.662%), neg=0, invalid=762
0047: dt=82.944000, rms=0.708 (0.591%), neg=0, invalid=762
0048: dt=82.944000, rms=0.705 (0.454%), neg=0, invalid=762
0049: dt=82.944000, rms=0.702 (0.383%), neg=0, invalid=762
0050: dt=82.944000, rms=0.700 (0.371%), neg=0, invalid=762
0051: dt=82.944000, rms=0.698 (0.291%), neg=0, invalid=762
0052: dt=82.944000, rms=0.696 (0.200%), neg=0, invalid=762
0053: dt=82.944000, rms=0.695 (0.166%), neg=0, invalid=762
0054: dt=82.944000, rms=0.694 (0.184%), neg=0, invalid=762
0055: dt=82.944000, rms=0.693 (0.137%), neg=0, invalid=762
0056: dt=82.944000, rms=0.692 (0.066%), neg=0, invalid=762
0057: dt=82.944000, rms=0.691 (0.112%), neg=0, invalid=762
0058: dt=82.944000, rms=0.690 (0.225%), neg=0, invalid=762
0059: dt=82.944000, rms=0.688 (0.280%), neg=0, invalid=762
0060: dt=82.944000, rms=0.687 (0.193%), neg=0, invalid=762
0061: dt=82.944000, rms=0.686 (0.092%), neg=0, invalid=762
0062: dt=82.944000, rms=0.685 (0.125%), neg=0, invalid=762
0063: dt=82.944000, rms=0.684 (0.134%), neg=0, invalid=762
0064: dt=82.944000, rms=0.684 (0.095%), neg=0, invalid=762
0065: dt=82.944000, rms=0.683 (0.066%), neg=0, invalid=762
0066: dt=145.152000, rms=0.683 (0.093%), neg=0, invalid=762
0067: dt=6.480000, rms=0.683 (0.001%), neg=0, invalid=762
0068: dt=6.480000, rms=0.683 (0.001%), neg=0, invalid=762
0069: dt=6.480000, rms=0.683 (-0.002%), neg=0, invalid=762
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.708, neg=0, invalid=762
0070: dt=6.400000, rms=0.707 (0.138%), neg=0, invalid=762
0071: dt=2.800000, rms=0.707 (0.017%), neg=0, invalid=762
0072: dt=2.800000, rms=0.707 (0.006%), neg=0, invalid=762
0073: dt=2.800000, rms=0.707 (-0.015%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.708, neg=0, invalid=762
0074: dt=0.000000, rms=0.707 (0.069%), neg=0, invalid=762
0075: dt=0.000000, rms=0.707 (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=0.776, neg=0, invalid=762
0076: dt=6.000000, rms=0.756 (2.530%), neg=0, invalid=762
0077: dt=8.098940, rms=0.752 (0.541%), neg=0, invalid=762
0078: dt=2.880000, rms=0.752 (0.018%), neg=0, invalid=762
0079: dt=2.880000, rms=0.752 (0.034%), neg=0, invalid=762
0080: dt=2.880000, rms=0.751 (0.038%), neg=0, invalid=762
0081: dt=2.880000, rms=0.751 (0.013%), neg=0, invalid=762
0082: dt=2.880000, rms=0.751 (-0.061%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.752, neg=0, invalid=762
0083: dt=0.000000, rms=0.751 (0.057%), neg=0, invalid=762
0084: dt=0.000000, rms=0.751 (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=0.792, neg=0, invalid=762
0085: dt=0.000000, rms=0.792 (0.051%), neg=0, invalid=762
0086: dt=0.000000, rms=0.792 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.792, neg=0, invalid=762
0087: dt=0.000000, rms=0.792 (0.051%), neg=0, invalid=762
0088: dt=0.000000, rms=0.792 (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=0.723, neg=0, invalid=762
0089: dt=0.922014, rms=0.703 (2.817%), neg=0, invalid=762
0090: dt=0.096000, rms=0.702 (0.175%), neg=0, invalid=762
0091: dt=0.096000, rms=0.702 (-0.102%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.702, neg=0, invalid=762
0092: dt=0.028000, rms=0.702 (0.093%), neg=0, invalid=762
0093: dt=0.020000, rms=0.702 (0.003%), neg=0, invalid=762
0094: dt=0.020000, rms=0.702 (-0.005%), neg=0, invalid=762
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.10027 (20)
mri peak = 0.09504 (30)
Left_Lateral_Ventricle (4): linear fit = 1.68 x + 0.0 (1149 voxels, overlap=0.298)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1149 voxels, peak = 34), gca=30.0
gca peak = 0.15565 (16)
mri peak = 0.10881 (31)
Right_Lateral_Ventricle (43): linear fit = 1.90 x + 0.0 (1263 voxels, overlap=0.129)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1263 voxels, peak = 30), gca=24.0
gca peak = 0.26829 (96)
mri peak = 0.06444 (96)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (901 voxels, overlap=0.955)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (901 voxels, peak = 96), gca=95.5
gca peak = 0.20183 (93)
mri peak = 0.07652 (84)
Left_Pallidum (13): linear fit = 0.90 x + 0.0 (763 voxels, overlap=0.559)
Left_Pallidum (13): linear fit = 0.90 x + 0.0 (763 voxels, peak = 84), gca=84.2
gca peak = 0.21683 (55)
mri peak = 0.08275 (72)
Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1012 voxels, overlap=0.020)
Right_Hippocampus (53): linear fit = 1.26 x + 0.0 (1012 voxels, peak = 70), gca=69.6
gca peak = 0.30730 (58)
mri peak = 0.08023 (69)
Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (704 voxels, overlap=0.044)
Left_Hippocampus (17): linear fit = 1.18 x + 0.0 (704 voxels, peak = 69), gca=68.7
gca peak = 0.11430 (101)
mri peak = 0.09011 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65574 voxels, overlap=0.687)
Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (65574 voxels, peak = 107), gca=106.6
gca peak = 0.12076 (102)
mri peak = 0.08743 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (68714 voxels, overlap=0.656)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (68714 voxels, peak = 107), gca=106.6
gca peak = 0.14995 (59)
mri peak = 0.04539 (74)
Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (23446 voxels, overlap=0.002)
Left_Cerebral_Cortex (3): linear fit = 1.29 x + 0.0 (23446 voxels, peak = 76), gca=76.4
gca peak = 0.15082 (58)
mri peak = 0.05316 (76)
Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (24764 voxels, overlap=0.000)
Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (24764 voxels, peak = 77), gca=76.9
gca peak = 0.14161 (67)
mri peak = 0.10185 (84)
Right_Caudate (50): linear fit = 1.25 x + 0.0 (679 voxels, overlap=0.011)
Right_Caudate (50): linear fit = 1.25 x + 0.0 (679 voxels, peak = 84), gca=84.1
gca peak = 0.15243 (71)
mri peak = 0.06370 (83)
Left_Caudate (11): linear fit = 1.18 x + 0.0 (946 voxels, overlap=0.032)
Left_Caudate (11): linear fit = 1.18 x + 0.0 (946 voxels, peak = 84), gca=84.1
gca peak = 0.13336 (57)
mri peak = 0.05901 (72)
Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (22716 voxels, overlap=0.010)
Left_Cerebellum_Cortex (8): linear fit = 1.29 x + 0.0 (22716 voxels, peak = 74), gca=73.8
gca peak = 0.13252 (56)
mri peak = 0.05907 (72)
Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (23782 voxels, overlap=0.001)
Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (23782 voxels, peak = 74), gca=74.2
gca peak = 0.18181 (84)
mri peak = 0.08760 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9161 voxels, overlap=0.784)
Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (9161 voxels, peak = 89), gca=89.5
gca peak = 0.20573 (83)
mri peak = 0.07913 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7754 voxels, overlap=0.807)
Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7754 voxels, peak = 88), gca=87.6
gca peak = 0.21969 (57)
mri peak = 0.08505 (72)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (389 voxels, overlap=0.053)
Left_Amygdala (18): linear fit = 1.23 x + 0.0 (389 voxels, peak = 70), gca=69.8
gca peak = 0.39313 (56)
mri peak = 0.08578 (71)
Right_Amygdala (54): linear fit = 1.23 x + 0.0 (446 voxels, overlap=0.018)
Right_Amygdala (54): linear fit = 1.23 x + 0.0 (446 voxels, peak = 69), gca=68.6
gca peak = 0.14181 (85)
mri peak = 0.07514 (96)
Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5827 voxels, overlap=0.415)
Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (5827 voxels, peak = 93), gca=93.1
gca peak = 0.11978 (83)
mri peak = 0.07075 (94)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4482 voxels, overlap=0.540)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4482 voxels, peak = 93), gca=92.5
gca peak = 0.13399 (79)
mri peak = 0.07103 (88)
Left_Putamen (12): linear fit = 1.14 x + 0.0 (2307 voxels, overlap=0.257)
Left_Putamen (12): linear fit = 1.14 x + 0.0 (2307 voxels, peak = 90), gca=90.5
gca peak = 0.14159 (79)
mri peak = 0.07604 (88)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (2412 voxels, overlap=0.454)
Right_Putamen (51): linear fit = 1.14 x + 0.0 (2412 voxels, peak = 90), gca=90.5
gca peak = 0.10025 (80)
mri peak = 0.09053 (87)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11580 voxels, overlap=0.402)
Brain_Stem (16): linear fit = 1.10 x + 0.0 (11580 voxels, peak = 88), gca=87.6
gca peak = 0.13281 (86)
mri peak = 0.07812 (90)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1015 voxels, overlap=0.648)
Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1015 voxels, peak = 93), gca=93.3
gca peak = 0.12801 (89)
mri peak = 0.09083 (90)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1288 voxels, overlap=0.667)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1288 voxels, peak = 92), gca=92.1
gca peak = 0.20494 (23)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.15061 (21)
mri peak = 0.14865 (29)
Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (532 voxels, overlap=0.280)
Fourth_Ventricle (15): linear fit = 1.36 x + 0.0 (532 voxels, peak = 28), gca=28.5
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.18056 (32)
gca peak Left_Thalamus = 0.64095 (94)
gca peak Third_Ventricle = 0.20494 (23)
gca peak CSF = 0.20999 (34)
gca peak Left_Accumbens_area = 0.39030 (62)
gca peak Left_undetermined = 0.95280 (25)
gca peak Left_vessel = 0.67734 (53)
gca peak Left_choroid_plexus = 0.09433 (44)
gca peak Right_Inf_Lat_Vent = 0.23544 (26)
gca peak Right_Accumbens_area = 0.30312 (64)
gca peak Right_vessel = 0.46315 (51)
gca peak Right_choroid_plexus = 0.14086 (44)
gca peak Fifth_Ventricle = 0.51669 (36)
gca peak WM_hypointensities = 0.09722 (76)
gca peak non_WM_hypointensities = 0.11899 (47)
gca peak Optic_Chiasm = 0.39033 (72)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 1.25 x + 0.0
estimating mean wm scale to be 1.05 x + 0.0
estimating mean csf scale to be 1.45 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=0.687, neg=0, invalid=762
0095: dt=64.861759, rms=0.673 (2.143%), neg=0, invalid=762
0096: dt=32.368000, rms=0.672 (0.133%), neg=0, invalid=762
0097: dt=32.368000, rms=0.671 (0.057%), neg=0, invalid=762
0098: dt=32.368000, rms=0.671 (0.041%), neg=0, invalid=762
0099: dt=32.368000, rms=0.671 (0.036%), neg=0, invalid=762
0100: dt=32.368000, rms=0.671 (0.022%), neg=0, invalid=762
0101: dt=32.368000, rms=0.671 (-0.028%), neg=0, invalid=762
0102: dt=129.472000, rms=0.670 (0.135%), neg=0, invalid=762
0103: dt=517.888000, rms=0.666 (0.617%), neg=0, invalid=762
0104: dt=517.888000, rms=0.661 (0.696%), neg=0, invalid=762
0105: dt=129.472000, rms=0.660 (0.205%), neg=0, invalid=762
0106: dt=73.984000, rms=0.660 (0.001%), neg=0, invalid=762
0107: dt=73.984000, rms=0.659 (0.032%), neg=0, invalid=762
0108: dt=73.984000, rms=0.659 (0.062%), neg=0, invalid=762
0109: dt=73.984000, rms=0.658 (0.093%), neg=0, invalid=762
0110: dt=73.984000, rms=0.657 (0.129%), neg=0, invalid=762
0111: dt=73.984000, rms=0.656 (0.152%), neg=0, invalid=762
0112: dt=73.984000, rms=0.655 (0.162%), neg=0, invalid=762
0113: dt=73.984000, rms=0.654 (0.148%), neg=0, invalid=762
0114: dt=73.984000, rms=0.654 (0.130%), neg=0, invalid=762
0115: dt=73.984000, rms=0.653 (0.111%), neg=0, invalid=762
0116: dt=73.984000, rms=0.652 (0.095%), neg=0, invalid=762
0117: dt=73.984000, rms=0.652 (0.083%), neg=0, invalid=762
0118: dt=73.984000, rms=0.651 (0.078%), neg=0, invalid=762
0119: dt=73.984000, rms=0.651 (0.077%), neg=0, invalid=762
0120: dt=73.984000, rms=0.650 (0.076%), neg=0, invalid=762
0121: dt=73.984000, rms=0.650 (0.073%), neg=0, invalid=762
0122: dt=73.984000, rms=0.649 (0.076%), neg=0, invalid=762
0123: dt=73.984000, rms=0.649 (0.075%), neg=0, invalid=762
0124: dt=73.984000, rms=0.648 (0.071%), neg=0, invalid=762
0125: dt=73.984000, rms=0.648 (0.070%), neg=0, invalid=762
0126: dt=73.984000, rms=0.647 (0.070%), neg=0, invalid=762
0127: dt=73.984000, rms=0.647 (0.063%), neg=0, invalid=762
0128: dt=73.984000, rms=0.647 (0.060%), neg=0, invalid=762
0129: dt=73.984000, rms=0.646 (0.051%), neg=0, invalid=762
0130: dt=73.984000, rms=0.646 (0.050%), neg=0, invalid=762
0131: dt=73.984000, rms=0.646 (0.052%), neg=0, invalid=762
0132: dt=73.984000, rms=0.645 (0.056%), neg=0, invalid=762
0133: dt=73.984000, rms=0.645 (0.059%), neg=0, invalid=762
0134: dt=73.984000, rms=0.644 (0.057%), neg=0, invalid=762
0135: dt=73.984000, rms=0.644 (0.049%), neg=0, invalid=762
0136: dt=73.984000, rms=0.644 (0.047%), neg=0, invalid=762
0137: dt=73.984000, rms=0.644 (0.046%), neg=0, invalid=762
0138: dt=73.984000, rms=0.643 (0.055%), neg=0, invalid=762
0139: dt=73.984000, rms=0.643 (0.059%), neg=0, invalid=762
0140: dt=73.984000, rms=0.642 (0.061%), neg=0, invalid=762
0141: dt=73.984000, rms=0.642 (0.058%), neg=0, invalid=762
0142: dt=73.984000, rms=0.642 (0.051%), neg=0, invalid=762
0143: dt=73.984000, rms=0.641 (0.046%), neg=0, invalid=762
0144: dt=73.984000, rms=0.641 (0.047%), neg=0, invalid=762
0145: dt=73.984000, rms=0.641 (0.048%), neg=0, invalid=762
0146: dt=73.984000, rms=0.640 (0.051%), neg=0, invalid=762
0147: dt=73.984000, rms=0.640 (0.048%), neg=0, invalid=762
0148: dt=73.984000, rms=0.640 (0.044%), neg=0, invalid=762
0149: dt=73.984000, rms=0.640 (0.038%), neg=0, invalid=762
0150: dt=73.984000, rms=0.639 (0.034%), neg=0, invalid=762
0151: dt=73.984000, rms=0.639 (0.033%), neg=0, invalid=762
0152: dt=73.984000, rms=0.639 (0.034%), neg=0, invalid=762
0153: dt=73.984000, rms=0.639 (0.034%), neg=0, invalid=762
0154: dt=73.984000, rms=0.639 (0.033%), neg=0, invalid=762
0155: dt=73.984000, rms=0.638 (0.030%), neg=0, invalid=762
0156: dt=73.984000, rms=0.638 (0.028%), neg=0, invalid=762
0157: dt=73.984000, rms=0.638 (0.025%), neg=0, invalid=762
0158: dt=73.984000, rms=0.638 (0.021%), neg=0, invalid=762
0159: dt=5918.720000, rms=0.637 (0.079%), neg=0, invalid=762
0160: dt=110.976000, rms=0.637 (0.077%), neg=0, invalid=762
0161: dt=73.984000, rms=0.637 (0.002%), neg=0, invalid=762
0162: dt=73.984000, rms=0.637 (0.005%), neg=0, invalid=762
0163: dt=73.984000, rms=0.637 (0.008%), neg=0, invalid=762
0164: dt=73.984000, rms=0.637 (0.009%), neg=0, invalid=762
0165: dt=73.984000, rms=0.637 (0.012%), neg=0, invalid=762
0166: dt=73.984000, rms=0.637 (0.013%), neg=0, invalid=762
0167: dt=73.984000, rms=0.637 (0.016%), neg=0, invalid=762
0168: dt=73.984000, rms=0.636 (0.013%), neg=0, invalid=762
0169: dt=73.984000, rms=0.636 (0.011%), neg=0, invalid=762
0170: dt=129.472000, rms=0.636 (0.001%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.637, neg=0, invalid=762
0171: dt=0.000000, rms=0.636 (0.051%), neg=0, invalid=762
0172: dt=0.000000, rms=0.636 (0.000%), neg=0, invalid=762
0173: dt=0.850000, rms=0.636 (-0.000%), neg=0, invalid=762
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.638, neg=0, invalid=762
0174: dt=497.664000, rms=0.623 (2.285%), neg=0, invalid=762
0175: dt=80.718802, rms=0.619 (0.596%), neg=0, invalid=762
0176: dt=145.152000, rms=0.616 (0.470%), neg=0, invalid=762
0177: dt=36.288000, rms=0.615 (0.191%), neg=0, invalid=762
0178: dt=145.152000, rms=0.614 (0.261%), neg=0, invalid=762
0179: dt=124.416000, rms=0.612 (0.235%), neg=0, invalid=762
0180: dt=36.288000, rms=0.611 (0.130%), neg=0, invalid=762
0181: dt=145.152000, rms=0.610 (0.191%), neg=0, invalid=762
0182: dt=124.416000, rms=0.609 (0.202%), neg=0, invalid=762
0183: dt=36.288000, rms=0.608 (0.088%), neg=0, invalid=762
0184: dt=145.152000, rms=0.608 (0.142%), neg=0, invalid=762
0185: dt=124.416000, rms=0.606 (0.182%), neg=0, invalid=762
0186: dt=36.288000, rms=0.606 (0.072%), neg=0, invalid=762
0187: dt=145.152000, rms=0.605 (0.121%), neg=0, invalid=762
0188: dt=124.416000, rms=0.604 (0.156%), neg=0, invalid=762
0189: dt=36.288000, rms=0.604 (0.053%), neg=0, invalid=762
0190: dt=248.832000, rms=0.603 (0.129%), neg=0, invalid=762
0191: dt=73.142857, rms=0.602 (0.166%), neg=0, invalid=762
0192: dt=36.288000, rms=0.602 (0.032%), neg=0, invalid=762
0193: dt=36.288000, rms=0.602 (0.027%), neg=0, invalid=762
0194: dt=36.288000, rms=0.602 (0.050%), neg=0, invalid=762
0195: dt=36.288000, rms=0.601 (0.072%), neg=0, invalid=762
0196: dt=36.288000, rms=0.601 (0.093%), neg=0, invalid=762
0197: dt=36.288000, rms=0.600 (0.104%), neg=0, invalid=762
0198: dt=36.288000, rms=0.599 (0.109%), neg=0, invalid=762
0199: dt=36.288000, rms=0.599 (0.118%), neg=0, invalid=762
0200: dt=36.288000, rms=0.599 (0.017%), neg=0, invalid=762
0201: dt=36.288000, rms=0.598 (0.035%), neg=0, invalid=762
0202: dt=36.288000, rms=0.598 (0.048%), neg=0, invalid=762
0203: dt=2.268000, rms=0.598 (0.001%), neg=0, invalid=762
0204: dt=0.283500, rms=0.598 (0.000%), neg=0, invalid=762
0205: dt=0.008859, rms=0.598 (0.000%), neg=0, invalid=762
0206: dt=0.004430, rms=0.598 (0.000%), neg=0, invalid=762
0207: dt=0.001107, rms=0.598 (0.000%), neg=0, invalid=762
0208: dt=0.000035, rms=0.598 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.598, neg=0, invalid=762
0209: dt=36.288000, rms=0.597 (0.165%), neg=0, invalid=762
0210: dt=82.944000, rms=0.597 (0.088%), neg=0, invalid=762
0211: dt=497.664000, rms=0.593 (0.631%), neg=0, invalid=762
0212: dt=25.920000, rms=0.593 (0.033%), neg=0, invalid=762
0213: dt=25.920000, rms=0.593 (0.020%), neg=0, invalid=762
0214: dt=25.920000, rms=0.593 (-0.009%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.598, neg=0, invalid=762
0215: dt=48.273245, rms=0.589 (1.620%), neg=0, invalid=762
0216: dt=11.200000, rms=0.586 (0.520%), neg=0, invalid=762
0217: dt=11.200000, rms=0.583 (0.371%), neg=0, invalid=762
0218: dt=11.200000, rms=0.582 (0.300%), neg=0, invalid=762
0219: dt=8.000000, rms=0.581 (0.184%), neg=0, invalid=762
0220: dt=0.700000, rms=0.581 (0.014%), neg=0, invalid=762
0221: dt=0.700000, rms=0.580 (0.015%), neg=0, invalid=762
0222: dt=0.087500, rms=0.580 (0.001%), neg=0, invalid=762
0223: dt=0.043750, rms=0.580 (0.001%), neg=0, invalid=762
0224: dt=0.010937, rms=0.580 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.581, neg=0, invalid=762
0225: dt=32.000000, rms=0.576 (0.762%), neg=0, invalid=762
0226: dt=72.615385, rms=0.569 (1.250%), neg=0, invalid=762
0227: dt=11.200000, rms=0.567 (0.384%), neg=0, invalid=762
0228: dt=11.200000, rms=0.566 (0.170%), neg=0, invalid=762
0229: dt=44.800000, rms=0.564 (0.295%), neg=0, invalid=762
0230: dt=52.528302, rms=0.561 (0.593%), neg=0, invalid=762
0231: dt=11.200000, rms=0.560 (0.231%), neg=0, invalid=762
0232: dt=24.387665, rms=0.559 (0.134%), neg=0, invalid=762
0233: dt=11.200000, rms=0.558 (0.141%), neg=0, invalid=762
0234: dt=9.600000, rms=0.558 (0.087%), neg=0, invalid=762
0235: dt=0.700000, rms=0.558 (0.007%), neg=0, invalid=762
0236: dt=0.175000, rms=0.558 (0.001%), neg=0, invalid=762
0237: dt=0.087500, rms=0.558 (0.001%), neg=0, invalid=762
0238: dt=0.043750, rms=0.558 (0.000%), neg=0, invalid=762
0239: dt=0.010937, rms=0.558 (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=0.572, neg=0, invalid=762
0240: dt=12.106339, rms=0.568 (0.813%), neg=0, invalid=762
0241: dt=0.003938, rms=0.568 (-0.000%), neg=0, invalid=762
0242: dt=0.003938, rms=0.568 (0.000%), neg=0, invalid=762
0243: dt=0.003938, rms=0.568 (0.000%), neg=0, invalid=762
0244: dt=0.001969, rms=0.568 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.568, neg=0, invalid=762
0245: dt=0.000984, rms=0.568 (0.066%), neg=0, invalid=762
0246: dt=0.000000, rms=0.568 (0.000%), neg=0, invalid=762
0247: dt=0.000073, rms=0.568 (0.000%), neg=0, invalid=762
0248: dt=0.000002, rms=0.568 (0.000%), neg=0, invalid=762
0249: dt=0.000001, rms=0.568 (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=0.594, neg=0, invalid=762
0250: dt=1.280000, rms=0.593 (0.203%), neg=0, invalid=762
0251: dt=1.024000, rms=0.592 (0.045%), neg=0, invalid=762
0252: dt=1.024000, rms=0.592 (0.019%), neg=0, invalid=762
0253: dt=1.024000, rms=0.592 (-0.054%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.593, neg=0, invalid=762
0254: dt=4.096000, rms=0.588 (0.748%), neg=0, invalid=762
0255: dt=6.144000, rms=0.584 (0.629%), neg=0, invalid=762
0256: dt=0.112000, rms=0.584 (-0.003%), neg=0, invalid=762
0257: dt=0.112000, rms=0.584 (0.000%), neg=0, invalid=762
0258: dt=0.112000, rms=0.584 (-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=0.562, neg=0, invalid=762
0259: dt=0.448000, rms=0.545 (3.082%), neg=0, invalid=762
0260: dt=0.448000, rms=0.540 (0.949%), neg=0, invalid=762
0261: dt=0.448000, rms=0.537 (0.542%), neg=0, invalid=762
0262: dt=0.448000, rms=0.535 (0.276%), neg=0, invalid=762
0263: dt=0.448000, rms=0.534 (0.230%), neg=0, invalid=762
0264: dt=0.448000, rms=0.533 (0.130%), neg=0, invalid=762
0265: dt=0.448000, rms=0.533 (0.143%), neg=0, invalid=762
0266: dt=0.448000, rms=0.532 (0.073%), neg=0, invalid=762
0267: dt=0.448000, rms=0.532 (0.101%), neg=0, invalid=762
0268: dt=0.448000, rms=0.531 (0.042%), neg=0, invalid=762
0269: dt=0.448000, rms=0.531 (0.076%), neg=0, invalid=762
0270: dt=0.448000, rms=0.530 (0.093%), neg=0, invalid=762
0271: dt=0.448000, rms=0.530 (0.027%), neg=0, invalid=762
0272: dt=0.448000, rms=0.530 (0.073%), neg=0, invalid=762
0273: dt=0.448000, rms=0.530 (0.028%), neg=0, invalid=762
0274: dt=0.448000, rms=0.530 (0.027%), neg=0, invalid=762
0275: dt=0.448000, rms=0.530 (0.026%), neg=0, invalid=762
0276: dt=0.448000, rms=0.529 (0.003%), neg=0, invalid=762
0277: dt=0.448000, rms=0.529 (0.019%), neg=0, invalid=762
0278: dt=0.448000, rms=0.529 (0.026%), neg=0, invalid=762
0279: dt=0.448000, rms=0.529 (0.026%), neg=0, invalid=762
0280: dt=0.448000, rms=0.529 (-0.008%), neg=0, invalid=762
0281: dt=0.112000, rms=0.529 (0.001%), neg=0, invalid=762
0282: dt=0.320000, rms=0.529 (0.005%), neg=0, invalid=762
0283: dt=0.448000, rms=0.529 (0.006%), neg=0, invalid=762
0284: dt=0.256000, rms=0.529 (0.005%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.529, neg=0, invalid=762
0285: dt=0.448000, rms=0.522 (1.366%), neg=0, invalid=762
0286: dt=0.112000, rms=0.522 (0.072%), neg=0, invalid=762
0287: dt=0.448000, rms=0.520 (0.258%), neg=0, invalid=762
0288: dt=0.448000, rms=0.520 (0.100%), neg=0, invalid=762
0289: dt=0.448000, rms=0.520 (0.047%), neg=0, invalid=762
0290: dt=0.448000, rms=0.520 (0.010%), neg=0, invalid=762
0291: dt=0.448000, rms=0.520 (0.008%), neg=0, invalid=762
0292: dt=0.448000, rms=0.520 (0.010%), neg=0, invalid=762
0293: dt=0.448000, rms=0.520 (-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=0.517, neg=0, invalid=762
0294: dt=0.000000, rms=0.517 (0.080%), neg=0, invalid=762
0295: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.517, neg=0, invalid=762
0296: dt=0.000000, rms=0.517 (0.080%), neg=0, invalid=762
0297: dt=0.000000, rms=0.517 (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=0.517, neg=0, invalid=762
0298: dt=0.567000, rms=0.517 (0.080%), neg=0, invalid=762
0299: dt=0.357143, rms=0.517 (0.000%), neg=0, invalid=762
0300: dt=0.357143, rms=0.517 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.517, neg=0, invalid=762
0301: dt=9.072000, rms=0.517 (0.091%), neg=0, invalid=762
0302: dt=20.736000, rms=0.517 (0.017%), neg=0, invalid=762
0303: dt=20.736000, rms=0.517 (0.050%), neg=0, invalid=762
0304: dt=20.736000, rms=0.516 (0.076%), neg=0, invalid=762
0305: dt=20.736000, rms=0.516 (0.091%), neg=0, invalid=762
0306: dt=20.736000, rms=0.515 (0.103%), neg=0, invalid=762
0307: dt=20.736000, rms=0.515 (0.117%), neg=0, invalid=762
0308: dt=20.736000, rms=0.514 (0.120%), neg=0, invalid=762
0309: dt=20.736000, rms=0.513 (0.107%), neg=0, invalid=762
0310: dt=20.736000, rms=0.513 (0.091%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.514, neg=0, invalid=762
0311: dt=22.936709, rms=0.510 (0.636%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 9 iterations, nbhd size=1, neg = 0
0312: dt=32.000000, rms=0.508 (0.388%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0313: dt=11.200000, rms=0.508 (0.138%), neg=0, invalid=762
0314: dt=11.200000, rms=0.507 (0.096%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0315: dt=11.200000, rms=0.507 (0.129%), neg=0, invalid=762
iter 0, gcam->neg = 6
after 8 iterations, nbhd size=1, neg = 0
0316: dt=11.200000, rms=0.506 (0.093%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 2 iterations, nbhd size=0, neg = 0
0317: dt=11.200000, rms=0.506 (0.071%), neg=0, invalid=762
iter 0, gcam->neg = 8
after 0 iterations, nbhd size=0, neg = 0
0318: dt=153.600000, rms=0.504 (0.375%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0319: dt=11.200000, rms=0.504 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0320: dt=11.200000, rms=0.504 (0.021%), neg=0, invalid=762
0321: dt=11.200000, rms=0.503 (0.022%), neg=0, invalid=762
0322: dt=11.200000, rms=0.503 (0.019%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0323: dt=11.200000, rms=0.503 (0.020%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 2 iterations, nbhd size=0, neg = 0
0324: dt=11.200000, rms=0.503 (0.025%), neg=0, invalid=762
iter 0, gcam->neg = 5
after 9 iterations, nbhd size=1, neg = 0
0325: dt=11.200000, rms=0.503 (0.047%), neg=0, invalid=762
iter 0, gcam->neg = 7
after 8 iterations, nbhd size=1, neg = 0
0326: dt=11.200000, rms=0.503 (0.038%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0327: dt=44.800000, rms=0.502 (0.059%), neg=0, invalid=762
0328: dt=19.200000, rms=0.502 (0.010%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.503, neg=0, invalid=762
0329: dt=27.886163, rms=0.497 (1.171%), neg=0, invalid=762
0330: dt=22.974359, rms=0.493 (0.706%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0331: dt=11.200000, rms=0.492 (0.282%), neg=0, invalid=762
0332: dt=102.400000, rms=0.488 (0.743%), neg=0, invalid=762
0333: dt=22.857143, rms=0.487 (0.295%), neg=0, invalid=762
0334: dt=9.600000, rms=0.487 (0.046%), neg=0, invalid=762
0335: dt=9.600000, rms=0.486 (0.024%), neg=0, invalid=762
0336: dt=9.600000, rms=0.486 (0.041%), neg=0, invalid=762
0337: dt=9.600000, rms=0.486 (0.066%), neg=0, invalid=762
0338: dt=9.600000, rms=0.486 (0.089%), neg=0, invalid=762
0339: dt=9.600000, rms=0.485 (0.094%), neg=0, invalid=762
0340: dt=9.600000, rms=0.485 (0.087%), neg=0, invalid=762
0341: dt=9.600000, rms=0.484 (0.081%), neg=0, invalid=762
0342: dt=44.800000, rms=0.484 (0.044%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.491, neg=0, invalid=762
0343: dt=2.000000, rms=0.490 (0.112%), neg=0, invalid=762
0344: dt=0.000000, rms=0.490 (0.003%), neg=0, invalid=762
0345: dt=0.150000, rms=0.490 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.491, neg=0, invalid=762
0346: dt=6.095238, rms=0.490 (0.221%), neg=0, invalid=762
0347: dt=10.084034, rms=0.489 (0.139%), neg=0, invalid=762
0348: dt=10.084034, rms=0.488 (0.191%), neg=0, invalid=762
0349: dt=10.084034, rms=0.487 (0.257%), neg=0, invalid=762
0350: dt=10.084034, rms=0.485 (0.262%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0351: dt=10.084034, rms=0.484 (0.388%), neg=0, invalid=762
0352: dt=10.084034, rms=0.481 (0.580%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 8 iterations, nbhd size=1, neg = 0
0353: dt=10.084034, rms=0.478 (0.617%), neg=0, invalid=762
0354: dt=10.084034, rms=0.476 (0.440%), neg=0, invalid=762
0355: dt=10.084034, rms=0.475 (0.168%), neg=0, invalid=762
iter 0, gcam->neg = 4
after 12 iterations, nbhd size=1, neg = 0
0356: dt=10.084034, rms=0.475 (-0.018%), neg=0, invalid=762
0357: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=762
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0358: dt=0.000000, rms=0.482 (0.095%), neg=0, invalid=762
0359: dt=0.000000, rms=0.482 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.483, neg=0, invalid=762
0360: dt=0.000000, rms=0.482 (0.095%), neg=0, invalid=762
0361: dt=0.000000, rms=0.482 (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=0.470, neg=0, invalid=762
iter 0, gcam->neg = 565
after 16 iterations, nbhd size=1, neg = 0
0362: dt=1.688703, rms=0.452 (3.866%), neg=0, invalid=762
0363: dt=0.028000, rms=0.452 (0.020%), neg=0, invalid=762
0364: dt=0.028000, rms=0.452 (-0.004%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.453, neg=0, invalid=762
0365: dt=0.112000, rms=0.451 (0.248%), neg=0, invalid=762
0366: dt=0.064000, rms=0.451 (0.026%), neg=0, invalid=762
0367: dt=0.064000, rms=0.451 (-0.004%), 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=0.444, neg=0, invalid=762
0368: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.444, neg=0, invalid=762
0369: dt=0.000000, rms=0.444 (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=0.444, neg=0, invalid=762
0370: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.444, neg=0, invalid=762
0371: dt=4.888889, rms=0.444 (0.002%), neg=0, invalid=762
0372: dt=1.620000, rms=0.444 (0.000%), neg=0, invalid=762
0373: dt=1.620000, rms=0.444 (0.000%), neg=0, invalid=762
0374: dt=1.620000, rms=0.444 (-0.001%), neg=0, invalid=762
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.444, neg=0, invalid=762
0375: dt=6.400000, rms=0.444 (0.072%), neg=0, invalid=762
0376: dt=2.800000, rms=0.444 (0.007%), neg=0, invalid=762
0377: dt=2.800000, rms=0.444 (-0.002%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.444, neg=0, invalid=762
0378: dt=25.600000, rms=0.443 (0.342%), neg=0, invalid=762
0379: dt=25.600000, rms=0.441 (0.294%), neg=0, invalid=762
0380: dt=11.200000, rms=0.441 (0.103%), neg=0, invalid=762
0381: dt=11.200000, rms=0.440 (0.073%), neg=0, invalid=762
0382: dt=11.200000, rms=0.440 (0.113%), neg=0, invalid=762
0383: dt=11.200000, rms=0.439 (0.134%), neg=0, invalid=762
0384: dt=11.200000, rms=0.439 (0.131%), neg=0, invalid=762
0385: dt=11.200000, rms=0.438 (0.127%), neg=0, invalid=762
iter 0, gcam->neg = 3
after 7 iterations, nbhd size=1, neg = 0
0386: dt=11.200000, rms=0.438 (0.108%), neg=0, invalid=762
0387: dt=11.200000, rms=0.437 (0.110%), neg=0, invalid=762
0388: dt=11.200000, rms=0.437 (0.100%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0389: dt=44.800000, rms=0.437 (0.062%), neg=0, invalid=762
0390: dt=44.800000, rms=0.437 (-0.062%), neg=0, invalid=762
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.439, neg=0, invalid=762
0391: dt=2.285714, rms=0.439 (0.037%), neg=0, invalid=762
0392: dt=0.000563, rms=0.439 (0.000%), neg=0, invalid=762
0393: dt=0.000563, 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
0394: dt=15.337931, rms=0.437 (0.452%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 9 iterations, nbhd size=1, neg = 0
0395: dt=15.117647, rms=0.435 (0.391%), neg=0, invalid=762
0396: dt=5.130435, rms=0.435 (0.122%), neg=0, invalid=762
0397: dt=5.130435, rms=0.435 (0.059%), neg=0, invalid=762
0398: dt=5.130435, rms=0.434 (0.100%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0399: dt=5.130435, rms=0.433 (0.141%), neg=0, invalid=762
0400: dt=5.130435, rms=0.433 (0.160%), neg=0, invalid=762
0401: dt=5.130435, rms=0.432 (0.159%), neg=0, invalid=762
iter 0, gcam->neg = 1
after 2 iterations, nbhd size=0, neg = 0
0402: dt=5.130435, rms=0.431 (0.144%), neg=0, invalid=762
0403: dt=5.130435, rms=0.431 (0.128%), neg=0, invalid=762
0404: dt=5.130435, rms=0.430 (0.111%), neg=0, invalid=762
iter 0, gcam->neg = 2
after 7 iterations, nbhd size=1, neg = 0
0405: dt=5.130435, rms=0.430 (0.085%), neg=0, invalid=762
0406: dt=2.880000, rms=0.430 (0.001%), neg=0, invalid=762
0407: dt=2.880000, rms=0.430 (0.000%), neg=0, invalid=762
0408: dt=2.880000, rms=0.430 (-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=0.435, neg=0, invalid=762
0409: dt=0.000000, rms=0.435 (0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.435, neg=0, invalid=762
0410: dt=0.000000, rms=0.435 (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=0.427, neg=0, invalid=762
iter 0, gcam->neg = 309
after 13 iterations, nbhd size=1, neg = 0
0411: dt=1.280000, rms=0.420 (1.726%), neg=0, invalid=762
0412: dt=0.000023, rms=0.420 (0.000%), neg=0, invalid=762
0413: dt=0.000023, rms=0.420 (-0.000%), neg=0, invalid=762
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=762
0414: dt=0.192000, rms=0.419 (0.226%), neg=0, invalid=762
0415: dt=0.256000, rms=0.418 (0.141%), neg=0, invalid=762
0416: dt=0.256000, rms=0.417 (0.190%), neg=0, invalid=762
0417: dt=0.256000, rms=0.416 (0.228%), neg=0, invalid=762
iter 0, gcam->neg = 17
after 9 iterations, nbhd size=1, neg = 0
0418: dt=0.256000, rms=0.416 (0.153%), neg=0, invalid=762
iter 0, gcam->neg = 14
after 11 iterations, nbhd size=1, neg = 0
0419: dt=0.256000, rms=0.415 (0.186%), neg=0, invalid=762
iter 0, gcam->neg = 20
after 9 iterations, nbhd size=1, neg = 0
0420: dt=0.256000, rms=0.414 (0.208%), neg=0, invalid=762
iter 0, gcam->neg = 24
after 10 iterations, nbhd size=1, neg = 0
0421: dt=0.256000, rms=0.414 (0.107%), neg=0, invalid=762
iter 0, gcam->neg = 24
after 10 iterations, nbhd size=1, neg = 0
0422: dt=0.256000, rms=0.414 (-0.051%), neg=0, invalid=762
0423: dt=0.048000, rms=0.414 (0.002%), neg=0, invalid=762
0424: dt=0.028000, rms=0.414 (0.001%), neg=0, invalid=762
writing output transformation to transforms/talairach.m3z...
GCAMwrite
mri_ca_register took 1 hours, 49 minutes and 18 seconds.
mri_ca_register utimesec    7253.512298
mri_ca_register stimesec    8.396723
mri_ca_register ru_maxrss   1350436
mri_ca_register ru_ixrss    0
mri_ca_register ru_idrss    0
mri_ca_register ru_isrss    0
mri_ca_register ru_minflt   4541415
mri_ca_register ru_majflt   0
mri_ca_register ru_nswap    0
mri_ca_register ru_inblock  0
mri_ca_register ru_oublock  67888
mri_ca_register ru_msgsnd   0
mri_ca_register ru_msgrcv   0
mri_ca_register ru_nsignals 0
mri_ca_register ru_nvcsw    3730
mri_ca_register ru_nivcsw   32511
FSRUNTIME@ mri_ca_register  1.8217 hours 2 threads
#--------------------------------------
#@# SubCort Seg Sat Oct  7 18:27:47 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-542
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-6.0.0/0050660/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 7.19
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 = 0.10476 (29)
Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (406 voxels, overlap=0.189)
Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (406 voxels, peak = 31), gca=30.0
gca peak = 0.17677 (13)
mri peak = 0.11901 (31)
Right_Lateral_Ventricle (43): linear fit = 2.15 x + 0.0 (1977 voxels, overlap=0.110)
Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1977 voxels, peak = 28), gca=19.5
gca peak = 0.28129 (95)
mri peak = 0.11811 (100)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (882 voxels, overlap=0.959)
Right_Pallidum (52): linear fit = 1.07 x + 0.0 (882 voxels, peak = 101), gca=101.2
gca peak = 0.16930 (96)
mri peak = 0.08976 (97)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (989 voxels, overlap=0.987)
Left_Pallidum (13): linear fit = 1.04 x + 0.0 (989 voxels, peak = 100), gca=100.3
gca peak = 0.24553 (55)
mri peak = 0.08358 (72)
Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1047 voxels, overlap=0.025)
Right_Hippocampus (53): linear fit = 1.27 x + 0.0 (1047 voxels, peak = 70), gca=70.1
gca peak = 0.30264 (59)
mri peak = 0.07350 (71)
Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1034 voxels, overlap=0.024)
Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1034 voxels, peak = 72), gca=72.3
gca peak = 0.07580 (103)
mri peak = 0.09607 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52018 voxels, overlap=0.643)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (52018 voxels, peak = 107), gca=106.6
gca peak = 0.07714 (104)
mri peak = 0.09706 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (51783 voxels, overlap=0.612)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (51783 voxels, peak = 107), gca=106.6
gca peak = 0.09712 (58)
mri peak = 0.04854 (74)
Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (32835 voxels, overlap=0.052)
Left_Cerebral_Cortex (3): linear fit = 1.26 x + 0.0 (32835 voxels, peak = 73), gca=73.4
gca peak = 0.11620 (58)
mri peak = 0.05644 (77)
Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (30959 voxels, overlap=0.001)
Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (30959 voxels, peak = 75), gca=75.1
gca peak = 0.30970 (66)
mri peak = 0.10463 (87)
Right_Caudate (50): linear fit = 1.26 x + 0.0 (1167 voxels, overlap=0.020)
Right_Caudate (50): linear fit = 1.26 x + 0.0 (1167 voxels, peak = 83), gca=83.5
gca peak = 0.15280 (69)
mri peak = 0.11535 (84)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (971 voxels, overlap=0.214)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (971 voxels, peak = 78), gca=77.6
gca peak = 0.13902 (56)
mri peak = 0.06272 (72)
Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (23514 voxels, overlap=0.014)
Left_Cerebellum_Cortex (8): linear fit = 1.26 x + 0.0 (23514 voxels, peak = 71), gca=70.8
gca peak = 0.14777 (55)
mri peak = 0.06852 (72)
Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (25164 voxels, overlap=0.003)
Right_Cerebellum_Cortex (47): linear fit = 1.29 x + 0.0 (25164 voxels, peak = 71), gca=71.2
gca peak = 0.16765 (84)
mri peak = 0.10701 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7540 voxels, overlap=0.810)
Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7540 voxels, peak = 88), gca=87.8
gca peak = 0.18739 (84)
mri peak = 0.10575 (88)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7302 voxels, overlap=0.742)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (7302 voxels, peak = 89), gca=89.5
gca peak = 0.29869 (57)
mri peak = 0.08661 (71)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (629 voxels, overlap=0.061)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (629 voxels, peak = 69), gca=69.3
gca peak = 0.33601 (57)
mri peak = 0.08442 (74)
Right_Amygdala (54): linear fit = 1.30 x + 0.0 (652 voxels, overlap=0.049)
Right_Amygdala (54): linear fit = 1.30 x + 0.0 (652 voxels, peak = 74), gca=74.4
gca peak = 0.11131 (90)
mri peak = 0.07244 (93)
Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5147 voxels, overlap=0.720)
Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5147 voxels, peak = 95), gca=94.9
gca peak = 0.11793 (83)
mri peak = 0.07083 (94)
Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4989 voxels, overlap=0.497)
Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (4989 voxels, peak = 92), gca=91.7
gca peak = 0.08324 (81)
mri peak = 0.08802 (90)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (1950 voxels, overlap=0.355)
Left_Putamen (12): linear fit = 1.12 x + 0.0 (1950 voxels, peak = 90), gca=90.3
gca peak = 0.10360 (77)
mri peak = 0.08380 (90)
Right_Putamen (51): linear fit = 1.16 x + 0.0 (2502 voxels, overlap=0.323)
Right_Putamen (51): linear fit = 1.16 x + 0.0 (2502 voxels, peak = 90), gca=89.7
gca peak = 0.08424 (78)
mri peak = 0.09690 (84)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (13507 voxels, overlap=0.476)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (13507 voxels, peak = 83), gca=83.1
gca peak = 0.12631 (89)
mri peak = 0.08881 (92)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1643 voxels, overlap=0.738)
Right_VentralDC (60): linear fit = 1.05 x + 0.0 (1643 voxels, peak = 94), gca=93.9
gca peak = 0.14500 (87)
mri peak = 0.08964 (90)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1871 voxels, overlap=0.843)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1871 voxels, peak = 90), gca=90.0
gca peak = 0.14975 (24)
mri peak = 0.20005 (36)
gca peak = 0.19357 (14)
mri peak = 0.12725 (29)
Fourth_Ventricle (15): linear fit = 1.84 x + 0.0 (302 voxels, overlap=0.172)
Fourth_Ventricle (15): linear fit = 1.84 x + 0.0 (302 voxels, peak = 26), gca=25.7
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16825 (27)
gca peak Left_Thalamus = 1.00000 (94)
gca peak Third_Ventricle = 0.14975 (24)
gca peak Fourth_Ventricle = 0.19357 (14)
gca peak CSF = 0.23379 (36)
gca peak Left_Accumbens_area = 0.70037 (62)
gca peak Left_undetermined = 1.00000 (26)
gca peak Left_vessel = 0.75997 (52)
gca peak Left_choroid_plexus = 0.12089 (35)
gca peak Right_Inf_Lat_Vent = 0.24655 (23)
gca peak Right_Accumbens_area = 0.45042 (65)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14516 (37)
gca peak Fifth_Ventricle = 0.65475 (32)
gca peak WM_hypointensities = 0.07854 (76)
gca peak non_WM_hypointensities = 0.08491 (43)
gca peak Optic_Chiasm = 0.71127 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.26 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.50 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.12544 (31)
mri peak = 0.10476 (29)
Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (406 voxels, overlap=0.834)
Left_Lateral_Ventricle (4): linear fit = 1.04 x + 0.0 (406 voxels, peak = 32), gca=32.4
gca peak = 0.13981 (19)
mri peak = 0.11901 (31)
Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (1977 voxels, overlap=0.329)
Right_Lateral_Ventricle (43): linear fit = 1.46 x + 0.0 (1977 voxels, peak = 28), gca=27.6
gca peak = 0.25726 (102)
mri peak = 0.11811 (100)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (882 voxels, overlap=1.011)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (882 voxels, peak = 103), gca=102.5
gca peak = 0.17215 (100)
mri peak = 0.08976 (97)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (989 voxels, overlap=1.005)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (989 voxels, peak = 100), gca=100.5
gca peak = 0.24040 (71)
mri peak = 0.08358 (72)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1047 voxels, overlap=1.003)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1047 voxels, peak = 71), gca=71.0
gca peak = 0.30146 (69)
mri peak = 0.07350 (71)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1034 voxels, overlap=1.007)
Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (1034 voxels, peak = 70), gca=70.0
gca peak = 0.07496 (106)
mri peak = 0.09607 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52018 voxels, overlap=0.787)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (52018 voxels, peak = 105), gca=105.5
gca peak = 0.07686 (107)
mri peak = 0.09706 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51783 voxels, overlap=0.722)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (51783 voxels, peak = 107), gca=107.0
gca peak = 0.07826 (73)
mri peak = 0.04854 (74)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (32835 voxels, overlap=0.960)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (32835 voxels, peak = 73), gca=73.0
gca peak = 0.09095 (75)
mri peak = 0.05644 (77)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (30959 voxels, overlap=0.939)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (30959 voxels, peak = 75), gca=75.0
gca peak = 0.21463 (83)
mri peak = 0.10463 (87)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1167 voxels, overlap=1.001)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (1167 voxels, peak = 83), gca=83.0
gca peak = 0.16640 (87)
mri peak = 0.11535 (84)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (971 voxels, overlap=0.977)
Left_Caudate (11): linear fit = 1.01 x + 0.0 (971 voxels, peak = 88), gca=88.3
gca peak = 0.11270 (70)
mri peak = 0.06272 (72)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23514 voxels, overlap=0.972)
Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (23514 voxels, peak = 70), gca=70.0
gca peak = 0.11145 (71)
mri peak = 0.06852 (72)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25164 voxels, overlap=0.975)
Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (25164 voxels, peak = 71), gca=71.0
gca peak = 0.15145 (88)
mri peak = 0.10701 (88)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7540 voxels, overlap=0.949)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7540 voxels, peak = 88), gca=88.0
gca peak = 0.15153 (90)
mri peak = 0.10575 (88)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7302 voxels, overlap=0.966)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (7302 voxels, peak = 89), gca=88.7
gca peak = 0.28119 (69)
mri peak = 0.08661 (71)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (629 voxels, overlap=1.016)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (629 voxels, peak = 69), gca=69.0
gca peak = 0.33194 (74)
mri peak = 0.08442 (74)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (652 voxels, overlap=1.001)
Right_Amygdala (54): linear fit = 0.99 x + 0.0 (652 voxels, peak = 73), gca=72.9
gca peak = 0.10670 (93)
mri peak = 0.07244 (93)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5147 voxels, overlap=0.917)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5147 voxels, peak = 93), gca=92.5
gca peak = 0.10075 (89)
mri peak = 0.07083 (94)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4989 voxels, overlap=0.925)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (4989 voxels, peak = 88), gca=87.7
gca peak = 0.07946 (92)
mri peak = 0.08802 (90)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1950 voxels, overlap=0.807)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1950 voxels, peak = 92), gca=91.5
gca peak = 0.08151 (87)
mri peak = 0.08380 (90)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2502 voxels, overlap=0.845)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2502 voxels, peak = 86), gca=85.7
gca peak = 0.07297 (83)
mri peak = 0.09690 (84)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (13507 voxels, overlap=0.704)
Brain_Stem (16): linear fit = 0.99 x + 0.0 (13507 voxels, peak = 82), gca=81.8
gca peak = 0.12764 (94)
mri peak = 0.08881 (92)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1643 voxels, overlap=0.827)
Right_VentralDC (60): linear fit = 1.01 x + 0.0 (1643 voxels, peak = 95), gca=95.4
gca peak = 0.15712 (90)
mri peak = 0.08964 (90)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1871 voxels, overlap=0.892)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1871 voxels, peak = 90), gca=89.6
gca peak = 0.12656 (38)
mri peak = 0.20005 (36)
gca peak = 0.16542 (24)
mri peak = 0.12725 (29)
Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (302 voxels, overlap=0.530)
Fourth_Ventricle (15): linear fit = 1.32 x + 0.0 (302 voxels, peak = 32), gca=31.6
gca peak Unknown = 0.94835 ( 0)
gca peak Left_Inf_Lat_Vent = 0.16283 (33)
gca peak Left_Thalamus = 0.36646 (105)
gca peak Third_Ventricle = 0.12656 (38)
gca peak CSF = 0.15446 (55)
gca peak Left_Accumbens_area = 0.61405 (70)
gca peak Left_undetermined = 0.95280 (34)
gca peak Left_vessel = 0.75962 (52)
gca peak Left_choroid_plexus = 0.12303 (35)
gca peak Right_Inf_Lat_Vent = 0.19636 (29)
gca peak Right_Accumbens_area = 0.29938 (82)
gca peak Right_vessel = 0.82168 (52)
gca peak Right_choroid_plexus = 0.14504 (37)
gca peak Fifth_Ventricle = 0.51780 (46)
gca peak WM_hypointensities = 0.08077 (80)
gca peak non_WM_hypointensities = 0.11678 (56)
gca peak Optic_Chiasm = 0.70876 (75)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.27 x + 0.0
Right_Pallidum too bright - rescaling by 1.005 (from 1.005) to 103.0 (was 102.5)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
91743 voxels changed in iteration 0 of unlikely voxel relabeling
453 voxels changed in iteration 1 of unlikely voxel relabeling
107 voxels changed in iteration 2 of unlikely voxel relabeling
2 voxels changed in iteration 3 of unlikely voxel relabeling
103 voxels changed in iteration 4 of unlikely voxel relabeling
80431 gm and wm labels changed (%35 to gray, %65 to white out of all changed labels)
634 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 87140 changed. image ll: -2.154, PF=0.500
pass 2: 22126 changed. image ll: -2.153, PF=0.500
pass 3: 6230 changed.
pass 4: 2220 changed.
65766 voxels changed in iteration 0 of unlikely voxel relabeling
579 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
13 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
9228 voxels changed in iteration 0 of unlikely voxel relabeling
166 voxels changed in iteration 1 of unlikely voxel relabeling
3 voxels changed in iteration 2 of unlikely voxel relabeling
0 voxels changed in iteration 3 of unlikely voxel relabeling
7603 voxels changed in iteration 0 of unlikely voxel relabeling
134 voxels changed in iteration 1 of unlikely voxel relabeling
8 voxels changed in iteration 2 of unlikely voxel relabeling
4 voxels changed in iteration 3 of unlikely voxel relabeling
0 voxels changed in iteration 4 of unlikely voxel relabeling
6625 voxels changed in iteration 0 of unlikely voxel relabeling
30 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    4547.352697
mri_ca_label stimesec    2.758580
mri_ca_label ru_maxrss   2126616
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   700517
mri_ca_label ru_majflt   0
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  67880
mri_ca_label ru_oublock  488
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    320
mri_ca_label ru_nivcsw   20246
auto-labeling took 74 minutes and 59 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/transforms/cc_up.lta 0050660 

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-6.0.0/0050660/mri/transforms/cc_up.lta
reading aseg from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.auto_noCCseg.mgz
reading norm from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/norm.mgz
64144 voxels in left wm, 90156 in right wm, xrange [114, 129]
searching rotation angles z=[-5  9], y=[-11  3]

searching scale 1 Z rot -5.2  
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  global minimum found at slice 122.2, rotations (-3.65, 1.81)
final transformation (x=122.2, yr=-3.652, zr=1.813):
 0.99747  -0.03163  -0.06366   15.38184;
 0.03157   0.99950  -0.00201   35.39107;
 0.06370   0.00000   0.99797   18.42117;
 0.00000   0.00000   0.00000   1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 128
cc center is found at 128 89 102
eigenvectors:
-0.00056   0.00389   0.99999;
-0.34416  -0.93891   0.00347;
 0.93891  -0.34415   0.00186;
writing aseg with callosum to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aseg.auto.mgz...
corpus callosum segmentation took 1.7 minutes
#--------------------------------------
#@# Merge ASeg Sat Oct  7 19:44:26 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Sat Oct  7 19:44:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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...
1315 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 82 (82), valley at 37 (37)
csf peak at 42, setting threshold to 68
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 81 (81), valley at 17 (17)
csf peak at 41, setting threshold to 67
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 8 seconds.
#--------------------------------------------
#@# Mask BFS Sat Oct  7 19:47:35 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1640741 voxels in mask (pct=  9.78)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Sat Oct  7 19:47:37 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 104.2 +- 6.5 [79.0 --> 125.0]
GM (76.0) : 72.5 +- 13.6 [30.0 --> 95.0]
setting bottom of white matter range to 86.0
setting top of gray matter range to 99.6
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
using local geometry to label remaining ambiguous voxels...

reclassifying voxels using Gaussian border classifier...

removing voxels with positive offset direction...
smoothing T1 volume with sigma = 0.250
removing 1-dimensional structures...
18472 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5422 filled
9866 bright non-wm voxels segmented.
9926 diagonally connected voxels added...
white matter segmentation took 2.1 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 0.53 minutes
reading wm segmentation from wm.seg.mgz...
690 voxels added to wm to prevent paths from MTL structures to cortex
4326 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 52618 voxels turned on, 57472 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  36 found -  36 modified     |    TOTAL:  36
pass   2 (xy+):   0 found -  36 modified     |    TOTAL:  36
pass   1 (xy-):  36 found -  36 modified     |    TOTAL:  72
pass   2 (xy-):   0 found -  36 modified     |    TOTAL:  72
pass   1 (yz+):  39 found -  39 modified     |    TOTAL: 111
pass   2 (yz+):   0 found -  39 modified     |    TOTAL: 111
pass   1 (yz-):  34 found -  34 modified     |    TOTAL: 145
pass   2 (yz-):   0 found -  34 modified     |    TOTAL: 145
pass   1 (xz+):  37 found -  37 modified     |    TOTAL: 182
pass   2 (xz+):   0 found -  37 modified     |    TOTAL: 182
pass   1 (xz-):  45 found -  45 modified     |    TOTAL: 227
pass   2 (xz-):   0 found -  45 modified     |    TOTAL: 227
Iteration Number : 1
pass   1 (+++):  68 found -  68 modified     |    TOTAL:  68
pass   2 (+++):   0 found -  68 modified     |    TOTAL:  68
pass   1 (+++):  65 found -  65 modified     |    TOTAL: 133
pass   2 (+++):   0 found -  65 modified     |    TOTAL: 133
pass   1 (+++): 104 found - 104 modified     |    TOTAL: 237
pass   2 (+++):   0 found - 104 modified     |    TOTAL: 237
pass   1 (+++):  92 found -  92 modified     |    TOTAL: 329
pass   2 (+++):   0 found -  92 modified     |    TOTAL: 329
Iteration Number : 1
pass   1 (++): 238 found - 238 modified     |    TOTAL: 238
pass   2 (++):   0 found - 238 modified     |    TOTAL: 238
pass   1 (+-): 253 found - 253 modified     |    TOTAL: 491
pass   2 (+-):   2 found - 255 modified     |    TOTAL: 493
pass   3 (+-):   0 found - 255 modified     |    TOTAL: 493
pass   1 (--): 268 found - 268 modified     |    TOTAL: 761
pass   2 (--):   1 found - 269 modified     |    TOTAL: 762
pass   3 (--):   0 found - 269 modified     |    TOTAL: 762
pass   1 (-+): 231 found - 231 modified     |    TOTAL: 993
pass   2 (-+):   0 found - 231 modified     |    TOTAL: 993
Iteration Number : 2
pass   1 (xy+):  18 found -  18 modified     |    TOTAL:  18
pass   2 (xy+):   0 found -  18 modified     |    TOTAL:  18
pass   1 (xy-):  23 found -  23 modified     |    TOTAL:  41
pass   2 (xy-):   0 found -  23 modified     |    TOTAL:  41
pass   1 (yz+):  24 found -  24 modified     |    TOTAL:  65
pass   2 (yz+):   0 found -  24 modified     |    TOTAL:  65
pass   1 (yz-):  19 found -  19 modified     |    TOTAL:  84
pass   2 (yz-):   0 found -  19 modified     |    TOTAL:  84
pass   1 (xz+):  18 found -  18 modified     |    TOTAL: 102
pass   2 (xz+):   0 found -  18 modified     |    TOTAL: 102
pass   1 (xz-):  12 found -  12 modified     |    TOTAL: 114
pass   2 (xz-):   0 found -  12 modified     |    TOTAL: 114
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  10
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  10
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  12
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  12
Iteration Number : 2
pass   1 (++):   8 found -   8 modified     |    TOTAL:   8
pass   2 (++):   0 found -   8 modified     |    TOTAL:   8
pass   1 (+-):  10 found -  10 modified     |    TOTAL:  18
pass   2 (+-):   0 found -  10 modified     |    TOTAL:  18
pass   1 (--):   6 found -   6 modified     |    TOTAL:  24
pass   2 (--):   0 found -   6 modified     |    TOTAL:  24
pass   1 (-+):   7 found -   7 modified     |    TOTAL:  31
pass   2 (-+):   0 found -   7 modified     |    TOTAL:  31
Iteration Number : 3
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   3
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   3
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 (++):   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 : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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
Iteration Number : 5
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 : 5
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 : 5
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 = 1712 (out of 584603: 0.292848)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Sat Oct  7 19:50:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36523;
 0.00000   0.00000   0.00000   1.00000;
voxel to talairach voxel transform
 1.03064  -0.08302  -0.11151   19.43493;
 0.10442   1.03170   0.46792  -50.75214;
 0.07140  -0.50700   0.79886   62.36523;
 0.00000   0.00000   0.00000   1.00000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 3007 (min = 350, max = 1400), aspect = 1.19 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 116, 89), TAL = (1.0, -39.0, 12.0)
talairach voxel to voxel transform
 0.95434   0.11046   0.06851  -17.21404;
-0.04496   0.74743  -0.44407   66.50200;
-0.11384   0.46448   0.96382  -34.32321;
 0.00000   0.00000   0.00000   1.00000;
segmentation indicates cc at (127,  116,  89) --> (1.0, -39.0, 12.0)
done.
writing output to filled.mgz...
filling took 0.7 minutes
talairach cc position changed to (1.00, -39.00, 12.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, -39.00, 12.00) SRC: (105.72, 108.78, 92.93)
search lh wm seed point around talairach space (-17.00, -39.00, 12.00), SRC: (140.08, 107.16, 88.83)
compute mri_fill using aseg
Erasing Brain Stem and Cerebellum ...
Define left and right masks using aseg:
Building Voronoi diagram ...
Using the Voronoi diagram to separate WM into two hemispheres ...
Find the largest connected component for each hemisphere ...
#--------------------------------------------
#@# Tessellate lh Sat Oct  7 19:50:59 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   6 found -   6 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   6 modified     |    TOTAL:   8
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:  10
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:  10
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:  12
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:  12
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  15
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  15
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:  16
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:  16
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   2 found -   2 modified     |    TOTAL:   4
pass   2 (--):   0 found -   2 modified     |    TOTAL:   4
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   5
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 22 (out of 270992: 0.008118)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 3002 vertices, 3259 faces
slice 50: 12198 vertices, 12610 faces
slice 60: 24806 vertices, 25273 faces
slice 70: 38576 vertices, 39102 faces
slice 80: 52130 vertices, 52631 faces
slice 90: 64138 vertices, 64592 faces
slice 100: 75789 vertices, 76248 faces
slice 110: 86714 vertices, 87208 faces
slice 120: 96907 vertices, 97392 faces
slice 130: 106880 vertices, 107339 faces
slice 140: 116764 vertices, 117195 faces
slice 150: 125173 vertices, 125599 faces
slice 160: 132940 vertices, 133293 faces
slice 170: 138663 vertices, 138987 faces
slice 180: 143709 vertices, 144019 faces
slice 190: 146441 vertices, 146653 faces
slice 200: 146666 vertices, 146830 faces
slice 210: 146666 vertices, 146830 faces
slice 220: 146666 vertices, 146830 faces
slice 230: 146666 vertices, 146830 faces
slice 240: 146666 vertices, 146830 faces
slice 250: 146666 vertices, 146830 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...
   146666 voxel in cpt #1: X=-164 [v=146666,e=440490,f=293660] located at (-22.299660, -27.050495, 30.157221)
For the whole surface: X=-164 [v=146666,e=440490,f=293660]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Tessellate rh Sat Oct  7 19:51:05 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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


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

Total Number of Modified Voxels = 7 (out of 283071: 0.002473)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
slice 40: 1268 vertices, 1403 faces
slice 50: 7850 vertices, 8170 faces
slice 60: 18936 vertices, 19358 faces
slice 70: 31614 vertices, 32111 faces
slice 80: 44991 vertices, 45472 faces
slice 90: 57135 vertices, 57571 faces
slice 100: 69227 vertices, 69693 faces
slice 110: 81116 vertices, 81596 faces
slice 120: 92933 vertices, 93421 faces
slice 130: 103836 vertices, 104350 faces
slice 140: 115093 vertices, 115608 faces
slice 150: 125588 vertices, 126074 faces
slice 160: 134583 vertices, 135045 faces
slice 170: 142013 vertices, 142395 faces
slice 180: 147794 vertices, 148130 faces
slice 190: 151706 vertices, 151981 faces
slice 200: 152648 vertices, 152834 faces
slice 210: 152648 vertices, 152834 faces
slice 220: 152648 vertices, 152834 faces
slice 230: 152648 vertices, 152834 faces
slice 240: 152648 vertices, 152834 faces
slice 250: 152648 vertices, 152834 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...
   152648 voxel in cpt #1: X=-186 [v=152648,e=458502,f=305668] located at (33.261925, -20.849012, 29.512178)
For the whole surface: X=-186 [v=152648,e=458502,f=305668]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Sat Oct  7 19:51:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

#--------------------------------------------
#@# Smooth1 rh Sat Oct  7 19:51:10 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

Waiting for PID 15802 of (15802 15805) to complete...
Waiting for PID 15805 of (15802 15805) 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 (15802 15805) completed and logs appended.
#--------------------------------------------
#@# Inflation1 lh Sat Oct  7 19:51:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

#--------------------------------------------
#@# Inflation1 rh Sat Oct  7 19:51:17 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

Waiting for PID 15849 of (15849 15852) to complete...
Waiting for PID 15852 of (15849 15852) 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 = 75555 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.166 (target=0.015)   
step 005: RMS=0.127 (target=0.015)   
step 010: RMS=0.097 (target=0.015)   
step 015: RMS=0.084 (target=0.015)   
step 020: RMS=0.074 (target=0.015)   
step 025: RMS=0.067 (target=0.015)   
step 030: RMS=0.061 (target=0.015)   
step 035: RMS=0.057 (target=0.015)   
step 040: RMS=0.054 (target=0.015)   
step 045: RMS=0.052 (target=0.015)   
step 050: RMS=0.051 (target=0.015)   
step 055: RMS=0.051 (target=0.015)   
step 060: RMS=0.050 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    45.048151
mris_inflate stimesec    0.127980
mris_inflate ru_maxrss   214712
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31135
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10328
mris_inflate ru_oublock  10344
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5233
mris_inflate ru_nivcsw   5882

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

Not saving sulc
Reading ../surf/rh.smoothwm.nofix
avg radius = 48.1 mm, total surface area = 77919 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes

step 000: RMS=0.169 (target=0.015)   
step 005: RMS=0.130 (target=0.015)   
step 010: RMS=0.102 (target=0.015)   
step 015: RMS=0.090 (target=0.015)   
step 020: RMS=0.079 (target=0.015)   
step 025: RMS=0.073 (target=0.015)   
step 030: RMS=0.067 (target=0.015)   
step 035: RMS=0.062 (target=0.015)   
step 040: RMS=0.060 (target=0.015)   
step 045: RMS=0.059 (target=0.015)   
step 050: RMS=0.058 (target=0.015)   
step 055: RMS=0.057 (target=0.015)   
step 060: RMS=0.056 (target=0.015)   
inflation complete.
Not saving sulc
mris_inflate utimesec    47.242818
mris_inflate stimesec    0.140978
mris_inflate ru_maxrss   223856
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   32394
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10744
mris_inflate ru_oublock  10768
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    5997
mris_inflate ru_nivcsw   5284
PIDs (15849 15852) completed and logs appended.
#--------------------------------------------
#@# QSphere lh Sat Oct  7 19:52:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

#--------------------------------------------
#@# QSphere rh Sat Oct  7 19:52:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

Waiting for PID 15951 of (15951 15954) to complete...
Waiting for PID 15954 of (15951 15954) 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 0.95 +- 0.62 (0.00-->11.65) (max @ vno 107643 --> 107644)
face area 0.03 +- 0.03 (-0.43-->0.96)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.318...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.394, avgs=0
005/300: dt: 0.9000, rms radial error=175.142, avgs=0
010/300: dt: 0.9000, rms radial error=174.602, avgs=0
015/300: dt: 0.9000, rms radial error=173.893, avgs=0
020/300: dt: 0.9000, rms radial error=173.084, avgs=0
025/300: dt: 0.9000, rms radial error=172.219, avgs=0
030/300: dt: 0.9000, rms radial error=171.321, avgs=0
035/300: dt: 0.9000, rms radial error=170.407, avgs=0
040/300: dt: 0.9000, rms radial error=169.484, avgs=0
045/300: dt: 0.9000, rms radial error=168.557, avgs=0
050/300: dt: 0.9000, rms radial error=167.630, avgs=0
055/300: dt: 0.9000, rms radial error=166.705, avgs=0
060/300: dt: 0.9000, rms radial error=165.782, avgs=0
065/300: dt: 0.9000, rms radial error=164.862, avgs=0
070/300: dt: 0.9000, rms radial error=163.946, avgs=0
075/300: dt: 0.9000, rms radial error=163.034, avgs=0
080/300: dt: 0.9000, rms radial error=162.125, avgs=0
085/300: dt: 0.9000, rms radial error=161.221, avgs=0
090/300: dt: 0.9000, rms radial error=160.321, avgs=0
095/300: dt: 0.9000, rms radial error=159.426, avgs=0
100/300: dt: 0.9000, rms radial error=158.535, avgs=0
105/300: dt: 0.9000, rms radial error=157.649, avgs=0
110/300: dt: 0.9000, rms radial error=156.767, avgs=0
115/300: dt: 0.9000, rms radial error=155.890, avgs=0
120/300: dt: 0.9000, rms radial error=155.016, avgs=0
125/300: dt: 0.9000, rms radial error=154.147, avgs=0
130/300: dt: 0.9000, rms radial error=153.281, avgs=0
135/300: dt: 0.9000, rms radial error=152.420, avgs=0
140/300: dt: 0.9000, rms radial error=151.563, avgs=0
145/300: dt: 0.9000, rms radial error=150.711, avgs=0
150/300: dt: 0.9000, rms radial error=149.863, avgs=0
155/300: dt: 0.9000, rms radial error=149.021, avgs=0
160/300: dt: 0.9000, rms radial error=148.183, avgs=0
165/300: dt: 0.9000, rms radial error=147.350, avgs=0
170/300: dt: 0.9000, rms radial error=146.521, avgs=0
175/300: dt: 0.9000, rms radial error=145.697, avgs=0
180/300: dt: 0.9000, rms radial error=144.877, avgs=0
185/300: dt: 0.9000, rms radial error=144.062, avgs=0
190/300: dt: 0.9000, rms radial error=143.251, avgs=0
195/300: dt: 0.9000, rms radial error=142.445, avgs=0
200/300: dt: 0.9000, rms radial error=141.643, avgs=0
205/300: dt: 0.9000, rms radial error=140.845, avgs=0
210/300: dt: 0.9000, rms radial error=140.052, avgs=0
215/300: dt: 0.9000, rms radial error=139.263, avgs=0
220/300: dt: 0.9000, rms radial error=138.479, avgs=0
225/300: dt: 0.9000, rms radial error=137.699, avgs=0
230/300: dt: 0.9000, rms radial error=136.923, avgs=0
235/300: dt: 0.9000, rms radial error=136.151, avgs=0
240/300: dt: 0.9000, rms radial error=135.384, avgs=0
245/300: dt: 0.9000, rms radial error=134.620, avgs=0
250/300: dt: 0.9000, rms radial error=133.862, avgs=0
255/300: dt: 0.9000, rms radial error=133.107, avgs=0
260/300: dt: 0.9000, rms radial error=132.356, avgs=0
265/300: dt: 0.9000, rms radial error=131.610, avgs=0
270/300: dt: 0.9000, rms radial error=130.868, avgs=0
275/300: dt: 0.9000, rms radial error=130.130, avgs=0
280/300: dt: 0.9000, rms radial error=129.396, avgs=0
285/300: dt: 0.9000, rms radial error=128.667, avgs=0
290/300: dt: 0.9000, rms radial error=127.941, avgs=0
295/300: dt: 0.9000, rms radial error=127.220, avgs=0
300/300: dt: 0.9000, rms radial error=126.502, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17159.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00008
epoch 2 (K=40.0), pass 1, starting sse = 2938.88
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00003
epoch 3 (K=160.0), pass 1, starting sse = 333.43
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00153
epoch 4 (K=640.0), pass 1, starting sse = 29.90
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00469
final distance error %29.86
writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    263.761902
mris_sphere stimesec    0.200969
mris_sphere ru_maxrss   214908
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   31180
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10368
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8212
mris_sphere ru_nivcsw   19294
FSRUNTIME@ mris_sphere  0.0733 hours 1 threads

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

doing quick spherical unfolding.
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
  $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.94 +- 0.58 (0.00-->10.49) (max @ vno 113661 --> 113662)
face area 0.03 +- 0.03 (-0.27-->0.50)

== Number of threads available to mris_sphere for OpenMP = 2 == 
scaling brain by 0.316...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=175.498, avgs=0
005/300: dt: 0.9000, rms radial error=175.242, avgs=0
010/300: dt: 0.9000, rms radial error=174.691, avgs=0
015/300: dt: 0.9000, rms radial error=173.966, avgs=0
020/300: dt: 0.9000, rms radial error=173.141, avgs=0
025/300: dt: 0.9000, rms radial error=172.259, avgs=0
030/300: dt: 0.9000, rms radial error=171.346, avgs=0
035/300: dt: 0.9000, rms radial error=170.415, avgs=0
040/300: dt: 0.9000, rms radial error=169.478, avgs=0
045/300: dt: 0.9000, rms radial error=168.543, avgs=0
050/300: dt: 0.9000, rms radial error=167.608, avgs=0
055/300: dt: 0.9000, rms radial error=166.675, avgs=0
060/300: dt: 0.9000, rms radial error=165.744, avgs=0
065/300: dt: 0.9000, rms radial error=164.817, avgs=0
070/300: dt: 0.9000, rms radial error=163.893, avgs=0
075/300: dt: 0.9000, rms radial error=162.974, avgs=0
080/300: dt: 0.9000, rms radial error=162.058, avgs=0
085/300: dt: 0.9000, rms radial error=161.146, avgs=0
090/300: dt: 0.9000, rms radial error=160.240, avgs=0
095/300: dt: 0.9000, rms radial error=159.338, avgs=0
100/300: dt: 0.9000, rms radial error=158.440, avgs=0
105/300: dt: 0.9000, rms radial error=157.547, avgs=0
110/300: dt: 0.9000, rms radial error=156.659, avgs=0
115/300: dt: 0.9000, rms radial error=155.780, avgs=0
120/300: dt: 0.9000, rms radial error=154.905, avgs=0
125/300: dt: 0.9000, rms radial error=154.035, avgs=0
130/300: dt: 0.9000, rms radial error=153.169, avgs=0
135/300: dt: 0.9000, rms radial error=152.309, avgs=0
140/300: dt: 0.9000, rms radial error=151.453, avgs=0
145/300: dt: 0.9000, rms radial error=150.602, avgs=0
150/300: dt: 0.9000, rms radial error=149.755, avgs=0
155/300: dt: 0.9000, rms radial error=148.914, avgs=0
160/300: dt: 0.9000, rms radial error=148.077, avgs=0
165/300: dt: 0.9000, rms radial error=147.245, avgs=0
170/300: dt: 0.9000, rms radial error=146.417, avgs=0
175/300: dt: 0.9000, rms radial error=145.594, avgs=0
180/300: dt: 0.9000, rms radial error=144.776, avgs=0
185/300: dt: 0.9000, rms radial error=143.962, avgs=0
190/300: dt: 0.9000, rms radial error=143.152, avgs=0
195/300: dt: 0.9000, rms radial error=142.347, avgs=0
200/300: dt: 0.9000, rms radial error=141.546, avgs=0
205/300: dt: 0.9000, rms radial error=140.750, avgs=0
210/300: dt: 0.9000, rms radial error=139.958, avgs=0
215/300: dt: 0.9000, rms radial error=139.171, avgs=0
220/300: dt: 0.9000, rms radial error=138.388, avgs=0
225/300: dt: 0.9000, rms radial error=137.609, avgs=0
230/300: dt: 0.9000, rms radial error=136.834, avgs=0
235/300: dt: 0.9000, rms radial error=136.064, avgs=0
240/300: dt: 0.9000, rms radial error=135.298, avgs=0
245/300: dt: 0.9000, rms radial error=134.537, avgs=0
250/300: dt: 0.9000, rms radial error=133.780, avgs=0
255/300: dt: 0.9000, rms radial error=133.028, avgs=0
260/300: dt: 0.9000, rms radial error=132.280, avgs=0
265/300: dt: 0.9000, rms radial error=131.536, avgs=0
270/300: dt: 0.9000, rms radial error=130.797, avgs=0
275/300: dt: 0.9000, rms radial error=130.062, avgs=0
280/300: dt: 0.9000, rms radial error=129.331, avgs=0
285/300: dt: 0.9000, rms radial error=128.604, avgs=0
290/300: dt: 0.9000, rms radial error=127.881, avgs=0
295/300: dt: 0.9000, rms radial error=127.162, avgs=0
300/300: dt: 0.9000, rms radial error=126.446, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17896.21
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 3041.67
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00018
epoch 3 (K=160.0), pass 1, starting sse = 337.71
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.02/10 = 0.00223
epoch 4 (K=640.0), pass 1, starting sse = 33.54
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00416
final distance error %27.59
writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.07 hours
mris_sphere utimesec    272.089636
mris_sphere stimesec    0.153976
mris_sphere ru_maxrss   224052
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   32441
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10792
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    8146
mris_sphere ru_nivcsw   18974
FSRUNTIME@ mris_sphere  0.0747 hours 1 threads
PIDs (15951 15954) completed and logs appended.
#--------------------------------------------
#@# Fix Topology Copy lh Sat Oct  7 19:56:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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


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

#--------------------------------------------
#@# Fix Topology Copy rh Sat Oct  7 19:56:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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


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

#@# Fix Topology lh Sat Oct  7 19:56:33 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 lh 

#@# Fix Topology rh Sat Oct  7 19:56:34 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 rh 

Waiting for PID 16152 of (16152 16155) to complete...
Waiting for PID 16155 of (16152 16155) to complete...

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 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=-164 (nv=146666, nf=293660, ne=440490, g=83)
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 10 iterations
marking ambiguous vertices...
8579 ambiguous faces found in tessellation
segmenting defects...
91 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 57 into 52
      -merging segment 79 into 73
      -merging segment 86 into 85
88 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.1234  (-4.5617)
      -vertex     loglikelihood: -5.9425  (-2.9713)
      -normal dot loglikelihood: -3.5911  (-3.5911)
      -quad curv  loglikelihood: -6.1749  (-3.0875)
      Total Loglikelihood : -24.8320

CORRECTING DEFECT 0 (vertices=23, convex hull=45, v0=17)
After retessellation of defect 0 (v0=17), euler #=-84 (141308,421372,279980) : difference with theory (-85) = -1 

CORRECTING DEFECT 1 (vertices=26, convex hull=63, v0=1685)
After retessellation of defect 1 (v0=1685), euler #=-83 (141319,421429,280027) : difference with theory (-84) = -1 

CORRECTING DEFECT 2 (vertices=17, convex hull=46, v0=6122)
After retessellation of defect 2 (v0=6122), euler #=-82 (141327,421466,280057) : difference with theory (-83) = -1 

CORRECTING DEFECT 3 (vertices=71, convex hull=88, v0=6942)
After retessellation of defect 3 (v0=6942), euler #=-81 (141359,421602,280162) : difference with theory (-82) = -1 

CORRECTING DEFECT 4 (vertices=178, convex hull=145, v0=10128)
After retessellation of defect 4 (v0=10128), euler #=-82 (141406,421847,280359) : difference with theory (-81) = 1 

CORRECTING DEFECT 5 (vertices=19, convex hull=22, v0=10178)
After retessellation of defect 5 (v0=10178), euler #=-81 (141408,421861,280372) : difference with theory (-80) = 1 

CORRECTING DEFECT 6 (vertices=48, convex hull=66, v0=13323)
After retessellation of defect 6 (v0=13323), euler #=-80 (141426,421940,280434) : difference with theory (-79) = 1 

CORRECTING DEFECT 7 (vertices=35, convex hull=68, v0=14449)
After retessellation of defect 7 (v0=14449), euler #=-79 (141438,422005,280488) : difference with theory (-78) = 1 

CORRECTING DEFECT 8 (vertices=33, convex hull=66, v0=14646)
After retessellation of defect 8 (v0=14646), euler #=-78 (141458,422092,280556) : difference with theory (-77) = 1 

CORRECTING DEFECT 9 (vertices=52, convex hull=97, v0=24211)
After retessellation of defect 9 (v0=24211), euler #=-77 (141484,422219,280658) : difference with theory (-76) = 1 

CORRECTING DEFECT 10 (vertices=73, convex hull=28, v0=25033)
After retessellation of defect 10 (v0=25033), euler #=-76 (141488,422242,280678) : difference with theory (-75) = 1 

CORRECTING DEFECT 11 (vertices=68, convex hull=86, v0=26771)
After retessellation of defect 11 (v0=26771), euler #=-76 (141502,422330,280752) : difference with theory (-74) = 2 

CORRECTING DEFECT 12 (vertices=18, convex hull=55, v0=27271)
After retessellation of defect 12 (v0=27271), euler #=-75 (141511,422377,280791) : difference with theory (-73) = 2 

CORRECTING DEFECT 13 (vertices=27, convex hull=57, v0=28558)
After retessellation of defect 13 (v0=28558), euler #=-74 (141522,422431,280835) : difference with theory (-72) = 2 

CORRECTING DEFECT 14 (vertices=180, convex hull=153, v0=34278)
After retessellation of defect 14 (v0=34278), euler #=-74 (141595,422728,281059) : difference with theory (-71) = 3 

CORRECTING DEFECT 15 (vertices=70, convex hull=78, v0=39550)
After retessellation of defect 15 (v0=39550), euler #=-73 (141619,422832,281140) : difference with theory (-70) = 3 

CORRECTING DEFECT 16 (vertices=39, convex hull=60, v0=39649)
After retessellation of defect 16 (v0=39649), euler #=-72 (141637,422909,281200) : difference with theory (-69) = 3 

CORRECTING DEFECT 17 (vertices=6, convex hull=24, v0=41241)
After retessellation of defect 17 (v0=41241), euler #=-71 (141638,422919,281210) : difference with theory (-68) = 3 

CORRECTING DEFECT 18 (vertices=78, convex hull=105, v0=42535)
After retessellation of defect 18 (v0=42535), euler #=-70 (141654,423012,281288) : difference with theory (-67) = 3 

CORRECTING DEFECT 19 (vertices=44, convex hull=82, v0=42850)
After retessellation of defect 19 (v0=42850), euler #=-69 (141678,423118,281371) : difference with theory (-66) = 3 

CORRECTING DEFECT 20 (vertices=6, convex hull=23, v0=42962)
After retessellation of defect 20 (v0=42962), euler #=-68 (141680,423130,281382) : difference with theory (-65) = 3 

CORRECTING DEFECT 21 (vertices=18, convex hull=47, v0=43252)
After retessellation of defect 21 (v0=43252), euler #=-67 (141689,423172,281416) : difference with theory (-64) = 3 

CORRECTING DEFECT 22 (vertices=43, convex hull=72, v0=43874)
After retessellation of defect 22 (v0=43874), euler #=-66 (141710,423268,281492) : difference with theory (-63) = 3 

CORRECTING DEFECT 23 (vertices=90, convex hull=147, v0=44052)
After retessellation of defect 23 (v0=44052), euler #=-65 (141757,423472,281650) : difference with theory (-62) = 3 

CORRECTING DEFECT 24 (vertices=53, convex hull=36, v0=45177)
After retessellation of defect 24 (v0=45177), euler #=-64 (141767,423514,281683) : difference with theory (-61) = 3 

CORRECTING DEFECT 25 (vertices=63, convex hull=28, v0=47909)
After retessellation of defect 25 (v0=47909), euler #=-63 (141772,423537,281702) : difference with theory (-60) = 3 

CORRECTING DEFECT 26 (vertices=13, convex hull=9, v0=48597)
After retessellation of defect 26 (v0=48597), euler #=-62 (141773,423541,281706) : difference with theory (-59) = 3 

CORRECTING DEFECT 27 (vertices=35, convex hull=71, v0=50832)
After retessellation of defect 27 (v0=50832), euler #=-61 (141788,423616,281767) : difference with theory (-58) = 3 

CORRECTING DEFECT 28 (vertices=112, convex hull=36, v0=52165)
After retessellation of defect 28 (v0=52165), euler #=-60 (141796,423656,281800) : difference with theory (-57) = 3 

CORRECTING DEFECT 29 (vertices=27, convex hull=60, v0=53452)
After retessellation of defect 29 (v0=53452), euler #=-59 (141809,423717,281849) : difference with theory (-56) = 3 

CORRECTING DEFECT 30 (vertices=21, convex hull=52, v0=59242)
After retessellation of defect 30 (v0=59242), euler #=-58 (141818,423764,281888) : difference with theory (-55) = 3 

CORRECTING DEFECT 31 (vertices=26, convex hull=61, v0=61418)
After retessellation of defect 31 (v0=61418), euler #=-57 (141833,423831,281941) : difference with theory (-54) = 3 

CORRECTING DEFECT 32 (vertices=14, convex hull=18, v0=66690)
After retessellation of defect 32 (v0=66690), euler #=-56 (141836,423844,281952) : difference with theory (-53) = 3 

CORRECTING DEFECT 33 (vertices=575, convex hull=220, v0=68481)
After retessellation of defect 33 (v0=68481), euler #=-55 (141990,424407,282362) : difference with theory (-52) = 3 

CORRECTING DEFECT 34 (vertices=21, convex hull=23, v0=69531)
After retessellation of defect 34 (v0=69531), euler #=-54 (141996,424435,282385) : difference with theory (-51) = 3 

CORRECTING DEFECT 35 (vertices=23, convex hull=35, v0=71638)
After retessellation of defect 35 (v0=71638), euler #=-53 (142001,424462,282408) : difference with theory (-50) = 3 

CORRECTING DEFECT 36 (vertices=6, convex hull=14, v0=72692)
After retessellation of defect 36 (v0=72692), euler #=-52 (142002,424470,282416) : difference with theory (-49) = 3 

CORRECTING DEFECT 37 (vertices=13, convex hull=21, v0=74327)
After retessellation of defect 37 (v0=74327), euler #=-51 (142005,424485,282429) : difference with theory (-48) = 3 

CORRECTING DEFECT 38 (vertices=80, convex hull=71, v0=75826)
After retessellation of defect 38 (v0=75826), euler #=-50 (142014,424541,282477) : difference with theory (-47) = 3 

CORRECTING DEFECT 39 (vertices=26, convex hull=71, v0=78286)
After retessellation of defect 39 (v0=78286), euler #=-49 (142030,424618,282539) : difference with theory (-46) = 3 

CORRECTING DEFECT 40 (vertices=51, convex hull=78, v0=86176)
After retessellation of defect 40 (v0=86176), euler #=-48 (142063,424755,282644) : difference with theory (-45) = 3 

CORRECTING DEFECT 41 (vertices=64, convex hull=23, v0=87861)
After retessellation of defect 41 (v0=87861), euler #=-47 (142068,424776,282661) : difference with theory (-44) = 3 

CORRECTING DEFECT 42 (vertices=48, convex hull=21, v0=95847)
After retessellation of defect 42 (v0=95847), euler #=-46 (142071,424793,282676) : difference with theory (-43) = 3 

CORRECTING DEFECT 43 (vertices=29, convex hull=54, v0=97158)
After retessellation of defect 43 (v0=97158), euler #=-45 (142085,424855,282725) : difference with theory (-42) = 3 

CORRECTING DEFECT 44 (vertices=34, convex hull=66, v0=98484)
After retessellation of defect 44 (v0=98484), euler #=-44 (142103,424938,282791) : difference with theory (-41) = 3 

CORRECTING DEFECT 45 (vertices=11, convex hull=30, v0=100649)
After retessellation of defect 45 (v0=100649), euler #=-43 (142105,424954,282806) : difference with theory (-40) = 3 

CORRECTING DEFECT 46 (vertices=10, convex hull=22, v0=103118)
After retessellation of defect 46 (v0=103118), euler #=-42 (142106,424965,282817) : difference with theory (-39) = 3 

CORRECTING DEFECT 47 (vertices=162, convex hull=143, v0=104539)
After retessellation of defect 47 (v0=104539), euler #=-41 (142164,425199,282994) : difference with theory (-38) = 3 

CORRECTING DEFECT 48 (vertices=64, convex hull=36, v0=105232)
After retessellation of defect 48 (v0=105232), euler #=-40 (142174,425239,283025) : difference with theory (-37) = 3 

CORRECTING DEFECT 49 (vertices=21, convex hull=29, v0=106628)
After retessellation of defect 49 (v0=106628), euler #=-39 (142179,425265,283047) : difference with theory (-36) = 3 

CORRECTING DEFECT 50 (vertices=16, convex hull=37, v0=106689)
After retessellation of defect 50 (v0=106689), euler #=-38 (142185,425298,283075) : difference with theory (-35) = 3 

CORRECTING DEFECT 51 (vertices=50, convex hull=47, v0=106853)
After retessellation of defect 51 (v0=106853), euler #=-37 (142208,425386,283141) : difference with theory (-34) = 3 

CORRECTING DEFECT 52 (vertices=71, convex hull=120, v0=107428)
After retessellation of defect 52 (v0=107428), euler #=-35 (142230,425507,283242) : difference with theory (-33) = 2 

CORRECTING DEFECT 53 (vertices=382, convex hull=289, v0=107445)
After retessellation of defect 53 (v0=107445), euler #=-34 (142338,425997,283625) : difference with theory (-32) = 2 

CORRECTING DEFECT 54 (vertices=33, convex hull=62, v0=109421)
After retessellation of defect 54 (v0=109421), euler #=-33 (142359,426083,283691) : difference with theory (-31) = 2 

CORRECTING DEFECT 55 (vertices=25, convex hull=55, v0=109545)
After retessellation of defect 55 (v0=109545), euler #=-32 (142370,426133,283731) : difference with theory (-30) = 2 

CORRECTING DEFECT 56 (vertices=20, convex hull=26, v0=111727)
After retessellation of defect 56 (v0=111727), euler #=-31 (142373,426148,283744) : difference with theory (-29) = 2 

CORRECTING DEFECT 57 (vertices=20, convex hull=33, v0=112706)
After retessellation of defect 57 (v0=112706), euler #=-30 (142378,426176,283768) : difference with theory (-28) = 2 

CORRECTING DEFECT 58 (vertices=24, convex hull=55, v0=114799)
After retessellation of defect 58 (v0=114799), euler #=-29 (142387,426223,283807) : difference with theory (-27) = 2 

CORRECTING DEFECT 59 (vertices=80, convex hull=119, v0=114936)
After retessellation of defect 59 (v0=114936), euler #=-28 (142403,426330,283899) : difference with theory (-26) = 2 

CORRECTING DEFECT 60 (vertices=79, convex hull=94, v0=115839)
After retessellation of defect 60 (v0=115839), euler #=-27 (142445,426494,284022) : difference with theory (-25) = 2 

CORRECTING DEFECT 61 (vertices=20, convex hull=32, v0=116240)
After retessellation of defect 61 (v0=116240), euler #=-26 (142450,426519,284043) : difference with theory (-24) = 2 

CORRECTING DEFECT 62 (vertices=132, convex hull=46, v0=118208)
After retessellation of defect 62 (v0=118208), euler #=-25 (142463,426577,284089) : difference with theory (-23) = 2 

CORRECTING DEFECT 63 (vertices=7, convex hull=16, v0=118247)
After retessellation of defect 63 (v0=118247), euler #=-24 (142463,426582,284095) : difference with theory (-22) = 2 

CORRECTING DEFECT 64 (vertices=27, convex hull=58, v0=118935)
After retessellation of defect 64 (v0=118935), euler #=-23 (142475,426641,284143) : difference with theory (-21) = 2 

CORRECTING DEFECT 65 (vertices=12, convex hull=27, v0=119736)
After retessellation of defect 65 (v0=119736), euler #=-22 (142478,426657,284157) : difference with theory (-20) = 2 

CORRECTING DEFECT 66 (vertices=18, convex hull=17, v0=119890)
After retessellation of defect 66 (v0=119890), euler #=-21 (142481,426669,284167) : difference with theory (-19) = 2 

CORRECTING DEFECT 67 (vertices=25, convex hull=62, v0=120312)
After retessellation of defect 67 (v0=120312), euler #=-20 (142489,426715,284206) : difference with theory (-18) = 2 

CORRECTING DEFECT 68 (vertices=63, convex hull=48, v0=120780)
After retessellation of defect 68 (v0=120780), euler #=-19 (142499,426767,284249) : difference with theory (-17) = 2 

CORRECTING DEFECT 69 (vertices=428, convex hull=166, v0=121501)
After retessellation of defect 69 (v0=121501), euler #=-18 (142607,427185,284560) : difference with theory (-16) = 2 

CORRECTING DEFECT 70 (vertices=48, convex hull=77, v0=122014)
After retessellation of defect 70 (v0=122014), euler #=-17 (142630,427292,284645) : difference with theory (-15) = 2 

CORRECTING DEFECT 71 (vertices=43, convex hull=86, v0=123135)
After retessellation of defect 71 (v0=123135), euler #=-16 (142645,427374,284713) : difference with theory (-14) = 2 

CORRECTING DEFECT 72 (vertices=83, convex hull=129, v0=123368)
After retessellation of defect 72 (v0=123368), euler #=-14 (142683,427544,284847) : difference with theory (-13) = 1 

CORRECTING DEFECT 73 (vertices=30, convex hull=76, v0=126173)
After retessellation of defect 73 (v0=126173), euler #=-13 (142698,427622,284911) : difference with theory (-12) = 1 

CORRECTING DEFECT 74 (vertices=21, convex hull=44, v0=126703)
After retessellation of defect 74 (v0=126703), euler #=-12 (142701,427647,284934) : difference with theory (-11) = 1 

CORRECTING DEFECT 75 (vertices=15, convex hull=56, v0=126737)
After retessellation of defect 75 (v0=126737), euler #=-11 (142710,427698,284977) : difference with theory (-10) = 1 

CORRECTING DEFECT 76 (vertices=28, convex hull=25, v0=127604)
After retessellation of defect 76 (v0=127604), euler #=-10 (142712,427712,284990) : difference with theory (-9) = 1 

CORRECTING DEFECT 77 (vertices=113, convex hull=72, v0=128238)
After retessellation of defect 77 (v0=128238), euler #=-9 (142734,427809,285066) : difference with theory (-8) = 1 

CORRECTING DEFECT 78 (vertices=24, convex hull=59, v0=131664)
After retessellation of defect 78 (v0=131664), euler #=-8 (142745,427867,285114) : difference with theory (-7) = 1 

CORRECTING DEFECT 79 (vertices=129, convex hull=159, v0=133466)
After retessellation of defect 79 (v0=133466), euler #=-7 (142777,428033,285249) : difference with theory (-6) = 1 

CORRECTING DEFECT 80 (vertices=23, convex hull=51, v0=137233)
After retessellation of defect 80 (v0=137233), euler #=-6 (142787,428081,285288) : difference with theory (-5) = 1 

CORRECTING DEFECT 81 (vertices=32, convex hull=64, v0=137784)
After retessellation of defect 81 (v0=137784), euler #=-5 (142796,428134,285333) : difference with theory (-4) = 1 

CORRECTING DEFECT 82 (vertices=139, convex hull=105, v0=138044)
After retessellation of defect 82 (v0=138044), euler #=-4 (142845,428330,285481) : difference with theory (-3) = 1 

CORRECTING DEFECT 83 (vertices=102, convex hull=136, v0=138750)
After retessellation of defect 83 (v0=138750), euler #=-2 (142865,428461,285594) : difference with theory (-2) = 0 

CORRECTING DEFECT 84 (vertices=50, convex hull=94, v0=142269)
After retessellation of defect 84 (v0=142269), euler #=-1 (142892,428584,285691) : difference with theory (-1) = 0 

CORRECTING DEFECT 85 (vertices=33, convex hull=73, v0=145238)
After retessellation of defect 85 (v0=145238), euler #=0 (142910,428666,285756) : difference with theory (0) = 0 

CORRECTING DEFECT 86 (vertices=30, convex hull=91, v0=145290)
After retessellation of defect 86 (v0=145290), euler #=1 (142925,428751,285827) : difference with theory (1) = 0 

CORRECTING DEFECT 87 (vertices=22, convex hull=48, v0=145393)
After retessellation of defect 87 (v0=145393), euler #=2 (142936,428802,285868) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.25 (0.05-->8.44) (max @ vno 133060 --> 136991)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.25 (0.05-->8.44) (max @ vno 133060 --> 136991)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
286 mutations (33.4%), 570 crossovers (66.6%), 256 vertices were eliminated
building final representation...
3730 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=142936, nf=285868, ne=428802, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 55.0 minutes
0 defective edges
removing intersecting faces
000: 602 intersecting
001: 10 intersecting
mris_fix_topology utimesec    3302.841891
mris_fix_topology stimesec    0.292955
mris_fix_topology ru_maxrss   458016
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   58086
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  30984
mris_fix_topology ru_oublock  13976
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    565
mris_fix_topology ru_nivcsw   8875
FSRUNTIME@ mris_fix_topology lh  0.9172 hours 1 threads

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050660 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=-186 (nv=152648, nf=305668, ne=458502, g=94)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 13 iterations
marking ambiguous vertices...
11866 ambiguous faces found in tessellation
segmenting defects...
112 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 4 into 3
      -merging segment 9 into 7
      -merging segment 23 into 22
      -merging segment 73 into 65
      -merging segment 82 into 69
      -merging segment 88 into 69
      -merging segment 81 into 76
      -merging segment 92 into 89
      -merging segment 95 into 89
      -merging segment 102 into 99
      -merging segment 101 into 99
      -merging segment 103 into 99
100 defects to be corrected 
0 vertices coincident
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.2148  (-4.6074)
      -vertex     loglikelihood: -5.9062  (-2.9531)
      -normal dot loglikelihood: -3.5490  (-3.5490)
      -quad curv  loglikelihood: -6.5135  (-3.2568)
      Total Loglikelihood : -25.1836

CORRECTING DEFECT 0 (vertices=60, convex hull=70, v0=159)
After retessellation of defect 0 (v0=159), euler #=-104 (145361,433107,287642) : difference with theory (-97) = 7 

CORRECTING DEFECT 1 (vertices=27, convex hull=25, v0=1319)
After retessellation of defect 1 (v0=1319), euler #=-103 (145367,433135,287665) : difference with theory (-96) = 7 

CORRECTING DEFECT 2 (vertices=32, convex hull=70, v0=1549)
After retessellation of defect 2 (v0=1549), euler #=-102 (145381,433203,287720) : difference with theory (-95) = 7 

CORRECTING DEFECT 3 (vertices=85, convex hull=137, v0=5450)
After retessellation of defect 3 (v0=5450), euler #=-100 (145411,433353,287842) : difference with theory (-94) = 6 

CORRECTING DEFECT 4 (vertices=34, convex hull=36, v0=7920)
After retessellation of defect 4 (v0=7920), euler #=-99 (145412,433372,287861) : difference with theory (-93) = 6 

CORRECTING DEFECT 5 (vertices=297, convex hull=185, v0=10734)
After retessellation of defect 5 (v0=10734), euler #=-98 (145488,433695,288109) : difference with theory (-92) = 6 

CORRECTING DEFECT 6 (vertices=80, convex hull=88, v0=11151)
After retessellation of defect 6 (v0=11151), euler #=-96 (145508,433795,288191) : difference with theory (-91) = 5 

CORRECTING DEFECT 7 (vertices=68, convex hull=38, v0=11271)
After retessellation of defect 7 (v0=11271), euler #=-95 (145511,433819,288213) : difference with theory (-90) = 5 

CORRECTING DEFECT 8 (vertices=7, convex hull=17, v0=19741)
After retessellation of defect 8 (v0=19741), euler #=-94 (145511,433821,288216) : difference with theory (-89) = 5 

CORRECTING DEFECT 9 (vertices=26, convex hull=20, v0=20437)
After retessellation of defect 9 (v0=20437), euler #=-93 (145513,433835,288229) : difference with theory (-88) = 5 

CORRECTING DEFECT 10 (vertices=25, convex hull=55, v0=20820)
After retessellation of defect 10 (v0=20820), euler #=-92 (145522,433882,288268) : difference with theory (-87) = 5 

CORRECTING DEFECT 11 (vertices=28, convex hull=59, v0=21012)
After retessellation of defect 11 (v0=21012), euler #=-91 (145530,433929,288308) : difference with theory (-86) = 5 

CORRECTING DEFECT 12 (vertices=50, convex hull=95, v0=21166)
After retessellation of defect 12 (v0=21166), euler #=-90 (145547,434017,288380) : difference with theory (-85) = 5 

CORRECTING DEFECT 13 (vertices=74, convex hull=87, v0=21556)
After retessellation of defect 13 (v0=21556), euler #=-89 (145582,434159,288488) : difference with theory (-84) = 5 

CORRECTING DEFECT 14 (vertices=92, convex hull=133, v0=22318)
After retessellation of defect 14 (v0=22318), euler #=-88 (145625,434341,288628) : difference with theory (-83) = 5 

CORRECTING DEFECT 15 (vertices=28, convex hull=59, v0=24583)
After retessellation of defect 15 (v0=24583), euler #=-87 (145635,434390,288668) : difference with theory (-82) = 5 

CORRECTING DEFECT 16 (vertices=25, convex hull=59, v0=24624)
After retessellation of defect 16 (v0=24624), euler #=-86 (145644,434441,288711) : difference with theory (-81) = 5 

CORRECTING DEFECT 17 (vertices=5, convex hull=19, v0=24941)
After retessellation of defect 17 (v0=24941), euler #=-85 (145644,434445,288716) : difference with theory (-80) = 5 

CORRECTING DEFECT 18 (vertices=50, convex hull=65, v0=25277)
After retessellation of defect 18 (v0=25277), euler #=-84 (145674,434559,288801) : difference with theory (-79) = 5 

CORRECTING DEFECT 19 (vertices=34, convex hull=56, v0=28661)
After retessellation of defect 19 (v0=28661), euler #=-83 (145683,434607,288841) : difference with theory (-78) = 5 

CORRECTING DEFECT 20 (vertices=15, convex hull=45, v0=28924)
After retessellation of defect 20 (v0=28924), euler #=-81 (145687,434638,288870) : difference with theory (-77) = 4 

CORRECTING DEFECT 21 (vertices=43, convex hull=65, v0=41923)
After retessellation of defect 21 (v0=41923), euler #=-80 (145712,434741,288949) : difference with theory (-76) = 4 

CORRECTING DEFECT 22 (vertices=14, convex hull=26, v0=42321)
After retessellation of defect 22 (v0=42321), euler #=-79 (145714,434754,288961) : difference with theory (-75) = 4 

CORRECTING DEFECT 23 (vertices=58, convex hull=100, v0=50977)
After retessellation of defect 23 (v0=50977), euler #=-78 (145742,434884,289064) : difference with theory (-74) = 4 

CORRECTING DEFECT 24 (vertices=17, convex hull=54, v0=55856)
After retessellation of defect 24 (v0=55856), euler #=-77 (145751,434932,289104) : difference with theory (-73) = 4 

CORRECTING DEFECT 25 (vertices=24, convex hull=59, v0=62724)
After retessellation of defect 25 (v0=62724), euler #=-76 (145762,434989,289151) : difference with theory (-72) = 4 

CORRECTING DEFECT 26 (vertices=20, convex hull=23, v0=62791)
After retessellation of defect 26 (v0=62791), euler #=-75 (145768,435014,289171) : difference with theory (-71) = 4 

CORRECTING DEFECT 27 (vertices=47, convex hull=34, v0=63173)
After retessellation of defect 27 (v0=63173), euler #=-74 (145772,435036,289190) : difference with theory (-70) = 4 

CORRECTING DEFECT 28 (vertices=18, convex hull=18, v0=63194)
After retessellation of defect 28 (v0=63194), euler #=-73 (145775,435051,289203) : difference with theory (-69) = 4 

CORRECTING DEFECT 29 (vertices=133, convex hull=164, v0=63942)
After retessellation of defect 29 (v0=63942), euler #=-72 (145789,435170,289309) : difference with theory (-68) = 4 

CORRECTING DEFECT 30 (vertices=5, convex hull=18, v0=65085)
After retessellation of defect 30 (v0=65085), euler #=-71 (145790,435177,289316) : difference with theory (-67) = 4 

CORRECTING DEFECT 31 (vertices=1268, convex hull=445, v0=66465)
L defect detected...
After retessellation of defect 31 (v0=66465), euler #=-70 (146007,436039,289962) : difference with theory (-66) = 4 

CORRECTING DEFECT 32 (vertices=23, convex hull=53, v0=66607)
After retessellation of defect 32 (v0=66607), euler #=-69 (146019,436092,290004) : difference with theory (-65) = 4 

CORRECTING DEFECT 33 (vertices=56, convex hull=67, v0=66918)
After retessellation of defect 33 (v0=66918), euler #=-68 (146029,436153,290056) : difference with theory (-64) = 4 

CORRECTING DEFECT 34 (vertices=19, convex hull=44, v0=68053)
After retessellation of defect 34 (v0=68053), euler #=-67 (146038,436195,290090) : difference with theory (-63) = 4 

CORRECTING DEFECT 35 (vertices=50, convex hull=86, v0=69210)
After retessellation of defect 35 (v0=69210), euler #=-66 (146055,436279,290158) : difference with theory (-62) = 4 

CORRECTING DEFECT 36 (vertices=32, convex hull=60, v0=71482)
After retessellation of defect 36 (v0=71482), euler #=-65 (146069,436346,290212) : difference with theory (-61) = 4 

CORRECTING DEFECT 37 (vertices=15, convex hull=32, v0=71689)
After retessellation of defect 37 (v0=71689), euler #=-64 (146070,436360,290226) : difference with theory (-60) = 4 

CORRECTING DEFECT 38 (vertices=19, convex hull=34, v0=74222)
After retessellation of defect 38 (v0=74222), euler #=-63 (146070,436375,290242) : difference with theory (-59) = 4 

CORRECTING DEFECT 39 (vertices=91, convex hull=95, v0=74550)
After retessellation of defect 39 (v0=74550), euler #=-63 (146109,436539,290367) : difference with theory (-58) = 5 

CORRECTING DEFECT 40 (vertices=17, convex hull=17, v0=75738)
After retessellation of defect 40 (v0=75738), euler #=-62 (146111,436550,290377) : difference with theory (-57) = 5 

CORRECTING DEFECT 41 (vertices=36, convex hull=68, v0=78220)
After retessellation of defect 41 (v0=78220), euler #=-61 (146135,436646,290450) : difference with theory (-56) = 5 

CORRECTING DEFECT 42 (vertices=7, convex hull=18, v0=81281)
After retessellation of defect 42 (v0=81281), euler #=-60 (146136,436654,290458) : difference with theory (-55) = 5 

CORRECTING DEFECT 43 (vertices=10, convex hull=32, v0=81981)
After retessellation of defect 43 (v0=81981), euler #=-59 (146140,436673,290474) : difference with theory (-54) = 5 

CORRECTING DEFECT 44 (vertices=18, convex hull=46, v0=82612)
After retessellation of defect 44 (v0=82612), euler #=-58 (146148,436714,290508) : difference with theory (-53) = 5 

CORRECTING DEFECT 45 (vertices=5, convex hull=18, v0=83734)
After retessellation of defect 45 (v0=83734), euler #=-57 (146149,436721,290515) : difference with theory (-52) = 5 

CORRECTING DEFECT 46 (vertices=81, convex hull=46, v0=83746)
After retessellation of defect 46 (v0=83746), euler #=-56 (146158,436761,290547) : difference with theory (-51) = 5 

CORRECTING DEFECT 47 (vertices=66, convex hull=38, v0=84607)
After retessellation of defect 47 (v0=84607), euler #=-55 (146170,436810,290585) : difference with theory (-50) = 5 

CORRECTING DEFECT 48 (vertices=16, convex hull=50, v0=84860)
After retessellation of defect 48 (v0=84860), euler #=-54 (146178,436851,290619) : difference with theory (-49) = 5 

CORRECTING DEFECT 49 (vertices=46, convex hull=90, v0=85165)
After retessellation of defect 49 (v0=85165), euler #=-53 (146211,436991,290727) : difference with theory (-48) = 5 

CORRECTING DEFECT 50 (vertices=65, convex hull=26, v0=87077)
After retessellation of defect 50 (v0=87077), euler #=-52 (146214,437005,290739) : difference with theory (-47) = 5 

CORRECTING DEFECT 51 (vertices=12, convex hull=22, v0=87487)
After retessellation of defect 51 (v0=87487), euler #=-51 (146216,437017,290750) : difference with theory (-46) = 5 

CORRECTING DEFECT 52 (vertices=20, convex hull=45, v0=87501)
After retessellation of defect 52 (v0=87501), euler #=-50 (146225,437061,290786) : difference with theory (-45) = 5 

CORRECTING DEFECT 53 (vertices=29, convex hull=51, v0=89393)
After retessellation of defect 53 (v0=89393), euler #=-49 (146244,437138,290845) : difference with theory (-44) = 5 

CORRECTING DEFECT 54 (vertices=25, convex hull=29, v0=93891)
After retessellation of defect 54 (v0=93891), euler #=-48 (146248,437159,290863) : difference with theory (-43) = 5 

CORRECTING DEFECT 55 (vertices=17, convex hull=22, v0=94477)
After retessellation of defect 55 (v0=94477), euler #=-47 (146251,437175,290877) : difference with theory (-42) = 5 

CORRECTING DEFECT 56 (vertices=65, convex hull=89, v0=96058)
After retessellation of defect 56 (v0=96058), euler #=-46 (146279,437295,290970) : difference with theory (-41) = 5 

CORRECTING DEFECT 57 (vertices=12, convex hull=22, v0=98488)
After retessellation of defect 57 (v0=98488), euler #=-45 (146281,437309,290983) : difference with theory (-40) = 5 

CORRECTING DEFECT 58 (vertices=68, convex hull=49, v0=101623)
After retessellation of defect 58 (v0=101623), euler #=-44 (146290,437355,291021) : difference with theory (-39) = 5 

CORRECTING DEFECT 59 (vertices=19, convex hull=52, v0=103510)
After retessellation of defect 59 (v0=103510), euler #=-43 (146302,437413,291068) : difference with theory (-38) = 5 

CORRECTING DEFECT 60 (vertices=10, convex hull=34, v0=103829)
After retessellation of defect 60 (v0=103829), euler #=-42 (146305,437432,291085) : difference with theory (-37) = 5 

CORRECTING DEFECT 61 (vertices=55, convex hull=103, v0=105005)
After retessellation of defect 61 (v0=105005), euler #=-41 (146343,437590,291206) : difference with theory (-36) = 5 

CORRECTING DEFECT 62 (vertices=110, convex hull=73, v0=105585)
After retessellation of defect 62 (v0=105585), euler #=-39 (146366,437689,291284) : difference with theory (-35) = 4 

CORRECTING DEFECT 63 (vertices=27, convex hull=62, v0=105723)
After retessellation of defect 63 (v0=105723), euler #=-38 (146377,437746,291331) : difference with theory (-34) = 4 

CORRECTING DEFECT 64 (vertices=60, convex hull=69, v0=105784)
After retessellation of defect 64 (v0=105784), euler #=-37 (146408,437872,291427) : difference with theory (-33) = 4 

CORRECTING DEFECT 65 (vertices=9, convex hull=14, v0=106251)
After retessellation of defect 65 (v0=106251), euler #=-36 (146409,437879,291434) : difference with theory (-32) = 4 

CORRECTING DEFECT 66 (vertices=795, convex hull=417, v0=108005)
L defect detected...
After retessellation of defect 66 (v0=108005), euler #=-35 (146546,438528,291947) : difference with theory (-31) = 4 

CORRECTING DEFECT 67 (vertices=28, convex hull=57, v0=108320)
After retessellation of defect 67 (v0=108320), euler #=-34 (146556,438580,291990) : difference with theory (-30) = 4 

CORRECTING DEFECT 68 (vertices=7, convex hull=15, v0=109352)
After retessellation of defect 68 (v0=109352), euler #=-33 (146557,438586,291996) : difference with theory (-29) = 4 

CORRECTING DEFECT 69 (vertices=46, convex hull=64, v0=110189)
After retessellation of defect 69 (v0=110189), euler #=-32 (146581,438684,292071) : difference with theory (-28) = 4 

CORRECTING DEFECT 70 (vertices=131, convex hull=61, v0=111617)
After retessellation of defect 70 (v0=111617), euler #=-32 (146605,438787,292150) : difference with theory (-27) = 5 

CORRECTING DEFECT 71 (vertices=32, convex hull=36, v0=111797)
After retessellation of defect 71 (v0=111797), euler #=-31 (146608,438808,292169) : difference with theory (-26) = 5 

CORRECTING DEFECT 72 (vertices=82, convex hull=139, v0=112405)
After retessellation of defect 72 (v0=112405), euler #=-29 (146656,439014,292329) : difference with theory (-25) = 4 

CORRECTING DEFECT 73 (vertices=49, convex hull=87, v0=117091)
After retessellation of defect 73 (v0=117091), euler #=-29 (146685,439143,292429) : difference with theory (-24) = 5 

CORRECTING DEFECT 74 (vertices=110, convex hull=34, v0=117789)
After retessellation of defect 74 (v0=117789), euler #=-28 (146695,439182,292459) : difference with theory (-23) = 5 

CORRECTING DEFECT 75 (vertices=22, convex hull=45, v0=117844)
After retessellation of defect 75 (v0=117844), euler #=-27 (146698,439208,292483) : difference with theory (-22) = 5 

CORRECTING DEFECT 76 (vertices=24, convex hull=15, v0=118215)
After retessellation of defect 76 (v0=118215), euler #=-26 (146699,439216,292491) : difference with theory (-21) = 5 

CORRECTING DEFECT 77 (vertices=112, convex hull=80, v0=122118)
After retessellation of defect 77 (v0=122118), euler #=-25 (146738,439372,292609) : difference with theory (-20) = 5 

CORRECTING DEFECT 78 (vertices=56, convex hull=39, v0=123226)
After retessellation of defect 78 (v0=123226), euler #=-24 (146739,439390,292627) : difference with theory (-19) = 5 

CORRECTING DEFECT 79 (vertices=32, convex hull=65, v0=123827)
After retessellation of defect 79 (v0=123827), euler #=-23 (146759,439479,292697) : difference with theory (-18) = 5 

CORRECTING DEFECT 80 (vertices=36, convex hull=21, v0=124386)
After retessellation of defect 80 (v0=124386), euler #=-22 (146766,439507,292719) : difference with theory (-17) = 5 

CORRECTING DEFECT 81 (vertices=99, convex hull=123, v0=125172)
After retessellation of defect 81 (v0=125172), euler #=-21 (146807,439690,292862) : difference with theory (-16) = 5 

CORRECTING DEFECT 82 (vertices=249, convex hull=299, v0=125497)
After retessellation of defect 82 (v0=125497), euler #=-18 (146926,440201,293257) : difference with theory (-15) = 3 

CORRECTING DEFECT 83 (vertices=59, convex hull=67, v0=126186)
After retessellation of defect 83 (v0=126186), euler #=-17 (146950,440306,293339) : difference with theory (-14) = 3 

CORRECTING DEFECT 84 (vertices=27, convex hull=20, v0=126211)
After retessellation of defect 84 (v0=126211), euler #=-16 (146956,440331,293359) : difference with theory (-13) = 3 

CORRECTING DEFECT 85 (vertices=66, convex hull=78, v0=126587)
After retessellation of defect 85 (v0=126587), euler #=-15 (146984,440448,293449) : difference with theory (-12) = 3 

CORRECTING DEFECT 86 (vertices=33, convex hull=68, v0=127831)
After retessellation of defect 86 (v0=127831), euler #=-14 (146993,440504,293497) : difference with theory (-11) = 3 

CORRECTING DEFECT 87 (vertices=14, convex hull=19, v0=129329)
After retessellation of defect 87 (v0=129329), euler #=-13 (146994,440513,293506) : difference with theory (-10) = 3 

CORRECTING DEFECT 88 (vertices=59, convex hull=85, v0=129869)
After retessellation of defect 88 (v0=129869), euler #=-12 (147021,440634,293601) : difference with theory (-9) = 3 

CORRECTING DEFECT 89 (vertices=58, convex hull=60, v0=131755)
After retessellation of defect 89 (v0=131755), euler #=-11 (147037,440709,293661) : difference with theory (-8) = 3 

CORRECTING DEFECT 90 (vertices=187, convex hull=201, v0=132609)
After retessellation of defect 90 (v0=132609), euler #=-7 (147105,441016,293904) : difference with theory (-7) = 0 

CORRECTING DEFECT 91 (vertices=46, convex hull=39, v0=133514)
After retessellation of defect 91 (v0=133514), euler #=-6 (147114,441056,293936) : difference with theory (-6) = 0 

CORRECTING DEFECT 92 (vertices=62, convex hull=68, v0=136970)
After retessellation of defect 92 (v0=136970), euler #=-5 (147124,441113,293984) : difference with theory (-5) = 0 

CORRECTING DEFECT 93 (vertices=496, convex hull=246, v0=138592)
After retessellation of defect 93 (v0=138592), euler #=-4 (147169,441372,294199) : difference with theory (-4) = 0 

CORRECTING DEFECT 94 (vertices=49, convex hull=54, v0=140593)
After retessellation of defect 94 (v0=140593), euler #=-3 (147180,441428,294245) : difference with theory (-3) = 0 

CORRECTING DEFECT 95 (vertices=20, convex hull=60, v0=142137)
After retessellation of defect 95 (v0=142137), euler #=-2 (147192,441485,294291) : difference with theory (-2) = 0 

CORRECTING DEFECT 96 (vertices=96, convex hull=91, v0=145260)
After retessellation of defect 96 (v0=145260), euler #=-1 (147217,441599,294381) : difference with theory (-1) = 0 

CORRECTING DEFECT 97 (vertices=59, convex hull=31, v0=149665)
After retessellation of defect 97 (v0=149665), euler #=0 (147222,441628,294406) : difference with theory (0) = 0 

CORRECTING DEFECT 98 (vertices=30, convex hull=24, v0=150810)
After retessellation of defect 98 (v0=150810), euler #=1 (147228,441654,294427) : difference with theory (1) = 0 

CORRECTING DEFECT 99 (vertices=24, convex hull=56, v0=152366)
After retessellation of defect 99 (v0=152366), euler #=2 (147238,441708,294472) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.25 (0.07-->8.74) (max @ vno 135352 --> 140393)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.25 (0.07-->8.74) (max @ vno 135352 --> 140393)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
349 mutations (36.5%), 608 crossovers (63.5%), 613 vertices were eliminated
building final representation...
5410 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=147238, nf=294472, ne=441708, g=0)
writing corrected surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 66.2 minutes
0 defective edges
removing intersecting faces
000: 682 intersecting
001: 5 intersecting
002: 2 intersecting
expanding nbhd size to 2
003: 5 intersecting
mris_fix_topology utimesec    3974.638763
mris_fix_topology stimesec    0.307953
mris_fix_topology ru_maxrss   493396
mris_fix_topology ru_ixrss    0
mris_fix_topology ru_idrss    0
mris_fix_topology ru_isrss    0
mris_fix_topology ru_minflt   57039
mris_fix_topology ru_majflt   0
mris_fix_topology ru_nswap    0
mris_fix_topology ru_inblock  21504
mris_fix_topology ru_oublock  14424
mris_fix_topology ru_msgsnd   0
mris_fix_topology ru_msgrcv   0
mris_fix_topology ru_nsignals 0
mris_fix_topology ru_nvcsw    720
mris_fix_topology ru_nivcsw   5407
FSRUNTIME@ mris_fix_topology rh  1.1034 hours 1 threads
PIDs (16152 16155) completed and logs appended.

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 142936 - 428802 + 285868 = 2 --> 0 holes
      F =2V-4:          285868 = 285872-4 (0)
      2E=3F:            857604 = 857604 (0)

total defect index = 0

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 147238 - 441708 + 294472 = 2 --> 0 holes
      F =2V-4:          294472 = 294476-4 (0)
      2E=3F:            883416 = 883416 (0)

total defect index = 0
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 90 intersecting
001: 2 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 71 intersecting
001: 4 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf lh Sat Oct  7 21:02:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 lh 

#--------------------------------------------
#@# Make White Surf rh Sat Oct  7 21:02:57 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 rh 

Waiting for PID 18583 of (18583 18586) to complete...
Waiting for PID 18586 of (18583 18586) to complete...

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 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-6.0.0/0050660/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
43243 bright wm thresholded.
11304 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.orig...
computing class statistics...
border white:    307857 voxels (1.83%)
border gray      349309 voxels (2.08%)
WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0]
GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 68.3 (was 70)
setting MAX_BORDER_WHITE to 110.8 (was 105)
setting MIN_BORDER_WHITE to 80.0 (was 85)
setting MAX_CSF to 56.6 (was 40)
setting MAX_GRAY to 97.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 68.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.9 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.23 (0.02-->4.53) (max @ vno 105751 --> 142272)
face area 0.27 +- 0.13 (0.00-->5.32)
mean absolute distance = 0.76 +- 0.95
3717 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=104+-5.2,    GM=80+-5.2
mean inside = 97.9, mean outside = 84.1
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=87.4, 116 (116) missing vertices, mean dist 0.3 [0.7 (%32.4)->0.8 (%67.6))]
%68 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.26 (0.05-->4.43) (max @ vno 142271 --> 142272)
face area 0.27 +- 0.13 (0.00-->4.49)
mean absolute distance = 0.38 +- 0.58
4173 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2237115.2, rms=7.734
001: dt: 0.5000, sse=1384283.2, rms=5.491 (29.004%)
002: dt: 0.5000, sse=1024193.1, rms=4.124 (24.890%)
003: dt: 0.5000, sse=859031.9, rms=3.343 (18.949%)
004: dt: 0.5000, sse=784022.9, rms=2.908 (13.009%)
005: dt: 0.5000, sse=754972.8, rms=2.710 (6.800%)
006: dt: 0.5000, sse=742163.1, rms=2.607 (3.818%)
rms = 2.57, time step reduction 1 of 3 to 0.250...
007: dt: 0.5000, sse=735211.8, rms=2.572 (1.331%)
008: dt: 0.2500, sse=663791.3, rms=1.880 (26.896%)
009: dt: 0.2500, sse=653436.4, rms=1.754 (6.722%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
010: dt: 0.2500, sse=650629.2, rms=1.727 (1.546%)
rms = 1.70, time step reduction 3 of 3 to 0.062...
011: dt: 0.1250, sse=647457.9, rms=1.703 (1.391%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
mean border=89.7, 121 (30) missing vertices, mean dist -0.2 [0.4 (%70.9)->0.3 (%29.1))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.26 (0.08-->4.37) (max @ vno 105751 --> 142272)
face area 0.34 +- 0.17 (0.00-->5.70)
mean absolute distance = 0.28 +- 0.40
4179 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1049101.5, rms=3.569
012: dt: 0.5000, sse=843576.1, rms=2.264 (36.574%)
013: dt: 0.5000, sse=824512.9, rms=2.091 (7.621%)
rms = 2.11, time step reduction 1 of 3 to 0.250...
014: dt: 0.2500, sse=782066.2, rms=1.731 (17.233%)
015: dt: 0.2500, sse=769284.2, rms=1.530 (11.626%)
rms = 1.49, time step reduction 2 of 3 to 0.125...
016: dt: 0.2500, sse=763040.8, rms=1.490 (2.620%)
rms = 1.46, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=761428.7, rms=1.464 (1.711%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=91.4, 143 (19) missing vertices, mean dist -0.1 [0.3 (%68.6)->0.2 (%31.4))]
%90 local maxima, % 5 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 +- 0.26 (0.08-->4.36) (max @ vno 142271 --> 142272)
face area 0.33 +- 0.16 (0.00-->5.79)
mean absolute distance = 0.24 +- 0.33
4006 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=866523.1, rms=2.561
018: dt: 0.5000, sse=793712.9, rms=1.894 (26.064%)
rms = 1.92, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=757049.6, rms=1.545 (18.424%)
020: dt: 0.2500, sse=745023.6, rms=1.368 (11.476%)
rms = 1.33, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=736452.4, rms=1.332 (2.608%)
rms = 1.31, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=733422.7, rms=1.309 (1.747%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=91.9, 171 (15) missing vertices, mean dist -0.0 [0.3 (%55.6)->0.2 (%44.4))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white.preaparc...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=743371.6, rms=1.516
023: dt: 0.5000, sse=730006.0, rms=1.186 (21.771%)
rms = 1.64, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=707105.6, rms=1.025 (13.569%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
rms = 1.01, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=704690.9, rms=1.013 (1.199%)
positioning took 0.5 minutes
generating cortex label...
17 non-cortical segments detected
only using segment with 7817 vertices
erasing segment 0 (vno[0] = 56287)
erasing segment 2 (vno[0] = 65714)
erasing segment 3 (vno[0] = 80862)
erasing segment 4 (vno[0] = 84792)
erasing segment 5 (vno[0] = 86834)
erasing segment 6 (vno[0] = 104720)
erasing segment 7 (vno[0] = 104826)
erasing segment 8 (vno[0] = 108390)
erasing segment 9 (vno[0] = 110202)
erasing segment 10 (vno[0] = 111163)
erasing segment 11 (vno[0] = 111246)
erasing segment 12 (vno[0] = 112149)
erasing segment 13 (vno[0] = 112970)
erasing segment 14 (vno[0] = 127928)
erasing segment 15 (vno[0] = 129027)
erasing segment 16 (vno[0] = 129041)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.area
vertex spacing 0.89 +- 0.26 (0.03-->4.43) (max @ vno 64534 --> 65725)
face area 0.33 +- 0.16 (0.00-->5.57)
refinement took 4.8 minutes

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs 0050660 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-6.0.0/0050660/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
43243 bright wm thresholded.
11304 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.orig...
computing class statistics...
border white:    307857 voxels (1.83%)
border gray      349309 voxels (2.08%)
WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0]
GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 69.3 (was 70)
setting MAX_BORDER_WHITE to 111.8 (was 105)
setting MIN_BORDER_WHITE to 81.0 (was 85)
setting MAX_CSF to 57.6 (was 40)
setting MAX_GRAY to 98.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 69.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.9 (was 40)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.81 +- 0.23 (0.01-->4.73) (max @ vno 88443 --> 145903)
face area 0.27 +- 0.13 (0.00-->4.33)
mean absolute distance = 0.77 +- 0.97
4600 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105+-5.2,    GM=81+-5.2
mean inside = 98.4, mean outside = 84.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=88.4, 224 (224) missing vertices, mean dist 0.3 [0.7 (%34.1)->0.8 (%65.9))]
%69 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.26 (0.07-->4.85) (max @ vno 88443 --> 145903)
face area 0.27 +- 0.13 (0.00-->3.71)
mean absolute distance = 0.40 +- 0.60
4885 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=2264461.0, rms=7.591
001: dt: 0.5000, sse=1399175.1, rms=5.396 (28.918%)
002: dt: 0.5000, sse=1042671.7, rms=4.075 (24.478%)
003: dt: 0.5000, sse=876481.7, rms=3.290 (19.268%)
004: dt: 0.5000, sse=798692.9, rms=2.828 (14.044%)
005: dt: 0.5000, sse=766698.9, rms=2.626 (7.127%)
006: dt: 0.5000, sse=779717.2, rms=2.527 (3.798%)
007: dt: 0.5000, sse=747066.6, rms=2.468 (2.328%)
rms = 2.43, time step reduction 1 of 3 to 0.250...
008: dt: 0.5000, sse=746688.8, rms=2.426 (1.672%)
009: dt: 0.2500, sse=680093.6, rms=1.791 (26.195%)
010: dt: 0.2500, sse=664924.8, rms=1.667 (6.932%)
rms = 1.66, time step reduction 2 of 3 to 0.125...
011: dt: 0.2500, sse=670105.4, rms=1.657 (0.582%)
rms = 1.62, time step reduction 3 of 3 to 0.062...
012: dt: 0.1250, sse=661498.6, rms=1.622 (2.097%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=90.7, 134 (42) missing vertices, mean dist -0.2 [0.4 (%71.4)->0.3 (%28.6))]
%84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.26 (0.06-->4.66) (max @ vno 88443 --> 145903)
face area 0.34 +- 0.17 (0.00-->4.85)
mean absolute distance = 0.29 +- 0.40
4860 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1068600.1, rms=3.488
013: dt: 0.5000, sse=873401.1, rms=2.219 (36.372%)
014: dt: 0.5000, sse=849802.9, rms=2.038 (8.166%)
rms = 2.04, time step reduction 1 of 3 to 0.250...
015: dt: 0.2500, sse=810634.9, rms=1.723 (15.451%)
016: dt: 0.2500, sse=792845.6, rms=1.542 (10.532%)
rms = 1.50, time step reduction 2 of 3 to 0.125...
017: dt: 0.2500, sse=813124.5, rms=1.497 (2.929%)
rms = 1.47, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=786193.6, rms=1.467 (1.989%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=92.3, 151 (21) missing vertices, mean dist -0.1 [0.3 (%69.1)->0.2 (%30.9))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.26 (0.05-->4.73) (max @ vno 145887 --> 84131)
face area 0.33 +- 0.16 (0.00-->4.87)
mean absolute distance = 0.24 +- 0.33
4186 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=889796.4, rms=2.541
019: dt: 0.5000, sse=838684.1, rms=1.874 (26.246%)
rms = 1.86, time step reduction 1 of 3 to 0.250...
020: dt: 0.5000, sse=808869.9, rms=1.856 (1.005%)
021: dt: 0.2500, sse=773662.1, rms=1.400 (24.542%)
022: dt: 0.2500, sse=763412.7, rms=1.325 (5.362%)
rms = 1.32, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=762087.8, rms=1.323 (0.149%)
rms = 1.30, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=774165.2, rms=1.296 (2.050%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=92.8, 165 (17) missing vertices, mean dist -0.0 [0.3 (%55.5)->0.2 (%44.5))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white.preaparc...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=782316.1, rms=1.499
025: dt: 0.5000, sse=759666.2, rms=1.188 (20.752%)
rms = 1.60, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=729637.8, rms=1.041 (12.384%)
rms = 1.08, time step reduction 2 of 3 to 0.125...
rms = 1.03, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=724795.3, rms=1.025 (1.505%)
positioning took 0.5 minutes
generating cortex label...
20 non-cortical segments detected
only using segment with 7437 vertices
erasing segment 1 (vno[0] = 66975)
erasing segment 2 (vno[0] = 67408)
erasing segment 3 (vno[0] = 80271)
erasing segment 4 (vno[0] = 94783)
erasing segment 5 (vno[0] = 98848)
erasing segment 6 (vno[0] = 102197)
erasing segment 7 (vno[0] = 103062)
erasing segment 8 (vno[0] = 107515)
erasing segment 9 (vno[0] = 110160)
erasing segment 10 (vno[0] = 110247)
erasing segment 11 (vno[0] = 110306)
erasing segment 12 (vno[0] = 111222)
erasing segment 13 (vno[0] = 112098)
erasing segment 14 (vno[0] = 112118)
erasing segment 15 (vno[0] = 114058)
erasing segment 16 (vno[0] = 115085)
erasing segment 17 (vno[0] = 115985)
erasing segment 18 (vno[0] = 116938)
erasing segment 19 (vno[0] = 117897)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.area
vertex spacing 0.88 +- 0.26 (0.04-->4.84) (max @ vno 84131 --> 145887)
face area 0.33 +- 0.16 (0.00-->4.88)
refinement took 5.1 minutes
PIDs (18583 18586) completed and logs appended.
#--------------------------------------------
#@# Smooth2 lh Sat Oct  7 21:08:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

#--------------------------------------------
#@# Smooth2 rh Sat Oct  7 21:08:01 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

Waiting for PID 18845 of (18845 18848) to complete...
Waiting for PID 18848 of (18845 18848) 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 (18845 18848) completed and logs appended.
#--------------------------------------------
#@# Inflation2 lh Sat Oct  7 21:08:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 

#--------------------------------------------
#@# Inflation2 rh Sat Oct  7 21:08:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

Waiting for PID 18894 of (18894 18897) to complete...
Waiting for PID 18897 of (18894 18897) to complete...

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated

Reading ../surf/lh.smoothwm
avg radius = 49.3 mm, total surface area = 85080 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.184 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.096 (target=0.015)   
step 015: RMS=0.081 (target=0.015)   
step 020: RMS=0.067 (target=0.015)   
step 025: RMS=0.057 (target=0.015)   
step 030: RMS=0.047 (target=0.015)   
step 035: RMS=0.040 (target=0.015)   
step 040: RMS=0.034 (target=0.015)   
step 045: RMS=0.031 (target=0.015)   
step 050: RMS=0.029 (target=0.015)   
step 055: RMS=0.027 (target=0.015)   
step 060: RMS=0.025 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    42.765498
mris_inflate stimesec    0.115982
mris_inflate ru_maxrss   209464
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   30458
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  0
mris_inflate ru_oublock  11192
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2333
mris_inflate ru_nivcsw   3306

 mris_inflate -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated

Reading ../surf/rh.smoothwm
avg radius = 48.3 mm, total surface area = 86882 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.184 (target=0.015)   
step 005: RMS=0.129 (target=0.015)   
step 010: RMS=0.098 (target=0.015)   
step 015: RMS=0.082 (target=0.015)   
step 020: RMS=0.068 (target=0.015)   
step 025: RMS=0.058 (target=0.015)   
step 030: RMS=0.048 (target=0.015)   
step 035: RMS=0.041 (target=0.015)   
step 040: RMS=0.037 (target=0.015)   
step 045: RMS=0.033 (target=0.015)   
step 050: RMS=0.030 (target=0.015)   
step 055: RMS=0.027 (target=0.015)   
step 060: RMS=0.026 (target=0.015)   
inflation complete.
inflation took 0.7 minutes
mris_inflate utimesec    44.374254
mris_inflate stimesec    0.118981
mris_inflate ru_maxrss   216116
mris_inflate ru_ixrss    0
mris_inflate ru_idrss    0
mris_inflate ru_isrss    0
mris_inflate ru_minflt   31609
mris_inflate ru_majflt   0
mris_inflate ru_nswap    0
mris_inflate ru_inblock  10360
mris_inflate ru_oublock  11528
mris_inflate ru_msgsnd   0
mris_inflate ru_msgrcv   0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw    2321
mris_inflate ru_nivcsw   3340
PIDs (18894 18897) completed and logs appended.
#--------------------------------------------
#@# Curv .H and .K lh Sat Oct  7 21:08:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 Sat Oct  7 21:08:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf
reconbatchjobs /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 18994 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 18997 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19000 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19003 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19006 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19009 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19012 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19015 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19018 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19022 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19025 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...
Waiting for PID 19028 of (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) to complete...

 mris_curvature -w lh.white.preaparc

total integrated curvature = 17.590*4pi (221.042) --> -17 handles
ICI = 211.1, FI = 2154.7, variation=33892.318
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
172 vertices thresholded to be in k1 ~ [-0.29 0.46], k2 ~ [-0.09 0.06]
total integrated curvature = 0.540*4pi (6.790) --> 0 handles
ICI = 1.5, FI = 10.1, variation=168.251
123 vertices thresholded to be in [-0.02 0.01]
writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
134 vertices thresholded to be in [-0.13 0.20]
done.
writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022
done.

 mris_curvature -w rh.white.preaparc

total integrated curvature = 19.193*4pi (241.185) --> -18 handles
ICI = 222.7, FI = 2146.1, variation=34182.067
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
234 vertices thresholded to be in k1 ~ [-0.26 1.05], k2 ~ [-0.15 0.30]
total integrated curvature = 0.473*4pi (5.938) --> 1 handles
ICI = 1.4, FI = 9.8, variation=163.019
170 vertices thresholded to be in [-0.07 0.01]
writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.002
128 vertices thresholded to be in [-0.13 0.35]
done.
writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022
done.
PIDs (18994 18997 19000 19003 19006 19009 19012 19015 19018 19022 19025 19028) completed and logs appended.

#-----------------------------------------
#@# Curvature Stats lh Sat Oct  7 21:10:22 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm 0050660 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      [ 0050660/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                      [ 264 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.618221
WARN:    S explicit min:                          0.000000	vertex = 317

#-----------------------------------------
#@# Curvature Stats rh Sat Oct  7 21:10:26 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm 0050660 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      [ 0050660/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                      [ 279 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.928958
WARN:    S explicit min:                          0.000000	vertex = 4
#--------------------------------------------
#@# Sphere lh Sat Oct  7 21:10:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

#--------------------------------------------
#@# Sphere rh Sat Oct  7 21:10:31 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

Waiting for PID 19187 of (19187 19191) to complete...
Waiting for PID 19191 of (19187 19191) to complete...

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0.298...
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 %20.11
pass 1: epoch 2 of 3 starting distance error %20.10
unfolding complete - removing small folds...
starting distance error %20.05
removing remaining folds...
final distance error %20.07
MRISunfold() return, current seed 1234
-01: dt=0.0000, 343 negative triangles
193: dt=0.9900, 343 negative triangles
194: dt=0.9900, 176 negative triangles
195: dt=0.9900, 138 negative triangles
196: dt=0.9900, 136 negative triangles
197: dt=0.9900, 124 negative triangles
198: dt=0.9900, 117 negative triangles
199: dt=0.9900, 120 negative triangles
200: dt=0.9900, 109 negative triangles
201: dt=0.9900, 117 negative triangles
202: dt=0.9900, 117 negative triangles
203: dt=0.9900, 113 negative triangles
204: dt=0.9900, 100 negative triangles
205: dt=0.9900, 99 negative triangles
206: dt=0.9900, 100 negative triangles
207: dt=0.9900, 102 negative triangles
208: dt=0.9900, 96 negative triangles
209: dt=0.9900, 88 negative triangles
210: dt=0.9900, 91 negative triangles
211: dt=0.9900, 98 negative triangles
212: dt=0.9900, 95 negative triangles
213: dt=0.9900, 93 negative triangles
214: dt=0.9900, 91 negative triangles
215: dt=0.9900, 89 negative triangles
216: dt=0.9900, 92 negative triangles
217: dt=0.9900, 88 negative triangles
218: dt=0.9900, 76 negative triangles
219: dt=0.9900, 90 negative triangles
220: dt=0.9900, 79 negative triangles
221: dt=0.9900, 83 negative triangles
222: dt=0.9900, 78 negative triangles
223: dt=0.9900, 83 negative triangles
224: dt=0.9900, 75 negative triangles
225: dt=0.9900, 82 negative triangles
226: dt=0.9900, 78 negative triangles
227: dt=0.9900, 79 negative triangles
228: dt=0.9900, 68 negative triangles
229: dt=0.9900, 73 negative triangles
230: dt=0.9900, 60 negative triangles
231: dt=0.9900, 72 negative triangles
232: dt=0.9900, 62 negative triangles
233: dt=0.9900, 66 negative triangles
234: dt=0.9900, 60 negative triangles
235: dt=0.9900, 68 negative triangles
236: dt=0.9900, 58 negative triangles
237: dt=0.9900, 64 negative triangles
238: dt=0.9900, 60 negative triangles
239: dt=0.9900, 55 negative triangles
240: dt=0.9900, 60 negative triangles
241: dt=0.9900, 58 negative triangles
242: dt=0.9900, 61 negative triangles
243: dt=0.9900, 57 negative triangles
244: dt=0.9900, 52 negative triangles
245: dt=0.9900, 52 negative triangles
246: dt=0.9900, 48 negative triangles
247: dt=0.9900, 46 negative triangles
248: dt=0.9900, 49 negative triangles
249: dt=0.9900, 44 negative triangles
250: dt=0.9900, 47 negative triangles
251: dt=0.9900, 49 negative triangles
252: dt=0.9900, 48 negative triangles
253: dt=0.9900, 44 negative triangles
254: dt=0.9900, 49 negative triangles
255: dt=0.9900, 43 negative triangles
256: dt=0.9900, 43 negative triangles
257: dt=0.9900, 46 negative triangles
258: dt=0.9900, 49 negative triangles
259: dt=0.9900, 45 negative triangles
260: dt=0.9900, 39 negative triangles
261: dt=0.9900, 38 negative triangles
262: dt=0.9900, 29 negative triangles
263: dt=0.9900, 28 negative triangles
264: dt=0.9900, 25 negative triangles
265: dt=0.9900, 28 negative triangles
266: dt=0.9900, 31 negative triangles
267: dt=0.9900, 30 negative triangles
268: dt=0.9900, 30 negative triangles
269: dt=0.9900, 26 negative triangles
270: dt=0.9900, 26 negative triangles
271: dt=0.9900, 20 negative triangles
272: dt=0.9900, 22 negative triangles
273: dt=0.9900, 18 negative triangles
274: dt=0.9900, 24 negative triangles
275: dt=0.9900, 17 negative triangles
276: dt=0.9900, 17 negative triangles
277: dt=0.9900, 17 negative triangles
278: dt=0.9900, 16 negative triangles
279: dt=0.9900, 13 negative triangles
280: dt=0.9900, 14 negative triangles
281: dt=0.9900, 15 negative triangles
282: dt=0.9900, 11 negative triangles
283: dt=0.9900, 11 negative triangles
284: dt=0.9900, 10 negative triangles
285: dt=0.9900, 10 negative triangles
286: dt=0.9900, 9 negative triangles
287: dt=0.9900, 14 negative triangles
288: dt=0.9900, 8 negative triangles
289: dt=0.9900, 6 negative triangles
290: dt=0.9900, 8 negative triangles
291: dt=0.9900, 6 negative triangles
292: dt=0.9900, 3 negative triangles
293: dt=0.9900, 7 negative triangles
294: dt=0.9900, 3 negative triangles
295: dt=0.9900, 5 negative triangles
296: dt=0.9900, 4 negative triangles
297: dt=0.9900, 3 negative triangles
298: dt=0.9900, 1 negative triangles
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.03 hours
mris_sphere utimesec    3829.167878
mris_sphere stimesec    1.925707
mris_sphere ru_maxrss   290884
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   50943
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10120
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    157319
mris_sphere ru_nivcsw   301698
FSRUNTIME@ mris_sphere  1.0291 hours 1 threads

 mris_sphere -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0.296...
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 %19.37
pass 1: epoch 2 of 3 starting distance error %19.31
unfolding complete - removing small folds...
starting distance error %19.23
removing remaining folds...
final distance error %19.25
MRISunfold() return, current seed 1234
-01: dt=0.0000, 280 negative triangles
215: dt=0.9900, 280 negative triangles
216: dt=0.9900, 118 negative triangles
217: dt=0.9900, 105 negative triangles
218: dt=0.9900, 90 negative triangles
219: dt=0.9900, 94 negative triangles
220: dt=0.9900, 83 negative triangles
221: dt=0.9900, 72 negative triangles
222: dt=0.9900, 65 negative triangles
223: dt=0.9900, 52 negative triangles
224: dt=0.9900, 61 negative triangles
225: dt=0.9900, 52 negative triangles
226: dt=0.9900, 40 negative triangles
227: dt=0.9900, 46 negative triangles
228: dt=0.9900, 46 negative triangles
229: dt=0.9900, 43 negative triangles
230: dt=0.9900, 37 negative triangles
231: dt=0.9900, 37 negative triangles
232: dt=0.9900, 43 negative triangles
233: dt=0.9900, 39 negative triangles
234: dt=0.9900, 38 negative triangles
235: dt=0.9900, 37 negative triangles
236: dt=0.9900, 41 negative triangles
237: dt=0.9900, 37 negative triangles
238: dt=0.9900, 39 negative triangles
239: dt=0.9900, 40 negative triangles
240: dt=0.9405, 38 negative triangles
241: dt=0.9405, 39 negative triangles
242: dt=0.9405, 34 negative triangles
243: dt=0.9405, 31 negative triangles
244: dt=0.9405, 29 negative triangles
245: dt=0.9405, 35 negative triangles
246: dt=0.9405, 35 negative triangles
247: dt=0.9405, 31 negative triangles
248: dt=0.9405, 33 negative triangles
249: dt=0.9405, 32 negative triangles
250: dt=0.9405, 33 negative triangles
251: dt=0.9405, 31 negative triangles
252: dt=0.9405, 31 negative triangles
253: dt=0.9405, 33 negative triangles
254: dt=0.8935, 34 negative triangles
255: dt=0.8935, 33 negative triangles
256: dt=0.8935, 30 negative triangles
257: dt=0.8935, 25 negative triangles
258: dt=0.8935, 24 negative triangles
259: dt=0.8935, 27 negative triangles
260: dt=0.8935, 27 negative triangles
261: dt=0.8935, 25 negative triangles
262: dt=0.8935, 26 negative triangles
263: dt=0.8935, 26 negative triangles
264: dt=0.8935, 27 negative triangles
265: dt=0.8935, 28 negative triangles
266: dt=0.8935, 26 negative triangles
267: dt=0.8935, 26 negative triangles
268: dt=0.8935, 23 negative triangles
269: dt=0.8935, 24 negative triangles
270: dt=0.8935, 25 negative triangles
271: dt=0.8935, 26 negative triangles
272: dt=0.8935, 26 negative triangles
273: dt=0.8935, 24 negative triangles
274: dt=0.8935, 27 negative triangles
275: dt=0.8935, 26 negative triangles
276: dt=0.8935, 24 negative triangles
277: dt=0.8935, 23 negative triangles
278: dt=0.8488, 26 negative triangles
279: dt=0.8488, 23 negative triangles
280: dt=0.8488, 23 negative triangles
281: dt=0.8488, 24 negative triangles
282: dt=0.8488, 24 negative triangles
283: dt=0.8488, 26 negative triangles
284: dt=0.8488, 24 negative triangles
285: dt=0.8488, 25 negative triangles
286: dt=0.8488, 24 negative triangles
287: dt=0.8488, 20 negative triangles
288: dt=0.8488, 20 negative triangles
289: dt=0.8488, 20 negative triangles
290: dt=0.8488, 21 negative triangles
291: dt=0.8488, 19 negative triangles
292: dt=0.8488, 21 negative triangles
293: dt=0.8488, 21 negative triangles
294: dt=0.8488, 19 negative triangles
295: dt=0.8488, 19 negative triangles
296: dt=0.8488, 17 negative triangles
297: dt=0.8488, 16 negative triangles
298: dt=0.8488, 16 negative triangles
299: dt=0.8488, 17 negative triangles
300: dt=0.8488, 13 negative triangles
301: dt=0.8488, 12 negative triangles
302: dt=0.8488, 9 negative triangles
303: dt=0.8488, 12 negative triangles
304: dt=0.8488, 10 negative triangles
305: dt=0.8488, 9 negative triangles
306: dt=0.8488, 9 negative triangles
307: dt=0.8488, 8 negative triangles
308: dt=0.8488, 3 negative triangles
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.99 hours
mris_sphere utimesec    3572.316925
mris_sphere stimesec    1.672745
mris_sphere ru_maxrss   299800
mris_sphere ru_ixrss    0
mris_sphere ru_idrss    0
mris_sphere ru_isrss    0
mris_sphere ru_minflt   52162
mris_sphere ru_majflt   0
mris_sphere ru_nswap    0
mris_sphere ru_inblock  0
mris_sphere ru_oublock  10456
mris_sphere ru_msgsnd   0
mris_sphere ru_msgrcv   0
mris_sphere ru_nsignals 0
mris_sphere ru_nvcsw    139107
mris_sphere ru_nivcsw   301499
FSRUNTIME@ mris_sphere  0.9914 hours 1 threads
PIDs (19187 19191) completed and logs appended.
#--------------------------------------------
#@# Surf Reg lh Sat Oct  7 22:12:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 Sat Oct  7 22:12:16 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 21737 of (21737 21740) to complete...
Waiting for PID 21740 of (21737 21740) to complete...

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 5.334
curvature mean = 0.040, std = 0.818
curvature mean = 0.019, std = 0.857
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, 0.00, -16.00) sse = 365414.2, tmin=1.0521
  d=32.00 min @ (8.00, 8.00, -8.00) sse = 304869.6, tmin=2.1364
  d=16.00 min @ (-4.00, 0.00, 4.00) sse = 299375.3, tmin=3.2420
  d=8.00 min @ (2.00, -2.00, -2.00) sse = 292485.5, tmin=4.3544
  d=4.00 min @ (0.00, 0.00, -1.00) sse = 291669.4, tmin=5.4752
  d=1.00 min @ (-0.25, 0.25, 0.25) sse = 291621.5, tmin=7.7291
  d=0.50 min @ (0.12, 0.00, -0.12) sse = 291602.3, tmin=8.8535
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   8.85 min
curvature mean = -0.004, std = 0.821
curvature mean = 0.007, std = 0.944
curvature mean = -0.011, std = 0.829
curvature mean = 0.003, std = 0.977
curvature mean = -0.016, std = 0.828
curvature mean = 0.001, std = 0.991
2 Reading smoothwm
curvature mean = -0.025, std = 0.335
curvature mean = 0.038, std = 0.247
curvature mean = 0.054, std = 0.295
curvature mean = 0.032, std = 0.307
curvature mean = 0.031, std = 0.457
curvature mean = 0.031, std = 0.333
curvature mean = 0.017, std = 0.588
curvature mean = 0.031, std = 0.344
curvature mean = 0.006, std = 0.716
MRISregister() return, current seed 0
-01: dt=0.0000, 138 negative triangles
115: dt=0.9900, 138 negative triangles
expanding nbhd size to 1
116: dt=0.9900, 166 negative triangles
117: dt=0.9900, 124 negative triangles
118: dt=0.9900, 119 negative triangles
119: dt=0.9900, 113 negative triangles
120: dt=0.9900, 105 negative triangles
121: dt=0.9900, 100 negative triangles
122: dt=0.9900, 94 negative triangles
123: dt=0.9900, 90 negative triangles
124: dt=0.9900, 89 negative triangles
125: dt=0.9900, 80 negative triangles
126: dt=0.9900, 72 negative triangles
127: dt=0.9900, 67 negative triangles
128: dt=0.9900, 64 negative triangles
129: dt=0.9900, 67 negative triangles
130: dt=0.9900, 60 negative triangles
131: dt=0.9900, 58 negative triangles
132: dt=0.9900, 58 negative triangles
133: dt=0.9900, 55 negative triangles
134: dt=0.9900, 49 negative triangles
135: dt=0.9900, 51 negative triangles
136: dt=0.9900, 50 negative triangles
137: dt=0.9900, 48 negative triangles
138: dt=0.9900, 50 negative triangles
139: dt=0.9900, 55 negative triangles
140: dt=0.9900, 47 negative triangles
141: dt=0.9900, 45 negative triangles
142: dt=0.9900, 40 negative triangles
143: dt=0.9900, 36 negative triangles
144: dt=0.9900, 35 negative triangles
145: dt=0.9900, 35 negative triangles
146: dt=0.9900, 31 negative triangles
147: dt=0.9900, 30 negative triangles
148: dt=0.9900, 32 negative triangles
149: dt=0.9900, 31 negative triangles
150: dt=0.9900, 28 negative triangles
151: dt=0.9900, 29 negative triangles
152: dt=0.9900, 30 negative triangles
153: dt=0.9900, 27 negative triangles
154: dt=0.9900, 23 negative triangles
155: dt=0.9900, 22 negative triangles
156: dt=0.9900, 22 negative triangles
157: dt=0.9900, 21 negative triangles
158: dt=0.9900, 19 negative triangles
159: dt=0.9900, 18 negative triangles
160: dt=0.9900, 20 negative triangles
161: dt=0.9900, 22 negative triangles
162: dt=0.9900, 17 negative triangles
163: dt=0.9900, 14 negative triangles
164: dt=0.9900, 10 negative triangles
165: dt=0.9900, 10 negative triangles
166: dt=0.9900, 9 negative triangles
167: dt=0.9900, 10 negative triangles
168: dt=0.9900, 9 negative triangles
169: dt=0.9900, 8 negative triangles
170: dt=0.9900, 7 negative triangles
171: dt=0.9900, 8 negative triangles
172: dt=0.9900, 7 negative triangles
173: dt=0.9900, 8 negative triangles
174: dt=0.9900, 5 negative triangles
175: dt=0.9900, 3 negative triangles
176: dt=0.9900, 4 negative triangles
177: dt=0.9900, 3 negative triangles
178: dt=0.9900, 2 negative triangles
179: dt=0.9900, 4 negative triangles
180: dt=0.9900, 3 negative triangles
181: dt=0.9900, 1 negative triangles
182: dt=0.9900, 3 negative triangles
183: dt=0.9900, 1 negative triangles
writing registered surface to ../surf/lh.sphere.reg...
registration took 1.53 hours
mris_register utimesec    5508.926515
mris_register stimesec    3.820419
mris_register ru_maxrss   262736
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38036
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10160
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    415602
mris_register ru_nivcsw   271577
FSRUNTIME@ mris_register  1.5305 hours 1 threads

 mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/scripts
cmdline mris_register -curv -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 5.400
curvature mean = 0.034, std = 0.811
curvature mean = 0.021, std = 0.856
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, -16.00) sse = 376287.2, tmin=1.0833
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 304890.1, tmin=2.2099
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 297809.7, tmin=4.4810
  d=2.00 min @ (0.50, 0.00, -0.50) sse = 297233.3, tmin=6.7609
  d=1.00 min @ (0.00, 0.25, 0.25) sse = 297124.0, tmin=7.9158
  d=0.50 min @ (0.00, -0.12, 0.00) sse = 297095.5, tmin=9.1034
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   9.10 min
curvature mean = 0.008, std = 0.822
curvature mean = 0.009, std = 0.945
curvature mean = 0.004, std = 0.831
curvature mean = 0.004, std = 0.977
curvature mean = 0.002, std = 0.833
curvature mean = 0.001, std = 0.990
2 Reading smoothwm
curvature mean = -0.029, std = 0.339
curvature mean = 0.034, std = 0.243
curvature mean = 0.065, std = 0.289
curvature mean = 0.029, std = 0.299
curvature mean = 0.040, std = 0.447
curvature mean = 0.028, std = 0.325
curvature mean = 0.023, std = 0.576
curvature mean = 0.028, std = 0.335
curvature mean = 0.008, std = 0.684
MRISregister() return, current seed 0
-01: dt=0.0000, 212 negative triangles
119: dt=0.9900, 212 negative triangles
120: dt=0.9405, 249 negative triangles
expanding nbhd size to 1
121: dt=0.9900, 243 negative triangles
122: dt=0.9900, 202 negative triangles
123: dt=0.9900, 190 negative triangles
124: dt=0.9900, 186 negative triangles
125: dt=0.9900, 165 negative triangles
126: dt=0.9900, 162 negative triangles
127: dt=0.9900, 150 negative triangles
128: dt=0.9900, 140 negative triangles
129: dt=0.9900, 138 negative triangles
130: dt=0.9900, 126 negative triangles
131: dt=0.9900, 119 negative triangles
132: dt=0.9900, 117 negative triangles
133: dt=0.9900, 108 negative triangles
134: dt=0.9900, 104 negative triangles
135: dt=0.9900, 99 negative triangles
136: dt=0.9900, 92 negative triangles
137: dt=0.9900, 91 negative triangles
138: dt=0.9900, 82 negative triangles
139: dt=0.9900, 87 negative triangles
140: dt=0.9900, 78 negative triangles
141: dt=0.9900, 80 negative triangles
142: dt=0.9900, 70 negative triangles
143: dt=0.9900, 65 negative triangles
144: dt=0.9900, 66 negative triangles
145: dt=0.9900, 57 negative triangles
146: dt=0.9900, 57 negative triangles
147: dt=0.9900, 51 negative triangles
148: dt=0.9900, 49 negative triangles
149: dt=0.9900, 46 negative triangles
150: dt=0.9900, 45 negative triangles
151: dt=0.9900, 42 negative triangles
152: dt=0.9900, 42 negative triangles
153: dt=0.9900, 44 negative triangles
154: dt=0.9900, 39 negative triangles
155: dt=0.9900, 41 negative triangles
156: dt=0.9900, 41 negative triangles
157: dt=0.9900, 39 negative triangles
158: dt=0.9900, 37 negative triangles
159: dt=0.9900, 37 negative triangles
160: dt=0.9900, 36 negative triangles
161: dt=0.9900, 42 negative triangles
162: dt=0.9900, 42 negative triangles
163: dt=0.9900, 35 negative triangles
164: dt=0.9900, 32 negative triangles
165: dt=0.9900, 34 negative triangles
166: dt=0.9900, 31 negative triangles
167: dt=0.9900, 33 negative triangles
168: dt=0.9900, 28 negative triangles
169: dt=0.9900, 28 negative triangles
170: dt=0.9900, 34 negative triangles
171: dt=0.9900, 32 negative triangles
172: dt=0.9900, 28 negative triangles
173: dt=0.9900, 24 negative triangles
174: dt=0.9900, 22 negative triangles
175: dt=0.9900, 24 negative triangles
176: dt=0.9900, 28 negative triangles
177: dt=0.9900, 26 negative triangles
178: dt=0.9900, 26 negative triangles
179: dt=0.9900, 25 negative triangles
180: dt=0.9900, 19 negative triangles
181: dt=0.9900, 18 negative triangles
182: dt=0.9900, 18 negative triangles
183: dt=0.9900, 16 negative triangles
184: dt=0.9900, 13 negative triangles
185: dt=0.9900, 12 negative triangles
186: dt=0.9900, 11 negative triangles
187: dt=0.9900, 10 negative triangles
188: dt=0.9900, 8 negative triangles
189: dt=0.9900, 6 negative triangles
190: dt=0.9900, 8 negative triangles
191: dt=0.9900, 7 negative triangles
192: dt=0.9900, 6 negative triangles
193: dt=0.9900, 7 negative triangles
194: dt=0.9900, 4 negative triangles
195: dt=0.9900, 2 negative triangles
196: dt=0.9900, 2 negative triangles
197: dt=0.9900, 1 negative triangles
198: dt=0.9900, 1 negative triangles
199: dt=0.9900, 2 negative triangles
writing registered surface to ../surf/rh.sphere.reg...
registration took 1.55 hours
mris_register utimesec    5610.953005
mris_register stimesec    3.844415
mris_register ru_maxrss   270668
mris_register ru_ixrss    0
mris_register ru_idrss    0
mris_register ru_isrss    0
mris_register ru_minflt   38678
mris_register ru_majflt   0
mris_register ru_nswap    0
mris_register ru_inblock  0
mris_register ru_oublock  10448
mris_register ru_msgsnd   0
mris_register ru_msgrcv   0
mris_register ru_nsignals 0
mris_register ru_nvcsw    408241
mris_register ru_nivcsw   271538
FSRUNTIME@ mris_register  1.5481 hours 1 threads
PIDs (21737 21740) completed and logs appended.
#--------------------------------------------
#@# Jacobian white lh Sat Oct  7 23:45:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

#--------------------------------------------
#@# Jacobian white rh Sat Oct  7 23:45:09 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

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

Waiting for PID 25704 of (25704 25707) to complete...
Waiting for PID 25707 of (25704 25707) 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 (25704 25707) completed and logs appended.
#--------------------------------------------
#@# AvgCurv lh Sat Oct  7 23:45:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 Sat Oct  7 23:45:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 25750 of (25750 25753) to complete...
Waiting for PID 25753 of (25750 25753) 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 (25750 25753) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc lh Sat Oct  7 23:45:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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 Sat Oct  7 23:45:13 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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 25796 of (25796 25799) to complete...
Waiting for PID 25799 of (25796 25799) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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...
1290 labels changed using aseg
relabeling using gibbs priors...
000:   3121 changed, 142936 examined...
001:    697 changed, 13222 examined...
002:    175 changed, 3811 examined...
003:     49 changed, 1089 examined...
004:     28 changed, 276 examined...
005:     20 changed, 177 examined...
006:      7 changed, 112 examined...
007:      4 changed, 44 examined...
008:      5 changed, 24 examined...
009:      2 changed, 18 examined...
010:      1 changed, 12 examined...
011:      3 changed, 9 examined...
012:      2 changed, 15 examined...
013:      1 changed, 14 examined...
014:      0 changed, 6 examined...
293 labels changed using aseg
000: 125 total segments, 83 labels (344 vertices) changed
001: 42 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2037 vertices marked for relabeling...
2037 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 14 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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...
1029 labels changed using aseg
relabeling using gibbs priors...
000:   3169 changed, 147238 examined...
001:    739 changed, 13552 examined...
002:    157 changed, 4080 examined...
003:     58 changed, 965 examined...
004:     15 changed, 365 examined...
005:      4 changed, 95 examined...
006:      1 changed, 26 examined...
007:      1 changed, 7 examined...
008:      2 changed, 7 examined...
009:      0 changed, 11 examined...
158 labels changed using aseg
000: 107 total segments, 64 labels (257 vertices) changed
001: 44 total segments, 1 labels (1 vertices) changed
002: 43 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 1 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2036 vertices marked for relabeling...
2036 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 0 minutes and 15 seconds.
PIDs (25796 25799) completed and logs appended.
#--------------------------------------------
#@# Make Pial Surf lh Sat Oct  7 23:45:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 lh 

#--------------------------------------------
#@# Make Pial Surf rh Sat Oct  7 23:45:28 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 rh 

Waiting for PID 25844 of (25844 25847) to complete...
Waiting for PID 25847 of (25844 25847) to complete...

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 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-6.0.0/0050660/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
43243 bright wm thresholded.
11304 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.orig...
computing class statistics...
border white:    307857 voxels (1.83%)
border gray      349309 voxels (2.08%)
WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0]
GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 68.3 (was 70)
setting MAX_BORDER_WHITE to 110.8 (was 105)
setting MIN_BORDER_WHITE to 80.0 (was 85)
setting MAX_CSF to 56.6 (was 40)
setting MAX_GRAY to 97.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 68.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.9 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=104+-5.2,    GM=80+-5.2
mean inside = 97.9, mean outside = 84.1
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.26 (0.03-->4.43) (max @ vno 64534 --> 65725)
face area 0.33 +- 0.16 (0.00-->5.58)
mean absolute distance = 0.67 +- 0.91
2971 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 44 points - only 0.00% unknown
deleting segment 1 with 17 points - only 0.00% unknown
deleting segment 2 with 104 points - only 0.00% unknown
deleting segment 3 with 16 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 284 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 7 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 11 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 22 points - only 0.00% unknown
deleting segment 14 with 28 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 15 with 2 points - only 0.00% unknown
mean border=87.2, 152 (152) missing vertices, mean dist 0.4 [1.2 (%12.9)->0.6 (%87.1))]
%65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.27 (0.08-->4.85) (max @ vno 65725 --> 64534)
face area 0.33 +- 0.17 (0.00-->5.26)
mean absolute distance = 0.37 +- 0.57
3541 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1662144.4, rms=5.995
001: dt: 0.5000, sse=1031686.4, rms=3.527 (41.164%)
002: dt: 0.5000, sse=867986.4, rms=2.567 (27.226%)
003: dt: 0.5000, sse=830388.2, rms=2.384 (7.122%)
004: dt: 0.5000, sse=818819.5, rms=2.292 (3.864%)
rms = 2.35, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=781209.2, rms=1.912 (16.569%)
006: dt: 0.2500, sse=769272.8, rms=1.735 (9.282%)
rms = 1.70, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=764582.8, rms=1.695 (2.273%)
rms = 1.67, time step reduction 3 of 3 to 0.062...
008: dt: 0.1250, sse=763054.5, rms=1.673 (1.337%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 37 points - only 0.00% unknown
deleting segment 1 with 13 points - only 0.00% unknown
deleting segment 2 with 98 points - only 0.00% unknown
deleting segment 3 with 13 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 6 with 183 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 15 points - only 0.00% unknown
deleting segment 9 with 33 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
mean border=89.6, 124 (32) missing vertices, mean dist -0.2 [0.4 (%70.6)->0.3 (%29.4))]
%83 local maxima, %13 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 +- 0.26 (0.07-->5.04) (max @ vno 65725 --> 64534)
face area 0.34 +- 0.17 (0.00-->5.78)
mean absolute distance = 0.28 +- 0.39
3940 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1040528.5, rms=3.448
009: dt: 0.5000, sse=844449.6, rms=2.155 (37.498%)
010: dt: 0.5000, sse=819941.4, rms=1.976 (8.318%)
rms = 2.03, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=784533.1, rms=1.620 (18.035%)
012: dt: 0.2500, sse=769961.3, rms=1.436 (11.316%)
rms = 1.41, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=782523.9, rms=1.407 (2.057%)
rms = 1.39, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=766032.9, rms=1.389 (1.271%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 44 points - only 0.00% unknown
deleting segment 1 with 16 points - only 0.00% unknown
deleting segment 2 with 99 points - only 0.00% unknown
deleting segment 3 with 13 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 229 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 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 20 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 29 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
mean border=91.3, 157 (19) missing vertices, mean dist -0.1 [0.3 (%68.6)->0.2 (%31.4))]
%90 local maxima, % 5 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 +- 0.26 (0.06-->5.15) (max @ vno 65725 --> 64534)
face area 0.34 +- 0.17 (0.00-->5.40)
mean absolute distance = 0.24 +- 0.33
3911 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=870098.4, rms=2.531
015: dt: 0.5000, sse=794961.1, rms=1.855 (26.707%)
rms = 1.88, time step reduction 1 of 3 to 0.250...
016: dt: 0.2500, sse=758971.2, rms=1.501 (19.113%)
017: dt: 0.2500, sse=745184.7, rms=1.321 (11.983%)
rms = 1.29, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=751846.6, rms=1.289 (2.382%)
rms = 1.27, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=740236.4, rms=1.270 (1.540%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 41 points - only 0.00% unknown
deleting segment 1 with 16 points - only 0.00% unknown
deleting segment 2 with 100 points - only 0.00% unknown
deleting segment 3 with 13 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 227 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 8 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 10 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 14 with 29 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
mean border=91.9, 197 (16) missing vertices, mean dist -0.0 [0.3 (%55.6)->0.2 (%44.4))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=749861.8, rms=1.489
020: dt: 0.5000, sse=740426.2, rms=1.168 (21.548%)
rms = 1.61, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=714586.5, rms=1.001 (14.337%)
rms = 1.03, time step reduction 2 of 3 to 0.125...
rms = 0.99, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=712339.4, rms=0.987 (1.398%)
positioning took 0.5 minutes
generating cortex label...
19 non-cortical segments detected
only using segment with 7837 vertices
erasing segment 0 (vno[0] = 56287)
erasing segment 2 (vno[0] = 65714)
erasing segment 3 (vno[0] = 66933)
erasing segment 4 (vno[0] = 79786)
erasing segment 5 (vno[0] = 85795)
erasing segment 6 (vno[0] = 88746)
erasing segment 7 (vno[0] = 89202)
erasing segment 8 (vno[0] = 96108)
erasing segment 9 (vno[0] = 104720)
erasing segment 10 (vno[0] = 104826)
erasing segment 11 (vno[0] = 108390)
erasing segment 12 (vno[0] = 110202)
erasing segment 13 (vno[0] = 111163)
erasing segment 14 (vno[0] = 111246)
erasing segment 15 (vno[0] = 112149)
erasing segment 16 (vno[0] = 112970)
erasing segment 17 (vno[0] = 127928)
erasing segment 18 (vno[0] = 129027)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.area
vertex spacing 0.89 +- 0.27 (0.05-->5.19) (max @ vno 64534 --> 65725)
face area 0.33 +- 0.17 (0.00-->5.40)
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 57 points - only 0.00% unknown
deleting segment 1 with 264 points - only 0.00% unknown
deleting segment 2 with 21 points - only 0.00% unknown
deleting segment 3 with 34 points - only 0.00% unknown
deleting segment 5 with 17 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 9 with 16 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 4 vertex label from ripped group
deleting segment 14 with 31 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 15 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=66.8, 166 (166) missing vertices, mean dist 1.5 [0.3 (%0.0)->3.3 (%100.0))]
%12 local maxima, %32 large gradients and %51 min vals, 267 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=19130522.0, rms=26.012
001: dt: 0.0500, sse=17186392.0, rms=24.603 (5.417%)
002: dt: 0.0500, sse=15780930.0, rms=23.532 (4.355%)
003: dt: 0.0500, sse=14705449.0, rms=22.678 (3.630%)
004: dt: 0.0500, sse=13841601.0, rms=21.968 (3.132%)
005: dt: 0.0500, sse=13121071.0, rms=21.357 (2.780%)
006: dt: 0.0500, sse=12502312.0, rms=20.818 (2.522%)
007: dt: 0.0500, sse=11959097.0, rms=20.333 (2.329%)
008: dt: 0.0500, sse=11475302.0, rms=19.892 (2.173%)
009: dt: 0.0500, sse=11039302.0, rms=19.485 (2.045%)
010: dt: 0.0500, sse=10642330.0, rms=19.107 (1.940%)
positioning took 1.0 minutes
mean border=66.5, 146 (90) missing vertices, mean dist 1.3 [0.1 (%0.0)->2.8 (%100.0))]
%14 local maxima, %33 large gradients and %49 min vals, 239 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=11592862.0, rms=20.003
011: dt: 0.0500, sse=11224382.0, rms=19.662 (1.706%)
012: dt: 0.0500, sse=10884491.0, rms=19.342 (1.628%)
013: dt: 0.0500, sse=10569034.0, rms=19.040 (1.561%)
014: dt: 0.0500, sse=10275266.0, rms=18.754 (1.500%)
015: dt: 0.0500, sse=10001329.0, rms=18.484 (1.442%)
016: dt: 0.0500, sse=9744793.0, rms=18.227 (1.390%)
017: dt: 0.0500, sse=9504022.0, rms=17.982 (1.342%)
018: dt: 0.0500, sse=9277411.0, rms=17.749 (1.298%)
019: dt: 0.0500, sse=9063554.0, rms=17.526 (1.257%)
020: dt: 0.0500, sse=8861249.0, rms=17.312 (1.220%)
positioning took 1.0 minutes
mean border=66.4, 168 (57) missing vertices, mean dist 1.2 [0.1 (%0.3)->2.5 (%99.7))]
%14 local maxima, %33 large gradients and %49 min vals, 232 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=8980241.0, rms=17.443
021: dt: 0.0500, sse=8785763.0, rms=17.236 (1.184%)
022: dt: 0.0500, sse=8601212.0, rms=17.038 (1.151%)
023: dt: 0.0500, sse=8424750.0, rms=16.846 (1.126%)
024: dt: 0.0500, sse=8255496.5, rms=16.660 (1.106%)
025: dt: 0.0500, sse=8092972.5, rms=16.479 (1.086%)
026: dt: 0.0500, sse=7936089.5, rms=16.302 (1.072%)
027: dt: 0.0500, sse=7783654.0, rms=16.129 (1.064%)
028: dt: 0.0500, sse=7635242.0, rms=15.958 (1.059%)
029: dt: 0.0500, sse=7489611.0, rms=15.789 (1.062%)
030: dt: 0.0500, sse=7346553.5, rms=15.620 (1.066%)
positioning took 1.0 minutes
mean border=66.3, 230 (48) missing vertices, mean dist 1.1 [0.1 (%1.8)->2.2 (%98.2))]
%14 local maxima, %33 large gradients and %48 min vals, 206 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=7444955.0, rms=15.738
031: dt: 0.5000, sse=6344280.0, rms=14.388 (8.579%)
032: dt: 0.5000, sse=5419289.0, rms=13.142 (8.659%)
033: dt: 0.5000, sse=4655352.5, rms=12.016 (8.565%)
034: dt: 0.5000, sse=4001545.0, rms=10.959 (8.795%)
035: dt: 0.5000, sse=3468365.5, rms=10.015 (8.616%)
036: dt: 0.5000, sse=3008430.5, rms=9.121 (8.927%)
037: dt: 0.5000, sse=2632061.8, rms=8.321 (8.767%)
038: dt: 0.5000, sse=2323722.5, rms=7.601 (8.662%)
039: dt: 0.5000, sse=2099456.5, rms=7.034 (7.462%)
040: dt: 0.5000, sse=1922194.1, rms=6.550 (6.879%)
041: dt: 0.5000, sse=1806286.1, rms=6.213 (5.144%)
042: dt: 0.5000, sse=1712135.0, rms=5.925 (4.624%)
043: dt: 0.5000, sse=1663987.9, rms=5.772 (2.592%)
044: dt: 0.5000, sse=1617624.4, rms=5.620 (2.635%)
045: dt: 0.5000, sse=1597751.2, rms=5.553 (1.189%)
046: dt: 0.5000, sse=1570023.6, rms=5.458 (1.711%)
rms = 5.44, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1564549.2, rms=5.440 (0.337%)
048: dt: 0.2500, sse=1438051.2, rms=4.945 (9.092%)
049: dt: 0.2500, sse=1399661.2, rms=4.800 (2.930%)
rms = 4.82, time step reduction 2 of 3 to 0.125...
050: dt: 0.1250, sse=1383011.0, rms=4.732 (1.411%)
051: dt: 0.1250, sse=1361759.9, rms=4.643 (1.883%)
rms = 4.63, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1357812.2, rms=4.626 (0.367%)
positioning took 3.2 minutes
mean border=65.4, 3968 (18) missing vertices, mean dist 0.1 [0.2 (%44.2)->0.6 (%55.8))]
%25 local maxima, %23 large gradients and %44 min vals, 150 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=1606659.8, rms=4.764
rms = 4.78, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1490080.9, rms=4.269 (10.377%)
054: dt: 0.2500, sse=1430163.4, rms=3.988 (6.583%)
rms = 3.95, time step reduction 2 of 3 to 0.125...
055: dt: 0.2500, sse=1419752.1, rms=3.946 (1.068%)
056: dt: 0.1250, sse=1363760.8, rms=3.662 (7.191%)
057: dt: 0.1250, sse=1348435.1, rms=3.587 (2.039%)
rms = 3.56, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1343571.1, rms=3.564 (0.645%)
positioning took 1.1 minutes
mean border=64.9, 4474 (16) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.4 (%56.3))]
%35 local maxima, %13 large gradients and %44 min vals, 186 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=1365464.1, rms=3.699
rms = 4.31, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1335099.1, rms=3.541 (4.273%)
rms = 3.56, time step reduction 2 of 3 to 0.125...
rms = 3.52, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1330460.6, rms=3.516 (0.709%)
positioning took 0.6 minutes
mean border=64.4, 7914 (15) missing vertices, mean dist 0.1 [0.2 (%43.4)->0.3 (%56.6))]
%36 local maxima, %12 large gradients and %42 min vals, 212 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-6.0.0/0050660/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1350630.4, rms=3.617
rms = 4.01, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1322391.5, rms=3.471 (4.029%)
062: dt: 0.2500, sse=1305931.2, rms=3.408 (1.824%)
rms = 3.46, time step reduction 2 of 3 to 0.125...
063: dt: 0.1250, sse=1296637.8, rms=3.354 (1.584%)
064: dt: 0.1250, sse=1282163.0, rms=3.274 (2.384%)
rms = 3.24, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1274684.4, rms=3.237 (1.129%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.area.pial
vertex spacing 1.02 +- 0.47 (0.09-->6.59) (max @ vno 64503 --> 64502)
face area 0.41 +- 0.35 (0.00-->7.83)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 142936 vertices processed
25000 of 142936 vertices processed
50000 of 142936 vertices processed
75000 of 142936 vertices processed
100000 of 142936 vertices processed
125000 of 142936 vertices processed
0 of 142936 vertices processed
25000 of 142936 vertices processed
50000 of 142936 vertices processed
75000 of 142936 vertices processed
100000 of 142936 vertices processed
125000 of 142936 vertices processed
thickness calculation complete, 558:1518 truncations.
25824 vertices at 0 distance
87942 vertices at 1 distance
90229 vertices at 2 distance
44182 vertices at 3 distance
16096 vertices at 4 distance
5455 vertices at 5 distance
1868 vertices at 6 distance
657 vertices at 7 distance
244 vertices at 8 distance
138 vertices at 9 distance
71 vertices at 10 distance
60 vertices at 11 distance
56 vertices at 12 distance
40 vertices at 13 distance
19 vertices at 14 distance
19 vertices at 15 distance
25 vertices at 16 distance
23 vertices at 17 distance
13 vertices at 18 distance
15 vertices at 19 distance
26 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.thickness
positioning took 15.8 minutes

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs 0050660 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-6.0.0/0050660/mri/filled.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/brain.finalsurfs.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/../mri/aseg.presurf.mgz...
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
43243 bright wm thresholded.
11304 bright non-wm voxels segmented.
reading original surface position from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.orig...
computing class statistics...
border white:    307857 voxels (1.83%)
border gray      349309 voxels (2.08%)
WM (102.0): 101.7 +- 6.8 [70.0 --> 110.0]
GM (82.0) : 80.2 +- 11.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 69.3 (was 70)
setting MAX_BORDER_WHITE to 111.8 (was 105)
setting MIN_BORDER_WHITE to 81.0 (was 85)
setting MAX_CSF to 57.6 (was 40)
setting MAX_GRAY to 98.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 69.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 45.9 (was 40)
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105+-5.2,    GM=81+-5.2
mean inside = 98.4, mean outside = 84.9
smoothing surface for 5 iterations...
reading initial white vertex positions from white.preaparc...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
smoothing T1 volume with sigma = 2.000
vertex spacing 0.88 +- 0.26 (0.04-->4.84) (max @ vno 84131 --> 145887)
face area 0.33 +- 0.16 (0.00-->4.88)
mean absolute distance = 0.69 +- 0.92
3487 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 11 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 19 points - only 0.00% unknown
deleting segment 7 with 130 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 37 points - only 0.00% unknown
deleting segment 11 with 17 points - only 0.00% unknown
deleting segment 12 with 19 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
mean border=88.3, 352 (351) missing vertices, mean dist 0.4 [1.2 (%12.9)->0.6 (%87.1))]
%67 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=tars-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.90 +- 0.27 (0.04-->4.88) (max @ vno 145887 --> 84131)
face area 0.33 +- 0.17 (0.00-->4.70)
mean absolute distance = 0.38 +- 0.57
4118 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1644972.1, rms=5.797
001: dt: 0.5000, sse=1037951.8, rms=3.438 (40.691%)
002: dt: 0.5000, sse=887113.8, rms=2.504 (27.182%)
003: dt: 0.5000, sse=846604.8, rms=2.292 (8.456%)
004: dt: 0.5000, sse=833308.2, rms=2.177 (4.994%)
rms = 2.23, time step reduction 1 of 3 to 0.250...
005: dt: 0.2500, sse=794641.2, rms=1.835 (15.707%)
006: dt: 0.2500, sse=785070.5, rms=1.676 (8.682%)
rms = 1.64, time step reduction 2 of 3 to 0.125...
007: dt: 0.2500, sse=777242.2, rms=1.640 (2.173%)
rms = 1.61, time step reduction 3 of 3 to 0.062...
008: dt: 0.1250, sse=775650.2, rms=1.614 (1.535%)
positioning took 1.0 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 1 with 2 points - only 0.00% unknown
deleting segment 2 with 78 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
mean border=90.6, 137 (44) missing vertices, mean dist -0.2 [0.4 (%71.8)->0.3 (%28.2))]
%83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=tars-, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.26 (0.06-->5.00) (max @ vno 145887 --> 84131)
face area 0.34 +- 0.17 (0.00-->5.22)
mean absolute distance = 0.29 +- 0.40
4390 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=1047880.8, rms=3.343
009: dt: 0.5000, sse=858062.8, rms=2.081 (37.738%)
010: dt: 0.5000, sse=840345.6, rms=1.878 (9.775%)
rms = 1.93, time step reduction 1 of 3 to 0.250...
011: dt: 0.2500, sse=798712.4, rms=1.561 (16.867%)
012: dt: 0.2500, sse=790508.3, rms=1.402 (10.219%)
rms = 1.37, time step reduction 2 of 3 to 0.125...
013: dt: 0.2500, sse=791362.4, rms=1.370 (2.221%)
rms = 1.35, time step reduction 3 of 3 to 0.062...
014: dt: 0.1250, sse=787017.2, rms=1.349 (1.580%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 8 points - only 0.00% unknown
deleting segment 2 with 102 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 11 points - only 0.00% unknown
deleting segment 6 with 13 points - only 0.00% unknown
deleting segment 7 with 13 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 14 points - only 0.00% unknown
mean border=92.2, 136 (22) missing vertices, mean dist -0.1 [0.3 (%69.1)->0.2 (%30.9))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=tars-, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.26 (0.06-->5.08) (max @ vno 145887 --> 84131)
face area 0.33 +- 0.17 (0.00-->5.27)
mean absolute distance = 0.24 +- 0.33
3954 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=887643.7, rms=2.474
015: dt: 0.5000, sse=820915.0, rms=1.802 (27.164%)
rms = 1.80, time step reduction 1 of 3 to 0.250...
016: dt: 0.5000, sse=805268.6, rms=1.795 (0.364%)
017: dt: 0.2500, sse=781915.5, rms=1.343 (25.204%)
018: dt: 0.2500, sse=760360.9, rms=1.276 (4.994%)
rms = 1.28, time step reduction 2 of 3 to 0.125...
rms = 1.26, time step reduction 3 of 3 to 0.062...
019: dt: 0.1250, sse=756671.7, rms=1.264 (0.958%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 9 points - only 0.00% unknown
deleting segment 1 with 8 points - only 0.00% unknown
deleting segment 2 with 102 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 15 points - only 0.00% unknown
deleting segment 6 with 14 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 12 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 4 points - only 0.00% unknown
deleting segment 10 with 14 points - only 0.00% unknown
mean border=92.8, 188 (14) missing vertices, mean dist -0.0 [0.3 (%55.6)->0.2 (%44.4))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=tars-, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
writing white matter surface to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=766493.4, rms=1.482
020: dt: 0.5000, sse=752034.1, rms=1.238 (16.463%)
rms = 1.67, time step reduction 1 of 3 to 0.250...
021: dt: 0.2500, sse=732014.0, rms=1.034 (16.450%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
rms = 1.01, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=730716.1, rms=1.015 (1.895%)
positioning took 0.5 minutes
generating cortex label...
25 non-cortical segments detected
only using segment with 7412 vertices
erasing segment 1 (vno[0] = 54235)
erasing segment 2 (vno[0] = 66276)
erasing segment 3 (vno[0] = 68539)
erasing segment 4 (vno[0] = 80271)
erasing segment 5 (vno[0] = 85273)
erasing segment 6 (vno[0] = 94783)
erasing segment 7 (vno[0] = 97800)
erasing segment 8 (vno[0] = 102197)
erasing segment 9 (vno[0] = 103062)
erasing segment 10 (vno[0] = 103304)
erasing segment 11 (vno[0] = 106192)
erasing segment 12 (vno[0] = 107515)
erasing segment 13 (vno[0] = 110160)
erasing segment 14 (vno[0] = 110247)
erasing segment 15 (vno[0] = 110306)
erasing segment 16 (vno[0] = 111222)
erasing segment 17 (vno[0] = 112098)
erasing segment 18 (vno[0] = 112118)
erasing segment 19 (vno[0] = 114058)
erasing segment 20 (vno[0] = 115085)
erasing segment 21 (vno[0] = 115985)
erasing segment 22 (vno[0] = 116938)
erasing segment 23 (vno[0] = 117897)
erasing segment 24 (vno[0] = 127144)
writing cortex label to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label...
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.area
vertex spacing 0.89 +- 0.27 (0.04-->5.05) (max @ vno 84131 --> 145887)
face area 0.33 +- 0.17 (0.00-->5.20)
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 14 points - only 0.00% unknown
deleting segment 1 with 28 points - only 0.00% unknown
deleting segment 2 with 48 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 3 points - only 0.00% unknown
deleting segment 7 with 6 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 10 points - only 0.00% unknown
deleting segment 13 with 9 points - only 0.00% unknown
deleting segment 16 with 41 points - only 0.00% unknown
deleting segment 17 with 6 points - only 0.00% unknown
smoothing surface for 5 iterations...
reading initial pial vertex positions from white.preaparc...
mean border=67.9, 355 (355) missing vertices, mean dist 1.5 [1.3 (%0.0)->3.4 (%100.0))]
%12 local maxima, %30 large gradients and %54 min vals, 234 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=19541948.0, rms=25.857
001: dt: 0.0500, sse=17601898.0, rms=24.489 (5.288%)
002: dt: 0.0500, sse=16205534.0, rms=23.455 (4.221%)
003: dt: 0.0500, sse=15143400.0, rms=22.637 (3.488%)
004: dt: 0.0500, sse=14290057.0, rms=21.958 (3.002%)
005: dt: 0.0500, sse=13579627.0, rms=21.376 (2.652%)
006: dt: 0.0500, sse=12968860.0, rms=20.862 (2.403%)
007: dt: 0.0500, sse=12433268.0, rms=20.401 (2.211%)
008: dt: 0.0500, sse=11956473.0, rms=19.981 (2.056%)
009: dt: 0.0500, sse=11525825.0, rms=19.594 (1.935%)
010: dt: 0.0500, sse=11133810.0, rms=19.236 (1.831%)
positioning took 1.0 minutes
mean border=67.6, 241 (151) missing vertices, mean dist 1.3 [0.1 (%0.1)->2.9 (%99.9))]
%13 local maxima, %31 large gradients and %52 min vals, 218 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=12310116.0, rms=20.286
011: dt: 0.0500, sse=11943799.0, rms=19.963 (1.593%)
012: dt: 0.0500, sse=11605339.0, rms=19.660 (1.519%)
013: dt: 0.0500, sse=11291073.0, rms=19.374 (1.454%)
014: dt: 0.0500, sse=10998360.0, rms=19.104 (1.395%)
015: dt: 0.0500, sse=10724568.0, rms=18.848 (1.342%)
016: dt: 0.0500, sse=10468399.0, rms=18.605 (1.290%)
017: dt: 0.0500, sse=10226968.0, rms=18.372 (1.248%)
018: dt: 0.0500, sse=9999295.0, rms=18.151 (1.207%)
019: dt: 0.0500, sse=9783662.0, rms=17.938 (1.171%)
020: dt: 0.0500, sse=9579177.0, rms=17.734 (1.137%)
positioning took 1.0 minutes
mean border=67.4, 219 (86) missing vertices, mean dist 1.2 [0.1 (%0.5)->2.6 (%99.5))]
%14 local maxima, %30 large gradients and %52 min vals, 228 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=9715544.0, rms=17.873
021: dt: 0.0500, sse=9515791.0, rms=17.673 (1.119%)
022: dt: 0.0500, sse=9325783.0, rms=17.481 (1.089%)
023: dt: 0.0500, sse=9143169.0, rms=17.294 (1.070%)
024: dt: 0.0500, sse=8967546.0, rms=17.112 (1.051%)
025: dt: 0.0500, sse=8797847.0, rms=16.935 (1.038%)
026: dt: 0.0500, sse=8633783.0, rms=16.761 (1.025%)
027: dt: 0.0500, sse=8473965.0, rms=16.590 (1.020%)
028: dt: 0.0500, sse=8317540.0, rms=16.421 (1.019%)
029: dt: 0.0500, sse=8164277.0, rms=16.254 (1.019%)
030: dt: 0.0500, sse=8013510.0, rms=16.087 (1.024%)
positioning took 1.0 minutes
mean border=67.3, 298 (68) missing vertices, mean dist 1.0 [0.1 (%1.9)->2.3 (%98.1))]
%14 local maxima, %31 large gradients and %51 min vals, 208 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=8117616.0, rms=16.204
031: dt: 0.5000, sse=6980306.0, rms=14.898 (8.057%)
032: dt: 0.5000, sse=6046142.5, rms=13.729 (7.849%)
033: dt: 0.5000, sse=5251323.0, rms=12.649 (7.863%)
034: dt: 0.5000, sse=4559655.5, rms=11.627 (8.084%)
035: dt: 0.5000, sse=3965775.0, rms=10.671 (8.216%)
036: dt: 0.5000, sse=3434142.5, rms=9.736 (8.763%)
037: dt: 0.5000, sse=2983715.5, rms=8.870 (8.896%)
038: dt: 0.5000, sse=2595282.8, rms=8.047 (9.276%)
039: dt: 0.5000, sse=2305278.0, rms=7.376 (8.346%)
040: dt: 0.5000, sse=2081590.6, rms=6.811 (7.652%)
041: dt: 0.5000, sse=1942855.8, rms=6.437 (5.502%)
042: dt: 0.5000, sse=1833828.0, rms=6.125 (4.839%)
043: dt: 0.5000, sse=1775930.5, rms=5.953 (2.802%)
044: dt: 0.5000, sse=1725695.4, rms=5.798 (2.611%)
045: dt: 0.5000, sse=1698680.5, rms=5.715 (1.438%)
046: dt: 0.5000, sse=1676140.8, rms=5.641 (1.292%)
rms = 5.61, time step reduction 1 of 3 to 0.250...
047: dt: 0.5000, sse=1666048.8, rms=5.609 (0.566%)
048: dt: 0.2500, sse=1531690.1, rms=5.118 (8.752%)
049: dt: 0.2500, sse=1490096.1, rms=4.971 (2.863%)
rms = 4.99, time step reduction 2 of 3 to 0.125...
050: dt: 0.1250, sse=1467199.8, rms=4.885 (1.736%)
051: dt: 0.1250, sse=1436874.1, rms=4.767 (2.409%)
rms = 4.75, time step reduction 3 of 3 to 0.062...
052: dt: 0.1250, sse=1431533.2, rms=4.746 (0.455%)
positioning took 3.4 minutes
mean border=66.6, 4994 (22) missing vertices, mean dist 0.1 [0.2 (%44.5)->0.6 (%55.5))]
%23 local maxima, %22 large gradients and %47 min vals, 153 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=1691833.1, rms=4.920
rms = 5.05, time step reduction 1 of 3 to 0.250...
053: dt: 0.2500, sse=1561506.1, rms=4.405 (10.471%)
054: dt: 0.2500, sse=1507521.2, rms=4.170 (5.331%)
rms = 4.17, time step reduction 2 of 3 to 0.125...
055: dt: 0.1250, sse=1479779.5, rms=4.044 (3.015%)
056: dt: 0.1250, sse=1439883.9, rms=3.860 (4.570%)
057: dt: 0.1250, sse=1421692.8, rms=3.776 (2.159%)
rms = 3.73, time step reduction 3 of 3 to 0.062...
058: dt: 0.1250, sse=1412254.1, rms=3.734 (1.109%)
positioning took 1.3 minutes
mean border=66.2, 5375 (16) missing vertices, mean dist 0.1 [0.2 (%44.6)->0.4 (%55.4))]
%32 local maxima, %13 large gradients and %47 min vals, 163 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=1434863.2, rms=3.870
rms = 4.58, time step reduction 1 of 3 to 0.250...
059: dt: 0.2500, sse=1398821.8, rms=3.700 (4.403%)
rms = 3.78, time step reduction 2 of 3 to 0.125...
rms = 3.67, time step reduction 3 of 3 to 0.062...
060: dt: 0.1250, sse=1393268.2, rms=3.673 (0.741%)
positioning took 0.6 minutes
mean border=65.8, 8839 (15) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.3 (%55.9))]
%33 local maxima, %12 large gradients and %45 min vals, 172 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-6.0.0/0050660/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=1408043.6, rms=3.739
rms = 4.24, time step reduction 1 of 3 to 0.250...
061: dt: 0.2500, sse=1376834.0, rms=3.590 (3.967%)
rms = 3.57, time step reduction 2 of 3 to 0.125...
062: dt: 0.2500, sse=1367459.0, rms=3.571 (0.550%)
063: dt: 0.1250, sse=1339061.9, rms=3.421 (4.183%)
064: dt: 0.1250, sse=1326661.8, rms=3.363 (1.704%)
rms = 3.34, time step reduction 3 of 3 to 0.062...
065: dt: 0.1250, sse=1321399.4, rms=3.341 (0.665%)
positioning took 1.1 minutes
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.area.pial
vertex spacing 1.01 +- 0.47 (0.05-->6.52) (max @ vno 66223 --> 63851)
face area 0.40 +- 0.34 (0.00-->10.40)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 147238 vertices processed
25000 of 147238 vertices processed
50000 of 147238 vertices processed
75000 of 147238 vertices processed
100000 of 147238 vertices processed
125000 of 147238 vertices processed
0 of 147238 vertices processed
25000 of 147238 vertices processed
50000 of 147238 vertices processed
75000 of 147238 vertices processed
100000 of 147238 vertices processed
125000 of 147238 vertices processed
thickness calculation complete, 537:1299 truncations.
27997 vertices at 0 distance
89294 vertices at 1 distance
92530 vertices at 2 distance
46325 vertices at 3 distance
17051 vertices at 4 distance
5803 vertices at 5 distance
1991 vertices at 6 distance
757 vertices at 7 distance
240 vertices at 8 distance
145 vertices at 9 distance
85 vertices at 10 distance
72 vertices at 11 distance
77 vertices at 12 distance
46 vertices at 13 distance
32 vertices at 14 distance
26 vertices at 15 distance
23 vertices at 16 distance
18 vertices at 17 distance
24 vertices at 18 distance
20 vertices at 19 distance
26 vertices at 20 distance
writing curvature file /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.thickness
positioning took 16.6 minutes
PIDs (25844 25847) completed and logs appended.
#--------------------------------------------
#@# Surf Volume lh Sun Oct  8 00:02:04 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label
Total face volume 285015
Total vertex volume 282017 (mask=0)
#@# 0050660 lh 282017
 
vertexvol Done
#--------------------------------------------
#@# Surf Volume rh Sun Oct  8 00:02:07 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.volume
masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label
Total face volume 291096
Total vertex volume 287734 (mask=0)
#@# 0050660 rh 287734
 
vertexvol Done
#--------------------------------------------
#@# Cortical ribbon mask Sun Oct  8 00:02:11 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 

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 = 95
writing volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/ribbon.mgz
mris_volmask took 15.01 minutes
 writing ribbon files
#-----------------------------------------
#@# Parcellation Stats lh Sun Oct  8 00:17:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 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 0050660 lh pial 

#-----------------------------------------
#@# Parcellation Stats rh Sun Oct  8 00:17:12 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 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 0050660 rh pial 

Waiting for PID 27287 of (27287 27290 27293 27296) to complete...
Waiting for PID 27290 of (27287 27290 27293 27296) to complete...
Waiting for PID 27293 of (27287 27290 27293 27296) to complete...
Waiting for PID 27296 of (27287 27290 27293 27296) 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 0050660 lh white

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015
Total vertex volume 282017 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1210    911   2327  2.539 0.421     0.109     0.022       12     1.0  bankssts
  875    596   1806  2.841 0.529     0.135     0.020       13     0.7  caudalanteriorcingulate
 3461   2286   7426  2.843 0.460     0.125     0.032       41     4.6  caudalmiddlefrontal
 2530   1623   3919  2.120 0.577     0.154     0.049       41     5.2  cuneus
  785    565   2501  3.225 0.757     0.153     0.056       14     2.0  entorhinal
 5543   3801  13707  3.038 0.623     0.139     0.041      104     9.5  fusiform
 7263   4845  14559  2.739 0.464     0.119     0.026       97     7.4  inferiorparietal
 6378   4395  16690  2.977 0.858     0.134     0.037      111    10.9  inferiortemporal
 1998   1331   3872  2.367 1.081     0.125     0.034       30     2.6  isthmuscingulate
 8727   5684  16613  2.559 0.615     0.140     0.035      127    12.3  lateraloccipital
 4006   2712   8602  2.921 0.810     0.140     0.049       66     9.6  lateralorbitofrontal
 4772   3139   7277  2.143 0.639     0.143     0.042       67     8.0  lingual
 3183   2136   7191  2.815 0.899     0.142     0.049       78     6.6  medialorbitofrontal
 5569   3923  15107  2.990 0.715     0.128     0.031       86     7.7  middletemporal
 1318    903   3290  3.023 0.651     0.101     0.031       13     1.5  parahippocampal
 2097   1212   3521  2.640 0.508     0.101     0.029       19     2.7  paracentral
 2220   1460   5186  2.952 0.479     0.112     0.029       27     2.3  parsopercularis
 1062    756   3256  3.121 0.585     0.160     0.054       27     2.4  parsorbitalis
 1898   1313   4198  2.746 0.485     0.123     0.029       27     2.2  parstriangularis
 1992   1347   1796  1.567 0.387     0.158     0.044       27     3.8  pericalcarine
 6846   4383  11441  2.343 0.688     0.121     0.030       83     8.2  postcentral
 1804   1183   3399  2.638 0.641     0.137     0.033       31     2.4  posteriorcingulate
 8716   5111  15207  2.738 0.560     0.111     0.034      107    12.2  precentral
 5563   3765  11280  2.755 0.504     0.123     0.027       73     6.2  precuneus
 1221    796   3007  3.222 0.718     0.131     0.044       27     1.6  rostralanteriorcingulate
 8730   5929  18701  2.698 0.511     0.141     0.037      171    14.0  rostralmiddlefrontal
 9670   6575  21551  2.892 0.605     0.132     0.034      137    13.6  superiorfrontal
 8262   5447  15922  2.560 0.541     0.125     0.028      103     9.1  superiorparietal
 5327   3724  12749  2.937 0.600     0.124     0.027       61     6.1  superiortemporal
 5996   4006  12686  2.851 0.477     0.131     0.034       94     7.9  supramarginal
  412    285   1287  3.100 0.544     0.160     0.052       11     0.9  frontalpole
  747    520   2425  3.116 0.896     0.147     0.053       15     1.7  temporalpole
  774    501   1331  2.381 0.628     0.150     0.057       12     1.8  transversetemporal
 3695   2431   8148  3.352 0.756     0.123     0.038       39     5.6  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 0050660 lh pial

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015
Total vertex volume 282017 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1210    979   2327  2.539 0.421     0.132     0.028       22     1.5  bankssts
  875    714   1806  2.841 0.529     0.149     0.029       34     0.8  caudalanteriorcingulate
 3461   2833   7426  2.843 0.460     0.141     0.037       71     5.1  caudalmiddlefrontal
 2530   1998   3919  2.120 0.577     0.149     0.041       40     4.6  cuneus
  785    997   2501  3.225 0.757     0.209     0.065       20     2.8  entorhinal
 5543   4930  13707  3.038 0.623     0.158     0.040      109     9.7  fusiform
 7263   5816  14559  2.739 0.464     0.139     0.054      159    22.2  inferiorparietal
 6378   6175  16690  2.977 0.858     0.161     0.038      119    12.1  inferiortemporal
 1998   1744   3872  2.367 1.081     0.160     0.041       43     3.5  isthmuscingulate
 8727   7023  16613  2.559 0.615     0.135     0.033      139    12.3  lateraloccipital
 4006   3061   8602  2.921 0.810     0.139     0.036       67     6.1  lateralorbitofrontal
 4772   3681   7277  2.143 0.639     0.140     0.040       75     8.1  lingual
 3183   2816   7191  2.815 0.899     0.165     0.050       80     7.1  medialorbitofrontal
 5569   5875  15107  2.990 0.715     0.157     0.031       70     8.4  middletemporal
 1318   1283   3290  3.023 0.651     0.141     0.029       10     2.0  parahippocampal
 2097   1437   3521  2.640 0.508     0.106     0.022       22     1.9  paracentral
 2220   2012   5186  2.952 0.479     0.145     0.033       29     3.2  parsopercularis
 1062   1257   3256  3.121 0.585     0.188     0.040       15     2.1  parsorbitalis
 1898   1697   4198  2.746 0.485     0.149     0.030       22     2.6  parstriangularis
 1992   1089   1796  1.567 0.387     0.110     0.032       35     2.6  pericalcarine
 6846   5283  11441  2.343 0.688     0.125     0.026       68     8.4  postcentral
 1804   1344   3399  2.638 0.641     0.150     0.044       79     3.2  posteriorcingulate
 8716   5788  15207  2.738 0.560     0.107     0.027      121    10.3  precentral
 5563   4212  11280  2.755 0.504     0.135     0.032      127     7.4  precuneus
 1221   1105   3007  3.222 0.718     0.175     0.046       45     2.5  rostralanteriorcingulate
 8730   7677  18701  2.698 0.511     0.160     0.038      135    14.8  rostralmiddlefrontal
 9670   7940  21551  2.892 0.605     0.142     0.035      167    14.7  superiorfrontal
 8262   6684  15922  2.560 0.541     0.137     0.036      127    10.8  superiorparietal
 5327   4775  12749  2.937 0.600     0.146     0.033       86     7.9  superiortemporal
 5996   4788  12686  2.851 0.477     0.143     0.052      275    17.0  supramarginal
  412    536   1287  3.100 0.544     0.205     0.041        6     0.7  frontalpole
  747   1025   2425  3.116 0.896     0.232     0.057       14     2.2  temporalpole
  774    577   1331  2.381 0.628     0.127     0.032        8     1.0  transversetemporal
 3695   2271   8148  3.352 0.756     0.134     0.040       71     6.6  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050660 rh white

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096
Total vertex volume 287734 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1615   1129   3224  3.033 0.468     0.113     0.023       14     1.6  bankssts
  891    611   1511  2.434 0.543     0.159     0.022       23     0.7  caudalanteriorcingulate
 3234   2173   6458  2.718 0.427     0.125     0.031       41     3.8  caudalmiddlefrontal
 2299   1465   3207  2.001 0.479     0.145     0.043       34     4.2  cuneus
  720    496   2302  3.282 0.780     0.129     0.046       10     1.5  entorhinal
 6132   3962  12865  2.823 0.729     0.134     0.049      119    11.9  fusiform
 9099   5996  18795  2.850 0.482     0.126     0.032      122    11.3  inferiorparietal
 5879   3837  14228  2.963 0.849     0.118     0.036       90     9.0  inferiortemporal
 1430    912   2682  2.430 0.972     0.129     0.029       24     1.7  isthmuscingulate
 7591   5004  14817  2.565 0.603     0.139     0.039      102    11.9  lateraloccipital
 3707   2524   8776  3.135 0.779     0.148     0.045       68     7.3  lateralorbitofrontal
 3887   2536   5494  2.031 0.609     0.146     0.051       64     7.7  lingual
 3410   2290   7595  2.767 0.680     0.127     0.038       63     5.2  medialorbitofrontal
 5957   4130  16241  3.170 0.737     0.127     0.033       92     8.0  middletemporal
 1336    855   2967  2.818 0.686     0.098     0.028       12     1.7  parahippocampal
 3150   1936   5371  2.591 0.502     0.126     0.036       42     4.8  paracentral
 2159   1429   5084  2.955 0.420     0.122     0.035       30     2.7  parsopercularis
 1310    872   3213  2.944 0.629     0.142     0.047       31     2.3  parsorbitalis
 2275   1542   5043  2.801 0.538     0.130     0.031       34     2.7  parstriangularis
 2164   1429   2149  1.693 0.443     0.144     0.044       27     3.9  pericalcarine
 7925   4792  12615  2.330 0.675     0.116     0.034       98    12.4  postcentral
 2126   1399   4219  2.579 0.721     0.132     0.030       33     2.7  posteriorcingulate
 9763   5839  16276  2.578 0.632     0.119     0.037      140    14.9  precentral
 5171   3418  10299  2.764 0.532     0.118     0.029       58     6.4  precuneus
  810    505   1853  2.997 0.783     0.129     0.031       14     1.1  rostralanteriorcingulate
 8124   5583  17973  2.765 0.576     0.143     0.037      149    13.1  rostralmiddlefrontal
10094   6789  22498  2.853 0.586     0.132     0.039      389    18.0  superiorfrontal
 8089   5237  14806  2.514 0.480     0.124     0.032      108    10.3  superiorparietal
 5989   4083  15625  3.194 0.660     0.119     0.027       71     6.5  superiortemporal
 7085   4749  15400  2.855 0.525     0.131     0.035      101    10.0  supramarginal
  500    334   1519  3.302 0.539     0.168     0.043       13     0.8  frontalpole
  674    448   2730  3.742 0.690     0.141     0.049       10     1.4  temporalpole
  590    360   1051  2.790 0.465     0.140     0.036        8     0.8  transversetemporal
 4321   2834   8780  3.038 0.970     0.127     0.040       58     6.2  insula

 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab 0050660 rh pial

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096
Total vertex volume 287734 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1615    980   3224  3.033 0.468     0.119     0.031       25     2.1  bankssts
  891    657   1511  2.434 0.543     0.177     0.044       66     1.4  caudalanteriorcingulate
 3234   2538   6458  2.718 0.427     0.132     0.030       62     4.2  caudalmiddlefrontal
 2299   1773   3207  2.001 0.479     0.136     0.035       29     3.6  cuneus
  720    827   2302  3.282 0.780     0.183     0.073       60     1.3  entorhinal
 6132   4852  12865  2.823 0.729     0.145     0.040      129    10.6  fusiform
 9099   7042  18795  2.850 0.482     0.137     0.033      139    13.3  inferiorparietal
 5879   5391  14228  2.963 0.849     0.147     0.034      116     9.3  inferiortemporal
 1430   1143   2682  2.430 0.972     0.149     0.040       26     2.2  isthmuscingulate
 7591   6331  14817  2.565 0.603     0.135     0.033      128    10.5  lateraloccipital
 3707   2969   8776  3.135 0.779     0.153     0.038      111     6.4  lateralorbitofrontal
 3887   2945   5494  2.031 0.609     0.139     0.038       60     6.6  lingual
 3410   3071   7595  2.767 0.680     0.158     0.038       50     5.6  medialorbitofrontal
 5957   5908  16241  3.170 0.737     0.155     0.035       91     9.0  middletemporal
 1336   1218   2967  2.818 0.686     0.136     0.037       17     2.5  parahippocampal
 3150   2128   5371  2.591 0.502     0.117     0.032       47     4.2  paracentral
 2159   1974   5084  2.955 0.420     0.156     0.034       28     3.5  parsopercularis
 1310   1279   3213  2.944 0.629     0.154     0.029       15     1.7  parsorbitalis
 2275   1984   5043  2.801 0.538     0.155     0.035       31     3.6  parstriangularis
 2164   1243   2149  1.693 0.443     0.107     0.030       47     2.6  pericalcarine
 7925   5939  12615  2.330 0.675     0.116     0.027       73     9.9  postcentral
 2126   1737   4219  2.579 0.721     0.154     0.034       58     3.2  posteriorcingulate
 9763   6461  16276  2.578 0.632     0.108     0.029      124    11.3  precentral
 5171   3848  10299  2.764 0.532     0.131     0.033       82     6.7  precuneus
  810    730   1853  2.997 0.783     0.199     0.076       26     3.3  rostralanteriorcingulate
 8124   7223  17973  2.765 0.576     0.161     0.038      144    14.4  rostralmiddlefrontal
10094   8510  22498  2.853 0.586     0.145     0.041      176    17.0  superiorfrontal
 8089   6390  14806  2.514 0.480     0.131     0.028      100     9.5  superiorparietal
 5989   5440  15625  3.194 0.660     0.137     0.029       62     7.8  superiortemporal
 7085   5767  15400  2.855 0.525     0.144     0.036      110    11.0  supramarginal
  500    587   1519  3.302 0.539     0.198     0.038        7     0.9  frontalpole
  674    970   2730  3.742 0.690     0.235     0.048        7     1.6  temporalpole
  590    395   1051  2.790 0.465     0.112     0.034        5     0.8  transversetemporal
 4321   2730   8780  3.038 0.970     0.135     0.043       99     8.0  insula
PIDs (27287 27290 27293 27296) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 2 lh Sun Oct  8 00:18:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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 00:18:32 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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 27374 of (27374 27377) to complete...
Waiting for PID 27377 of (27374 27377) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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...
40 labels changed using aseg
relabeling using gibbs priors...
000:   9013 changed, 142936 examined...
001:   2095 changed, 35640 examined...
002:    664 changed, 10990 examined...
003:    283 changed, 3670 examined...
004:    130 changed, 1631 examined...
005:     65 changed, 734 examined...
006:     36 changed, 377 examined...
007:     25 changed, 197 examined...
008:      7 changed, 126 examined...
009:      2 changed, 38 examined...
010:      2 changed, 11 examined...
011:      1 changed, 8 examined...
012:      2 changed, 8 examined...
013:      0 changed, 12 examined...
10 labels changed using aseg
000: 254 total segments, 170 labels (1460 vertices) changed
001: 88 total segments, 4 labels (9 vertices) changed
002: 84 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 42 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1224 vertices marked for relabeling...
1224 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 0 minutes and 19 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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...
7 labels changed using aseg
relabeling using gibbs priors...
000:   9597 changed, 147238 examined...
001:   2179 changed, 37405 examined...
002:    651 changed, 11445 examined...
003:    277 changed, 3670 examined...
004:    140 changed, 1578 examined...
005:     66 changed, 785 examined...
006:     30 changed, 373 examined...
007:     15 changed, 167 examined...
008:      8 changed, 97 examined...
009:      4 changed, 35 examined...
010:      2 changed, 24 examined...
011:      0 changed, 9 examined...
14 labels changed using aseg
000: 288 total segments, 202 labels (2388 vertices) changed
001: 104 total segments, 18 labels (128 vertices) changed
002: 87 total segments, 1 labels (1 vertices) changed
003: 86 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 52 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1553 vertices marked for relabeling...
1553 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 0 minutes and 20 seconds.
PIDs (27374 27377) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 2 lh Sun Oct  8 00:18:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white 

#-----------------------------------------
#@# Parcellation Stats 2 rh Sun Oct  8 00:18:52 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white 

Waiting for PID 27443 of (27443 27446) to complete...
Waiting for PID 27446 of (27443 27446) 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 0050660 lh white

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015
Total vertex volume 282017 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1546   1078   3738  2.833 0.735     0.144     0.036       29     2.3  G&S_frontomargin
 1653   1140   4008  2.944 0.568     0.149     0.035       28     2.2  G&S_occipital_inf
 1579    824   2538  2.506 0.490     0.106     0.034       19     1.9  G&S_paracentral
 1631   1096   4159  3.126 0.621     0.134     0.033       23     2.1  G&S_subcentral
  746    520   2009  2.922 0.423     0.159     0.048       20     1.5  G&S_transv_frontopol
 2379   1609   5606  3.170 0.587     0.136     0.044       43     3.6  G&S_cingul-Ant
 1025    736   2187  2.815 0.421     0.111     0.019       10     0.7  G&S_cingul-Mid-Ant
 1199    842   2352  2.751 0.393     0.126     0.034       15     1.8  G&S_cingul-Mid-Post
  861    580   2420  3.134 0.733     0.148     0.039       14     1.3  G_cingul-Post-dorsal
  323    214    911  2.910 1.185     0.144     0.044        6     0.4  G_cingul-Post-ventral
 2272   1443   3759  2.079 0.717     0.150     0.050       38     4.7  G_cuneus
 1514    978   4086  3.056 0.491     0.128     0.037       26     2.0  G_front_inf-Opercular
  407    267   1321  3.246 0.367     0.130     0.032        6     0.6  G_front_inf-Orbital
 1162    766   3099  2.881 0.508     0.144     0.040       24     2.0  G_front_inf-Triangul
 4955   3259  12653  2.876 0.480     0.150     0.045      118     9.4  G_front_middle
 7088   4654  17296  2.978 0.622     0.139     0.040      131    12.1  G_front_sup
  716    494   1830  3.533 0.775     0.164     0.059       14     1.8  G_Ins_lg&S_cent_ins
  845    524   2803  3.876 0.716     0.122     0.042       12     1.4  G_insular_short
 3106   1950   7710  2.923 0.511     0.134     0.032       59     3.7  G_occipital_middle
 1604    975   2942  2.399 0.656     0.136     0.037       25     2.4  G_occipital_sup
 2193   1444   6102  3.093 0.553     0.151     0.050       49     4.4  G_oc-temp_lat-fusifor
 3322   2138   5232  2.053 0.643     0.159     0.053       59     7.0  G_oc-temp_med-Lingual
 1728   1210   5165  3.149 0.745     0.130     0.047       27     3.2  G_oc-temp_med-Parahip
 2689   1764   7230  2.972 0.859     0.162     0.069       75     9.1  G_orbital
 2648   1721   6680  2.932 0.565     0.137     0.038       54     4.0  G_pariet_inf-Angular
 2959   1935   7246  2.996 0.477     0.142     0.040       58     4.6  G_pariet_inf-Supramar
 3031   1994   7296  2.773 0.519     0.137     0.035       52     3.7  G_parietal_sup
 2554   1549   4523  2.294 0.581     0.131     0.037       40     4.0  G_postcentral
 3396   1698   6653  2.917 0.570     0.107     0.042       63     6.0  G_precentral
 2651   1760   7026  2.979 0.519     0.144     0.036       58     3.9  G_precuneus
  938    606   2795  2.957 0.899     0.160     0.055       35     2.4  G_rectus
  738    478   1425  2.473 1.270     0.122     0.066       15     1.7  G_subcallosal
  698    435   1352  2.404 0.651     0.160     0.065       14     1.7  G_temp_sup-G_T_transv
 1762   1253   6112  3.162 0.613     0.143     0.038       32     2.7  G_temp_sup-Lateral
  601    475   2097  3.532 0.726     0.105     0.021        4     0.5  G_temp_sup-Plan_polar
  824    580   1913  2.808 0.356     0.093     0.019        6     0.5  G_temp_sup-Plan_tempo
 3421   2346  10882  3.035 0.964     0.150     0.048       85     7.8  G_temporal_inf
 3170   2261  10499  3.182 0.774     0.139     0.035       63     5.0  G_temporal_middle
  380    265    677  2.851 0.583     0.097     0.017        2     0.2  Lat_Fis-ant-Horizont
  330    231    610  2.620 0.438     0.085     0.014        1     0.2  Lat_Fis-ant-Vertical
 1165    775   1654  2.672 0.455     0.111     0.025        8     1.1  Lat_Fis-post
 2061   1317   3857  2.380 0.694     0.145     0.046       32     3.6  Pole_occipital
 2092   1433   6901  3.198 0.830     0.154     0.054       45     5.0  Pole_temporal
 2509   1733   2617  1.815 0.601     0.142     0.034       28     3.6  S_calcarine
 3563   2313   4024  2.063 0.518     0.114     0.028       27     4.3  S_central
  884    633   1405  2.519 0.350     0.093     0.015        4     0.6  S_cingul-Marginalis
  540    361   1062  3.304 0.530     0.099     0.020        2     0.5  S_circular_insula_ant
 1410    972   2249  3.007 0.604     0.101     0.022        7     1.3  S_circular_insula_inf
 1712   1168   2564  2.765 0.425     0.103     0.021        8     1.6  S_circular_insula_sup
 1232    835   2504  3.049 0.830     0.113     0.029       23     1.7  S_collat_transv_ant
  635    445    839  2.356 0.344     0.135     0.028        5     0.8  S_collat_transv_post
 1843   1271   2832  2.617 0.387     0.111     0.025       16     1.9  S_front_inf
 1558   1068   2382  2.471 0.331     0.117     0.024       14     1.5  S_front_middle
 2532   1781   4355  2.556 0.410     0.114     0.024       19     2.8  S_front_sup
  265    180    385  2.493 0.249     0.114     0.020        2     0.3  S_interm_prim-Jensen
 3162   2120   4705  2.520 0.378     0.108     0.019       25     2.5  S_intrapariet&P_trans
 1515   1033   2090  2.335 0.456     0.128     0.025       13     1.6  S_oc_middle&Lunatus
 1519   1024   2028  2.215 0.386     0.121     0.025       14     1.5  S_oc_sup&transversal
  775    538   1243  2.676 0.379     0.127     0.024       11     0.8  S_occipital_ant
 1017    718   1785  2.869 0.508     0.119     0.027        7     1.2  S_oc-temp_lat
 2438   1716   4184  2.757 0.482     0.112     0.024       17     2.3  S_oc-temp_med&Lingual
  391    263    659  2.757 0.444     0.098     0.017        2     0.3  S_orbital_lateral
  687    500   1182  2.778 0.715     0.126     0.024        5     0.8  S_orbital_med-olfact
 1422   1007   2872  2.877 0.744     0.134     0.036       18     2.2  S_orbital-H_Shaped
 2274   1529   3396  2.373 0.397     0.125     0.029       22     2.7  S_parieto_occipital
 1627    951   1435  1.998 1.006     0.122     0.025       29     1.5  S_pericallosal
 3476   2328   5354  2.498 0.375     0.113     0.023       28     3.3  S_postcentral
 1648   1110   3043  2.825 0.373     0.103     0.019       12     1.2  S_precentral-inf-part
 1680   1135   2567  2.615 0.397     0.121     0.025       13     1.8  S_precentral-sup-part
  785    539   1296  2.671 0.573     0.129     0.026        8     0.9  S_suborbital
 1459   1000   2314  2.641 0.345     0.108     0.021       11     1.2  S_subparietal
 2337   1623   3588  2.640 0.460     0.109     0.021       16     2.0  S_temporal_inf
 5423   3803   9120  2.657 0.462     0.113     0.022       46     5.0  S_temporal_sup
  419    303    581  2.332 0.472     0.137     0.023        4     0.5  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 0050660 rh white

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096
Total vertex volume 287734 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1009    680   2366  2.981 0.598     0.152     0.039       22     1.6  G&S_frontomargin
 1548   1043   3846  2.901 0.561     0.137     0.038       24     2.3  G&S_occipital_inf
 1774   1053   2886  2.353 0.545     0.129     0.042       28     3.2  G&S_paracentral
 1767   1206   4665  3.215 0.447     0.142     0.039       25     2.8  G&S_subcentral
  984    711   3087  3.310 0.596     0.175     0.050       26     1.9  G&S_transv_frontopol
 3395   2287   7183  2.897 0.525     0.130     0.032       50     4.5  G&S_cingul-Ant
 1307    916   2646  2.823 0.423     0.127     0.026       18     1.3  G&S_cingul-Mid-Ant
 1773   1187   3446  2.730 0.424     0.121     0.028       21     2.1  G&S_cingul-Mid-Post
  522    364   1703  3.054 0.783     0.152     0.035        9     0.8  G_cingul-Post-dorsal
  343    219   1005  3.182 0.881     0.152     0.044        9     0.6  G_cingul-Post-ventral
 2135   1339   3016  1.949 0.525     0.146     0.046       34     4.1  G_cuneus
 1665   1077   4511  3.102 0.406     0.134     0.041       30     2.5  G_front_inf-Opercular
  429    287   1177  2.968 0.608     0.145     0.037       10     0.6  G_front_inf-Orbital
  757    513   2084  2.983 0.433     0.143     0.037       16     1.0  G_front_inf-Triangul
 4088   2766  10604  2.794 0.569     0.157     0.048      103     8.5  G_front_middle
 6641   4254  15793  2.877 0.616     0.140     0.047      365    14.9  G_front_sup
  850    570   2131  3.608 0.659     0.140     0.041       14     1.2  G_Ins_lg&S_cent_ins
 1064    695   2923  3.282 0.905     0.153     0.053       23     2.1  G_insular_short
 2136   1343   5409  3.003 0.472     0.143     0.043       38     3.4  G_occipital_middle
 1536    880   2733  2.417 0.623     0.134     0.042       25     2.9  G_occipital_sup
 2597   1642   6229  2.944 0.735     0.144     0.048       52     5.0  G_oc-temp_lat-fusifor
 2139   1371   3373  2.051 0.632     0.156     0.057       40     4.5  G_oc-temp_med-Lingual
 1830   1206   4969  2.981 0.808     0.125     0.047       28     4.0  G_oc-temp_med-Parahip
 2699   1811   8158  3.284 0.777     0.154     0.053       69     6.0  G_orbital
 4004   2563  10618  3.036 0.522     0.145     0.046       86     7.2  G_pariet_inf-Angular
 3596   2412   8867  2.956 0.569     0.140     0.035       59     5.2  G_pariet_inf-Supramar
 2682   1773   6030  2.669 0.464     0.139     0.036       49     4.0  G_parietal_sup
 3079   1579   4625  2.211 0.573     0.123     0.049       53     7.1  G_postcentral
 3894   2100   7223  2.673 0.627     0.121     0.047       58     8.0  G_precentral
 2294   1503   5837  2.911 0.571     0.135     0.036       39     3.7  G_precuneus
  946    648   2929  2.973 0.817     0.166     0.060       30     2.0  G_rectus
  746    423    896  1.872 1.325     0.100     0.049       10     1.2  G_subcallosal
  444    264    948  2.842 0.484     0.141     0.035        7     0.6  G_temp_sup-G_T_transv
 2087   1407   7303  3.603 0.640     0.148     0.041       42     3.3  G_temp_sup-Lateral
  740    516   2136  3.480 0.567     0.094     0.019        4     0.6  G_temp_sup-Plan_polar
 1184    805   2639  2.936 0.582     0.114     0.028       11     1.3  G_temp_sup-Plan_tempo
 3086   1959   8882  3.154 0.876     0.128     0.044       64     5.9  G_temporal_inf
 3617   2459  12155  3.445 0.724     0.140     0.042       74     5.9  G_temporal_middle
  542    357   1049  2.712 0.560     0.109     0.024        6     0.5  Lat_Fis-ant-Horizont
  204    148    312  2.409 0.512     0.118     0.019        1     0.2  Lat_Fis-ant-Vertical
 1591   1077   2465  2.710 0.416     0.118     0.027       14     1.8  Lat_Fis-post
 3391   2200   5374  2.112 0.662     0.154     0.055       57     7.3  Pole_occipital
 2040   1408   7374  3.391 0.842     0.157     0.060       43     5.1  Pole_temporal
 2011   1382   2348  1.987 0.663     0.133     0.036       20     3.0  S_calcarine
 3622   2316   3794  1.940 0.609     0.112     0.031       52     4.4  S_central
 1626   1116   2788  2.652 0.323     0.118     0.027       14     1.7  S_cingul-Marginalis
  628    420   1058  3.129 0.459     0.101     0.021        3     0.5  S_circular_insula_ant
 1036    717   1605  2.829 0.526     0.088     0.018        4     0.8  S_circular_insula_inf
 1379    928   2280  2.939 0.505     0.103     0.020        6     1.2  S_circular_insula_sup
 1353    873   2321  2.777 0.715     0.106     0.038       13     1.9  S_collat_transv_ant
  532    367    755  2.279 0.391     0.133     0.041        6     0.9  S_collat_transv_post
 1866   1265   3145  2.569 0.356     0.115     0.024       18     1.8  S_front_inf
 1878   1304   3016  2.553 0.458     0.126     0.027       14     2.2  S_front_middle
 2856   1947   5239  2.622 0.451     0.117     0.025       30     2.8  S_front_sup
  263    177    435  2.890 0.345     0.116     0.025        2     0.3  S_interm_prim-Jensen
 3702   2476   6157  2.533 0.360     0.106     0.021       32     3.0  S_intrapariet&P_trans
  776    520    990  2.321 0.318     0.120     0.030        5     1.0  S_oc_middle&Lunatus
 1071    739   1415  2.220 0.481     0.123     0.027        9     1.1  S_oc_sup&transversal
 1139    743   1676  2.556 0.410     0.116     0.023       10     1.2  S_occipital_ant
 1488   1010   2423  2.650 0.663     0.102     0.023       12     1.6  S_oc-temp_lat
 2618   1709   3867  2.476 0.579     0.115     0.037       41     3.6  S_oc-temp_med&Lingual
  595    394   1017  2.850 0.644     0.123     0.025        6     0.6  S_orbital_lateral
  747    526   1263  2.606 0.593     0.099     0.019        5     0.4  S_orbital_med-olfact
 1542   1046   3150  3.014 0.716     0.144     0.044       22     2.9  S_orbital-H_Shaped
 2149   1416   3113  2.407 0.478     0.114     0.027       20     2.4  S_parieto_occipital
 1493    874   1179  1.808 0.680     0.135     0.025       29     1.4  S_pericallosal
 3278   2184   4618  2.461 0.410     0.110     0.021       26     2.8  S_postcentral
 1699   1148   2806  2.794 0.354     0.109     0.021       12     1.5  S_precentral-inf-part
 2245   1479   3529  2.601 0.384     0.107     0.020       19     1.7  S_precentral-sup-part
  417    294    650  2.551 0.478     0.133     0.028        4     0.6  S_suborbital
 1043    701   1821  2.822 0.463     0.104     0.019        6     0.8  S_subparietal
 1758   1198   2513  2.595 0.471     0.100     0.016       11     1.1  S_temporal_inf
 7266   5018  12669  2.821 0.439     0.106     0.019       52     6.2  S_temporal_sup
  297    201    488  2.970 0.409     0.111     0.022        2     0.3  S_temporal_transverse
PIDs (27443 27446) completed and logs appended.
#-----------------------------------------
#@# Cortical Parc 3 lh Sun Oct  8 00:19:33 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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 00:19:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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 27498 of (27498 27501) to complete...
Waiting for PID 27501 of (27498 27501) to complete...

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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...
1376 labels changed using aseg
relabeling using gibbs priors...
000:   2077 changed, 142936 examined...
001:    484 changed, 9606 examined...
002:    118 changed, 2767 examined...
003:     46 changed, 738 examined...
004:     20 changed, 297 examined...
005:     11 changed, 109 examined...
006:     14 changed, 73 examined...
007:      7 changed, 78 examined...
008:      7 changed, 47 examined...
009:      1 changed, 41 examined...
010:      1 changed, 6 examined...
011:      1 changed, 7 examined...
012:      1 changed, 7 examined...
013:      2 changed, 7 examined...
014:      0 changed, 8 examined...
202 labels changed using aseg
000: 55 total segments, 22 labels (183 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 5 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1020 vertices marked for relabeling...
1020 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classification took 0 minutes and 15 seconds.

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 0050660 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...
1393 labels changed using aseg
relabeling using gibbs priors...
000:   2253 changed, 147238 examined...
001:    564 changed, 10452 examined...
002:    160 changed, 3153 examined...
003:     64 changed, 906 examined...
004:     48 changed, 392 examined...
005:     25 changed, 246 examined...
006:     19 changed, 162 examined...
007:      6 changed, 105 examined...
008:      2 changed, 39 examined...
009:      1 changed, 14 examined...
010:      0 changed, 7 examined...
299 labels changed using aseg
000: 69 total segments, 36 labels (499 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, 15 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1127 vertices marked for relabeling...
1127 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classification took 0 minutes and 16 seconds.
PIDs (27498 27501) completed and logs appended.
#-----------------------------------------
#@# Parcellation Stats 3 lh Sun Oct  8 00:19:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white 

#-----------------------------------------
#@# Parcellation Stats 3 rh Sun Oct  8 00:19:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white 

Waiting for PID 27552 of (27552 27555) to complete...
Waiting for PID 27555 of (27552 27555) 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 0050660 lh white

computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 285015
Total vertex volume 282017 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1502   1030   2954  2.818 0.473     0.133     0.022       20     1.3  caudalanteriorcingulate
 3711   2455   7864  2.856 0.455     0.126     0.032       43     4.9  caudalmiddlefrontal
 3365   2178   5557  2.239 0.631     0.143     0.042       49     5.8  cuneus
  677    493   2096  3.180 0.792     0.149     0.051       12     1.5  entorhinal
 5013   3430  11805  2.993 0.573     0.138     0.040       92     8.3  fusiform
 7377   4908  14956  2.748 0.475     0.122     0.027      107     7.9  inferiorparietal
 6382   4378  17671  3.057 0.888     0.139     0.041      119    12.0  inferiortemporal
 1998   1318   3805  2.365 1.075     0.124     0.034       31     2.5  isthmuscingulate
 8742   5685  16844  2.563 0.625     0.138     0.035      126    12.0  lateraloccipital
 4396   2989  10024  2.919 0.832     0.146     0.051       82    10.8  lateralorbitofrontal
 4939   3256   7485  2.134 0.636     0.144     0.042       69     8.2  lingual
 2472   1655   5887  2.833 0.814     0.142     0.048       60     4.9  medialorbitofrontal
 7088   5058  18143  2.909 0.692     0.125     0.029      102     9.1  middletemporal
 1371    939   3438  3.039 0.643     0.102     0.033       14     1.6  parahippocampal
 2477   1466   4248  2.666 0.513     0.102     0.028       21     3.1  paracentral
 2058   1352   4672  2.932 0.463     0.112     0.029       26     2.0  parsopercularis
 1095    720   2798  3.059 0.543     0.127     0.043       18     2.1  parsorbitalis
 2342   1603   4905  2.715 0.489     0.123     0.029       30     2.8  parstriangularis
 1998   1348   1822  1.575 0.394     0.158     0.044       27     3.9  pericalcarine
 7724   4978  12879  2.366 0.672     0.122     0.030       92     9.5  postcentral
 1929   1259   3543  2.633 0.651     0.134     0.033       31     2.5  posteriorcingulate
 8533   4994  14932  2.733 0.560     0.110     0.034      105    12.1  precentral
 5403   3679  11369  2.774 0.506     0.124     0.028       74     6.2  precuneus
 1771   1144   3808  3.037 0.929     0.131     0.048       36     3.0  rostralanteriorcingulate
 6221   4235  13891  2.755 0.528     0.143     0.039      122    10.6  rostralmiddlefrontal
11086   7594  25238  2.853 0.610     0.137     0.036      191    16.6  superiorfrontal
 6625   4351  12620  2.562 0.508     0.125     0.028       82     7.2  superiorparietal
 7096   4954  16990  2.928 0.630     0.127     0.031       87     9.4  superiortemporal
 5478   3641  11311  2.834 0.462     0.129     0.034       79     7.1  supramarginal
  752    485   1288  2.375 0.625     0.149     0.058       12     1.7  transversetemporal
 3078   2039   7175  3.458 0.724     0.118     0.033       31     4.0  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 0050660 rh white

computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 291096
Total vertex volume 287734 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1106    752   2110  2.544 0.615     0.157     0.024       27     1.0  caudalanteriorcingulate
 3376   2267   6720  2.713 0.425     0.125     0.030       44     3.8  caudalmiddlefrontal
 2682   1715   3785  2.061 0.494     0.140     0.041       36     4.6  cuneus
  642    449   2074  3.374 0.615     0.125     0.039        6     1.0  entorhinal
 5568   3594  11284  2.803 0.699     0.132     0.048      104    10.3  fusiform
 8900   5875  18548  2.854 0.484     0.129     0.033      124    11.4  inferiorparietal
 6356   4175  15920  2.982 0.867     0.120     0.038      101    10.1  inferiortemporal
 1451    925   2709  2.443 0.963     0.128     0.029       24     1.7  isthmuscingulate
 7773   5095  14952  2.535 0.611     0.138     0.039      104    12.2  lateraloccipital
 4513   3043  11117  3.154 0.787     0.150     0.048       94     8.8  lateralorbitofrontal
 3789   2483   5399  2.045 0.601     0.150     0.051       64     7.7  lingual
 2647   1720   5882  2.599 1.011     0.134     0.046       52     4.4  medialorbitofrontal
 7309   5053  18954  3.137 0.705     0.123     0.031      101     9.2  middletemporal
 1446    915   3096  2.776 0.713     0.101     0.033       17     2.3  parahippocampal
 3294   2025   5752  2.608 0.522     0.126     0.037       43     5.0  paracentral
 2459   1649   5617  2.912 0.424     0.124     0.034       33     3.1  parsopercularis
 1130    738   2123  2.619 0.510     0.113     0.027       15     1.2  parsorbitalis
 2270   1533   5158  2.832 0.537     0.128     0.031       36     2.6  parstriangularis
 2180   1405   2140  1.693 0.445     0.144     0.048       29     4.3  pericalcarine
 8673   5287  13646  2.335 0.659     0.119     0.034      107    13.3  postcentral
 2169   1418   4251  2.599 0.719     0.131     0.031       32     2.8  posteriorcingulate
 9258   5535  15696  2.594 0.638     0.119     0.038      133    14.5  precentral
 5324   3523  10782  2.751 0.537     0.118     0.029       61     6.5  precuneus
 1115    710   2235  2.865 0.786     0.117     0.027       16     1.3  rostralanteriorcingulate
 5793   3927  12192  2.713 0.567     0.143     0.039      103     9.8  rostralmiddlefrontal
13261   8971  29507  2.840 0.580     0.136     0.040      459    23.8  superiorfrontal
 6769   4393  12614  2.547 0.476     0.122     0.031       90     8.6  superiorparietal
 7702   5260  20233  3.200 0.662     0.121     0.029       94     8.9  superiortemporal
 6692   4483  14644  2.856 0.534     0.130     0.034       94     9.4  supramarginal
  585    358   1029  2.772 0.459     0.141     0.036        8     0.8  transversetemporal
 3296   2234   7567  3.337 0.670     0.125     0.032       39     4.2  insula
PIDs (27552 27555) completed and logs appended.
#-----------------------------------------
#@# WM/GM Contrast lh Sun Oct  8 00:20:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 pctsurfcon --s 0050660 --lh-only 

#-----------------------------------------
#@# WM/GM Contrast rh Sun Oct  8 00:20:30 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts

 pctsurfcon --s 0050660 --rh-only 

Waiting for PID 27636 of (27636 27648) to complete...
Waiting for PID 27648 of (27636 27648) to complete...

 pctsurfcon --s 0050660 --lh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts/pctsurfcon.log
Sun Oct  8 00:20:30 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-6.0.0/0050660/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-542 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-6.0.0/0050660/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.wm.mgh --regheader 0050660 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 77480
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.wm.mgh
Dim: 142936 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.gm.mgh --projfrac 0.3 --regheader 0050660 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 93123
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.gm.mgh
Dim: 142936 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27636/lh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/lh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.w-g.pct.mgh --annot 0050660 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/lh.w-g.pct.mgh --annot 0050660 lh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/lh.w-g.pct.mgh
Vertex Area is 0.664865 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 0050660 --rh-only

Log file is /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/scripts/pctsurfcon.log
Sun Oct  8 00:20:30 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-6.0.0/0050660/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-542 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-6.0.0/0050660/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.wm.mgh --regheader 0050660 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 78821
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.wm.mgh
Dim: 147238 1 1
mri_vol2surf --mov /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.gm.mgh --projfrac 0.3 --regheader 0050660 --cortex
srcvol = /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Loading label /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label
Reading surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white
Done reading source surface
Reading thickness /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 95188
Masking with /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.cortex.label
Writing to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.gm.mgh
Dim: 147238 1 1
mri_concat /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.wm.mgh /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/tmp.pctsurfcon.27648/rh.gm.mgh --paired-diff-norm --mul 100 --o /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.w-g.pct.mgh
mri_segstats --in /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.w-g.pct.mgh --annot 0050660 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.w-g.pct.mgh --annot 0050660 rh aparc --sum /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut
UseRobust  0
Constructing seg from annotation

Reading annotation /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.w-g.pct.mgh
Vertex Area is 0.657735 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 (27636 27648) completed and logs appended.
#-----------------------------------------
#@# Relabel Hypointensities Sun Oct  8 00:20:36 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

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

reading input surface ../surf/lh.white...
relabeling lh hypointensities...
2795 voxels changed to hypointensity...
reading input surface ../surf/rh.white...
relabeling rh hypointensities...
3281 voxels changed to hypointensity...
5979 hypointense voxels neighboring cortex changed
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Oct  8 00:21:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660

 mri_aparc2aseg --s 0050660 --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 00:21:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660

 mri_aparc2aseg --s 0050660 --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 00:21:00 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660

 mri_aparc2aseg --s 0050660 --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 27815 of (27815 27818 27821) to complete...
Waiting for PID 27818 of (27815 27818 27821) to complete...
Waiting for PID 27821 of (27815 27818 27821) to complete...

 mri_aparc2aseg --s 0050660 --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 0050660
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/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-6.0.0/0050660/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 7.19
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 107
rescaling Left_Cerebral_Cortex from 61 --> 73
rescaling Left_Lateral_Ventricle from 13 --> 32
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 70
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 92
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 48
rescaling Fourth_Ventricle from 22 --> 32
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 70
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 70
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 75
rescaling Right_Lateral_Ventricle from 13 --> 28
rescaling Right_Inf_Lat_Vent from 25 --> 29
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 71
rescaling Right_Thalamus_Proper from 85 --> 88
rescaling Right_Caudate from 62 --> 83
rescaling Right_Putamen from 80 --> 86
rescaling Right_Pallidum from 97 --> 103
rescaling Right_Hippocampus from 53 --> 71
rescaling Right_Amygdala from 55 --> 73
rescaling Right_Accumbens_area from 65 --> 82
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 58
rescaling WM_hypointensities from 78 --> 80
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 564001
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 184 changed.
pass 2: 15 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc+aseg.mgz

 mri_aparc2aseg --s 0050660 --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 0050660
outvol /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/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-6.0.0/0050660/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 7.19
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 107
rescaling Left_Cerebral_Cortex from 61 --> 73
rescaling Left_Lateral_Ventricle from 13 --> 32
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 70
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 92
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 48
rescaling Fourth_Ventricle from 22 --> 32
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 70
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 70
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 75
rescaling Right_Lateral_Ventricle from 13 --> 28
rescaling Right_Inf_Lat_Vent from 25 --> 29
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 71
rescaling Right_Thalamus_Proper from 85 --> 88
rescaling Right_Caudate from 62 --> 83
rescaling Right_Putamen from 80 --> 86
rescaling Right_Pallidum from 97 --> 103
rescaling Right_Hippocampus from 53 --> 71
rescaling Right_Amygdala from 55 --> 73
rescaling Right_Accumbens_area from 65 --> 82
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 58
rescaling WM_hypointensities from 78 --> 80
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 564054
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 184 changed.
pass 2: 15 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/aparc.a2009s+aseg.mgz

 mri_aparc2aseg --s 0050660 --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 0050660
outvol mri/aparc.DKTatlas+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/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-6.0.0/0050660/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 7.19
reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt
rescaling Left_Cerebral_White_Matter from 107 --> 107
rescaling Left_Cerebral_Cortex from 61 --> 73
rescaling Left_Lateral_Ventricle from 13 --> 32
rescaling Left_Inf_Lat_Vent from 34 --> 33
rescaling Left_Cerebellum_White_Matter from 86 --> 88
rescaling Left_Cerebellum_Cortex from 60 --> 70
rescaling Left_Thalamus from 94 --> 105
rescaling Left_Thalamus_Proper from 84 --> 93
rescaling Left_Caudate from 75 --> 88
rescaling Left_Putamen from 80 --> 92
rescaling Left_Pallidum from 98 --> 100
rescaling Third_Ventricle from 25 --> 48
rescaling Fourth_Ventricle from 22 --> 32
rescaling Brain_Stem from 81 --> 82
rescaling Left_Hippocampus from 57 --> 70
rescaling Left_Amygdala from 56 --> 69
rescaling CSF from 32 --> 70
rescaling Left_Accumbens_area from 62 --> 71
rescaling Left_VentralDC from 87 --> 90
rescaling Right_Cerebral_White_Matter from 105 --> 105
rescaling Right_Cerebral_Cortex from 58 --> 75
rescaling Right_Lateral_Ventricle from 13 --> 28
rescaling Right_Inf_Lat_Vent from 25 --> 29
rescaling Right_Cerebellum_White_Matter from 87 --> 89
rescaling Right_Cerebellum_Cortex from 59 --> 71
rescaling Right_Thalamus_Proper from 85 --> 88
rescaling Right_Caudate from 62 --> 83
rescaling Right_Putamen from 80 --> 86
rescaling Right_Pallidum from 97 --> 103
rescaling Right_Hippocampus from 53 --> 71
rescaling Right_Amygdala from 55 --> 73
rescaling Right_Accumbens_area from 65 --> 82
rescaling Right_VentralDC from 86 --> 95
rescaling Fifth_Ventricle from 40 --> 58
rescaling WM_hypointensities from 78 --> 80
rescaling non_WM_hypointensities from 40 --> 56
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 564054
Used brute-force search on 0 voxels
relabeling unlikely voxels in interior of white matter
average std[0] = 7.3
pass 1: 184 changed.
pass 2: 15 changed.
pass 3: 0 changed.
nchanged = 0
Writing output aseg to mri/aparc.DKTatlas+aseg.mgz
PIDs (27815 27818 27821) completed and logs appended.
#-----------------------------------------
#@# APas-to-ASeg Sun Oct  8 00:28:44 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri

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

Sun Oct  8 00:28:44 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-6.0.0/0050660/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-542 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-6.0.0/0050660/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-542
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 00:28:44 CEST 2017 
Ended   at Sun Oct  8 00:28:50 CEST 2017
Apas2aseg-Run-Time-Sec 6
 
apas2aseg Done
#--------------------------------------------
#@# ASeg Stats Sun Oct  8 00:28:50 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660

 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 0050660 


$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 0050660 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1471526 mm^3    (det: 1.323867 )
Computing euler number
orig.nofix lheno = -164, rheno = -186
orig.nofix lhholes =   83, rhholes = 94
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
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 00:30:34 CEST 2017
/pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660

 mri_aparc2aseg --s 0050660 --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 0050660
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-6.0.0/0050660/mri/aparc+aseg.mgz

Reading lh white surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white

Reading lh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial

Loading lh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/surf/rh.white

Reading rh pial surface 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial

Loading rh annotations from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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-6.0.0/0050660/mri/ribbon.mgz
Loading filled from /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/ribbon.mgz
Ripping vertices labeled as unkown
Ripped 8286 vertices from left hemi
Ripped 7732 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-6.0.0/0050660/mri/aseg.mgz
Loading Ctx Seg File /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 = 1033055
Used brute-force search on 169 voxels
Fixing Parahip LH WM
  Found 17 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 2.000000
     3 k 9.000000
     4 k 101.000000
     5 k 2.000000
     6 k 1.000000
     7 k 1.000000
     8 k 6.000000
     9 k 1.000000
     10 k 1.000000
     11 k 1.000000
     12 k 1.000000
     13 k 1720.000000
     14 k 42.000000
     15 k 2.000000
     16 k 10.000000
Fixing Parahip RH WM
  Found 20 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 4.000000
     3 k 5.000000
     4 k 1.000000
     5 k 7.000000
     6 k 1.000000
     7 k 122.000000
     8 k 4.000000
     9 k 4.000000
     10 k 44.000000
     11 k 1627.000000
     12 k 3.000000
     13 k 1.000000
     14 k 1.000000
     15 k 1.000000
     16 k 1.000000
     17 k 1.000000
     18 k 1.000000
     19 k 1.000000
Writing output aseg to mri/wmparc.mgz

 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject 0050660 --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 0050660 --surf-wm-vol --ctab /pasteur/homes/ntraut/bin/freesurfer-6.0.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname tars-542
machine  x86_64
user     ntraut
UseRobust  0
atlas_icv (eTIV) = 1471526 mm^3    (det: 1.323867 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
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-6.0.0/0050660/label
#--------------------------------------------
#@# BA_exvivo Labels lh Sun Oct  8 00:39:15 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 28514 of (28514 28520 28526 28531 28537) to complete...
Waiting for PID 28520 of (28514 28520 28526 28531 28537) to complete...
Waiting for PID 28526 of (28514 28520 28526 28531 28537) to complete...
Waiting for PID 28531 of (28514 28520 28526 28531 28537) to complete...
Waiting for PID 28537 of (28514 28520 28526 28531 28537) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 423
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.label 4552
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 797
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.label 8706
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 274
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.label 4351
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 517
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.label 6500
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 947
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.label 6731
mri_label2label: Done

PIDs (28514 28520 28526 28531 28537) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 28579 of (28579 28585 28591 28596) to complete...
Waiting for PID 28585 of (28579 28585 28591 28596) to complete...
Waiting for PID 28591 of (28579 28585 28591 28596) to complete...
Waiting for PID 28596 of (28579 28585 28591 28596) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 514
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.label 4584
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 1730
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.label 15319
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 269
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.label 4450
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 633
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.label 4055
mri_label2label: Done

PIDs (28579 28585 28591 28596) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 

Waiting for PID 28671 of (28671 28677 28683 28688 28693) to complete...
Waiting for PID 28677 of (28671 28677 28683 28688 28693) to complete...
Waiting for PID 28683 of (28671 28677 28683 28688 28693) to complete...
Waiting for PID 28688 of (28671 28677 28683 28688 28693) to complete...
Waiting for PID 28693 of (28671 28677 28683 28688 28693) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 1382
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.label 6023
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 3232
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.label 11346
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 585
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.label 2603
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 272
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.label 1562
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 284
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.label 1483
mri_label2label: Done

PIDs (28671 28677 28683 28688 28693) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 28738 of (28738 28744 28750 28756 28761) to complete...
Waiting for PID 28744 of (28738 28744 28750 28756 28761) to complete...
Waiting for PID 28750 of (28738 28744 28750 28756 28761) to complete...
Waiting for PID 28756 of (28738 28744 28750 28756 28761) to complete...
Waiting for PID 28761 of (28738 28744 28750 28756 28761) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 162
Checking for and removing duplicates
Writing label file ./lh.BA1_exvivo.thresh.label 1176
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 186
Checking for and removing duplicates
Writing label file ./lh.BA2_exvivo.thresh.label 2278
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 72
Checking for and removing duplicates
Writing label file ./lh.BA3a_exvivo.thresh.label 1576
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 182
Checking for and removing duplicates
Writing label file ./lh.BA3b_exvivo.thresh.label 2178
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 501
Checking for and removing duplicates
Writing label file ./lh.BA4a_exvivo.thresh.label 2820
mri_label2label: Done

PIDs (28738 28744 28750 28756 28761) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 28808 of (28808 28814 28820 28825) to complete...
Waiting for PID 28814 of (28808 28814 28820 28825) to complete...
Waiting for PID 28820 of (28808 28814 28820 28825) to complete...
Waiting for PID 28825 of (28808 28814 28820 28825) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 148
Checking for and removing duplicates
Writing label file ./lh.BA4p_exvivo.thresh.label 1697
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 813
Checking for and removing duplicates
Writing label file ./lh.BA6_exvivo.thresh.label 7848
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 156
Checking for and removing duplicates
Writing label file ./lh.BA44_exvivo.thresh.label 2068
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 256
Checking for and removing duplicates
Writing label file ./lh.BA45_exvivo.thresh.label 1407
mri_label2label: Done

PIDs (28808 28814 28820 28825) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 

Waiting for PID 28892 of (28892 28898 28904 28910 28916) to complete...
Waiting for PID 28898 of (28892 28898 28904 28910 28916) to complete...
Waiting for PID 28904 of (28892 28898 28904 28910 28916) to complete...
Waiting for PID 28910 of (28892 28898 28904 28910 28916) to complete...
Waiting for PID 28916 of (28892 28898 28904 28910 28916) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 912
Checking for and removing duplicates
Writing label file ./lh.V1_exvivo.thresh.label 4317
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 1426
Checking for and removing duplicates
Writing label file ./lh.V2_exvivo.thresh.label 4760
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 143
Checking for and removing duplicates
Writing label file ./lh.MT_exvivo.thresh.label 656
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 109
Checking for and removing duplicates
Writing label file ./lh.entorhinal_exvivo.thresh.label 579
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/lh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 142936
Number of reverse mapping hits = 94
Checking for and removing duplicates
Writing label file ./lh.perirhinal_exvivo.thresh.label 544
mri_label2label: Done

PIDs (28892 28898 28904 28910 28916) completed and logs appended.

 mris_label2annot --s 0050660 --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-6.0.0/0050660/label
cmdline mris_label2annot --s 0050660 --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-542
machine  x86_64
user     ntraut

subject 0050660
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-6.0.0/0050660/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 98817 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/lh.BA_exvivo.annot

 mris_label2annot --s 0050660 --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-6.0.0/0050660/label
cmdline mris_label2annot --s 0050660 --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-542
machine  x86_64
user     ntraut

subject 0050660
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-6.0.0/0050660/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 116936 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 285015
Total vertex volume 282017 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1265    750   2282  2.301 0.560     0.142     0.043       25     2.3  BA1_exvivo
 4513   2964   7790  2.543 0.456     0.117     0.025       43     4.6  BA2_exvivo
 1093    744   1074  1.896 0.376     0.142     0.036       11     1.6  BA3a_exvivo
 2566   1640   4280  2.161 0.740     0.118     0.029       34     2.9  BA3b_exvivo
 2072    985   3221  2.761 0.516     0.098     0.040       23     4.0  BA4a_exvivo
 1542    897   2096  2.529 0.454     0.103     0.031       10     1.9  BA4p_exvivo
 9735   6167  20973  2.892 0.577     0.124     0.034      143    13.5  BA6_exvivo
 2129   1394   4685  2.936 0.470     0.114     0.029       27     2.3  BA44_exvivo
 2918   1995   6550  2.750 0.505     0.126     0.034       47     4.0  BA45_exvivo
 3475   2324   4440  1.781 0.656     0.152     0.045       50     6.5  V1_exvivo
 8870   5660  14235  2.235 0.638     0.147     0.044      139    15.7  V2_exvivo
 2333   1568   4797  2.788 0.509     0.129     0.025       26     2.7  MT_exvivo
  747    506   2146  3.085 0.745     0.115     0.040       10     1.2  perirhinal_exvivo
  861    656   3062  3.333 0.719     0.146     0.051       16     1.7  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 0050660 lh white 

computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 285015
Total vertex volume 282017 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
  895    504   1474  2.153 0.545     0.147     0.047       19     1.7  BA1_exvivo
 1699   1100   2903  2.461 0.396     0.110     0.025       15     1.5  BA2_exvivo
  880    594    819  1.886 0.355     0.143     0.037        9     1.4  BA3a_exvivo
 1568   1015   1833  1.742 0.382     0.103     0.021       13     1.4  BA3b_exvivo
 2166   1022   3248  2.770 0.503     0.093     0.036       21     3.5  BA4a_exvivo
 1213    730   1648  2.484 0.451     0.108     0.034        9     1.6  BA4p_exvivo
 5514   3363  11416  2.864 0.581     0.123     0.036       92     8.1  BA6_exvivo
 1419    920   3230  2.948 0.430     0.115     0.028       20     1.6  BA44_exvivo
 1227    832   3417  2.921 0.530     0.141     0.041       23     1.9  BA45_exvivo
 3670   2451   4851  1.817 0.674     0.149     0.044       53     6.6  V1_exvivo
 4362   2766   6737  2.166 0.631     0.152     0.048       72     8.5  V2_exvivo
  594    388   1355  2.849 0.480     0.132     0.029        8     0.7  MT_exvivo
  356    253   1056  3.091 0.721     0.083     0.019        1     0.3  perirhinal_exvivo
  437    348   1447  3.415 0.749     0.150     0.050        8     0.8  entorhinal_exvivo
#--------------------------------------------
#@# BA_exvivo Labels rh Sun Oct  8 00:42:17 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29032 of (29032 29038 29044 29050 29056) to complete...
Waiting for PID 29038 of (29032 29038 29044 29050 29056) to complete...
Waiting for PID 29044 of (29032 29038 29044 29050 29056) to complete...
Waiting for PID 29050 of (29032 29038 29044 29050 29056) to complete...
Waiting for PID 29056 of (29032 29038 29044 29050 29056) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 826
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.label 4788
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 1070
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.label 7757
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 317
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.label 4297
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 540
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.label 5062
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 1150
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.label 6897
mri_label2label: Done

PIDs (29032 29038 29044 29050 29056) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29099 of (29099 29105 29111 29116) to complete...
Waiting for PID 29105 of (29099 29105 29111 29116) to complete...
Waiting for PID 29111 of (29099 29105 29111 29116) to complete...
Waiting for PID 29116 of (29099 29105 29111 29116) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 514
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.label 4987
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 2175
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.label 14431
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 789
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.label 7701
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 1013
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.label 6368
mri_label2label: Done

PIDs (29099 29105 29111 29116) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 

Waiting for PID 29177 of (29177 29183 29189 29194 29199) to complete...
Waiting for PID 29183 of (29177 29183 29189 29194 29199) to complete...
Waiting for PID 29189 of (29177 29183 29189 29194 29199) to complete...
Waiting for PID 29194 of (29177 29183 29189 29194 29199) to complete...
Waiting for PID 29199 of (29177 29183 29189 29194 29199) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 1468
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.label 6195
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 2056
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.label 10072
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 867
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.label 2799
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 346
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.label 1384
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 275
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.label 1027
mri_label2label: Done

PIDs (29177 29183 29189 29194 29199) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 29245 of (29245 29251 29257 29263 29269) to complete...
Waiting for PID 29251 of (29245 29251 29257 29263 29269) to complete...
Waiting for PID 29257 of (29245 29251 29257 29263 29269) to complete...
Waiting for PID 29263 of (29245 29251 29257 29263 29269) to complete...
Waiting for PID 29269 of (29245 29251 29257 29263 29269) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 353
Checking for and removing duplicates
Writing label file ./rh.BA1_exvivo.thresh.label 1229
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 358
Checking for and removing duplicates
Writing label file ./rh.BA2_exvivo.thresh.label 3046
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 104
Checking for and removing duplicates
Writing label file ./rh.BA3a_exvivo.thresh.label 1802
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 284
Checking for and removing duplicates
Writing label file ./rh.BA3b_exvivo.thresh.label 2467
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 185
Checking for and removing duplicates
Writing label file ./rh.BA4a_exvivo.thresh.label 1573
mri_label2label: Done

PIDs (29245 29251 29257 29263 29269) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 29315 of (29315 29321 29327 29333) to complete...
Waiting for PID 29321 of (29315 29321 29327 29333) to complete...
Waiting for PID 29327 of (29315 29321 29327 29333) to complete...
Waiting for PID 29333 of (29315 29321 29327 29333) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 210
Checking for and removing duplicates
Writing label file ./rh.BA4p_exvivo.thresh.label 1699
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 1543
Checking for and removing duplicates
Writing label file ./rh.BA6_exvivo.thresh.label 8502
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 196
Checking for and removing duplicates
Writing label file ./rh.BA44_exvivo.thresh.label 1208
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 162
Checking for and removing duplicates
Writing label file ./rh.BA45_exvivo.thresh.label 1340
mri_label2label: Done

PIDs (29315 29321 29327 29333) 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 0050660 --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 0050660 --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 0050660 --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 0050660 --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 0050660 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 

Waiting for PID 29386 of (29386 29392 29398 29404 29410) to complete...
Waiting for PID 29392 of (29386 29392 29398 29404 29410) to complete...
Waiting for PID 29398 of (29386 29392 29398 29404 29410) to complete...
Waiting for PID 29404 of (29386 29392 29398 29404 29410) to complete...
Waiting for PID 29410 of (29386 29392 29398 29404 29410) 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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 1052
Checking for and removing duplicates
Writing label file ./rh.V1_exvivo.thresh.label 4284
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 911
Checking for and removing duplicates
Writing label file ./rh.V2_exvivo.thresh.label 4348
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 155
Checking for and removing duplicates
Writing label file ./rh.MT_exvivo.thresh.label 423
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 234
Checking for and removing duplicates
Writing label file ./rh.entorhinal_exvivo.thresh.label 928
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 0050660 --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 = 0050660
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-6.0.0/0050660/surf/rh.white
Reading target registration 
 /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 147238
Number of reverse mapping hits = 157
Checking for and removing duplicates
Writing label file ./rh.perirhinal_exvivo.thresh.label 448
mri_label2label: Done

PIDs (29386 29392 29398 29404 29410) completed and logs appended.

 mris_label2annot --s 0050660 --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-6.0.0/0050660/label
cmdline mris_label2annot --s 0050660 --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-542
machine  x86_64
user     ntraut

subject 0050660
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-6.0.0/0050660/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 102130 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/label/rh.BA_exvivo.annot

 mris_label2annot --s 0050660 --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-6.0.0/0050660/label
cmdline mris_label2annot --s 0050660 --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-542
machine  x86_64
user     ntraut

subject 0050660
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-6.0.0/0050660/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 120851 unhit vertices
Writing annot to /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/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 0050660 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 291096
Total vertex volume 287734 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1295    656   1851  2.140 0.662     0.131     0.056       24     3.5  BA1_exvivo
 4236   2674   6511  2.440 0.445     0.111     0.028       44     5.4  BA2_exvivo
 1257    833   1143  1.827 0.535     0.133     0.033       12     1.6  BA3a_exvivo
 2389   1463   3412  2.067 0.647     0.106     0.027       23     2.5  BA3b_exvivo
 2039   1065   3079  2.549 0.605     0.107     0.039       22     3.5  BA4a_exvivo
 1599    949   1976  2.257 0.667     0.123     0.048       43     3.1  BA4p_exvivo
 9632   5999  18875  2.726 0.575     0.125     0.039      377    16.6  BA6_exvivo
 3760   2481   8067  2.922 0.468     0.120     0.031       46     4.2  BA44_exvivo
 4232   2842   9580  2.810 0.532     0.130     0.034       70     5.5  BA45_exvivo
 3796   2441   4857  1.843 0.595     0.147     0.053       59     8.1  V1_exvivo
 6973   4552  10646  2.147 0.598     0.146     0.044      102    12.4  V2_exvivo
 2577   1654   4990  2.687 0.449     0.127     0.034       33     3.3  MT_exvivo
  736    529   2234  3.189 0.669     0.112     0.040        9     1.2  perirhinal_exvivo
  587    378   1758  3.004 1.057     0.172     0.085       18     2.3  entorhinal_exvivo

 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab 0050660 rh white 

computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading volume /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/mri/wm.mgz...
reading input surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
reading input pial surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.pial...
reading input white surface /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050660/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Total face volume 291096
Total vertex volume 287734 (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) = 1471526 mm^3    (det: 1.323867 )
lhCtxGM: 279280.808 278491.000  diff=  789.8  pctdiff= 0.283
rhCtxGM: 284870.137 284689.000  diff=  181.1  pctdiff= 0.064
lhCtxWM: 233480.686 233866.500  diff= -385.8  pctdiff=-0.165
rhCtxWM: 237715.068 238592.500  diff= -877.4  pctdiff=-0.369
SubCortGMVol  68130.000
SupraTentVol  1124469.700 (1120363.000) diff=4106.700 pctdiff=0.365
SupraTentVolNotVent  1107906.700 (1103800.000) diff=4106.700 pctdiff=0.371
BrainSegVol  1281366.000 (1278704.000) diff=2662.000 pctdiff=0.208
BrainSegVolNotVent  1261243.000 (1260795.700) diff=447.300 pctdiff=0.035
BrainSegVolNotVent  1261243.000
CerebellumVol 157288.000
VentChorVol   16563.000
3rd4th5thCSF   3560.000
CSFVol   898.000, OptChiasmVol   155.000
MaskVol 1664570.000
 1097    483   1181  1.878 0.474     0.122     0.058       21     3.0  BA1_exvivo
 2422   1490   3891  2.383 0.398     0.112     0.027       29     3.1  BA2_exvivo
 1108    735    941  1.757 0.474     0.136     0.034       11     1.4  BA3a_exvivo
 1903   1167   2373  1.917 0.586     0.102     0.025       16     1.9  BA3b_exvivo
 1179    620   1675  2.359 0.582     0.120     0.045       16     2.4  BA4a_exvivo
 1317    797   1645  2.298 0.711     0.123     0.043       38     2.2  BA4p_exvivo
 6771   4097  12802  2.701 0.594     0.124     0.042      342    12.8  BA6_exvivo
  982    661   2195  2.849 0.405     0.127     0.040       18     1.3  BA44_exvivo
 1032    705   2688  2.927 0.496     0.141     0.040       19     1.6  BA45_exvivo
 3614   2325   4451  1.820 0.580     0.147     0.054       56     7.8  V1_exvivo
 3678   2457   5500  1.983 0.547     0.154     0.046       59     6.7  V2_exvivo
  413    248    812  2.595 0.380     0.123     0.032        5     0.5  MT_exvivo
  468    325   1196  3.104 0.647     0.118     0.046        7     1.0  perirhinal_exvivo
  403    270    959  2.560 1.001     0.191     0.092       13     1.9  entorhinal_exvivo

Started at Sat Oct 7 16:10:09 CEST 2017 
Ended   at Sun Oct 8 00:45:20 CEST 2017
#@#%# recon-all-run-time-hours 8.586
recon-all -s 0050660 finished without error at Sun Oct  8 00:45:20 CEST 2017