cortical-surfaces-freesurfer/sub-21/scripts/recon-all.log

Fri Jun 20 09:58:04 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T
/opt/freesurfer/5.3/bin/recon-all
-s surface_3T -i 3T_scan/NIFTI/MPRAGE_T1_0.7/MPRAGE_T1_0.7.nii -sd .
subjid surface_3T
setenv SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Actual FREESURFER_HOME /opt/freesurfer/5.3
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    8000000 kbytes
vmemoryuse   18000000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      300 
maxlocks     unlimited
maxsignal    2067069 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:     264664500  150074316  114590184          0     736828  136772104
-/+ buffers/cache:   12565384  252099116
Swap:    293227320       5876  293221444

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:04-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:05-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:06-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:07-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:08-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:08-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:08-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /opt/freesurfer/5.3/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /opt/freesurfer/5.3/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 mri_convert /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/3T_scan/NIFTI/MPRAGE_T1_0.7/MPRAGE_T1_0.7.nii /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig/001.mgz 

mri_convert /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/3T_scan/NIFTI/MPRAGE_T1_0.7/MPRAGE_T1_0.7.nii /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig/001.mgz 
INFO: using NIfTI-1 qform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/3T_scan/NIFTI/MPRAGE_T1_0.7/MPRAGE_T1_0.7.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.033078, -0.999453, 0.000121699)
j_ras = (0.0158229, -0.000401944, 0.999875)
k_ras = (0.999327, -0.0330758, -0.0158275)
writing to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig/001.mgz...

#------------------------------------------

Started at Fri Jun 20 09:58:04 CEST 2014 
Ended   at Fri Jun 20 09:58:19 CEST 2014
#@#%# recon-all-run-time-hours 0.004
recon-all -s surface_3T finished without error at Fri Jun 20 09:58:19 CEST 2014



New invocation of recon-all 



Fri Jun 20 09:58:54 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T
/opt/freesurfer/5.3/bin/recon-all
-s surface_3T -sd . -all
subjid surface_3T
setenv SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Actual FREESURFER_HOME /opt/freesurfer/5.3
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    8000000 kbytes
vmemoryuse   18000000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      300 
maxlocks     unlimited
maxsignal    2067069 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:     264664500  150096676  114567824          0     736840  136789400
-/+ buffers/cache:   12570436  252094064
Swap:    293227320       5876  293221444

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:54-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:54-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:54-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:54-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:55-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:56-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/06/20-07:58:57-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /opt/freesurfer/5.3/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /opt/freesurfer/5.3/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Fri Jun 20 09:58:58 CEST 2014
Found 1 runs
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig/001.mgz /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz 

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 mri_convert /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz --conform 

mri_convert /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.033078, -0.999453, 0.000121699)
j_ras = (0.0158229, -0.000401944, 0.999875)
k_ras = (0.999327, -0.0330758, -0.0158275)
Original Data has (0.666667, 0.666667, 0.699913) mm size and (384, 384, 274) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/transforms/talairach.xfm /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Fri Jun 20 09:59:18 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 


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


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

#--------------------------------------------
#@# Talairach Failure Detection Fri Jun 20 10:02:00 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5106, pval=0.1531 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3/bin/extract_talairach_avi_QA.awk /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/transforms/talairach_avi.log 

TalAviQA: 0.96717
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Fri Jun 20 10:02:00 CEST 2014

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
/opt/freesurfer/5.3/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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
Fri Jun 20 10:02:00 CEST 2014
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
tmpdir is ./tmp.mri_nu_correct.mni.17604
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17604/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17604/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 3.72529e-08, 7.07805e-08)
j_ras = (-1.37836e-07, 5.00586e-09, -1)
k_ras = (-1.11759e-08, 1, 1.86265e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.17604/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Fri Jun 20 10:02:04 CEST 2014
nu_correct -clobber ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.17604/0/
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:04] running:
  /opt/freesurfer/5.3/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17604/0/ ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/nu1.imp

Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
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Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
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Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Number of iterations: 37 
CV of field change: 0.000995657
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:41] running:
  /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17604/nu0.mnc ./tmp.mri_nu_correct.mni.17604/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Fri Jun 20 10:02:47 CEST 2014
nu_correct -clobber ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.17604/1/
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:02:47] running:
  /opt/freesurfer/5.3/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 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.17604/1/ ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/nu2.imp

Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Use of ?PATTERN? without explicit operator is deprecated at /opt/freesurfer/5.3/mni/bin/sharpen_volume line 153.
Processing:.................................................................Done
Number of iterations: 34 
CV of field change: 0.000989176
[spark@medusa:/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/] [2014-06-20 10:03:24] running:
  /opt/freesurfer/5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.17604/nu1.mnc ./tmp.mri_nu_correct.mni.17604/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17604/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.17604/ones.mgz 
sysname  Linux
hostname medusa
machine  x86_64
user     spark

input      ./tmp.mri_nu_correct.mni.17604/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.17604/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
Found 16777216 values in range
Counting number of voxels
Found 16777216 voxels in final mask
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/input.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/input.mean.dat 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.17604/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                     16777216  16777216.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.17604/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/output.mean.dat

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.17604/ones.mgz --i ./tmp.mri_nu_correct.mni.17604/nu2.mnc --sum ./tmp.mri_nu_correct.mni.17604/sum.junk --avgwf ./tmp.mri_nu_correct.mni.17604/output.mean.dat 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.17604/ones.mgz
Loading ./tmp.mri_nu_correct.mni.17604/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0     1                                     16777216  16777216.000

Reporting on   1 segmentations
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.17604/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.17604/nu2.mnc ./tmp.mri_nu_correct.mni.17604/nu2.mnc mul .90202857338110148963
Saving result to './tmp.mri_nu_correct.mni.17604/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.17604/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.17604/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.17604/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 3.72529e-08, 7.07805e-08)
j_ras = (-1.37836e-07, 5.00586e-09, -1)
k_ras = (-1.11759e-08, 1, 1.86265e-09)
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 (18, 177) to ( 3, 110)
 
 
Fri Jun 20 10:04:10 CEST 2014
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Fri Jun 20 10:04:11 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.118  -0.020  -0.000  -1.042;
 0.026   1.091   0.463  -32.658;
 0.007  -0.576   1.226  -1.136;
 0.000   0.000   0.000   1.000;
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 111
white matter peak found at 109
gm peak at 47 (47), valley at 33 (33)
csf peak at 23, setting threshold to 39
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 48 (48), valley at 34 (34)
csf peak at 24, setting threshold to 40
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 54 seconds.
#--------------------------------------------
#@# Skull Stripping Fri Jun 20 10:07:06 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_em_register -skull nu.mgz /opt/freesurfer/5.3/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta 



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
reading 1 input volumes...
logging results to talairach_with_skull.log
reading '/opt/freesurfer/5.3/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7 
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=41.0
skull bounding box = (61, 41, 33) --> (194, 255, 139)
using (105, 112, 86) as brain centroid...
mean wm in atlas = 126, using box (89,86,73) --> (121, 138,98) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 108, scaling input intensities by 1.167
scaling channel 0 by 1.16667
initial log_p = -4.9
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.571380 @ (-9.091, 9.091, -9.091)
max log p =    -4.435192 @ (4.545, 4.545, -4.545)
max log p =    -4.435192 @ (0.000, 0.000, 0.000)
max log p =    -4.426252 @ (-1.136, 1.136, 5.682)
max log p =    -4.422502 @ (1.705, 1.705, 0.568)
max log p =    -4.422502 @ (0.000, 0.000, 0.000)
Found translation: (-4.0, 16.5, -7.4): log p = -4.423
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.4 (thresh=-4.4)
 1.075   0.000   0.000  -13.708;
 0.000   1.142   0.473  -44.555;
 0.000  -0.407   0.983   37.161;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.156   0.000   0.000  -24.168;
 0.000   1.228   0.509  -56.980;
 0.000  -0.407   0.983   37.161;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.156   0.000   0.000  -24.168;
 0.000   1.366   0.404  -59.035;
 0.000  -0.225   0.963   21.370;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.156   0.000   0.000  -24.168;
 0.000   1.366   0.404  -59.035;
 0.000  -0.225   0.963   21.370;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.133  -0.045  -0.015  -15.079;
 0.036   1.357   0.435  -66.333;
 0.000  -0.275   0.967   27.708;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.154  -0.046  -0.015  -17.719;
 0.036   1.357   0.435  -66.333;
 0.000  -0.275   0.967   27.708;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.154  -0.046  -0.015  -17.719;
 0.036   1.357   0.435  -66.333;
 0.000  -0.275   0.967   27.708;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.156  -0.026   0.000  -22.033;
 0.017   1.357   0.444  -64.327;
-0.010  -0.286   0.964   30.335;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.156  -0.026   0.000  -22.033;
 0.017   1.355   0.443  -63.641;
-0.010  -0.286   0.966   30.246;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.15552  -0.02635   0.00031  -22.03295;
 0.01747   1.35522   0.44314  -63.64138;
-0.00978  -0.28608   0.96550   30.24647;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.15552  -0.02635   0.00031  -22.03295;
 0.01747   1.35522   0.44314  -63.64138;
-0.00978  -0.28608   0.96550   30.24647;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.156  -0.026   0.000  -22.033;
 0.017   1.355   0.443  -63.641;
-0.010  -0.286   0.966   30.246;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.9)
transform before final EM align:
 1.156  -0.026   0.000  -22.033;
 0.017   1.355   0.443  -63.641;
-0.010  -0.286   0.966   30.246;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 382743 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.15552  -0.02635   0.00031  -22.03295;
 0.01747   1.35522   0.44314  -63.64138;
-0.00978  -0.28608   0.96550   30.24647;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.15552  -0.02635   0.00031  -22.03295;
 0.01747   1.35522   0.44314  -63.64138;
-0.00978  -0.28608   0.96550   30.24647;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) =    4.4  tol 0.000000
final transform:
 1.156  -0.026   0.000  -22.033;
 0.017   1.355   0.443  -63.641;
-0.010  -0.286   0.966   30.246;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 44 minutes and 40 seconds.

 mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3/average/RB_all_withskull_2008-03-26.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=131 y=90 z=115 r=88
      first estimation of the main basin volume: 2917376 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        15 found in the rest of the brain 
      global maximum in x=150, y=89, z=74, Imax=255
      CSF=14, 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=19278313046 voxels, voxel volume =1.000 
                     = 19278313046 mmm3 = 19278313.472 cm3
done.
PostAnalyze...Basin Prior
 61 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=130,y=98, z=107, r=9361 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 45930
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1031227685
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1092288354
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1075455182
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1074922978
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082177556
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    3,      3,        26,   50
  after  analyzing :    3,      18,        26,   26
   RIGHT_CER   
  before analyzing :    4,      5,        27,   59
  after  analyzing :    4,      19,        27,   29
   LEFT_CER    
  before analyzing :    4,      5,        28,   59
  after  analyzing :    4,      20,        28,   29
  RIGHT_BRAIN  
  before analyzing :    3,      3,        25,   50
  after  analyzing :    3,      17,        25,   25
  LEFT_BRAIN   
  before analyzing :    3,      4,        27,   50
  after  analyzing :    3,      19,        27,   26
     OTHER     
  before analyzing :    4,      18,        82,   91
  after  analyzing :    4,      60,        82,   67
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...64 iterations

*********************VALIDATION*********************
curvature mean = -0.013, std = 0.011
curvature mean = 70.564, std = 8.017

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.84, sigma = 6.37
      after  rotation: sse = 3.84, sigma = 6.37
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  4.57, its var is  8.35   
      before Erosion-Dilatation  2.85% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...30 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1677683 voxels, voxel volume = 1.000 mm3
           = 1677683 mmm3 = 1677.683 cm3


******************************
Saving brainmask.auto.mgz
done

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Fri Jun 20 10:52:13 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3/average/RB_all_2008-03-26.gca transforms/talairach.lta 



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes...
logging results to talairach.log
reading '/opt/freesurfer/5.3/average/RB_all_2008-03-26.gca'...
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 1812 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 14.9 or > 790.2 
total sample mean = 84.4 (994 zeros)
************************************************
spacing=8, using 2772 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2772, passno 0, spacing 8
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=23.0
skull bounding box = (61, 41, 32) --> (199, 179, 193)
using (107, 87, 113) as brain centroid...
mean wm in atlas = 107, using box (90,70,93) --> (123, 103,132) to find MRI wm
before smoothing, mri peak at 104
after smoothing, mri peak at 104, scaling input intensities by 1.029
scaling channel 0 by 1.02885
initial log_p = -4.5
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.023337 @ (-9.091, 27.273, -9.091)
max log p =    -3.914176 @ (4.545, -4.545, 4.545)
max log p =    -3.842072 @ (-2.273, -2.273, -6.818)
max log p =    -3.814302 @ (1.136, -1.136, 1.136)
max log p =    -3.794145 @ (-0.568, 0.568, 0.568)
max log p =    -3.794145 @ (0.000, 0.000, 0.000)
Found translation: (-6.3, 19.9, -9.7): log p = -3.794
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.8 (thresh=-3.8)
 1.000   0.000   0.000  -6.250;
 0.000   1.068   0.421  -35.226;
 0.000  -0.402   0.919   46.925;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 1.000   0.000   0.000  -6.250;
 0.000   1.068   0.421  -35.226;
 0.000  -0.402   0.919   46.925;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.4 (thresh=-3.4)
 1.057   0.000   0.000  -11.953;
 0.000   1.154   0.381  -35.796;
 0.000  -0.337   0.961   33.934;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.057   0.000   0.000  -11.953;
 0.000   1.154   0.381  -35.796;
 0.000  -0.337   0.961   33.934;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.053  -0.012   0.005  -11.227;
 0.009   1.152   0.380  -37.689;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2772 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.05070  -0.01215   0.00472  -10.90334;
 0.00861   1.15091   0.37985  -37.50603;
-0.00864  -0.33648   0.96027   34.20784;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 1.05070  -0.01215   0.00472  -10.90334;
 0.00861   1.15091   0.37985  -37.50603;
-0.00864  -0.33648   0.96027   34.20784;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.2 (old=-4.5)
transform before final EM align:
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 312841 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.05070  -0.01215   0.00472  -10.90334;
 0.00861   1.15091   0.37985  -37.50603;
-0.00864  -0.33648   0.96027   34.20784;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 1.05070  -0.01215   0.00472  -10.90334;
 0.00861   1.15091   0.37985  -37.50603;
-0.00864  -0.33648   0.96027   34.20784;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =    3.8  tol 0.000000
final transform:
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 27 minutes and 25 seconds.
#--------------------------------------
#@# CA Normalize Fri Jun 20 11:19:38 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3/average/RB_all_2008-03-26.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 '/opt/freesurfer/5.3/average/RB_all_2008-03-26.gca'...
reading transform from 'transforms/talairach.lta'...
reading input volume from nu.mgz...
resetting wm mean[0]: 102 --> 107
resetting gm mean[0]: 64 --> 64
input volume #1 is the most T1-like
using real data threshold=23.0
skull bounding box = (61, 41, 32) --> (199, 179, 193)
using (107, 87, 113) as brain centroid...
mean wm in atlas = 107, using box (90,70,93) --> (123, 103,132) to find MRI wm
before smoothing, mri peak at 104
after smoothing, mri peak at 104, scaling input intensities by 1.029
scaling channel 0 by 1.02885
using 244171 sample points...
INFO: compute sample coordinates transform
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
INFO: transform used
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (130, 43, 37) --> (194, 146, 196)
Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 147.0
0 of 534 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (70, 43, 37) --> (131, 139, 196)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 147.0
0 of 345 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (133, 120, 68) --> (179, 158, 118)
Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 147.0
0 of 9 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (88, 120, 64) --> (132, 157, 119)
Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 147.0
0 of 9 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (116, 108, 99) --> (147, 166, 129)
Brain_Stem: limiting intensities to 95.0 --> 147.0
6 of 12 (50.0%) samples deleted
using 909 total control points for intensity normalization...
bias field = 0.976 +- 0.039
0 of 903 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (130, 43, 37) --> (194, 146, 196)
Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 141.0
0 of 635 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (70, 43, 37) --> (131, 139, 196)
Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 141.0
0 of 460 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (133, 120, 68) --> (179, 158, 118)
Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 141.0
0 of 45 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (88, 120, 64) --> (132, 157, 119)
Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 141.0
0 of 71 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (116, 108, 99) --> (147, 166, 129)
Brain_Stem: limiting intensities to 76.0 --> 141.0
0 of 100 (0.0%) samples deleted
using 1311 total control points for intensity normalization...
bias field = 0.997 +- 0.040
2 of 1311 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (130, 43, 37) --> (194, 146, 196)
Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 139.0
0 of 705 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (70, 43, 37) --> (131, 139, 196)
Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 139.0
0 of 546 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (133, 120, 68) --> (179, 158, 118)
Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 139.0
0 of 91 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (88, 120, 64) --> (132, 157, 119)
Right_Cerebellum_White_Matter: limiting intensities to 77.0 --> 139.0
0 of 69 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (116, 108, 99) --> (147, 166, 129)
Brain_Stem: limiting intensities to 71.0 --> 139.0
0 of 158 (0.0%) samples deleted
using 1569 total control points for intensity normalization...
bias field = 1.004 +- 0.034
4 of 1569 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 1 minutes and 58 seconds.
#--------------------------------------
#@# CA Reg Fri Jun 20 11:21:36 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3/average/RB_all_2008-03-26.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...
reading 1 input volumes...
logging results to talairach.log


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
reading input volume 'norm.mgz'...
reading GCA '/opt/freesurfer/5.3/average/RB_all_2008-03-26.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.30 (predicted orig area = 6.2)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.840, neg=0, invalid=96777
0001: dt=129.472000, rms=0.775 (7.692%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.760 (1.977%), neg=0, invalid=96777
0003: dt=295.936000, rms=0.747 (1.664%), neg=0, invalid=96777
0004: dt=129.472000, rms=0.741 (0.853%), neg=0, invalid=96777
0005: dt=129.472000, rms=0.737 (0.560%), neg=0, invalid=96777
0006: dt=295.936000, rms=0.731 (0.737%), neg=0, invalid=96777
0007: dt=92.480000, rms=0.728 (0.424%), neg=0, invalid=96777
0008: dt=443.904000, rms=0.724 (0.606%), neg=0, invalid=96777
0009: dt=73.984000, rms=0.721 (0.329%), neg=0, invalid=96777
0010: dt=1775.616000, rms=0.714 (1.105%), neg=0, invalid=96777
0011: dt=92.480000, rms=0.710 (0.461%), neg=0, invalid=96777
0012: dt=129.472000, rms=0.708 (0.310%), neg=0, invalid=96777
0013: dt=129.472000, rms=0.708 (0.074%), neg=0, invalid=96777
0014: dt=129.472000, rms=0.707 (0.123%), neg=0, invalid=96777
0015: dt=129.472000, rms=0.706 (0.151%), neg=0, invalid=96777
0016: dt=129.472000, rms=0.704 (0.172%), neg=0, invalid=96777
0017: dt=129.472000, rms=0.703 (0.202%), neg=0, invalid=96777
0018: dt=129.472000, rms=0.701 (0.217%), neg=0, invalid=96777
0019: dt=129.472000, rms=0.700 (0.234%), neg=0, invalid=96777
0020: dt=129.472000, rms=0.698 (0.296%), neg=0, invalid=96777
0021: dt=129.472000, rms=0.696 (0.289%), neg=0, invalid=96777
0022: dt=129.472000, rms=0.694 (0.298%), neg=0, invalid=96777
0023: dt=129.472000, rms=0.692 (0.292%), neg=0, invalid=96777
0024: dt=129.472000, rms=0.690 (0.285%), neg=0, invalid=96777
0025: dt=129.472000, rms=0.688 (0.269%), neg=0, invalid=96777
0026: dt=129.472000, rms=0.686 (0.259%), neg=0, invalid=96777
0027: dt=129.472000, rms=0.685 (0.207%), neg=0, invalid=96777
0028: dt=129.472000, rms=0.683 (0.168%), neg=0, invalid=96777
0029: dt=129.472000, rms=0.682 (0.151%), neg=0, invalid=96777
0030: dt=129.472000, rms=0.681 (0.153%), neg=0, invalid=96777
0031: dt=129.472000, rms=0.680 (0.157%), neg=0, invalid=96777
0032: dt=129.472000, rms=0.679 (0.160%), neg=0, invalid=96777
0033: dt=129.472000, rms=0.678 (0.157%), neg=0, invalid=96777
0034: dt=129.472000, rms=0.677 (0.154%), neg=0, invalid=96777
0035: dt=129.472000, rms=0.676 (0.149%), neg=0, invalid=96777
0036: dt=129.472000, rms=0.675 (0.112%), neg=0, invalid=96777
0037: dt=129.472000, rms=0.675 (0.101%), neg=0, invalid=96777
0038: dt=443.904000, rms=0.674 (0.039%), neg=0, invalid=96777
0039: dt=443.904000, rms=0.674 (-0.505%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.674, neg=0, invalid=96777
0040: dt=92.480000, rms=0.674 (0.064%), neg=0, invalid=96777
0041: dt=110.976000, rms=0.674 (0.036%), neg=0, invalid=96777
0042: dt=110.976000, rms=0.674 (0.030%), neg=0, invalid=96777
0043: dt=110.976000, rms=0.673 (0.035%), neg=0, invalid=96777
0044: dt=110.976000, rms=0.673 (0.023%), neg=0, invalid=96777
0045: dt=110.976000, rms=0.673 (0.034%), neg=0, invalid=96777
0046: dt=110.976000, rms=0.672 (0.062%), neg=0, invalid=96777
0047: dt=110.976000, rms=0.672 (0.061%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.678, neg=0, invalid=96777
0048: dt=124.416000, rms=0.671 (1.045%), neg=0, invalid=96777
0049: dt=103.680000, rms=0.666 (0.843%), neg=0, invalid=96777
0050: dt=36.288000, rms=0.661 (0.653%), neg=0, invalid=96777
0051: dt=82.944000, rms=0.660 (0.251%), neg=0, invalid=96777
0052: dt=36.288000, rms=0.656 (0.555%), neg=0, invalid=96777
0053: dt=36.288000, rms=0.655 (0.136%), neg=0, invalid=96777
0054: dt=36.288000, rms=0.653 (0.281%), neg=0, invalid=96777
0055: dt=36.288000, rms=0.651 (0.379%), neg=0, invalid=96777
0056: dt=36.288000, rms=0.648 (0.480%), neg=0, invalid=96777
0057: dt=36.288000, rms=0.644 (0.558%), neg=0, invalid=96777
0058: dt=36.288000, rms=0.640 (0.645%), neg=0, invalid=96777
0059: dt=36.288000, rms=0.636 (0.653%), neg=0, invalid=96777
0060: dt=36.288000, rms=0.632 (0.613%), neg=0, invalid=96777
0061: dt=36.288000, rms=0.628 (0.542%), neg=0, invalid=96777
0062: dt=36.288000, rms=0.625 (0.499%), neg=0, invalid=96777
0063: dt=36.288000, rms=0.623 (0.445%), neg=0, invalid=96777
0064: dt=36.288000, rms=0.620 (0.372%), neg=0, invalid=96777
0065: dt=36.288000, rms=0.618 (0.339%), neg=0, invalid=96777
0066: dt=36.288000, rms=0.616 (0.280%), neg=0, invalid=96777
0067: dt=36.288000, rms=0.615 (0.286%), neg=0, invalid=96777
0068: dt=36.288000, rms=0.613 (0.224%), neg=0, invalid=96777
0069: dt=36.288000, rms=0.612 (0.184%), neg=0, invalid=96777
0070: dt=36.288000, rms=0.611 (0.165%), neg=0, invalid=96777
0071: dt=36.288000, rms=0.610 (0.132%), neg=0, invalid=96777
0072: dt=36.288000, rms=0.610 (0.120%), neg=0, invalid=96777
0073: dt=36.288000, rms=0.609 (0.151%), neg=0, invalid=96777
0074: dt=36.288000, rms=0.608 (0.118%), neg=0, invalid=96777
0075: dt=36.288000, rms=0.607 (0.102%), neg=0, invalid=96777
0076: dt=103.680000, rms=0.607 (0.054%), neg=0, invalid=96777
0077: dt=103.680000, rms=0.607 (-0.324%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.607, neg=0, invalid=96777
0078: dt=25.920000, rms=0.607 (0.056%), neg=0, invalid=96777
0079: dt=36.288000, rms=0.606 (0.087%), neg=0, invalid=96777
0080: dt=15.552000, rms=0.606 (-0.002%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.633, neg=0, invalid=96777
0081: dt=4.000000, rms=0.633 (0.026%), neg=0, invalid=96777
0082: dt=0.700000, rms=0.633 (0.003%), neg=0, invalid=96777
0083: dt=0.700000, rms=0.633 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.633, neg=0, invalid=96777
0084: dt=0.000488, rms=0.633 (0.000%), neg=0, invalid=96777
0085: dt=0.000488, rms=0.633 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.707, neg=0, invalid=96777
0086: dt=5.150235, rms=0.686 (3.077%), neg=0, invalid=96777
0087: dt=3.068493, rms=0.684 (0.199%), neg=0, invalid=96777
0088: dt=3.068493, rms=0.684 (-0.041%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.684, neg=0, invalid=96777
0089: dt=0.000000, rms=0.684 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 5.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.752, neg=0, invalid=96777
0090: dt=1.098655, rms=0.748 (0.553%), neg=0, invalid=96777
0091: dt=1.792000, rms=0.742 (0.830%), neg=0, invalid=96777
0092: dt=0.515625, rms=0.741 (0.067%), neg=0, invalid=96777
0093: dt=0.515625, rms=0.741 (0.053%), neg=0, invalid=96777
0094: dt=0.515625, rms=0.740 (0.060%), neg=0, invalid=96777
0095: dt=0.515625, rms=0.740 (0.010%), neg=0, invalid=96777
0096: dt=0.515625, rms=0.740 (-0.095%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.740, neg=0, invalid=96777
0097: dt=1.625000, rms=0.738 (0.240%), neg=0, invalid=96777
0098: dt=0.000000, rms=0.738 (-0.000%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.696, neg=0, invalid=96777
0099: dt=0.384000, rms=0.679 (2.466%), neg=0, invalid=96777
0100: dt=0.000000, rms=0.679 (0.000%), neg=0, invalid=96777
0101: dt=0.050000, rms=0.679 (-0.406%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.679, neg=0, invalid=96777
0102: dt=0.000000, rms=0.679 (0.000%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.15066 (10)
Left_Lateral_Ventricle (4): linear fit = 0.31 x + 0.0 (860 voxels, overlap=0.005)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (860 voxels, peak =  8), gca=9.6
gca peak = 0.14022 (22)
mri peak = 0.10789 (11)
Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (492 voxels, overlap=0.006)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (492 voxels, peak =  7), gca=8.8
gca peak = 0.24234 (100)
mri peak = 0.11642 (100)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (378 voxels, overlap=0.921)
Right_Pallidum (52): linear fit = 1.01 x + 0.0 (378 voxels, peak = 102), gca=101.5
gca peak = 0.19192 (97)
mri peak = 0.10959 (99)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (326 voxels, overlap=0.998)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (326 voxels, peak = 98), gca=98.5
gca peak = 0.24007 (63)
mri peak = 0.05558 (52)
Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (357 voxels, overlap=0.757)
Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (357 voxels, peak = 57), gca=57.0
gca peak = 0.29892 (64)
mri peak = 0.07382 (62)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (414 voxels, overlap=0.993)
Left_Hippocampus (17): linear fit = 0.94 x + 0.0 (414 voxels, peak = 60), gca=59.8
gca peak = 0.12541 (104)
mri peak = 0.07736 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (62192 voxels, overlap=0.696)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (62192 voxels, peak = 109), gca=108.7
gca peak = 0.13686 (104)
mri peak = 0.08360 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (70030 voxels, overlap=0.713)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (70030 voxels, peak = 107), gca=106.6
gca peak = 0.11691 (63)
mri peak = 0.04702 (53)
Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (18461 voxels, overlap=0.186)
Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (18461 voxels, peak = 53), gca=53.2
gca peak = 0.13270 (63)
mri peak = 0.04765 (50)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (18063 voxels, overlap=0.058)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (18063 voxels, peak = 52), gca=52.0
gca peak = 0.15182 (70)
mri peak = 0.07595 (70)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (506 voxels, overlap=0.909)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (506 voxels, peak = 69), gca=69.0
gca peak = 0.14251 (76)
mri peak = 0.05662 (78)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (582 voxels, overlap=0.814)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (582 voxels, peak = 72), gca=71.8
gca peak = 0.12116 (60)
mri peak = 0.03987 (57)
Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (14121 voxels, overlap=0.845)
Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (14121 voxels, peak = 55), gca=54.9
gca peak = 0.12723 (61)
mri peak = 0.04047 (52)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (14283 voxels, overlap=0.845)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (14283 voxels, peak = 56), gca=55.8
gca peak = 0.22684 (88)
mri peak = 0.09166 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7012 voxels, overlap=0.770)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (7012 voxels, peak = 91), gca=91.1
gca peak = 0.21067 (87)
mri peak = 0.09815 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6498 voxels, overlap=0.731)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6498 voxels, peak = 91), gca=90.9
gca peak = 0.25455 (62)
mri peak = 0.08659 (63)
Left_Amygdala (18): linear fit = 0.95 x + 0.0 (225 voxels, overlap=0.981)
Left_Amygdala (18): linear fit = 0.95 x + 0.0 (225 voxels, peak = 59), gca=59.2
gca peak = 0.39668 (62)
mri peak = 0.10072 (61)
Right_Amygdala (54): linear fit = 0.96 x + 0.0 (277 voxels, overlap=0.999)
Right_Amygdala (54): linear fit = 0.96 x + 0.0 (277 voxels, peak = 60), gca=59.8
gca peak = 0.10129 (93)
mri peak = 0.06152 (97)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5173 voxels, overlap=0.748)
Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (5173 voxels, peak = 96), gca=96.3
gca peak = 0.12071 (89)
mri peak = 0.05942 (95)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4279 voxels, overlap=0.849)
Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (4279 voxels, peak = 94), gca=93.9
gca peak = 0.13716 (82)
mri peak = 0.05739 (82)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2252 voxels, overlap=1.000)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (2252 voxels, peak = 82), gca=81.6
gca peak = 0.15214 (84)
mri peak = 0.04879 (85)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2037 voxels, overlap=0.994)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (2037 voxels, peak = 83), gca=82.7
gca peak = 0.08983 (85)
mri peak = 0.06290 (87)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (12106 voxels, overlap=0.778)
Brain_Stem (16): linear fit = 1.07 x + 0.0 (12106 voxels, peak = 91), gca=90.5
gca peak = 0.11809 (92)
mri peak = 0.06265 (107)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (932 voxels, overlap=0.713)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (932 voxels, peak = 103), gca=102.6
gca peak = 0.12914 (94)
mri peak = 0.06792 (98)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1159 voxels, overlap=0.679)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1159 voxels, peak = 104), gca=103.9
gca peak = 0.21100 (36)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.13542 (27)
mri peak = 0.16861 ( 9)
Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (170 voxels, overlap=0.015)
Fourth_Ventricle (15): linear fit = 0.28 x + 0.0 (170 voxels, peak =  7), gca=7.4
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.21802 (40)
gca peak Third_Ventricle = 0.21100 (36)
gca peak Fourth_Ventricle = 0.13542 (27)
gca peak CSF = 0.17123 (45)
gca peak Left_Accumbens_area = 0.25875 (69)
gca peak Left_undetermined = 0.96240 (36)
gca peak Left_vessel = 0.33262 (65)
gca peak Left_choroid_plexus = 0.09846 (46)
gca peak Right_Inf_Lat_Vent = 0.28113 (34)
gca peak Right_Accumbens_area = 0.27120 (72)
gca peak Right_vessel = 0.61915 (60)
gca peak Right_choroid_plexus = 0.12775 (51)
gca peak Fifth_Ventricle = 0.45329 (44)
gca peak WM_hypointensities = 0.11729 (81)
gca peak non_WM_hypointensities = 0.10912 (56)
gca peak Optic_Chiasm = 0.33287 (75)
label assignment complete, 0 changed (0.00%)
not using caudate to estimate GM means
estimating mean gm scale to be 0.90 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
saving intensity scales to talairach.label_intensities.txt
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.718, neg=0, invalid=96777
0103: dt=129.472000, rms=0.711 (0.875%), neg=0, invalid=96777
0104: dt=295.936000, rms=0.707 (0.630%), neg=0, invalid=96777
0105: dt=73.984000, rms=0.705 (0.255%), neg=0, invalid=96777
0106: dt=129.472000, rms=0.704 (0.159%), neg=0, invalid=96777
0107: dt=129.472000, rms=0.703 (0.147%), neg=0, invalid=96777
0108: dt=55.488000, rms=0.702 (0.094%), neg=0, invalid=96777
0109: dt=443.904000, rms=0.701 (0.233%), neg=0, invalid=96777
0110: dt=32.368000, rms=0.700 (0.148%), neg=0, invalid=96777
0111: dt=73.984000, rms=0.699 (0.044%), neg=0, invalid=96777
0112: dt=73.984000, rms=0.699 (0.044%), neg=0, invalid=96777
0113: dt=73.984000, rms=0.698 (0.075%), neg=0, invalid=96777
0114: dt=73.984000, rms=0.698 (0.112%), neg=0, invalid=96777
0115: dt=73.984000, rms=0.697 (0.102%), neg=0, invalid=96777
0116: dt=73.984000, rms=0.696 (0.130%), neg=0, invalid=96777
0117: dt=73.984000, rms=0.695 (0.117%), neg=0, invalid=96777
0118: dt=73.984000, rms=0.694 (0.128%), neg=0, invalid=96777
0119: dt=73.984000, rms=0.693 (0.116%), neg=0, invalid=96777
0120: dt=73.984000, rms=0.693 (0.113%), neg=0, invalid=96777
0121: dt=73.984000, rms=0.692 (0.110%), neg=0, invalid=96777
0122: dt=73.984000, rms=0.691 (0.104%), neg=0, invalid=96777
0123: dt=73.984000, rms=0.691 (0.095%), neg=0, invalid=96777
0124: dt=73.984000, rms=0.690 (0.078%), neg=0, invalid=96777
0125: dt=73.984000, rms=0.689 (0.094%), neg=0, invalid=96777
0126: dt=73.984000, rms=0.689 (0.088%), neg=0, invalid=96777
0127: dt=73.984000, rms=0.688 (0.078%), neg=0, invalid=96777
0128: dt=73.984000, rms=0.688 (0.077%), neg=0, invalid=96777
0129: dt=73.984000, rms=0.687 (0.092%), neg=0, invalid=96777
0130: dt=73.984000, rms=0.687 (0.075%), neg=0, invalid=96777
0131: dt=73.984000, rms=0.686 (0.083%), neg=0, invalid=96777
0132: dt=73.984000, rms=0.685 (0.077%), neg=0, invalid=96777
0133: dt=73.984000, rms=0.685 (0.088%), neg=0, invalid=96777
0134: dt=73.984000, rms=0.684 (0.068%), neg=0, invalid=96777
0135: dt=73.984000, rms=0.684 (0.073%), neg=0, invalid=96777
0136: dt=73.984000, rms=0.683 (0.066%), neg=0, invalid=96777
0137: dt=73.984000, rms=0.683 (0.068%), neg=0, invalid=96777
0138: dt=73.984000, rms=0.683 (0.054%), neg=0, invalid=96777
0139: dt=73.984000, rms=0.682 (0.057%), neg=0, invalid=96777
0140: dt=73.984000, rms=0.682 (0.062%), neg=0, invalid=96777
0141: dt=73.984000, rms=0.681 (0.062%), neg=0, invalid=96777
0142: dt=73.984000, rms=0.681 (0.045%), neg=0, invalid=96777
0143: dt=73.984000, rms=0.681 (0.045%), neg=0, invalid=96777
0144: dt=73.984000, rms=0.680 (0.049%), neg=0, invalid=96777
0145: dt=73.984000, rms=0.680 (0.043%), neg=0, invalid=96777
0146: dt=73.984000, rms=0.680 (0.043%), neg=0, invalid=96777
0147: dt=73.984000, rms=0.680 (0.035%), neg=0, invalid=96777
0148: dt=73.984000, rms=0.679 (0.046%), neg=0, invalid=96777
0149: dt=73.984000, rms=0.679 (0.030%), neg=0, invalid=96777
0150: dt=73.984000, rms=0.679 (0.017%), neg=0, invalid=96777
0151: dt=73.984000, rms=0.679 (0.019%), neg=0, invalid=96777
0152: dt=73.984000, rms=0.679 (0.017%), neg=0, invalid=96777
0153: dt=92.480000, rms=0.679 (0.015%), neg=0, invalid=96777
0154: dt=92.480000, rms=0.679 (0.003%), neg=0, invalid=96777
0155: dt=92.480000, rms=0.678 (0.024%), neg=0, invalid=96777
0156: dt=92.480000, rms=0.678 (0.009%), neg=0, invalid=96777
0157: dt=92.480000, rms=0.678 (0.013%), neg=0, invalid=96777
0158: dt=92.480000, rms=0.678 (0.008%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.678, neg=0, invalid=96777
0159: dt=73.984000, rms=0.678 (0.050%), neg=0, invalid=96777
0160: dt=73.984000, rms=0.678 (0.023%), neg=0, invalid=96777
0161: dt=73.984000, rms=0.678 (0.032%), neg=0, invalid=96777
0162: dt=73.984000, rms=0.677 (0.031%), neg=0, invalid=96777
0163: dt=73.984000, rms=0.677 (0.044%), neg=0, invalid=96777
0164: dt=73.984000, rms=0.677 (0.054%), neg=0, invalid=96777
0165: dt=73.984000, rms=0.676 (0.061%), neg=0, invalid=96777
0166: dt=73.984000, rms=0.676 (0.062%), neg=0, invalid=96777
0167: dt=73.984000, rms=0.675 (0.048%), neg=0, invalid=96777
0168: dt=73.984000, rms=0.675 (0.031%), neg=0, invalid=96777
0169: dt=73.984000, rms=0.675 (0.021%), neg=0, invalid=96777
0170: dt=73.984000, rms=0.675 (0.004%), neg=0, invalid=96777
0171: dt=129.472000, rms=0.675 (0.052%), neg=0, invalid=96777
0172: dt=5.780000, rms=0.675 (0.003%), neg=0, invalid=96777
0173: dt=5.780000, rms=0.675 (-0.002%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.675, neg=0, invalid=96777
0174: dt=82.944000, rms=0.671 (0.721%), neg=0, invalid=96777
0175: dt=36.288000, rms=0.668 (0.425%), neg=0, invalid=96777
0176: dt=145.152000, rms=0.663 (0.777%), neg=0, invalid=96777
0177: dt=25.920000, rms=0.659 (0.461%), neg=0, invalid=96777
0178: dt=82.944000, rms=0.656 (0.481%), neg=0, invalid=96777
0179: dt=31.104000, rms=0.654 (0.273%), neg=0, invalid=96777
0180: dt=62.208000, rms=0.653 (0.284%), neg=0, invalid=96777
0181: dt=36.288000, rms=0.651 (0.242%), neg=0, invalid=96777
0182: dt=36.288000, rms=0.650 (0.195%), neg=0, invalid=96777
0183: dt=36.288000, rms=0.649 (0.195%), neg=0, invalid=96777
0184: dt=62.208000, rms=0.647 (0.224%), neg=0, invalid=96777
0185: dt=36.288000, rms=0.646 (0.206%), neg=0, invalid=96777
0186: dt=36.288000, rms=0.645 (0.148%), neg=0, invalid=96777
0187: dt=36.288000, rms=0.644 (0.191%), neg=0, invalid=96777
0188: dt=62.208000, rms=0.643 (0.158%), neg=0, invalid=96777
0189: dt=31.104000, rms=0.641 (0.190%), neg=0, invalid=96777
0190: dt=36.288000, rms=0.641 (0.121%), neg=0, invalid=96777
0191: dt=82.944000, rms=0.639 (0.215%), neg=0, invalid=96777
0192: dt=25.920000, rms=0.638 (0.164%), neg=0, invalid=96777
0193: dt=103.680000, rms=0.636 (0.334%), neg=0, invalid=96777
0194: dt=36.288000, rms=0.635 (0.085%), neg=0, invalid=96777
0195: dt=36.288000, rms=0.635 (0.127%), neg=0, invalid=96777
0196: dt=36.288000, rms=0.634 (0.064%), neg=0, invalid=96777
0197: dt=103.680000, rms=0.633 (0.228%), neg=0, invalid=96777
0198: dt=25.920000, rms=0.632 (0.123%), neg=0, invalid=96777
0199: dt=124.416000, rms=0.630 (0.280%), neg=0, invalid=96777
0200: dt=36.288000, rms=0.630 (0.084%), neg=0, invalid=96777
0201: dt=31.104000, rms=0.629 (0.083%), neg=0, invalid=96777
0202: dt=124.416000, rms=0.629 (0.100%), neg=0, invalid=96777
0203: dt=9.072000, rms=0.628 (0.105%), neg=0, invalid=96777
0204: dt=9.072000, rms=0.628 (0.045%), neg=0, invalid=96777
0205: dt=9.072000, rms=0.627 (0.034%), neg=0, invalid=96777
0206: dt=9.072000, rms=0.627 (0.046%), neg=0, invalid=96777
0207: dt=4.536000, rms=0.627 (0.004%), neg=0, invalid=96777
0208: dt=1.134000, rms=0.627 (0.001%), neg=0, invalid=96777
0209: dt=0.567000, rms=0.627 (0.001%), neg=0, invalid=96777
0210: dt=0.008859, rms=0.627 (0.000%), neg=0, invalid=96777
0211: dt=0.000554, rms=0.627 (0.000%), neg=0, invalid=96777
0212: dt=0.000138, rms=0.627 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.627, neg=0, invalid=96777
0213: dt=0.000000, rms=0.627 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.631, neg=0, invalid=96777
0214: dt=44.800000, rms=0.607 (3.848%), neg=0, invalid=96777
0215: dt=44.800000, rms=0.596 (1.856%), neg=0, invalid=96777
0216: dt=8.000000, rms=0.592 (0.665%), neg=0, invalid=96777
0217: dt=44.800000, rms=0.583 (1.460%), neg=0, invalid=96777
0218: dt=8.052863, rms=0.581 (0.432%), neg=0, invalid=96777
0219: dt=44.800000, rms=0.575 (0.908%), neg=0, invalid=96777
0220: dt=9.714286, rms=0.573 (0.393%), neg=0, invalid=96777
0221: dt=44.800000, rms=0.569 (0.735%), neg=0, invalid=96777
0222: dt=8.184615, rms=0.567 (0.339%), neg=0, invalid=96777
0223: dt=44.800000, rms=0.565 (0.381%), neg=0, invalid=96777
0224: dt=10.890052, rms=0.563 (0.398%), neg=0, invalid=96777
0225: dt=11.200000, rms=0.562 (0.158%), neg=0, invalid=96777
0226: dt=11.200000, rms=0.561 (0.161%), neg=0, invalid=96777
0227: dt=44.800000, rms=0.559 (0.304%), neg=0, invalid=96777
0228: dt=8.067511, rms=0.558 (0.279%), neg=0, invalid=96777
0229: dt=11.200000, rms=0.557 (0.107%), neg=0, invalid=96777
0230: dt=11.200000, rms=0.556 (0.109%), neg=0, invalid=96777
0231: dt=44.800000, rms=0.555 (0.224%), neg=0, invalid=96777
0232: dt=9.600000, rms=0.554 (0.240%), neg=0, invalid=96777
0233: dt=11.200000, rms=0.553 (0.073%), neg=0, invalid=96777
0234: dt=11.200000, rms=0.553 (0.103%), neg=0, invalid=96777
0235: dt=32.000000, rms=0.552 (0.126%), neg=0, invalid=96777
0236: dt=11.200000, rms=0.551 (0.190%), neg=0, invalid=96777
0237: dt=8.000000, rms=0.551 (0.033%), neg=0, invalid=96777
0238: dt=8.000000, rms=0.550 (0.060%), neg=0, invalid=96777
0239: dt=8.000000, rms=0.550 (0.086%), neg=0, invalid=96777
0240: dt=8.000000, rms=0.549 (0.139%), neg=0, invalid=96777
0241: dt=8.000000, rms=0.548 (0.158%), neg=0, invalid=96777
0242: dt=8.000000, rms=0.547 (0.190%), neg=0, invalid=96777
0243: dt=8.000000, rms=0.546 (0.210%), neg=0, invalid=96777
0244: dt=8.000000, rms=0.545 (0.212%), neg=0, invalid=96777
0245: dt=8.000000, rms=0.544 (0.236%), neg=0, invalid=96777
0246: dt=8.000000, rms=0.542 (0.242%), neg=0, invalid=96777
0247: dt=8.000000, rms=0.541 (0.253%), neg=0, invalid=96777
0248: dt=8.000000, rms=0.540 (0.234%), neg=0, invalid=96777
0249: dt=8.000000, rms=0.539 (0.218%), neg=0, invalid=96777
0250: dt=8.000000, rms=0.537 (0.217%), neg=0, invalid=96777
0251: dt=8.000000, rms=0.536 (0.197%), neg=0, invalid=96777
0252: dt=8.000000, rms=0.535 (0.208%), neg=0, invalid=96777
0253: dt=8.000000, rms=0.534 (0.184%), neg=0, invalid=96777
0254: dt=8.000000, rms=0.533 (0.153%), neg=0, invalid=96777
0255: dt=8.000000, rms=0.533 (0.136%), neg=0, invalid=96777
0256: dt=8.000000, rms=0.532 (0.130%), neg=0, invalid=96777
0257: dt=8.000000, rms=0.531 (0.127%), neg=0, invalid=96777
0258: dt=8.000000, rms=0.531 (0.131%), neg=0, invalid=96777
0259: dt=8.000000, rms=0.530 (0.142%), neg=0, invalid=96777
0260: dt=8.000000, rms=0.529 (0.113%), neg=0, invalid=96777
0261: dt=8.000000, rms=0.529 (0.102%), neg=0, invalid=96777
0262: dt=8.000000, rms=0.528 (0.087%), neg=0, invalid=96777
0263: dt=8.000000, rms=0.528 (0.077%), neg=0, invalid=96777
0264: dt=8.000000, rms=0.528 (0.077%), neg=0, invalid=96777
0265: dt=8.000000, rms=0.527 (0.083%), neg=0, invalid=96777
0266: dt=8.000000, rms=0.527 (0.085%), neg=0, invalid=96777
0267: dt=8.000000, rms=0.526 (0.069%), neg=0, invalid=96777
0268: dt=8.000000, rms=0.526 (0.065%), neg=0, invalid=96777
0269: dt=8.000000, rms=0.526 (0.040%), neg=0, invalid=96777
0270: dt=8.000000, rms=0.525 (0.063%), neg=0, invalid=96777
0271: dt=8.000000, rms=0.525 (0.047%), neg=0, invalid=96777
0272: dt=8.000000, rms=0.525 (0.047%), neg=0, invalid=96777
0273: dt=8.000000, rms=0.525 (0.043%), neg=0, invalid=96777
0274: dt=8.000000, rms=0.524 (0.059%), neg=0, invalid=96777
0275: dt=8.000000, rms=0.524 (0.045%), neg=0, invalid=96777
0276: dt=8.000000, rms=0.524 (0.045%), neg=0, invalid=96777
0277: dt=8.000000, rms=0.524 (0.064%), neg=0, invalid=96777
0278: dt=8.000000, rms=0.523 (0.047%), neg=0, invalid=96777
0279: dt=8.000000, rms=0.523 (0.043%), neg=0, invalid=96777
0280: dt=8.000000, rms=0.523 (0.034%), neg=0, invalid=96777
0281: dt=8.000000, rms=0.523 (0.039%), neg=0, invalid=96777
0282: dt=8.000000, rms=0.523 (0.030%), neg=0, invalid=96777
0283: dt=8.000000, rms=0.522 (0.039%), neg=0, invalid=96777
0284: dt=8.000000, rms=0.522 (0.044%), neg=0, invalid=96777
0285: dt=8.000000, rms=0.522 (0.028%), neg=0, invalid=96777
0286: dt=8.000000, rms=0.522 (0.022%), neg=0, invalid=96777
0287: dt=8.000000, rms=0.522 (0.021%), neg=0, invalid=96777
0288: dt=11.200000, rms=0.522 (0.033%), neg=0, invalid=96777
0289: dt=9.600000, rms=0.522 (0.000%), neg=0, invalid=96777
0290: dt=9.600000, rms=0.522 (0.007%), neg=0, invalid=96777
0291: dt=9.600000, rms=0.522 (-0.006%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.522, neg=0, invalid=96777
0292: dt=25.600000, rms=0.520 (0.337%), neg=0, invalid=96777
0293: dt=11.200000, rms=0.519 (0.126%), neg=0, invalid=96777
0294: dt=32.000000, rms=0.519 (0.101%), neg=0, invalid=96777
0295: dt=9.600000, rms=0.518 (0.061%), neg=0, invalid=96777
0296: dt=11.200000, rms=0.518 (0.035%), neg=0, invalid=96777
0297: dt=11.200000, rms=0.518 (0.018%), neg=0, invalid=96777
0298: dt=11.200000, rms=0.518 (0.043%), neg=0, invalid=96777
0299: dt=11.200000, rms=0.518 (0.045%), neg=0, invalid=96777
0300: dt=11.200000, rms=0.517 (0.027%), neg=0, invalid=96777
0301: dt=11.200000, rms=0.517 (0.031%), neg=0, invalid=96777
0302: dt=11.200000, rms=0.517 (0.027%), neg=0, invalid=96777
0303: dt=11.200000, rms=0.517 (0.047%), neg=0, invalid=96777
0304: dt=11.200000, rms=0.517 (0.019%), neg=0, invalid=96777
0305: dt=11.200000, rms=0.517 (-0.033%), neg=0, invalid=96777
0306: dt=6.400000, rms=0.517 (0.005%), neg=0, invalid=96777
0307: dt=9.600000, rms=0.517 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.540, neg=0, invalid=96777
0308: dt=0.000000, rms=0.540 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.540, neg=0, invalid=96777
0309: dt=0.000000, rms=0.540 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.585, neg=0, invalid=96777
0310: dt=1.064865, rms=0.582 (0.571%), neg=0, invalid=96777
0311: dt=0.256000, rms=0.582 (0.022%), neg=0, invalid=96777
0312: dt=0.256000, rms=0.582 (-0.012%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.582, neg=0, invalid=96777
0313: dt=0.531250, rms=0.581 (0.088%), neg=0, invalid=96777
0314: dt=0.112000, rms=0.581 (0.009%), neg=0, invalid=96777
0315: dt=0.112000, rms=0.581 (0.003%), neg=0, invalid=96777
0316: dt=0.112000, rms=0.581 (-0.009%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.530, neg=0, invalid=96777
0317: dt=0.112000, rms=0.525 (0.906%), neg=0, invalid=96777
0318: dt=0.080000, rms=0.522 (0.508%), neg=0, invalid=96777
0319: dt=0.028000, rms=0.521 (0.156%), neg=0, invalid=96777
0320: dt=0.137605, rms=0.518 (0.712%), neg=0, invalid=96777
0321: dt=0.112000, rms=0.515 (0.443%), neg=0, invalid=96777
0322: dt=0.116453, rms=0.513 (0.371%), neg=0, invalid=96777
0323: dt=0.112000, rms=0.512 (0.294%), neg=0, invalid=96777
0324: dt=0.104701, rms=0.511 (0.232%), neg=0, invalid=96777
0325: dt=0.028000, rms=0.510 (0.048%), neg=0, invalid=96777
0326: dt=0.028000, rms=0.510 (0.051%), neg=0, invalid=96777
0327: dt=0.028000, rms=0.510 (0.103%), neg=0, invalid=96777
0328: dt=0.028000, rms=0.509 (0.127%), neg=0, invalid=96777
0329: dt=0.028000, rms=0.508 (0.147%), neg=0, invalid=96777
0330: dt=0.028000, rms=0.508 (0.035%), neg=0, invalid=96777
0331: dt=0.028000, rms=0.508 (0.070%), neg=0, invalid=96777
0332: dt=0.028000, rms=0.507 (0.090%), neg=0, invalid=96777
0333: dt=0.028000, rms=0.507 (0.025%), neg=0, invalid=96777
0334: dt=0.028000, rms=0.507 (0.047%), neg=0, invalid=96777
0335: dt=0.028000, rms=0.506 (0.078%), neg=0, invalid=96777
0336: dt=0.028000, rms=0.506 (0.091%), neg=0, invalid=96777
0337: dt=0.028000, rms=0.506 (0.030%), neg=0, invalid=96777
0338: dt=0.028000, rms=0.506 (0.029%), neg=0, invalid=96777
0339: dt=0.028000, rms=0.506 (0.021%), neg=0, invalid=96777
0340: dt=0.028000, rms=0.505 (0.046%), neg=0, invalid=96777
0341: dt=0.028000, rms=0.505 (0.052%), neg=0, invalid=96777
0342: dt=0.028000, rms=0.505 (0.054%), neg=0, invalid=96777
0343: dt=0.028000, rms=0.505 (0.071%), neg=0, invalid=96777
0344: dt=0.028000, rms=0.504 (0.083%), neg=0, invalid=96777
0345: dt=0.028000, rms=0.504 (0.090%), neg=0, invalid=96777
0346: dt=0.028000, rms=0.503 (0.084%), neg=0, invalid=96777
0347: dt=0.028000, rms=0.503 (0.088%), neg=0, invalid=96777
0348: dt=0.028000, rms=0.502 (0.079%), neg=0, invalid=96777
0349: dt=0.028000, rms=0.502 (0.069%), neg=0, invalid=96777
0350: dt=0.028000, rms=0.502 (0.073%), neg=0, invalid=96777
0351: dt=0.028000, rms=0.502 (0.012%), neg=0, invalid=96777
0352: dt=0.028000, rms=0.502 (0.003%), neg=0, invalid=96777
0353: dt=0.028000, rms=0.502 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.502, neg=0, invalid=96777
0354: dt=0.028000, rms=0.501 (0.075%), neg=0, invalid=96777
0355: dt=0.080000, rms=0.500 (0.205%), neg=0, invalid=96777
0356: dt=0.028000, rms=0.500 (0.052%), neg=0, invalid=96777
0357: dt=0.112000, rms=0.499 (0.219%), neg=0, invalid=96777
0358: dt=0.028000, rms=0.499 (0.044%), neg=0, invalid=96777
0359: dt=0.028000, rms=0.498 (0.041%), neg=0, invalid=96777
0360: dt=0.028000, rms=0.498 (0.076%), neg=0, invalid=96777
0361: dt=0.028000, rms=0.498 (0.090%), neg=0, invalid=96777
0362: dt=0.028000, rms=0.497 (0.107%), neg=0, invalid=96777
0363: dt=0.028000, rms=0.496 (0.117%), neg=0, invalid=96777
0364: dt=0.028000, rms=0.496 (0.024%), neg=0, invalid=96777
0365: dt=0.028000, rms=0.496 (0.023%), neg=0, invalid=96777
0366: dt=0.112000, rms=0.496 (0.046%), neg=0, invalid=96777
0367: dt=0.112000, rms=0.496 (0.042%), neg=0, invalid=96777
0368: dt=0.056000, rms=0.496 (0.007%), neg=0, invalid=96777
0369: dt=0.028000, rms=0.496 (0.015%), neg=0, invalid=96777
0370: dt=0.028000, rms=0.496 (0.004%), neg=0, invalid=96777
0371: dt=0.028000, rms=0.496 (0.013%), neg=0, invalid=96777
0372: dt=0.028000, rms=0.496 (0.020%), neg=0, invalid=96777
0373: dt=0.028000, rms=0.495 (0.017%), neg=0, invalid=96777
label assignment complete, 0 changed (0.00%)
*********************************************************************************************
*********************************************************************************************
*********************************************************************************************
********************* ALLOWING NEGATIVE NODES IN DEFORMATION ********************************
*********************************************************************************************
*********************************************************************************************
*********************************************************************************************
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.493, neg=0, invalid=96777
0374: dt=0.000000, rms=0.493 (0.003%), neg=0, invalid=96777
0375: dt=0.000000, rms=0.493 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.493, neg=0, invalid=96777
0376: dt=129.472000, rms=0.493 (0.062%), neg=0, invalid=96777
0377: dt=32.368000, rms=0.493 (0.010%), neg=0, invalid=96777
0378: dt=32.368000, rms=0.493 (0.003%), neg=0, invalid=96777
0379: dt=32.368000, rms=0.493 (0.024%), neg=0, invalid=96777
0380: dt=32.368000, rms=0.493 (0.014%), neg=0, invalid=96777
0381: dt=32.368000, rms=0.493 (0.011%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.493, neg=0, invalid=96777
0382: dt=20.736000, rms=0.493 (0.032%), neg=0, invalid=96777
0383: dt=20.736000, rms=0.493 (0.020%), neg=0, invalid=96777
0384: dt=20.736000, rms=0.493 (0.009%), neg=0, invalid=96777
0385: dt=20.736000, rms=0.493 (0.005%), neg=0, invalid=96777
0386: dt=20.736000, rms=0.492 (-0.028%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.492, neg=0, invalid=96777
0387: dt=36.288000, rms=0.491 (0.332%), neg=0, invalid=96777
0388: dt=36.288000, rms=0.490 (0.127%), neg=0, invalid=96777
0389: dt=36.288000, rms=0.490 (0.115%), neg=0, invalid=96777
0390: dt=36.288000, rms=0.489 (0.154%), neg=0, invalid=96777
0391: dt=36.288000, rms=0.488 (0.144%), neg=0, invalid=96777
0392: dt=36.288000, rms=0.488 (0.120%), neg=0, invalid=96777
0393: dt=36.288000, rms=0.487 (0.177%), neg=0, invalid=96777
0394: dt=36.288000, rms=0.486 (0.138%), neg=0, invalid=96777
0395: dt=36.288000, rms=0.486 (0.070%), neg=0, invalid=96777
0396: dt=36.288000, rms=0.485 (0.059%), neg=0, invalid=96777
0397: dt=82.944000, rms=0.485 (0.059%), neg=0, invalid=96777
0398: dt=82.944000, rms=0.485 (-0.128%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.485, neg=0, invalid=96777
0399: dt=11.200000, rms=0.484 (0.226%), neg=0, invalid=96777
iter 0, gcam->neg = 17
after 7 iterations, nbhd size=1, neg = 0
0400: dt=32.000000, rms=0.483 (0.316%), neg=0, invalid=96777
0401: dt=11.200000, rms=0.482 (0.209%), neg=0, invalid=96777
0402: dt=11.200000, rms=0.481 (0.185%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 14 iterations, nbhd size=2, neg = 0
0403: dt=11.200000, rms=0.480 (0.265%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0404: dt=11.200000, rms=0.478 (0.277%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 7 iterations, nbhd size=1, neg = 0
0405: dt=11.200000, rms=0.477 (0.257%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0406: dt=11.200000, rms=0.476 (0.232%), neg=0, invalid=96777
0407: dt=11.200000, rms=0.475 (0.201%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0408: dt=11.200000, rms=0.474 (0.185%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0409: dt=11.200000, rms=0.473 (0.205%), neg=0, invalid=96777
0410: dt=11.200000, rms=0.472 (0.213%), neg=0, invalid=96777
0411: dt=11.200000, rms=0.471 (0.187%), neg=0, invalid=96777
0412: dt=11.200000, rms=0.470 (0.208%), neg=0, invalid=96777
0413: dt=11.200000, rms=0.470 (0.170%), neg=0, invalid=96777
0414: dt=11.200000, rms=0.469 (0.170%), neg=0, invalid=96777
0415: dt=11.200000, rms=0.468 (0.139%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 9 iterations, nbhd size=1, neg = 0
0416: dt=11.200000, rms=0.468 (0.097%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 8 iterations, nbhd size=1, neg = 0
0417: dt=11.200000, rms=0.467 (0.086%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0418: dt=11.200000, rms=0.467 (0.086%), neg=0, invalid=96777
0419: dt=11.200000, rms=0.467 (0.017%), neg=0, invalid=96777
0420: dt=11.200000, rms=0.467 (0.045%), neg=0, invalid=96777
0421: dt=11.200000, rms=0.466 (0.080%), neg=0, invalid=96777
0422: dt=11.200000, rms=0.466 (0.042%), neg=0, invalid=96777
0423: dt=11.200000, rms=0.466 (0.023%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.466, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 8 iterations, nbhd size=1, neg = 0
0424: dt=38.400000, rms=0.462 (0.761%), neg=0, invalid=96777
0425: dt=11.200000, rms=0.461 (0.203%), neg=0, invalid=96777
0426: dt=11.200000, rms=0.461 (0.103%), neg=0, invalid=96777
0427: dt=11.200000, rms=0.460 (0.107%), neg=0, invalid=96777
0428: dt=11.200000, rms=0.460 (0.154%), neg=0, invalid=96777
0429: dt=11.200000, rms=0.459 (0.124%), neg=0, invalid=96777
0430: dt=11.200000, rms=0.458 (0.163%), neg=0, invalid=96777
0431: dt=11.200000, rms=0.458 (0.120%), neg=0, invalid=96777
0432: dt=11.200000, rms=0.458 (0.063%), neg=0, invalid=96777
0433: dt=8.000000, rms=0.457 (0.035%), neg=0, invalid=96777
0434: dt=8.000000, rms=0.457 (0.001%), neg=0, invalid=96777
0435: dt=8.000000, rms=0.457 (0.023%), neg=0, invalid=96777
0436: dt=8.000000, rms=0.457 (0.015%), neg=0, invalid=96777
0437: dt=8.000000, rms=0.457 (0.020%), neg=0, invalid=96777
0438: dt=8.000000, rms=0.457 (0.027%), neg=0, invalid=96777
0439: dt=8.000000, rms=0.457 (0.029%), neg=0, invalid=96777
0440: dt=8.000000, rms=0.457 (0.035%), neg=0, invalid=96777
0441: dt=8.000000, rms=0.457 (0.026%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.462, neg=0, invalid=96777
0442: dt=0.000563, rms=0.462 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.462, neg=0, invalid=96777
0443: dt=2.880000, rms=0.461 (0.035%), neg=0, invalid=96777
0444: dt=2.880000, rms=0.461 (0.028%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0445: dt=2.880000, rms=0.461 (0.002%), neg=0, invalid=96777
iter 0, gcam->neg = 9
after 8 iterations, nbhd size=1, neg = 0
0446: dt=2.880000, rms=0.461 (-0.071%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.469, neg=0, invalid=96777
0447: dt=0.001750, rms=0.469 (0.000%), neg=0, invalid=96777
0448: dt=0.001250, rms=0.469 (0.000%), neg=0, invalid=96777
0449: dt=0.001250, rms=0.469 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.469, neg=0, invalid=96777
iter 0, gcam->neg = 5
after 7 iterations, nbhd size=1, neg = 0
0450: dt=0.460000, rms=0.469 (0.073%), neg=0, invalid=96777
iter 0, gcam->neg = 9
after 8 iterations, nbhd size=1, neg = 0
0451: dt=0.256000, rms=0.468 (0.024%), neg=0, invalid=96777
iter 0, gcam->neg = 29
after 9 iterations, nbhd size=1, neg = 0
0452: dt=0.256000, rms=0.468 (0.024%), neg=0, invalid=96777
iter 0, gcam->neg = 32
after 8 iterations, nbhd size=1, neg = 0
0453: dt=0.256000, rms=0.468 (0.015%), neg=0, invalid=96777
iter 0, gcam->neg = 41
after 10 iterations, nbhd size=1, neg = 0
0454: dt=0.256000, rms=0.468 (-0.032%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.459, neg=0, invalid=96777
iter 0, gcam->neg = 810
after 26 iterations, nbhd size=2, neg = 0
0455: dt=1.724643, rms=0.419 (8.566%), neg=0, invalid=96777
0456: dt=0.000094, rms=0.419 (-0.007%), neg=0, invalid=96777
0457: dt=0.000094, rms=0.419 (0.001%), neg=0, invalid=96777
0458: dt=0.000094, rms=0.419 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=96777
0459: dt=0.000188, rms=0.419 (0.000%), neg=0, invalid=96777
0460: dt=0.000000, rms=0.419 (-0.001%), neg=0, invalid=96777
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 ************************
setting smoothness coefficient to 0.008
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=96777
0461: dt=0.000000, rms=0.407 (-0.358%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.407, neg=0, invalid=96777
0462: dt=32.368000, rms=0.407 (0.014%), neg=0, invalid=96777
0463: dt=32.368000, rms=0.407 (0.003%), neg=0, invalid=96777
0464: dt=32.368000, rms=0.407 (0.001%), neg=0, invalid=96777
0465: dt=32.368000, rms=0.407 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.407, neg=0, invalid=96777
0466: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.407, neg=0, invalid=96777
0467: dt=36.288000, rms=0.407 (0.020%), neg=0, invalid=96777
0468: dt=36.288000, rms=0.407 (0.006%), neg=0, invalid=96777
0469: dt=36.288000, rms=0.407 (0.007%), neg=0, invalid=96777
0470: dt=36.288000, rms=0.407 (0.005%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 7 iterations, nbhd size=1, neg = 0
0471: dt=36.288000, rms=0.407 (-0.062%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.408, neg=0, invalid=96777
0472: dt=0.010937, rms=0.408 (0.000%), neg=0, invalid=96777
0473: dt=1.600000, rms=0.408 (0.002%), neg=0, invalid=96777
0474: dt=2.400000, rms=0.408 (0.004%), neg=0, invalid=96777
0475: dt=0.700000, rms=0.408 (0.001%), neg=0, invalid=96777
0476: dt=0.700000, rms=0.408 (0.000%), neg=0, invalid=96777
0477: dt=0.700000, rms=0.408 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.408, neg=0, invalid=96777
iter 0, gcam->neg = 18
after 200 iterations, nbhd size=1, neg = 1
starting rms=0.005, neg=1, removing folds in lattice....
iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.003 (36.614%)
0478: dt=44.800000, rms=0.406 (0.350%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 5 iterations, nbhd size=1, neg = 0
0479: dt=11.200000, rms=0.406 (0.106%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 200 iterations, nbhd size=1, neg = 3
starting rms=0.005, neg=3, removing folds in lattice....
iter 1, dt=0.000047: new neg 0, old_neg 3, delta 3, rms=0.003 (49.334%)
0480: dt=11.200000, rms=0.406 (0.021%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0481: dt=11.200000, rms=0.406 (0.084%), neg=0, invalid=96777
iter 0, gcam->neg = 9
after 15 iterations, nbhd size=2, neg = 0
0482: dt=11.200000, rms=0.405 (0.059%), neg=0, invalid=96777
iter 0, gcam->neg = 15
after 38 iterations, nbhd size=4, neg = 0
0483: dt=11.200000, rms=0.405 (-0.038%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.407, neg=0, invalid=96777
iter 0, gcam->neg = 15
after 11 iterations, nbhd size=1, neg = 0
0484: dt=1.800000, rms=0.407 (0.049%), neg=0, invalid=96777
iter 0, gcam->neg = 16
after 16 iterations, nbhd size=2, neg = 0
0485: dt=2.304000, rms=0.407 (0.068%), neg=0, invalid=96777
0486: dt=0.027000, rms=0.407 (0.000%), neg=0, invalid=96777
0487: dt=0.027000, rms=0.407 (0.001%), neg=0, invalid=96777
0488: dt=0.027000, rms=0.407 (0.003%), neg=0, invalid=96777
0489: dt=0.027000, rms=0.407 (0.004%), neg=0, invalid=96777
0490: dt=0.027000, rms=0.407 (0.005%), neg=0, invalid=96777
0491: dt=0.027000, rms=0.407 (0.006%), neg=0, invalid=96777
0492: dt=0.027000, rms=0.407 (0.007%), neg=0, invalid=96777
0493: dt=0.027000, rms=0.407 (0.007%), neg=0, invalid=96777
0494: dt=0.027000, rms=0.407 (0.008%), neg=0, invalid=96777
0495: dt=0.027000, rms=0.407 (0.009%), neg=0, invalid=96777
0496: dt=0.027000, rms=0.407 (0.009%), neg=0, invalid=96777
0497: dt=0.027000, rms=0.407 (0.009%), neg=0, invalid=96777
0498: dt=0.027000, rms=0.407 (0.010%), neg=0, invalid=96777
0499: dt=0.027000, rms=0.407 (0.010%), neg=0, invalid=96777
0500: dt=0.027000, rms=0.407 (0.010%), neg=0, invalid=96777
0501: dt=0.027000, rms=0.407 (0.010%), neg=0, invalid=96777
0502: dt=0.027000, rms=0.407 (0.010%), neg=0, invalid=96777
0503: dt=0.027000, rms=0.406 (0.010%), neg=0, invalid=96777
0504: dt=0.027000, rms=0.406 (0.010%), neg=0, invalid=96777
0505: dt=0.027000, rms=0.406 (0.010%), neg=0, invalid=96777
0506: dt=0.027000, rms=0.406 (0.010%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.406, neg=0, invalid=96777
iter 0, gcam->neg = 126
after 36 iterations, nbhd size=2, neg = 0
0507: dt=13.356932, rms=0.403 (0.832%), neg=0, invalid=96777
0508: dt=0.009000, rms=0.403 (0.000%), neg=0, invalid=96777
0509: dt=0.009000, rms=0.403 (0.000%), neg=0, invalid=96777
0510: dt=0.009000, rms=0.403 (0.000%), neg=0, invalid=96777
0511: dt=0.009000, rms=0.403 (0.001%), neg=0, invalid=96777
0512: dt=0.009000, rms=0.403 (0.001%), neg=0, invalid=96777
0513: dt=0.009000, rms=0.403 (0.001%), neg=0, invalid=96777
0514: dt=0.009000, rms=0.403 (0.002%), neg=0, invalid=96777
0515: dt=0.009000, rms=0.403 (0.002%), neg=0, invalid=96777
0516: dt=0.009000, rms=0.403 (0.002%), neg=0, invalid=96777
0517: dt=0.009000, rms=0.403 (0.002%), neg=0, invalid=96777
0518: dt=0.009000, rms=0.403 (0.002%), neg=0, invalid=96777
0519: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0520: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0521: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0522: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0523: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0524: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0525: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0526: dt=0.009000, rms=0.403 (0.003%), neg=0, invalid=96777
0527: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0528: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0529: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0530: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0531: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0532: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0533: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0534: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0535: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
0536: dt=0.009000, rms=0.403 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 78
after 200 iterations, nbhd size=3, neg = 1
starting rms=0.004, neg=1, removing folds in lattice....
iter 1, dt=0.000055: new neg 0, old_neg 1, delta 1, rms=0.003 (23.042%)
0537: dt=8.680851, rms=0.402 (0.181%), neg=0, invalid=96777
0538: dt=0.000000, rms=0.402 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.407, neg=0, invalid=96777
0539: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.407, neg=0, invalid=96777
0540: dt=0.000000, rms=0.407 (0.000%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.399, neg=0, invalid=96777
iter 0, gcam->neg = 268
after 21 iterations, nbhd size=2, neg = 0
0541: dt=0.448000, rms=0.390 (2.068%), neg=0, invalid=96777
0542: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 622
after 10 iterations, nbhd size=1, neg = 0
0543: dt=0.050000, rms=0.390 (-0.097%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.390, neg=0, invalid=96777
0544: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 3 hours, 45 minutes and 19 seconds.
#--------------------------------------
#@# CA Reg Inv Fri Jun 20 15:06:55 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_ca_register -invert-and-save transforms/talairach.m3z 

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z 
Inverting GCAM
Saving inverse 
#--------------------------------------
#@# Remove Neck Fri Jun 20 15:08:15 CEST 2014

 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3/average/RB_all_2008-03-26.gca nu_noneck.mgz 

erasing everything more than 25 mm from possible brain
reading atlas '/opt/freesurfer/5.3/average/RB_all_2008-03-26.gca'...
reading input volume 'nu.mgz'...
reading transform 'transforms/talairach.m3z'...
removing structures at least 25 mm from brain...
11249179 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 34 seconds.
#--------------------------------------
#@# SkullLTA Fri Jun 20 15:09:49 CEST 2014

 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 



 ======= NUMBER OF OPENMP THREADS = 1 ======= 
aligning to atlas containing skull, setting unknown_nbr_spacing = 5
using previously computed transform transforms/talairach.lta
reading 1 input volumes...
logging results to talairach_with_skull_2.log
reading '/opt/freesurfer/5.3/average/RB_all_withskull_2008-03-26.gca'...
average std = 23.1   using min determinant for regularization = 53.4
0 singular and 5702 ill-conditioned covariance matrices regularized
reading 'nu_noneck.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 20.2 or > 943.7 
total sample mean = 92.0 (1443 zeros)
************************************************
spacing=8, using 3481 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 3481, passno 0, spacing 8
resetting wm mean[0]: 117 --> 126
resetting gm mean[0]: 74 --> 74
input volume #1 is the most T1-like
using real data threshold=11.0
skull bounding box = (47, 20, 13) --> (211, 201, 167)
using (102, 80, 90) as brain centroid...
mean wm in atlas = 126, using box (82,58,71) --> (122, 102,108) to find MRI wm
before smoothing, mri peak at 107
after smoothing, mri peak at 107, scaling input intensities by 1.178
scaling channel 0 by 1.17757
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2)
 1.051  -0.012   0.005  -10.903;
 0.009   1.237   0.408  -49.402;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.051  -0.012   0.005  -10.903;
 0.009   1.237   0.408  -49.402;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.031  -0.012   0.005  -8.341;
 0.009   1.180   0.423  -43.307;
-0.009  -0.363   0.911   44.183;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.031  -0.012   0.005  -8.341;
 0.009   1.180   0.423  -43.307;
-0.009  -0.363   0.911   44.183;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.032  -0.015   0.012  -9.471;
 0.009   1.181   0.432  -44.851;
-0.017  -0.371   0.904   46.843;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.032  -0.015   0.012  -9.471;
 0.009   1.182   0.432  -45.046;
-0.017  -0.371   0.904   46.843;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03210  -0.01498   0.01218  -9.47110;
 0.00864   1.18218   0.43236  -45.04571;
-0.01720  -0.37076   0.90420   46.84279;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.03210  -0.01498   0.01218  -9.47110;
 0.00864   1.18218   0.43236  -45.04571;
-0.01720  -0.37076   0.90420   46.84279;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.032  -0.015   0.012  -9.471;
 0.009   1.182   0.432  -45.046;
-0.017  -0.371   0.904   46.843;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
transform before final EM align:
 1.032  -0.015   0.012  -9.471;
 0.009   1.182   0.432  -45.046;
-0.017  -0.371   0.904   46.843;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 382743 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.03210  -0.01498   0.01218  -9.47110;
 0.00864   1.18218   0.43236  -45.04571;
-0.01720  -0.37076   0.90420   46.84279;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.03210  -0.01498   0.01218  -9.47110;
 0.00864   1.18218   0.43236  -45.04571;
-0.01720  -0.37076   0.90420   46.84279;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =    4.4  tol 0.000000
final transform:
 1.032  -0.015   0.012  -9.471;
 0.009   1.182   0.432  -45.046;
-0.017  -0.371   0.904   46.843;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 30 minutes and 8 seconds.
#--------------------------------------
#@# SubCort Seg Fri Jun 20 15:39:58 CEST 2014

 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 

sysname  Linux
hostname medusa
machine  x86_64

setenv SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
cd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri
mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 

renormalizing sequences with structure alignment, equivalent to:
	-renormalize
	-renormalize_mean 0.500
	-regularize 0.500
reading 1 input volumes...
reading classifier array from /opt/freesurfer/5.3/average/RB_all_2008-03-26.gca...
reading input volume from norm.mgz...
average std[0] = 6.9
reading transform from transforms/talairach.m3z...
Atlas used for the 3D morph was /opt/freesurfer/5.3/average/RB_all_2008-03-26.gca
average std = 6.9   using min determinant for regularization = 4.7
0 singular and 0 ill-conditioned covariance matrices regularized
labeling volume...
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15151 (27)
mri peak = 0.13514 (10)
Left_Lateral_Ventricle (4): linear fit = 0.34 x + 0.0 (170 voxels, overlap=0.006)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (170 voxels, peak =  9), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.09742 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.35 x + 0.0 (148 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (148 voxels, peak =  7), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.12229 (100)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (386 voxels, overlap=0.901)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (386 voxels, peak = 97), gca=96.5
gca peak = 0.18160 (96)
mri peak = 0.11202 (97)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (361 voxels, overlap=1.007)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (361 voxels, peak = 96), gca=96.5
gca peak = 0.27536 (62)
mri peak = 0.07460 (55)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (550 voxels, overlap=0.191)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (550 voxels, peak = 52), gca=51.8
gca peak = 0.32745 (63)
mri peak = 0.09202 (61)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (489 voxels, overlap=0.832)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (489 voxels, peak = 58), gca=58.3
gca peak = 0.08597 (105)
mri peak = 0.08416 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (41213 voxels, overlap=0.608)
Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (41213 voxels, peak = 110), gca=109.7
gca peak = 0.09209 (106)
mri peak = 0.08990 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (46219 voxels, overlap=0.613)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (46219 voxels, peak = 111), gca=110.8
gca peak = 0.07826 (63)
mri peak = 0.04436 (53)
Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14403 voxels, overlap=0.375)
Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (14403 voxels, peak = 52), gca=52.0
gca peak = 0.08598 (64)
mri peak = 0.04537 (53)
Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13543 voxels, overlap=0.157)
Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (13543 voxels, peak = 51), gca=50.9
gca peak = 0.24164 (71)
mri peak = 0.09434 (70)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (583 voxels, overlap=1.009)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (583 voxels, peak = 70), gca=69.9
gca peak = 0.18227 (75)
mri peak = 0.08302 (77)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (1001 voxels, overlap=0.784)
Left_Caudate (11): linear fit = 0.94 x + 0.0 (1001 voxels, peak = 71), gca=70.9
gca peak = 0.10629 (62)
mri peak = 0.04723 (57)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (11566 voxels, overlap=0.927)
Left_Cerebellum_Cortex (8): linear fit = 0.94 x + 0.0 (11566 voxels, peak = 58), gca=58.0
gca peak = 0.11668 (59)
mri peak = 0.04817 (56)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (11725 voxels, overlap=0.897)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (11725 voxels, peak = 54), gca=54.0
gca peak = 0.17849 (88)
mri peak = 0.09746 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6277 voxels, overlap=0.921)
Left_Cerebellum_White_Matter (7): linear fit = 1.03 x + 0.0 (6277 voxels, peak = 91), gca=91.1
gca peak = 0.16819 (86)
mri peak = 0.10688 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6135 voxels, overlap=0.827)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6135 voxels, peak = 90), gca=89.9
gca peak = 0.41688 (64)
mri peak = 0.08147 (65)
Left_Amygdala (18): linear fit = 0.95 x + 0.0 (228 voxels, overlap=1.032)
Left_Amygdala (18): linear fit = 0.95 x + 0.0 (228 voxels, peak = 61), gca=61.1
gca peak = 0.42394 (62)
mri peak = 0.11744 (61)
Right_Amygdala (54): linear fit = 0.98 x + 0.0 (257 voxels, overlap=1.036)
Right_Amygdala (54): linear fit = 0.98 x + 0.0 (257 voxels, peak = 60), gca=60.5
gca peak = 0.10041 (96)
mri peak = 0.08190 (97)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3714 voxels, overlap=0.860)
Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3714 voxels, peak = 98), gca=98.4
gca peak = 0.13978 (88)
mri peak = 0.06596 (94)
Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3606 voxels, overlap=0.889)
Right_Thalamus_Proper (49): linear fit = 1.07 x + 0.0 (3606 voxels, peak = 94), gca=93.7
gca peak = 0.08514 (81)
mri peak = 0.06798 (83)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1588 voxels, overlap=0.861)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1588 voxels, peak = 80), gca=79.8
gca peak = 0.09624 (82)
mri peak = 0.05714 (81)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (1645 voxels, overlap=0.925)
Right_Putamen (51): linear fit = 0.96 x + 0.0 (1645 voxels, peak = 79), gca=79.1
gca peak = 0.07543 (88)
mri peak = 0.07209 (84)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (12266 voxels, overlap=0.765)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (12266 voxels, peak = 89), gca=89.3
gca peak = 0.12757 (95)
mri peak = 0.06780 (107)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1146 voxels, overlap=0.707)
Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1146 voxels, peak = 106), gca=105.9
gca peak = 0.17004 (92)
mri peak = 0.06932 (103)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1254 voxels, overlap=0.821)
Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1254 voxels, peak = 102), gca=101.7
gca peak = 0.21361 (36)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.26069 (23)
mri peak = 0.17544 ( 7)
Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (57 voxels, overlap=0.022)
Fourth_Ventricle (15): linear fit = 0.26 x + 0.0 (57 voxels, peak =  6), gca=6.1
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak Third_Ventricle = 0.21361 (36)
gca peak Fourth_Ventricle = 0.26069 (23)
gca peak CSF = 0.14367 (38)
gca peak Left_Accumbens_area = 0.57033 (70)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.65201 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.31129 (32)
gca peak Right_Accumbens_area = 0.30219 (72)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.72939 (42)
gca peak WM_hypointensities = 0.14821 (82)
gca peak non_WM_hypointensities = 0.10354 (53)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 0.88 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.40 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.31600 (11)
mri peak = 0.13514 (10)
Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (170 voxels, overlap=0.941)
Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (170 voxels, peak =  9), gca=8.9
gca peak = 0.29325 ( 9)
mri peak = 0.09742 ( 8)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (148 voxels, overlap=0.968)
Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (148 voxels, peak =  9), gca=9.5
gca peak = 0.27897 (97)
mri peak = 0.12229 (100)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (386 voxels, overlap=0.930)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (386 voxels, peak = 97), gca=96.5
gca peak = 0.16495 (96)
mri peak = 0.11202 (97)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (361 voxels, overlap=0.997)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (361 voxels, peak = 96), gca=96.5
gca peak = 0.30643 (52)
mri peak = 0.07460 (55)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (550 voxels, overlap=1.002)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (550 voxels, peak = 52), gca=52.0
gca peak = 0.31501 (58)
mri peak = 0.09202 (61)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (489 voxels, overlap=1.005)
Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (489 voxels, peak = 57), gca=57.1
gca peak = 0.08168 (110)
mri peak = 0.08416 (109)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41213 voxels, overlap=0.789)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41213 voxels, peak = 110), gca=110.0
gca peak = 0.08583 (111)
mri peak = 0.08990 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46219 voxels, overlap=0.753)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (46219 voxels, peak = 111), gca=111.0
gca peak = 0.09514 (52)
mri peak = 0.04436 (53)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (14403 voxels, overlap=0.995)
Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (14403 voxels, peak = 53), gca=53.3
gca peak = 0.11043 (51)
mri peak = 0.04537 (53)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13543 voxels, overlap=0.995)
Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (13543 voxels, peak = 50), gca=50.2
gca peak = 0.21322 (73)
mri peak = 0.09434 (70)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (583 voxels, overlap=1.008)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (583 voxels, peak = 73), gca=73.0
gca peak = 0.17375 (71)
mri peak = 0.08302 (77)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1001 voxels, overlap=1.003)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1001 voxels, peak = 71), gca=71.0
gca peak = 0.11357 (57)
mri peak = 0.04723 (57)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (11566 voxels, overlap=1.000)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (11566 voxels, peak = 58), gca=58.4
gca peak = 0.13049 (54)
mri peak = 0.04817 (56)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (11725 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (11725 voxels, peak = 55), gca=55.3
gca peak = 0.16819 (91)
mri peak = 0.09746 (91)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6277 voxels, overlap=0.989)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6277 voxels, peak = 91), gca=90.5
gca peak = 0.15955 (90)
mri peak = 0.10688 (90)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6135 voxels, overlap=0.982)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6135 voxels, peak = 90), gca=89.6
gca peak = 0.46581 (61)
mri peak = 0.08147 (65)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (228 voxels, overlap=1.027)
Left_Amygdala (18): linear fit = 0.99 x + 0.0 (228 voxels, peak = 60), gca=60.1
gca peak = 0.36912 (61)
mri peak = 0.11744 (61)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (257 voxels, overlap=1.015)
Right_Amygdala (54): linear fit = 1.02 x + 0.0 (257 voxels, peak = 63), gca=62.5
gca peak = 0.09773 (97)
mri peak = 0.08190 (97)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3714 voxels, overlap=0.882)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3714 voxels, peak = 96), gca=95.5
gca peak = 0.09400 (91)
mri peak = 0.06596 (94)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3606 voxels, overlap=0.939)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3606 voxels, peak = 91), gca=91.0
gca peak = 0.09432 (81)
mri peak = 0.06798 (83)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1588 voxels, overlap=0.938)
Left_Putamen (12): linear fit = 0.99 x + 0.0 (1588 voxels, peak = 80), gca=79.8
gca peak = 0.10052 (73)
mri peak = 0.05714 (81)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1645 voxels, overlap=1.000)
Right_Putamen (51): linear fit = 1.00 x + 0.0 (1645 voxels, peak = 73), gca=73.0
gca peak = 0.07468 (87)
mri peak = 0.07209 (84)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12266 voxels, overlap=0.797)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12266 voxels, peak = 87), gca=86.6
gca peak = 0.10599 (106)
mri peak = 0.06780 (107)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1146 voxels, overlap=0.875)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1146 voxels, peak = 106), gca=106.0
gca peak = 0.14356 (102)
mri peak = 0.06932 (103)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1254 voxels, overlap=0.881)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1254 voxels, peak = 102), gca=102.0
gca peak = 0.35640 (14)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.33827 ( 9)
mri peak = 0.17544 ( 7)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (57 voxels, overlap=0.708)
Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (57 voxels, peak =  6), gca=6.3
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.24950 (33)
gca peak Third_Ventricle = 0.35640 (14)
gca peak CSF = 0.30128 (18)
gca peak Left_Accumbens_area = 0.67614 (66)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.61822 (62)
gca peak Left_choroid_plexus = 0.09164 (48)
gca peak Right_Inf_Lat_Vent = 0.30433 (27)
gca peak Right_Accumbens_area = 0.30120 (71)
gca peak Right_vessel = 0.53048 (60)
gca peak Right_choroid_plexus = 0.10321 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.16373 (85)
gca peak non_WM_hypointensities = 0.11664 (55)
gca peak Optic_Chiasm = 0.34840 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.00 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.85 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt
13968 gm and wm labels changed (%11 to gray, %89 to white out of all changed labels)
362 hippocampal voxels changed.
4 amygdala voxels changed.
pass 1: 84963 changed. image ll: -2.195, PF=1.000
pass 2: 15236 changed. image ll: -2.192, PF=1.000
pass 3: 5545 changed.
pass 4: 2415 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 19 minutes and 26 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/transforms/cc_up.lta surface_3T 

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/norm.mgz
21653 voxels in left wm, 28087 in right wm, xrange [127, 134]
searching rotation angles z=[-9  5], y=[-6  8]

searching scale 1 Z rot -8.7  
searching scale 1 Z rot -8.5  
searching scale 1 Z rot -8.2  
searching scale 1 Z rot -8.0  
searching scale 1 Z rot -7.7  
searching scale 1 Z rot -7.5  
searching scale 1 Z rot -7.2  
searching scale 1 Z rot -7.0  
searching scale 1 Z rot -6.7  
searching scale 1 Z rot -6.5  
searching scale 1 Z rot -6.2  
searching scale 1 Z rot -6.0  
searching scale 1 Z rot -5.7  
searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.2  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.7  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.2  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.7  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.2  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.7  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.2  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.7  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.2  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.7  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.2  
searching scale 1 Z rot 0.0  
searching scale 1 Z rot 0.3  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.8  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.3  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.8  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.3  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.8  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.3  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.8  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.3  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.8  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.3  
searching scale 1 Z rot 5.5  global minimum found at slice 131.0, rotations (0.99, -1.23)
final transformation (x=131.0, yr=0.988, zr=-1.226):
 1.000   0.021   0.017  -6.441;
-0.021   1.000  -0.000   45.857;
-0.017  -0.000   1.000   33.273;
 0.000   0.000   0.000   1.000;
updating x range to be [127, 131] in xformed coordinates
best xformed slice 129
cc center is found at 129 149 123
eigenvectors:
-0.001   0.006   1.000;
-0.205  -0.979   0.006;
 0.979  -0.205   0.002;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 0.6 minutes
#--------------------------------------
#@# Merge ASeg Fri Jun 20 15:59:58 CEST 2014

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Fri Jun 20 15:59:58 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz 

using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
normalizing image...
processing with aseg
removing outliers in the aseg WM...
5169 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 111
white matter peak found at 110
gm peak at 56 (56), valley at 34 (34)
csf peak at 10, setting threshold to 40
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 58 (58), valley at 34 (34)
csf peak at 10, setting threshold to 42
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 26 seconds.
#--------------------------------------------
#@# Mask BFS Fri Jun 20 16:04:27 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1528611 voxels in mask (pct=  9.11)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Fri Jun 20 16:04:29 CEST 2014

 mri_segment brain.mgz wm.seg.mgz 

doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (107.0): 107.0 +- 5.0 [80.0 --> 125.0]
GM (68.0) : 67.3 +- 9.5 [30.0 --> 96.0]
setting bottom of white matter range to 76.8
setting top of gray matter range to 86.2
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...
4893 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5464 filled
462 bright non-wm voxels segmented.
2629 diagonally connected voxels added...
white matter segmentation took 1.9 minutes
writing output to wm.seg.mgz...

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

preserving editing changes in input volume...
auto filling took 0.79 minutes
reading wm segmentation from wm.seg.mgz...
347 voxels added to wm to prevent paths from MTL structures to cortex
1712 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 35072 voxels turned on, 41604 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 0   new 0
115,126,128 old 0   new 0
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  27 found -  27 modified     |    TOTAL:  27
pass   2 (xy+):   0 found -  27 modified     |    TOTAL:  27
pass   1 (xy-):  18 found -  18 modified     |    TOTAL:  45
pass   2 (xy-):   0 found -  18 modified     |    TOTAL:  45
pass   1 (yz+):  51 found -  51 modified     |    TOTAL:  96
pass   2 (yz+):   0 found -  51 modified     |    TOTAL:  96
pass   1 (yz-):  31 found -  31 modified     |    TOTAL: 127
pass   2 (yz-):   0 found -  31 modified     |    TOTAL: 127
pass   1 (xz+):  24 found -  24 modified     |    TOTAL: 151
pass   2 (xz+):   0 found -  24 modified     |    TOTAL: 151
pass   1 (xz-):  20 found -  20 modified     |    TOTAL: 171
pass   2 (xz-):   0 found -  20 modified     |    TOTAL: 171
Iteration Number : 1
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):   8 found -   8 modified     |    TOTAL:  14
pass   2 (+++):   0 found -   8 modified     |    TOTAL:  14
pass   1 (+++):   8 found -   8 modified     |    TOTAL:  22
pass   2 (+++):   0 found -   8 modified     |    TOTAL:  22
pass   1 (+++):   6 found -   6 modified     |    TOTAL:  28
pass   2 (+++):   0 found -   6 modified     |    TOTAL:  28
Iteration Number : 1
pass   1 (++): 118 found - 118 modified     |    TOTAL: 118
pass   2 (++):   0 found - 118 modified     |    TOTAL: 118
pass   1 (+-): 123 found - 123 modified     |    TOTAL: 241
pass   2 (+-):   0 found - 123 modified     |    TOTAL: 241
pass   1 (--): 102 found - 102 modified     |    TOTAL: 343
pass   2 (--):   0 found - 102 modified     |    TOTAL: 343
pass   1 (-+): 109 found - 109 modified     |    TOTAL: 452
pass   2 (-+):   0 found - 109 modified     |    TOTAL: 452
Iteration Number : 2
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   4
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz+):   4 found -   4 modified     |    TOTAL:  10
pass   2 (xz+):   0 found -   4 modified     |    TOTAL:  10
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:  13
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:  13
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 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 = 667 (out of 589158: 0.113212)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Fri Jun 20 16:07:12 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.051  -0.012   0.005  -10.903;
 0.009   1.151   0.380  -37.506;
-0.009  -0.336   0.960   34.208;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 3310 (min = 350, max = 1400), aspect = 1.37 (min = 0.10, max = 0.75)
need search nearby
using seed (127, 106, 92), TAL = (1.0, -36.0, 22.0)
talairach voxel to voxel transform
 0.952   0.008  -0.008   10.933;
-0.009   0.779  -0.308   39.646;
 0.005   0.273   0.933  -21.633;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (127,  106,  92) --> (1.0, -36.0, 22.0)
done.
writing output to filled.mgz...
filling took 0.9 minutes
talairach cc position changed to (1.00, -36.00, 22.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(19.00, -36.00, 22.00) SRC: (114.77, 92.89, 93.76)
search lh wm seed point around talairach space (-17.00, -36.00, 22.00), SRC: (149.03, 92.56, 93.96)
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 Fri Jun 20 16:08:05 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

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


Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   3
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   6
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   7
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   1 found -   1 modified     |    TOTAL:   2
pass   2 (--):   0 found -   1 modified     |    TOTAL:   2
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 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 = 11 (out of 284263: 0.003870)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 40: 2464 vertices, 2644 faces
slice 50: 10480 vertices, 10825 faces
slice 60: 21981 vertices, 22385 faces
slice 70: 34592 vertices, 35010 faces
slice 80: 46705 vertices, 47096 faces
slice 90: 57534 vertices, 57906 faces
slice 100: 68915 vertices, 69357 faces
slice 110: 79945 vertices, 80345 faces
slice 120: 90913 vertices, 91324 faces
slice 130: 101147 vertices, 101528 faces
slice 140: 111459 vertices, 111859 faces
slice 150: 121494 vertices, 121805 faces
slice 160: 129833 vertices, 130131 faces
slice 170: 136447 vertices, 136667 faces
slice 180: 141651 vertices, 141834 faces
slice 190: 145144 vertices, 145252 faces
slice 200: 145934 vertices, 145960 faces
slice 210: 145934 vertices, 145960 faces
slice 220: 145934 vertices, 145960 faces
slice 230: 145934 vertices, 145960 faces
slice 240: 145934 vertices, 145960 faces
slice 250: 145934 vertices, 145960 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;

 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 


counting number of connected components...
   145934 voxel in cpt #1: X=-26 [v=145934,e=437880,f=291920] located at (-30.925631, -23.116100, 35.443195)
For the whole surface: X=-26 [v=145934,e=437880,f=291920]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Fri Jun 20 16:08:16 CEST 2014

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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 lh Fri Jun 20 16:08:22 CEST 2014

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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
avg radius = 48.0 mm, total surface area = 77519 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.7 minutes
Not saving sulc

step 000: RMS=0.098 (target=0.015)   
step 005: RMS=0.071 (target=0.015)   
step 010: RMS=0.052 (target=0.015)   
step 015: RMS=0.044 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.030 (target=0.015)   
step 035: RMS=0.027 (target=0.015)   
step 040: RMS=0.026 (target=0.015)   
step 045: RMS=0.025 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.023 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Fri Jun 20 16:09:03 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 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 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.97 +- 0.57 (0.00-->8.09) (max @ vno 75461 --> 76582)
face area 0.03 +- 0.03 (-0.18-->0.86)
scaling brain by 0.309...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.225, avgs=0
005/300: dt: 0.9000, rms radial error=175.966, avgs=0
010/300: dt: 0.9000, rms radial error=175.410, avgs=0
015/300: dt: 0.9000, rms radial error=174.679, avgs=0
020/300: dt: 0.9000, rms radial error=173.845, avgs=0
025/300: dt: 0.9000, rms radial error=172.952, avgs=0
030/300: dt: 0.9000, rms radial error=172.027, avgs=0
035/300: dt: 0.9000, rms radial error=171.084, avgs=0
040/300: dt: 0.9000, rms radial error=170.132, avgs=0
045/300: dt: 0.9000, rms radial error=169.178, avgs=0
050/300: dt: 0.9000, rms radial error=168.225, avgs=0
055/300: dt: 0.9000, rms radial error=167.279, avgs=0
060/300: dt: 0.9000, rms radial error=166.342, avgs=0
065/300: dt: 0.9000, rms radial error=165.412, avgs=0
070/300: dt: 0.9000, rms radial error=164.486, avgs=0
075/300: dt: 0.9000, rms radial error=163.565, avgs=0
080/300: dt: 0.9000, rms radial error=162.650, avgs=0
085/300: dt: 0.9000, rms radial error=161.739, avgs=0
090/300: dt: 0.9000, rms radial error=160.834, avgs=0
095/300: dt: 0.9000, rms radial error=159.933, avgs=0
100/300: dt: 0.9000, rms radial error=159.037, avgs=0
105/300: dt: 0.9000, rms radial error=158.146, avgs=0
110/300: dt: 0.9000, rms radial error=157.259, avgs=0
115/300: dt: 0.9000, rms radial error=156.378, avgs=0
120/300: dt: 0.9000, rms radial error=155.500, avgs=0
125/300: dt: 0.9000, rms radial error=154.628, avgs=0
130/300: dt: 0.9000, rms radial error=153.760, avgs=0
135/300: dt: 0.9000, rms radial error=152.897, avgs=0
140/300: dt: 0.9000, rms radial error=152.039, avgs=0
145/300: dt: 0.9000, rms radial error=151.186, avgs=0
150/300: dt: 0.9000, rms radial error=150.337, avgs=0
155/300: dt: 0.9000, rms radial error=149.493, avgs=0
160/300: dt: 0.9000, rms radial error=148.653, avgs=0
165/300: dt: 0.9000, rms radial error=147.819, avgs=0
170/300: dt: 0.9000, rms radial error=146.988, avgs=0
175/300: dt: 0.9000, rms radial error=146.163, avgs=0
180/300: dt: 0.9000, rms radial error=145.342, avgs=0
185/300: dt: 0.9000, rms radial error=144.525, avgs=0
190/300: dt: 0.9000, rms radial error=143.713, avgs=0
195/300: dt: 0.9000, rms radial error=142.905, avgs=0
200/300: dt: 0.9000, rms radial error=142.102, avgs=0
205/300: dt: 0.9000, rms radial error=141.303, avgs=0
210/300: dt: 0.9000, rms radial error=140.509, avgs=0
215/300: dt: 0.9000, rms radial error=139.719, avgs=0
220/300: dt: 0.9000, rms radial error=138.934, avgs=0
225/300: dt: 0.9000, rms radial error=138.153, avgs=0
230/300: dt: 0.9000, rms radial error=137.377, avgs=0
235/300: dt: 0.9000, rms radial error=136.605, avgs=0
240/300: dt: 0.9000, rms radial error=135.837, avgs=0
245/300: dt: 0.9000, rms radial error=135.073, avgs=0
250/300: dt: 0.9000, rms radial error=134.313, avgs=0
255/300: dt: 0.9000, rms radial error=133.558, avgs=0
260/300: dt: 0.9000, rms radial error=132.806, avgs=0
265/300: dt: 0.9000, rms radial error=132.059, avgs=0
270/300: dt: 0.9000, rms radial error=131.316, avgs=0
275/300: dt: 0.9000, rms radial error=130.577, avgs=0
280/300: dt: 0.9000, rms radial error=129.842, avgs=0
285/300: dt: 0.9000, rms radial error=129.111, avgs=0
290/300: dt: 0.9000, rms radial error=128.384, avgs=0
295/300: dt: 0.9000, rms radial error=127.661, avgs=0
300/300: dt: 0.9000, rms radial error=126.942, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17105.33
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00012
epoch 2 (K=40.0), pass 1, starting sse = 2885.88
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 = 305.13
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.04/10 = 0.00359
epoch 4 (K=640.0), pass 1, starting sse = 23.17
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.08/12 = 0.00627
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Fri Jun 20 16:14:55 CEST 2014

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


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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 surface_3T 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 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
before topology correction, eno=-26 (nv=145934, nf=291920, ne=437880, g=14)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
4529 ambiguous faces found in tessellation
segmenting defects...
16 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 8 into 6
15 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8045  (-4.9023)
      -vertex     loglikelihood: -6.5739  (-3.2870)
      -normal dot loglikelihood: -3.4956  (-3.4956)
      -quad curv  loglikelihood: -6.5127  (-3.2564)
      Total Loglikelihood : -26.3868

CORRECTING DEFECT 0 (vertices=87, convex hull=77)
After retessellation of defect 0, euler #=-13 (143343,429324,285968) : difference with theory (-12) = 1 

CORRECTING DEFECT 1 (vertices=71, convex hull=79)
After retessellation of defect 1, euler #=-12 (143359,429403,286032) : difference with theory (-11) = 1 

CORRECTING DEFECT 2 (vertices=72, convex hull=77)
After retessellation of defect 2, euler #=-11 (143375,429482,286096) : difference with theory (-10) = 1 

CORRECTING DEFECT 3 (vertices=272, convex hull=121)
After retessellation of defect 3, euler #=-10 (143450,429763,286303) : difference with theory (-9) = 1 

CORRECTING DEFECT 4 (vertices=24, convex hull=49)
After retessellation of defect 4, euler #=-9 (143461,429817,286347) : difference with theory (-8) = 1 

CORRECTING DEFECT 5 (vertices=114, convex hull=114)
After retessellation of defect 5, euler #=-8 (143470,429897,286419) : difference with theory (-7) = 1 

CORRECTING DEFECT 6 (vertices=1536, convex hull=666)
After retessellation of defect 6, euler #=-6 (143958,431715,287751) : difference with theory (-6) = 0 

CORRECTING DEFECT 7 (vertices=12, convex hull=20)
After retessellation of defect 7, euler #=-5 (143959,431723,287759) : difference with theory (-5) = 0 

CORRECTING DEFECT 8 (vertices=56, convex hull=48)
After retessellation of defect 8, euler #=-4 (143963,431756,287789) : difference with theory (-4) = 0 

CORRECTING DEFECT 9 (vertices=29, convex hull=56)
After retessellation of defect 9, euler #=-3 (143974,431810,287833) : difference with theory (-3) = 0 

CORRECTING DEFECT 10 (vertices=60, convex hull=33)
After retessellation of defect 10, euler #=-2 (143985,431852,287865) : difference with theory (-2) = 0 

CORRECTING DEFECT 11 (vertices=108, convex hull=68)
After retessellation of defect 11, euler #=-1 (143992,431912,287919) : difference with theory (-1) = 0 

CORRECTING DEFECT 12 (vertices=10, convex hull=15)
After retessellation of defect 12, euler #=0 (143993,431917,287924) : difference with theory (0) = 0 

CORRECTING DEFECT 13 (vertices=40, convex hull=41)
After retessellation of defect 13, euler #=1 (144005,431969,287965) : difference with theory (1) = 0 

CORRECTING DEFECT 14 (vertices=121, convex hull=97)
After retessellation of defect 14, euler #=2 (144053,432153,288102) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.06-->6.43) (max @ vno 121087 --> 125277)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.06-->6.43) (max @ vno 121087 --> 125277)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
43 mutations (37.7%), 71 crossovers (62.3%), 36 vertices were eliminated
building final representation...
1881 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=144053, nf=288102, ne=432153, g=0)
writing corrected surface to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 9.5 minutes
0 defective edges
removing intersecting faces
000: 267 intersecting
001: 50 intersecting
002: 5 intersecting
003: 3 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 144053 - 432153 + 288102 = 2 --> 0 holes
      F =2V-4:          288102 = 288106-4 (0)
      2E=3F:            864306 = 864306 (0)

total defect index = 0
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 151 intersecting
001: 43 intersecting
002: 5 intersecting
003: 3 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Fri Jun 20 16:24:34 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs surface_3T lh 

only generating white matter surface
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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/filled.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
17992 bright wm thresholded.
469 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.orig...
computing class statistics...
border white:    270110 voxels (1.61%)
border gray      299704 voxels (1.79%)
WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0]
GM (76.0) : 74.9 +- 12.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 49.6 (was 70)
setting MAX_BORDER_WHITE to 114.7 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 37.2 (was 40)
setting MAX_GRAY to 95.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 24.8 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.01-->3.49) (max @ vno 78135 --> 143735)
face area 0.28 +- 0.12 (0.00-->3.03)
mean absolute distance = 0.70 +- 0.88
3365 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=62
mean inside = 93.4, mean outside = 70.7
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=75.2, 63 (63) missing vertices, mean dist 0.3 [0.6 (%34.1)->0.8 (%65.9))]
%69 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=medus, 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 0.92 +- 0.26 (0.12-->5.50) (max @ vno 143753 --> 143794)
face area 0.28 +- 0.13 (0.00-->3.09)
mean absolute distance = 0.34 +- 0.55
3661 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7090387.0, rms=12.84
001: dt: 0.5000, sse=7081053.0, rms=9.173 (0.000%)
002: dt: 0.5000, sse=7390670.5, rms=7.035 (0.000%)
003: dt: 0.5000, sse=7519892.5, rms=5.687 (0.000%)
004: dt: 0.5000, sse=7813698.0, rms=4.882 (0.000%)
005: dt: 0.5000, sse=7900933.0, rms=4.478 (0.000%)
006: dt: 0.5000, sse=8053252.0, rms=4.270 (0.000%)
007: dt: 0.5000, sse=8016944.0, rms=4.176 (0.000%)
008: dt: 0.5000, sse=8050999.5, rms=4.106 (0.000%)
rms = 4.08, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8002147.5, rms=4.083 (0.000%)
010: dt: 0.2500, sse=4962068.5, rms=2.760 (0.000%)
011: dt: 0.2500, sse=4492659.5, rms=2.336 (0.000%)
012: dt: 0.2500, sse=4222224.5, rms=2.229 (0.000%)
013: dt: 0.2500, sse=4151532.5, rms=2.154 (0.000%)
rms = 2.12, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4060428.8, rms=2.122 (0.000%)
015: dt: 0.1250, sse=3880930.5, rms=1.932 (0.000%)
rms = 1.91, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=3841376.5, rms=1.908 (0.000%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
mean border=79.3, 90 (25) missing vertices, mean dist -0.2 [0.4 (%76.2)->0.2 (%23.8))]
%81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=medus, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.06-->5.25) (max @ vno 143753 --> 143794)
face area 0.35 +- 0.16 (0.00-->3.95)
mean absolute distance = 0.22 +- 0.34
3034 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4812490.5, rms=5.94
017: dt: 0.5000, sse=5061609.5, rms=4.148 (0.000%)
rms = 4.30, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=4590226.5, rms=3.167 (0.000%)
019: dt: 0.2500, sse=4388129.0, rms=2.510 (0.000%)
020: dt: 0.2500, sse=4300910.0, rms=2.100 (0.000%)
021: dt: 0.2500, sse=4270513.5, rms=1.963 (0.000%)
022: dt: 0.2500, sse=4203805.5, rms=1.833 (0.000%)
023: dt: 0.2500, sse=4213706.0, rms=1.771 (0.000%)
024: dt: 0.2500, sse=4171308.5, rms=1.715 (0.000%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=4193827.5, rms=1.680 (0.000%)
026: dt: 0.1250, sse=4075113.5, rms=1.533 (0.000%)
rms = 1.52, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4044842.8, rms=1.523 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=82.3, 84 (17) missing vertices, mean dist -0.1 [0.2 (%75.7)->0.2 (%24.3))]
%89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=medus, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.08-->4.87) (max @ vno 143718 --> 143798)
face area 0.34 +- 0.16 (0.00-->4.34)
mean absolute distance = 0.17 +- 0.27
3001 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4370020.0, rms=3.90
028: dt: 0.5000, sse=4811670.5, rms=3.750 (0.000%)
rms = 3.96, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=4357362.5, rms=2.382 (0.000%)
030: dt: 0.2500, sse=4225725.5, rms=1.865 (0.000%)
031: dt: 0.2500, sse=4261176.0, rms=1.581 (0.000%)
rms = 1.60, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=4209492.5, rms=1.486 (0.000%)
033: dt: 0.1250, sse=4138702.8, rms=1.354 (0.000%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=4113217.8, rms=1.344 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=83.2, 93 (14) missing vertices, mean dist -0.0 [0.2 (%57.6)->0.2 (%42.4))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=medus, 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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=4135331.8, rms=1.73
rms = 2.37, time step reduction 1 of 3 to 0.250...
035: dt: 0.2500, sse=4221079.0, rms=1.190 (0.000%)
036: dt: 0.2500, sse=4370153.0, rms=1.031 (0.000%)
rms = 1.05, time step reduction 2 of 3 to 0.125...
rms = 1.02, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=4371043.0, rms=1.024 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
16 non-cortical segments detected
only using segment with 2174 vertices
erasing segment 0 (vno[0] = 56537)
erasing segment 1 (vno[0] = 65312)
erasing segment 2 (vno[0] = 66351)
erasing segment 4 (vno[0] = 88716)
erasing segment 5 (vno[0] = 91805)
erasing segment 6 (vno[0] = 93818)
erasing segment 7 (vno[0] = 93846)
erasing segment 8 (vno[0] = 97709)
erasing segment 9 (vno[0] = 101822)
erasing segment 10 (vno[0] = 104834)
erasing segment 11 (vno[0] = 105779)
erasing segment 12 (vno[0] = 108766)
erasing segment 13 (vno[0] = 110778)
erasing segment 14 (vno[0] = 111809)
erasing segment 15 (vno[0] = 112976)
writing cortex label to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.cortex.label...
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.08-->4.80) (max @ vno 143718 --> 143798)
face area 0.34 +- 0.16 (0.00-->4.44)
refinement took 6.7 minutes
#--------------------------------------------
#@# Smooth2 lh Fri Jun 20 16:31:18 CEST 2014

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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
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...
#--------------------------------------------
#@# Inflation2 lh Fri Jun 20 16:31:23 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated 

avg radius = 48.3 mm, total surface area = 88436 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.114 (target=0.015)   
step 005: RMS=0.079 (target=0.015)   
step 010: RMS=0.056 (target=0.015)   
step 015: RMS=0.046 (target=0.015)   
step 020: RMS=0.039 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
inflation complete.
inflation took 0.6 minutes

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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
156 vertices thresholded to be in k1 ~ [-0.19 0.55], k2 ~ [-0.12 0.13]
total integrated curvature = 0.517*4pi (6.495) --> 0 handles
ICI = 1.7, FI = 12.5, variation=208.693
137 vertices thresholded to be in [-0.03 0.01]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
139 vertices thresholded to be in [-0.12 0.25]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.026
done.

#-----------------------------------------
#@# Curvature Stats lh Fri Jun 20 16:33:38 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm surface_3T 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   [ surface_3T/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                      [ 235 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.152200
WARN:    S explicit min:                          0.000000	vertex = 1047
#--------------------------------------------
#@# Sphere lh Fri Jun 20 16:33:43 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
scaling brain by 0.287...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=medus, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %19.38
pass 1: epoch 2 of 3 starting distance error %19.38
unfolding complete - removing small folds...
starting distance error %19.30
removing remaining folds...
final distance error %19.32
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.95 hours
#--------------------------------------------
#@# Surf Reg lh Fri Jun 20 17:30:51 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 

using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading surface from ../surf/lh.sphere...
reading template parameterization from /opt/freesurfer/5.3/average/lh.average.curvature.filled.buckner40.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=medus, 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=medus, 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 = 0.589
curvature mean = 0.021, std = 0.935
curvature mean = 0.024, std = 0.852
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, -16.00) sse = 369714.5, tmin=1.1172
  d=32.00 min @ (0.00, 8.00, 8.00) sse = 252393.2, tmin=2.3154
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 239807.5, tmin=3.5274
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 239103.9, tmin=4.7752
  d=4.00 min @ (1.00, 1.00, -1.00) sse = 236426.4, tmin=6.0542
  d=2.00 min @ (0.00, -0.50, 0.50) sse = 236047.3, tmin=7.3456
  d=1.00 min @ (0.00, 0.25, 0.00) sse = 235954.0, tmin=8.6424
  d=0.50 min @ (0.12, 0.00, 0.00) sse = 235942.6, tmin=9.9486
tol=1.0e+00, sigma=0.5, host=medus, 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   9.95 min
curvature mean = -0.000, std = 0.950
curvature mean = 0.012, std = 0.938
curvature mean = -0.001, std = 0.962
curvature mean = 0.006, std = 0.973
curvature mean = -0.004, std = 0.963
curvature mean = 0.002, std = 0.988
2 Reading smoothwm
curvature mean = -0.023, std = 0.283
curvature mean = 0.003, std = 0.067
curvature mean = 0.066, std = 0.341
curvature mean = 0.003, std = 0.079
curvature mean = 0.025, std = 0.543
curvature mean = 0.003, std = 0.085
curvature mean = 0.013, std = 0.688
curvature mean = 0.003, std = 0.088
curvature mean = 0.004, std = 0.798
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Fri Jun 20 18:04:43 CEST 2014

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

reading surface from ../surf/lh.white...
writing curvature file ../surf/lh.jacobian_white
#--------------------------------------------
#@# AvgCurv lh Fri Jun 20 18:04:45 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3/average/lh.average.curvature.filled.buckner40.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 /opt/freesurfer/5.3/average/lh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/lh.avg_curv...
#-----------------------------------------
#@# Cortical Parc lh Fri Jun 20 18:04:47 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 surface_3T lh ../surf/lh.sphere.reg /opt/freesurfer/5.3/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file....
average std = 1.0   using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1380 labels changed using aseg
relabeling using gibbs priors...
000:   3175 changed, 144053 examined...
001:    768 changed, 13564 examined...
002:    184 changed, 4206 examined...
003:     48 changed, 1092 examined...
004:     17 changed, 300 examined...
005:      7 changed, 108 examined...
006:      5 changed, 45 examined...
007:      4 changed, 27 examined...
008:      0 changed, 23 examined...
247 labels changed using aseg
000: 127 total segments, 77 labels (361 vertices) changed
001: 50 total segments, 5 labels (16 vertices) changed
002: 45 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 43 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1204 vertices marked for relabeling...
1204 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 1 minutes and 9 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Fri Jun 20 18:05:56 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs surface_3T lh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/filled.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
17992 bright wm thresholded.
469 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.orig...
computing class statistics...
border white:    270110 voxels (1.61%)
border gray      299704 voxels (1.79%)
WM (92.0): 93.5 +- 9.7 [70.0 --> 110.0]
GM (76.0) : 74.9 +- 12.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 49.6 (was 70)
setting MAX_BORDER_WHITE to 114.7 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 37.2 (was 40)
setting MAX_GRAY to 95.3 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.8 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 24.8 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=62
mean inside = 93.4, mean outside = 70.7
smoothing surface for 5 iterations...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.01-->3.49) (max @ vno 78135 --> 143735)
face area 0.28 +- 0.12 (0.00-->3.03)
mean absolute distance = 0.70 +- 0.88
2970 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
deleting segment 4 with 39 points - only 15.38% unknown
removing 2 vertex label from ripped group
deleting segment 5 with 2 points - only 0.00% unknown
deleting segment 6 with 570 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 5 points - only 0.00% unknown
deleting segment 12 with 14 points - only 0.00% unknown
deleting segment 13 with 30 points - only 0.00% unknown
deleting segment 14 with 16 points - only 0.00% unknown
mean border=75.2, 63 (63) missing vertices, mean dist 0.3 [0.6 (%34.2)->0.8 (%65.8))]
%70 local maxima, %26 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=medus, 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 0.92 +- 0.26 (0.12-->5.50) (max @ vno 143753 --> 143794)
face area 0.28 +- 0.13 (0.00-->3.09)
mean absolute distance = 0.34 +- 0.56
3697 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7115943.5, rms=12.83
001: dt: 0.5000, sse=7113592.5, rms=9.165 (0.000%)
002: dt: 0.5000, sse=7421116.5, rms=7.030 (0.000%)
003: dt: 0.5000, sse=7550660.0, rms=5.683 (0.000%)
004: dt: 0.5000, sse=7848439.5, rms=4.879 (0.000%)
005: dt: 0.5000, sse=7930777.0, rms=4.475 (0.000%)
006: dt: 0.5000, sse=8086472.0, rms=4.267 (0.000%)
007: dt: 0.5000, sse=8046547.0, rms=4.172 (0.000%)
008: dt: 0.5000, sse=8087585.0, rms=4.103 (0.000%)
rms = 4.08, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8033021.0, rms=4.079 (0.000%)
010: dt: 0.2500, sse=4980875.5, rms=2.761 (0.000%)
011: dt: 0.2500, sse=4511365.5, rms=2.338 (0.000%)
012: dt: 0.2500, sse=4240376.5, rms=2.233 (0.000%)
013: dt: 0.2500, sse=4170084.5, rms=2.159 (0.000%)
rms = 2.13, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4079090.5, rms=2.126 (0.000%)
015: dt: 0.1250, sse=3900515.8, rms=1.938 (0.000%)
rms = 1.92, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=3861434.0, rms=1.915 (0.000%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 87 points - only 29.89% unknown
deleting segment 1 with 29 points - only 0.00% unknown
deleting segment 4 with 13 points - only 0.00% unknown
deleting segment 5 with 563 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 11 with 7 points - only 0.00% unknown
deleting segment 12 with 11 points - only 0.00% unknown
mean border=79.3, 93 (25) missing vertices, mean dist -0.2 [0.4 (%76.1)->0.2 (%23.9))]
%82 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=medus, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.90 +- 0.25 (0.06-->5.25) (max @ vno 143753 --> 143794)
face area 0.35 +- 0.16 (0.00-->3.95)
mean absolute distance = 0.22 +- 0.34
3089 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4846599.0, rms=5.93
017: dt: 0.5000, sse=5099007.5, rms=4.149 (0.000%)
rms = 4.30, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=4625593.5, rms=3.172 (0.000%)
019: dt: 0.2500, sse=4424021.0, rms=2.520 (0.000%)
020: dt: 0.2500, sse=4336209.0, rms=2.114 (0.000%)
021: dt: 0.2500, sse=4306657.5, rms=1.980 (0.000%)
022: dt: 0.2500, sse=4239219.0, rms=1.851 (0.000%)
023: dt: 0.2500, sse=4249065.5, rms=1.790 (0.000%)
024: dt: 0.2500, sse=4209810.5, rms=1.736 (0.000%)
rms = 1.70, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=4232154.5, rms=1.702 (0.000%)
026: dt: 0.1250, sse=4112669.0, rms=1.558 (0.000%)
rms = 1.55, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4082893.0, rms=1.548 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 84 points - only 29.76% unknown
deleting segment 1 with 43 points - only 0.00% unknown
deleting segment 2 with 16 points - only 0.00% unknown
deleting segment 3 with 586 points - only 0.00% unknown
deleting segment 4 with 14 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 7 with 11 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
mean border=82.2, 88 (17) missing vertices, mean dist -0.1 [0.2 (%75.6)->0.2 (%24.4))]
%89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=medus, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.06-->4.87) (max @ vno 143718 --> 143798)
face area 0.34 +- 0.16 (0.00-->4.01)
mean absolute distance = 0.17 +- 0.27
3088 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4410764.5, rms=3.90
028: dt: 0.5000, sse=4856837.0, rms=3.753 (0.000%)
rms = 3.96, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=4401837.0, rms=2.393 (0.000%)
030: dt: 0.2500, sse=4269038.0, rms=1.880 (0.000%)
031: dt: 0.2500, sse=4304632.5, rms=1.600 (0.000%)
rms = 1.62, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=4252965.5, rms=1.506 (0.000%)
033: dt: 0.1250, sse=4182856.5, rms=1.376 (0.000%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=4154740.0, rms=1.365 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 64 points - only 7.81% unknown
deleting segment 1 with 46 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 596 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 8 points - only 0.00% unknown
deleting segment 8 with 13 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
mean border=83.2, 95 (14) missing vertices, mean dist -0.0 [0.2 (%57.5)->0.2 (%42.5))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=medus, 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
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4174573.5, rms=1.74
rms = 2.37, time step reduction 1 of 3 to 0.250...
035: dt: 0.2500, sse=4263359.0, rms=1.210 (0.000%)
036: dt: 0.2500, sse=4415932.5, rms=1.051 (0.000%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
rms = 1.04, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=4417091.0, rms=1.044 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=51.7, 86 (86) missing vertices, mean dist 1.7 [0.6 (%0.0)->2.2 (%100.0))]
%16 local maxima, %55 large gradients and %25 min vals, 1537 gradients ignored
tol=1.0e-04, sigma=2.0, host=medus, 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=29601440.0, rms=31.17
001: dt: 0.5000, sse=21495474.0, rms=26.020 (0.000%)
002: dt: 0.5000, sse=15801634.0, rms=21.712 (0.000%)
003: dt: 0.5000, sse=11990055.0, rms=18.203 (0.000%)
004: dt: 0.5000, sse=9612066.0, rms=15.370 (0.000%)
005: dt: 0.5000, sse=8214975.5, rms=13.117 (0.000%)
006: dt: 0.5000, sse=7371863.5, rms=11.330 (0.000%)
007: dt: 0.5000, sse=6815936.0, rms=9.770 (0.000%)
008: dt: 0.5000, sse=6528006.5, rms=8.382 (0.000%)
009: dt: 0.5000, sse=6316188.5, rms=7.114 (0.000%)
010: dt: 0.5000, sse=6365918.5, rms=6.020 (0.000%)
011: dt: 0.5000, sse=6348263.0, rms=5.110 (0.000%)
012: dt: 0.5000, sse=6546598.5, rms=4.508 (0.000%)
013: dt: 0.5000, sse=6617556.0, rms=4.169 (0.000%)
014: dt: 0.5000, sse=6787489.0, rms=4.027 (0.000%)
015: dt: 0.5000, sse=6783916.0, rms=3.920 (0.000%)
rms = 3.88, time step reduction 1 of 3 to 0.250...
016: dt: 0.5000, sse=6856976.5, rms=3.876 (0.000%)
017: dt: 0.2500, sse=4724653.0, rms=3.120 (0.000%)
018: dt: 0.2500, sse=4558770.0, rms=2.915 (0.000%)
rms = 2.89, time step reduction 2 of 3 to 0.125...
019: dt: 0.2500, sse=4429819.5, rms=2.887 (0.000%)
020: dt: 0.1250, sse=4205765.5, rms=2.730 (0.000%)
rms = 2.70, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=4179722.5, rms=2.704 (0.000%)
positioning took 2.5 minutes
mean border=49.3, 1059 (19) missing vertices, mean dist 0.2 [0.2 (%47.9)->0.6 (%52.1))]
%30 local maxima, %45 large gradients and %21 min vals, 483 gradients ignored
tol=1.0e-04, sigma=1.0, host=medus, 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=4867615.0, rms=4.92
022: dt: 0.5000, sse=5156227.5, rms=4.119 (0.000%)
023: dt: 0.5000, sse=6538912.0, rms=3.966 (0.000%)
rms = 4.02, time step reduction 1 of 3 to 0.250...
024: dt: 0.2500, sse=5378944.5, rms=3.216 (0.000%)
025: dt: 0.2500, sse=4957089.5, rms=2.900 (0.000%)
026: dt: 0.2500, sse=4926088.5, rms=2.839 (0.000%)
rms = 2.80, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=4894162.0, rms=2.800 (0.000%)
028: dt: 0.1250, sse=4693361.5, rms=2.612 (0.000%)
rms = 2.58, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=4674194.0, rms=2.576 (0.000%)
positioning took 1.0 minutes
mean border=47.0, 1220 (16) missing vertices, mean dist 0.1 [0.2 (%38.3)->0.4 (%61.7))]
%48 local maxima, %26 large gradients and %21 min vals, 633 gradients ignored
tol=1.0e-04, sigma=0.5, host=medus, 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=4990622.5, rms=4.15
030: dt: 0.5000, sse=5284355.0, rms=3.914 (0.000%)
rms = 3.92, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=4926338.5, rms=3.094 (0.000%)
032: dt: 0.2500, sse=5073594.5, rms=2.756 (0.000%)
033: dt: 0.2500, sse=5035135.0, rms=2.703 (0.000%)
rms = 2.67, time step reduction 2 of 3 to 0.125...
034: dt: 0.2500, sse=5090435.5, rms=2.669 (0.000%)
035: dt: 0.1250, sse=4885995.5, rms=2.470 (0.000%)
rms = 2.44, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4878434.5, rms=2.440 (0.000%)
positioning took 0.9 minutes
mean border=45.8, 2420 (15) missing vertices, mean dist 0.1 [0.2 (%44.0)->0.3 (%56.0))]
%52 local maxima, %21 large gradients and %20 min vals, 480 gradients ignored
tol=1.0e-04, sigma=0.2, host=medus, 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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=4937401.5, rms=2.85
rms = 3.60, time step reduction 1 of 3 to 0.250...
037: dt: 0.2500, sse=4810293.5, rms=2.556 (0.000%)
038: dt: 0.2500, sse=4969370.5, rms=2.465 (0.000%)
rms = 2.47, time step reduction 2 of 3 to 0.125...
rms = 2.43, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=4926072.0, rms=2.429 (0.000%)
positioning took 0.5 minutes
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.area.pial
vertex spacing 1.00 +- 0.41 (0.06-->6.66) (max @ vno 117092 --> 117093)
face area 0.40 +- 0.29 (0.00-->6.57)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 144053 vertices processed
25000 of 144053 vertices processed
50000 of 144053 vertices processed
75000 of 144053 vertices processed
100000 of 144053 vertices processed
125000 of 144053 vertices processed
0 of 144053 vertices processed
25000 of 144053 vertices processed
50000 of 144053 vertices processed
75000 of 144053 vertices processed
100000 of 144053 vertices processed
125000 of 144053 vertices processed
thickness calculation complete, 109:336 truncations.
37767 vertices at 0 distance
106961 vertices at 1 distance
88502 vertices at 2 distance
30966 vertices at 3 distance
8346 vertices at 4 distance
2226 vertices at 5 distance
665 vertices at 6 distance
215 vertices at 7 distance
84 vertices at 8 distance
45 vertices at 9 distance
33 vertices at 10 distance
20 vertices at 11 distance
25 vertices at 12 distance
8 vertices at 13 distance
8 vertices at 14 distance
9 vertices at 15 distance
5 vertices at 16 distance
4 vertices at 17 distance
2 vertices at 18 distance
2 vertices at 19 distance
13 vertices at 20 distance
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.thickness
positioning took 12.7 minutes
#--------------------------------------------
#@# Surf Volume lh Fri Jun 20 18:18:39 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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_calc -o lh.volume lh.area.mid mul lh.thickness 

Saving result to 'lh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#-----------------------------------------
#@# WM/GM Contrast lh Fri Jun 20 18:18:39 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 pctsurfcon --s surface_3T --lh-only 

Log file is /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts/pctsurfcon.log
Fri Jun 20 18:18:39 CEST 2014
setenv SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
cd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
/opt/freesurfer/5.3/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3
mri_vol2surf --mov /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.60357/lh.wm.mgh --regheader surface_3T --cortex
srcvol = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.cortex.label
Reading surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 = 111863
Masking with /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.cortex.label
Writing to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.60357/lh.wm.mgh
Dim: 144053 1 1
mri_vol2surf --mov /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.60357/lh.gm.mgh --projfrac 0.3 --regheader surface_3T --cortex
srcvol = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.cortex.label
Reading surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 = 128428
Masking with /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.cortex.label
Writing to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.60357/lh.gm.mgh
Dim: 144053 1 1
mri_concat /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.60357/lh.wm.mgh /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.60357/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.w-g.pct.mgh --annot surface_3T lh aparc --sum /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/stats/lh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --in /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.w-g.pct.mgh --annot surface_3T lh aparc --sum /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
Constructing seg from annotation

Reading annotation
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 1000
Loading /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.w-g.pct.mgh
Vertex Area is 0.668747 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    1519    1112.312
  2   1002            caudalanteriorcingulate    1076     766.886
  3   1003                caudalmiddlefrontal    3421    2341.754
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    2691    1846.188
  6   1006                         entorhinal     617     416.017
  7   1007                           fusiform    5192    3558.504
  8   1008                   inferiorparietal    7311    4916.325
  9   1009                   inferiortemporal    5087    3459.084
 10   1010                   isthmuscingulate    1978    1270.505
 11   1011                   lateraloccipital    8151    5363.607
 12   1012               lateralorbitofrontal    3836    2601.234
 13   1013                            lingual    4783    3261.594
 14   1014                medialorbitofrontal    2107    1396.708
 15   1015                     middletemporal    5138    3583.106
 16   1016                    parahippocampal    1151     797.835
 17   1017                        paracentral    2162    1352.895
 18   1018                    parsopercularis    2396    1591.979
 19   1019                      parsorbitalis     985     661.911
 20   1020                   parstriangularis    2328    1573.185
 21   1021                      pericalcarine    2499    1688.990
 22   1022                        postcentral    6404    4131.953
 23   1023                 posteriorcingulate    1990    1346.636
 24   1024                         precentral    7664    4781.467
 25   1025                          precuneus    6411    4316.344
 26   1026           rostralanteriorcingulate    1410     948.940
 27   1027               rostralmiddlefrontal    9013    6127.417
 28   1028                    superiorfrontal   11047    7618.643
 29   1029                   superiorparietal    8952    5759.208
 30   1030                   superiortemporal    6403    4287.505
 31   1031                      supramarginal    6682    4489.393
 32   1032                        frontalpole     272     178.886
 33   1033                       temporalpole     605     426.008
 34   1034                 transversetemporal     787     501.945
 35   1035                             insula    3243    2100.993

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Fri Jun 20 18:18:50 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab surface_3T lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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

 1519   1112   2653  2.409 0.391     0.114     0.022       12     1.5  bankssts
 1076    767   2335  2.572 0.705     0.156     0.034       19     1.6  caudalanteriorcingulate
 3421   2342   6505  2.597 0.399     0.119     0.030       33     4.4  caudalmiddlefrontal
 2691   1846   4058  2.039 0.485     0.169     0.062       53     6.6  cuneus
  617    416   1577  2.812 0.910     0.120     0.041        6     1.0  entorhinal
 5192   3559  10483  2.672 0.565     0.153     0.055      105    12.0  fusiform
 7311   4916  13119  2.368 0.487     0.144     0.047      123    13.8  inferiorparietal
 5087   3459   9212  2.323 0.671     0.146     0.059      109    11.5  inferiortemporal
 1978   1271   3367  2.468 0.764     0.161     0.086       56     5.7  isthmuscingulate
 8151   5364  13184  2.273 0.518     0.160     0.061      170    18.1  lateraloccipital
 3836   2601   7402  2.525 0.660     0.153     0.058       62     9.5  lateralorbitofrontal
 4783   3262   7166  2.073 0.596     0.165     0.081       96    14.3  lingual
 2107   1397   3096  1.904 0.594     0.160     0.094       56     5.9  medialorbitofrontal
 5138   3583  11300  2.528 0.674     0.150     0.115     1916    33.9  middletemporal
 1151    798   2264  2.629 0.885     0.133     0.075       27     4.4  parahippocampal
 2162   1353   3853  2.531 0.678     0.118     0.033       20     3.1  paracentral
 2396   1592   4600  2.565 0.420     0.128     0.037       29     3.7  parsopercularis
  985    662   1933  2.354 0.508     0.150     0.057       19     2.1  parsorbitalis
 2328   1573   4406  2.454 0.402     0.130     0.037       30     3.4  parstriangularis
 2499   1689   2580  1.657 0.384     0.150     0.054       33     5.4  pericalcarine
 6404   4132   9634  2.057 0.510     0.123     0.036       80     9.9  postcentral
 1990   1347   3349  2.296 0.599     0.149     0.050       48     4.6  posteriorcingulate
 7664   4781  14404  2.741 0.557     0.112     0.038       82    12.5  precentral
 6411   4316  10854  2.336 0.523     0.151     0.054      123    12.9  precuneus
 1410    949   2980  2.585 0.610     0.167     0.073       33     4.6  rostralanteriorcingulate
 9013   6127  16048  2.262 0.514     0.144     0.047      151    17.1  rostralmiddlefrontal
11047   7619  22100  2.534 0.554     0.140     0.042      157    19.5  superiorfrontal
 8952   5759  14049  2.219 0.432     0.129     0.037      109    12.9  superiorparietal
 6403   4287  13083  2.727 0.567     0.124     0.039       74     9.1  superiortemporal
 6682   4489  12448  2.507 0.521     0.134     0.039       92    10.5  supramarginal
  272    179    640  2.698 0.496     0.203     0.068        8     0.7  frontalpole
  605    426   2291  3.790 0.549     0.190     0.094       17     2.2  temporalpole
  787    502   1239  2.342 0.473     0.161     0.055       16     1.8  transversetemporal
 3243   2101   6385  2.928 0.634     0.123     0.042       39     5.3  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Fri Jun 20 18:19:17 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 surface_3T lh ../surf/lh.sphere.reg /opt/freesurfer/5.3/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3/average/lh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 3.9 0.2   using min determinant for regularization = 0.000
0 singular and 1066 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
82 labels changed using aseg
relabeling using gibbs priors...
000:   9733 changed, 144053 examined...
001:   2233 changed, 37326 examined...
002:    668 changed, 11689 examined...
003:    288 changed, 3845 examined...
004:    143 changed, 1589 examined...
005:     77 changed, 817 examined...
006:     44 changed, 440 examined...
007:     30 changed, 248 examined...
008:     21 changed, 176 examined...
009:     19 changed, 118 examined...
010:     14 changed, 92 examined...
011:      2 changed, 80 examined...
012:      2 changed, 15 examined...
013:      2 changed, 12 examined...
014:      0 changed, 9 examined...
9 labels changed using aseg
000: 261 total segments, 179 labels (2190 vertices) changed
001: 94 total segments, 12 labels (27 vertices) changed
002: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 131 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
641 vertices marked for relabeling...
641 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 20 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Fri Jun 20 18:20:37 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_anatomical_stats -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 surface_3T lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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

 1248    832   1949  2.077 0.542     0.156     0.059       25     3.0  G_and_S_frontomargin
 2200   1444   4170  2.572 0.543     0.174     0.065       55     5.6  G_and_S_occipital_inf
 1605    947   2631  2.420 0.707     0.127     0.041       20     2.8  G_and_S_paracentral
 1432    976   2937  2.605 0.376     0.148     0.054       28     3.0  G_and_S_subcentral
  751    499   1658  2.547 0.372     0.171     0.068       20     1.8  G_and_S_transv_frontopol
 2614   1783   4571  2.329 0.597     0.136     0.043       35     4.3  G_and_S_cingul-Ant
 1337    959   2755  2.671 0.501     0.122     0.028       12     1.4  G_and_S_cingul-Mid-Ant
 1383    979   2520  2.474 0.403     0.133     0.035       17     2.1  G_and_S_cingul-Mid-Post
  861    566   2065  2.913 0.571     0.192     0.108       39     3.4  G_cingul-Post-dorsal
  484    293    652  2.138 0.730     0.176     0.129       27     2.2  G_cingul-Post-ventral
 2524   1682   3530  1.915 0.502     0.175     0.068       51     7.0  G_cuneus
 1413    945   3285  2.698 0.456     0.153     0.049       27     2.9  G_front_inf-Opercular
  430    277    970  2.607 0.286     0.157     0.049        9     0.8  G_front_inf-Orbital
 1347    874   2951  2.614 0.356     0.148     0.048       25     2.5  G_front_inf-Triangul
 4745   3228  10339  2.531 0.492     0.152     0.049       93     9.7  G_front_middle
 7835   5339  17601  2.647 0.585     0.152     0.050      138    16.2  G_front_sup
  518    312   1149  3.115 0.544     0.128     0.049       10     1.0  G_Ins_lg_and_S_cent_ins
  705    457   2029  3.357 0.630     0.144     0.060       13     1.8  G_insular_short
 2230   1449   4545  2.496 0.401     0.171     0.068       69     5.6  G_occipital_middle
 1901   1207   3278  2.223 0.561     0.149     0.047       30     3.4  G_occipital_sup
 2231   1462   4815  2.764 0.556     0.157     0.059       54     5.8  G_oc-temp_lat-fusifor
 3148   2141   5009  2.022 0.577     0.178     0.081       74    10.1  G_oc-temp_med-Lingual
 1339    888   3002  2.650 0.927     0.140     0.071       29     4.7  G_oc-temp_med-Parahip
 2684   1802   5971  2.559 0.689     0.167     0.070       57     7.8  G_orbital
 2866   1895   6409  2.643 0.479     0.160     0.057       61     6.4  G_pariet_inf-Angular
 3592   2415   7670  2.647 0.522     0.147     0.044       63     6.5  G_pariet_inf-Supramar
 3227   2029   5759  2.318 0.436     0.137     0.043       51     5.2  G_parietal_sup
 2597   1571   4314  2.168 0.449     0.135     0.043       38     4.8  G_postcentral
 3182   1824   7231  2.997 0.462     0.114     0.046       47     6.6  G_precentral
 2964   1958   6099  2.494 0.464     0.163     0.058       71     7.1  G_precuneus
  845    523   1451  2.038 0.608     0.207     0.181       44     4.0  G_rectus
  103     66    208  2.686 0.544     0.101     0.026        1     0.1  G_subcallosal
  592    385   1105  2.370 0.527     0.145     0.051       12     1.3  G_temp_sup-G_T_transv
 2347   1533   5957  2.876 0.493     0.151     0.060       44     4.7  G_temp_sup-Lateral
  718    478   1914  3.360 0.637     0.095     0.026        4     0.7  G_temp_sup-Plan_polar
 1086    759   2161  2.564 0.428     0.112     0.028       11     1.2  G_temp_sup-Plan_tempo
 2960   1963   6130  2.382 0.628     0.170     0.081       95     9.5  G_temporal_inf
 3181   2227   8015  2.672 0.648     0.166     0.167     1894    31.0  G_temporal_middle
  465    316    634  2.144 0.323     0.100     0.019        2     0.4  Lat_Fis-ant-Horizont
  300    200    527  2.650 0.291     0.120     0.028        2     0.4  Lat_Fis-ant-Vertical
 1292    853   1688  2.420 0.422     0.127     0.037       13     1.9  Lat_Fis-post
 2449   1586   3485  2.037 0.458     0.164     0.070       51     5.5  Pole_occipital
 1660   1172   5166  3.336 0.663     0.181     0.083       44     5.2  Pole_temporal
 3301   2277   3829  1.816 0.571     0.151     0.079       61     8.1  S_calcarine
 3183   2185   3876  2.004 0.647     0.110     0.030       22     4.1  S_central
 1089    739   1520  2.173 0.456     0.105     0.025        6     1.1  S_cingul-Marginalis
  627    437   1153  2.845 0.488     0.125     0.032        5     0.9  S_circular_insula_ant
 1389    945   2328  2.842 0.551     0.099     0.023        7     1.3  S_circular_insula_inf
 1823   1230   2697  2.510 0.418     0.113     0.029       12     2.1  S_circular_insula_sup
 1187    850   2033  2.570 0.474     0.114     0.026        8     1.3  S_collat_transv_ant
  397    269    466  2.215 0.427     0.178     0.092       10     1.7  S_collat_transv_post
 2553   1720   3934  2.311 0.373     0.108     0.027       21     3.0  S_front_inf
 1862   1308   2658  2.020 0.430     0.120     0.030       15     2.2  S_front_middle
 2364   1656   3860  2.426 0.499     0.117     0.029       18     2.7  S_front_sup
  404    275    462  1.765 0.352     0.115     0.025        3     0.5  S_interm_prim-Jensen
 3569   2360   4854  2.144 0.358     0.106     0.026       25     3.8  S_intrapariet_and_P_trans
 1417    952   1810  2.024 0.385     0.134     0.039       14     2.2  S_oc_middle_and_Lunatus
 1293    869   1722  2.100 0.294     0.125     0.031       11     1.7  S_oc_sup_and_transversal
  619    423    855  2.402 0.444     0.125     0.030        5     0.8  S_occipital_ant
  920    624   1250  2.241 0.460     0.131     0.035        9     1.3  S_oc-temp_lat
 2135   1534   3518  2.539 0.564     0.131     0.041       24     3.5  S_oc-temp_med_and_Lingual
  491    327    669  2.230 0.427     0.109     0.022        3     0.5  S_orbital_lateral
  464    318    672  1.970 0.721     0.122     0.041        4     0.6  S_orbital_med-olfact
 1257    878   2108  2.386 0.666     0.148     0.056       18     2.9  S_orbital-H_Shaped
 2590   1760   3740  2.193 0.498     0.138     0.042       33     4.1  S_parieto_occipital
 1411    885   1495  1.939 0.761     0.162     0.058       30     3.9  S_pericallosal
 3103   2035   4117  2.146 0.383     0.116     0.030       26     3.8  S_postcentral
 1373    909   2242  2.587 0.462     0.102     0.023        8     1.3  S_precentral-inf-part
 1522   1045   2146  2.406 0.392     0.097     0.021        7     1.5  S_precentral-sup-part
  523    379    674  1.692 0.438     0.155     0.042        7     1.0  S_suborbital
  993    670   1563  2.524 0.377     0.135     0.037        9     1.6  S_subparietal
 1746   1202   2221  1.953 0.636     0.123     0.032       18     2.3  S_temporal_inf
 5841   4082   9086  2.296 0.437     0.120     0.031       58     7.3  S_temporal_sup
  474    340    729  2.393 0.388     0.118     0.024        4     0.5  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Fri Jun 20 18:21:06 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 surface_3T lh ../surf/lh.sphere.reg /opt/freesurfer/5.3/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3/average/lh.DKTatlas40.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.007
0 singular and 293 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1391 labels changed using aseg
relabeling using gibbs priors...
000:   2902 changed, 144053 examined...
001:    642 changed, 12590 examined...
002:    160 changed, 3509 examined...
003:     74 changed, 977 examined...
004:     39 changed, 403 examined...
005:     26 changed, 217 examined...
006:     14 changed, 147 examined...
007:      5 changed, 81 examined...
008:      4 changed, 31 examined...
009:      3 changed, 35 examined...
010:      4 changed, 18 examined...
011:      4 changed, 30 examined...
012:      1 changed, 21 examined...
013:      1 changed, 7 examined...
014:      0 changed, 6 examined...
211 labels changed using aseg
000: 83 total segments, 50 labels (281 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, 60 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
712 vertices marked for relabeling...
712 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 1 minutes and 11 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Fri Jun 20 18:22:17 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab surface_3T lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.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

 1677   1181   3196  2.530 0.620     0.139     0.031       22     2.2  caudalanteriorcingulate
 3498   2384   6706  2.614 0.406     0.119     0.030       34     4.5  caudalmiddlefrontal
 3687   2489   5632  2.074 0.498     0.159     0.054       63     8.1  cuneus
  617    417   1546  2.757 0.921     0.122     0.041        6     1.1  entorhinal
 4732   3222   9075  2.625 0.554     0.149     0.052       90    10.4  fusiform
 6991   4694  12560  2.363 0.483     0.144     0.047      118    13.1  inferiorparietal
 5169   3503   9905  2.407 0.692     0.151     0.064      120    13.0  inferiortemporal
 2019   1303   3427  2.453 0.766     0.164     0.086       58     6.0  isthmuscingulate
 8374   5517  13558  2.271 0.519     0.161     0.060      173    18.0  lateraloccipital
 4014   2686   7779  2.501 0.701     0.158     0.063       73    10.7  lateralorbitofrontal
 4829   3304   7245  2.070 0.595     0.165     0.081       97    14.2  lingual
 1786   1187   2735  1.894 0.604     0.168     0.106       54     5.6  medialorbitofrontal
 6722   4698  14010  2.477 0.658     0.146     0.097     1938    36.4  middletemporal
 1107    764   2213  2.666 0.870     0.129     0.074       25     4.2  parahippocampal
 2518   1587   4614  2.581 0.666     0.117     0.032       23     3.4  paracentral
 2153   1426   4184  2.589 0.431     0.135     0.040       29     3.6  parsopercularis
 1135    777   2309  2.479 0.376     0.143     0.048       19     2.1  parsorbitalis
 2853   1919   5310  2.452 0.387     0.125     0.034       34     3.9  parstriangularis
 2481   1683   2562  1.653 0.382     0.152     0.055       33     5.5  pericalcarine
 7109   4612  10512  2.064 0.503     0.125     0.037       87    10.9  postcentral
 2051   1390   3406  2.301 0.589     0.148     0.049       48     4.6  posteriorcingulate
 7542   4706  14118  2.735 0.557     0.112     0.038       81    12.3  precentral
 6103   4110  10607  2.362 0.519     0.151     0.055      119    12.4  precuneus
 1771   1181   3404  2.489 0.615     0.160     0.066       37     5.0  rostralanteriorcingulate
 6019   4091  10720  2.284 0.526     0.139     0.044       90    10.9  rostralmiddlefrontal
12654   8738  25167  2.458 0.571     0.145     0.045      203    23.6  superiorfrontal
 7285   4658  11498  2.233 0.418     0.125     0.036       88    10.2  superiorparietal
 8208   5570  17479  2.775 0.619     0.128     0.042      103    12.8  superiortemporal
 6460   4350  11967  2.497 0.521     0.134     0.038       88    10.2  supramarginal
  754    477   1187  2.341 0.477     0.162     0.056       16     1.8  transversetemporal
 2993   1953   5964  2.951 0.601     0.119     0.039       33     4.6  insula
#--------------------------------------------
#@# Tessellate rh Fri Jun 20 18:22:44 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (xy-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz-):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   2 modified     |    TOTAL:   6
pass   1 (xz+):   2 found -   2 modified     |    TOTAL:   8
pass   2 (xz+):   0 found -   2 modified     |    TOTAL:   8
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  10
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  10
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   2
pass   1 (--):   0 found -   0 modified     |    TOTAL:   2
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   3
Iteration Number : 2
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 13 (out of 281290: 0.004622)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 40: 1627 vertices, 1822 faces
slice 50: 8780 vertices, 9070 faces
slice 60: 19722 vertices, 20155 faces
slice 70: 31900 vertices, 32290 faces
slice 80: 44237 vertices, 44631 faces
slice 90: 55866 vertices, 56265 faces
slice 100: 67642 vertices, 68050 faces
slice 110: 79297 vertices, 79707 faces
slice 120: 90398 vertices, 90814 faces
slice 130: 101432 vertices, 101832 faces
slice 140: 112364 vertices, 112746 faces
slice 150: 121874 vertices, 122186 faces
slice 160: 130292 vertices, 130603 faces
slice 170: 137202 vertices, 137438 faces
slice 180: 142825 vertices, 143016 faces
slice 190: 146657 vertices, 146774 faces
slice 200: 147348 vertices, 147376 faces
slice 210: 147348 vertices, 147376 faces
slice 220: 147348 vertices, 147376 faces
slice 230: 147348 vertices, 147376 faces
slice 240: 147348 vertices, 147376 faces
slice 250: 147348 vertices, 147376 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;

 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 


counting number of connected components...
   147348 voxel in cpt #1: X=-28 [v=147348,e=442128,f=294752] located at (26.491598, -21.702534, 36.800140)
For the whole surface: X=-28 [v=147348,e=442128,f=294752]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Fri Jun 20 18:22:56 CEST 2014

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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
#--------------------------------------------
#@# Inflation1 rh Fri Jun 20 18:23:01 CEST 2014

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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
avg radius = 47.5 mm, total surface area = 78052 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.098 (target=0.015)   
step 005: RMS=0.072 (target=0.015)   
step 010: RMS=0.053 (target=0.015)   
step 015: RMS=0.044 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.034 (target=0.015)   
step 030: RMS=0.030 (target=0.015)   
step 035: RMS=0.028 (target=0.015)   
step 040: RMS=0.026 (target=0.015)   
step 045: RMS=0.025 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.024 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Fri Jun 20 18:23:38 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 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 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
vertex spacing 0.96 +- 0.56 (0.00-->7.20) (max @ vno 112058 --> 113037)
face area 0.03 +- 0.03 (-0.24-->0.60)
scaling brain by 0.309...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.170, avgs=0
005/300: dt: 0.9000, rms radial error=175.908, avgs=0
010/300: dt: 0.9000, rms radial error=175.346, avgs=0
015/300: dt: 0.9000, rms radial error=174.608, avgs=0
020/300: dt: 0.9000, rms radial error=173.771, avgs=0
025/300: dt: 0.9000, rms radial error=172.877, avgs=0
030/300: dt: 0.9000, rms radial error=171.950, avgs=0
035/300: dt: 0.9000, rms radial error=171.007, avgs=0
040/300: dt: 0.9000, rms radial error=170.062, avgs=0
045/300: dt: 0.9000, rms radial error=169.115, avgs=0
050/300: dt: 0.9000, rms radial error=168.171, avgs=0
055/300: dt: 0.9000, rms radial error=167.230, avgs=0
060/300: dt: 0.9000, rms radial error=166.292, avgs=0
065/300: dt: 0.9000, rms radial error=165.360, avgs=0
070/300: dt: 0.9000, rms radial error=164.432, avgs=0
075/300: dt: 0.9000, rms radial error=163.509, avgs=0
080/300: dt: 0.9000, rms radial error=162.591, avgs=0
085/300: dt: 0.9000, rms radial error=161.678, avgs=0
090/300: dt: 0.9000, rms radial error=160.771, avgs=0
095/300: dt: 0.9000, rms radial error=159.868, avgs=0
100/300: dt: 0.9000, rms radial error=158.970, avgs=0
105/300: dt: 0.9000, rms radial error=158.077, avgs=0
110/300: dt: 0.9000, rms radial error=157.189, avgs=0
115/300: dt: 0.9000, rms radial error=156.306, avgs=0
120/300: dt: 0.9000, rms radial error=155.430, avgs=0
125/300: dt: 0.9000, rms radial error=154.560, avgs=0
130/300: dt: 0.9000, rms radial error=153.694, avgs=0
135/300: dt: 0.9000, rms radial error=152.834, avgs=0
140/300: dt: 0.9000, rms radial error=151.977, avgs=0
145/300: dt: 0.9000, rms radial error=151.126, avgs=0
150/300: dt: 0.9000, rms radial error=150.279, avgs=0
155/300: dt: 0.9000, rms radial error=149.437, avgs=0
160/300: dt: 0.9000, rms radial error=148.599, avgs=0
165/300: dt: 0.9000, rms radial error=147.766, avgs=0
170/300: dt: 0.9000, rms radial error=146.938, avgs=0
175/300: dt: 0.9000, rms radial error=146.114, avgs=0
180/300: dt: 0.9000, rms radial error=145.294, avgs=0
185/300: dt: 0.9000, rms radial error=144.479, avgs=0
190/300: dt: 0.9000, rms radial error=143.668, avgs=0
195/300: dt: 0.9000, rms radial error=142.862, avgs=0
200/300: dt: 0.9000, rms radial error=142.061, avgs=0
205/300: dt: 0.9000, rms radial error=141.263, avgs=0
210/300: dt: 0.9000, rms radial error=140.470, avgs=0
215/300: dt: 0.9000, rms radial error=139.682, avgs=0
220/300: dt: 0.9000, rms radial error=138.898, avgs=0
225/300: dt: 0.9000, rms radial error=138.118, avgs=0
230/300: dt: 0.9000, rms radial error=137.343, avgs=0
235/300: dt: 0.9000, rms radial error=136.572, avgs=0
240/300: dt: 0.9000, rms radial error=135.805, avgs=0
245/300: dt: 0.9000, rms radial error=135.042, avgs=0
250/300: dt: 0.9000, rms radial error=134.284, avgs=0
255/300: dt: 0.9000, rms radial error=133.530, avgs=0
260/300: dt: 0.9000, rms radial error=132.780, avgs=0
265/300: dt: 0.9000, rms radial error=132.034, avgs=0
270/300: dt: 0.9000, rms radial error=131.292, avgs=0
275/300: dt: 0.9000, rms radial error=130.555, avgs=0
280/300: dt: 0.9000, rms radial error=129.821, avgs=0
285/300: dt: 0.9000, rms radial error=129.092, avgs=0
290/300: dt: 0.9000, rms radial error=128.366, avgs=0
295/300: dt: 0.9000, rms radial error=127.645, avgs=0
300/300: dt: 0.9000, rms radial error=126.928, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 17267.81
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00010
epoch 2 (K=40.0), pass 1, starting sse = 2899.09
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00002
epoch 3 (K=160.0), pass 1, starting sse = 291.45
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00501
epoch 4 (K=640.0), pass 1, starting sse = 17.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/13 = 0.00697
final writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology rh Fri Jun 20 18:28:19 CEST 2014

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


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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 surface_3T 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 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
before topology correction, eno=-28 (nv=147348, nf=294752, ne=442128, g=15)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
2758 ambiguous faces found in tessellation
segmenting defects...
25 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 14 into 13
      -merging segment 16 into 15
23 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.7779  (-4.8890)
      -vertex     loglikelihood: -6.7072  (-3.3536)
      -normal dot loglikelihood: -3.5839  (-3.5839)
      -quad curv  loglikelihood: -6.3884  (-3.1942)
      Total Loglikelihood : -26.4574

CORRECTING DEFECT 0 (vertices=48, convex hull=86)
After retessellation of defect 0, euler #=-22 (145667,436381,290692) : difference with theory (-20) = 2 

CORRECTING DEFECT 1 (vertices=15, convex hull=27)
After retessellation of defect 1, euler #=-21 (145670,436399,290708) : difference with theory (-19) = 2 

CORRECTING DEFECT 2 (vertices=33, convex hull=74)
After retessellation of defect 2, euler #=-20 (145686,436475,290769) : difference with theory (-18) = 2 

CORRECTING DEFECT 3 (vertices=18, convex hull=54)
After retessellation of defect 3, euler #=-19 (145694,436519,290806) : difference with theory (-17) = 2 

CORRECTING DEFECT 4 (vertices=75, convex hull=80)
After retessellation of defect 4, euler #=-18 (145711,436605,290876) : difference with theory (-16) = 2 

CORRECTING DEFECT 5 (vertices=400, convex hull=196)
After retessellation of defect 5, euler #=-17 (145756,436831,291058) : difference with theory (-15) = 2 

CORRECTING DEFECT 6 (vertices=78, convex hull=43)
After retessellation of defect 6, euler #=-16 (145765,436871,291090) : difference with theory (-14) = 2 

CORRECTING DEFECT 7 (vertices=149, convex hull=192)
After retessellation of defect 7, euler #=-15 (145835,437166,291316) : difference with theory (-13) = 2 

CORRECTING DEFECT 8 (vertices=38, convex hull=73)
After retessellation of defect 8, euler #=-14 (145859,437264,291391) : difference with theory (-12) = 2 

CORRECTING DEFECT 9 (vertices=8, convex hull=33)
Warning - incorrect dp selected!!!!(-100.293008 >= -100.293009 ) 
After retessellation of defect 9, euler #=-13 (145863,437284,291408) : difference with theory (-11) = 2 

CORRECTING DEFECT 10 (vertices=19, convex hull=44)
After retessellation of defect 10, euler #=-12 (145872,437327,291443) : difference with theory (-10) = 2 

CORRECTING DEFECT 11 (vertices=27, convex hull=29)
After retessellation of defect 11, euler #=-11 (145878,437354,291465) : difference with theory (-9) = 2 

CORRECTING DEFECT 12 (vertices=47, convex hull=49)
Warning - incorrect dp selected!!!!(-85.124201 >= -85.124203 ) 
After retessellation of defect 12, euler #=-10 (145882,437386,291494) : difference with theory (-8) = 2 

CORRECTING DEFECT 13 (vertices=207, convex hull=128)
After retessellation of defect 13, euler #=-8 (145901,437506,291597) : difference with theory (-7) = 1 

CORRECTING DEFECT 14 (vertices=48, convex hull=70)
After retessellation of defect 14, euler #=-6 (145919,437596,291671) : difference with theory (-6) = 0 

CORRECTING DEFECT 15 (vertices=166, convex hull=67)
After retessellation of defect 15, euler #=-5 (145929,437648,291714) : difference with theory (-5) = 0 

CORRECTING DEFECT 16 (vertices=12, convex hull=17)
After retessellation of defect 16, euler #=-4 (145932,437660,291724) : difference with theory (-4) = 0 

CORRECTING DEFECT 17 (vertices=30, convex hull=78)
After retessellation of defect 17, euler #=-3 (145949,437743,291791) : difference with theory (-3) = 0 

CORRECTING DEFECT 18 (vertices=41, convex hull=35)
After retessellation of defect 18, euler #=-2 (145952,437764,291810) : difference with theory (-2) = 0 

CORRECTING DEFECT 19 (vertices=13, convex hull=25)
After retessellation of defect 19, euler #=-1 (145957,437786,291828) : difference with theory (-1) = 0 

CORRECTING DEFECT 20 (vertices=36, convex hull=32)
After retessellation of defect 20, euler #=0 (145965,437824,291859) : difference with theory (0) = 0 

CORRECTING DEFECT 21 (vertices=151, convex hull=91)
After retessellation of defect 21, euler #=1 (145981,437910,291930) : difference with theory (1) = 0 

CORRECTING DEFECT 22 (vertices=38, convex hull=74)
After retessellation of defect 22, euler #=2 (145997,437985,291990) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.10-->14.35) (max @ vno 64618 --> 66904)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.10-->14.35) (max @ vno 64618 --> 66904)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
99 mutations (34.5%), 188 crossovers (65.5%), 162 vertices were eliminated
building final representation...
1351 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=145997, nf=291990, ne=437985, g=0)
writing corrected surface to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 21.9 minutes
0 defective edges
removing intersecting faces
000: 138 intersecting
001: 13 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 145997 - 437985 + 291990 = 2 --> 0 holes
      F =2V-4:          291990 = 291994-4 (0)
      2E=3F:            875970 = 875970 (0)

total defect index = 0
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 13 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Fri Jun 20 18:50:21 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs surface_3T rh 

only generating white matter surface
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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/filled.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
18488 bright wm thresholded.
490 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.orig...
computing class statistics...
border white:    270110 voxels (1.61%)
border gray      299704 voxels (1.79%)
WM (93.0): 93.9 +- 9.5 [70.0 --> 110.0]
GM (77.0) : 74.5 +- 13.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 45.5 (was 70)
setting MAX_BORDER_WHITE to 114.5 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 32.0 (was 40)
setting MAX_GRAY to 95.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.2 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->5.29) (max @ vno 64618 --> 66904)
face area 0.28 +- 0.12 (0.00-->5.08)
mean absolute distance = 0.68 +- 0.82
4006 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 93.1, mean outside = 68.9
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=73.2, 84 (84) missing vertices, mean dist 0.3 [0.5 (%32.6)->0.8 (%67.4))]
%73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=medus, 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 0.92 +- 0.26 (0.03-->7.17) (max @ vno 64618 --> 66904)
face area 0.28 +- 0.13 (0.00-->5.05)
mean absolute distance = 0.32 +- 0.51
3467 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8121419.0, rms=14.07
001: dt: 0.5000, sse=7789942.5, rms=10.165 (0.000%)
002: dt: 0.5000, sse=7907496.0, rms=7.816 (0.000%)
003: dt: 0.5000, sse=7976806.5, rms=6.282 (0.000%)
004: dt: 0.5000, sse=8173508.0, rms=5.345 (0.000%)
005: dt: 0.5000, sse=8271251.0, rms=4.843 (0.000%)
006: dt: 0.5000, sse=8395748.0, rms=4.594 (0.000%)
007: dt: 0.5000, sse=8396715.0, rms=4.467 (0.000%)
008: dt: 0.5000, sse=8415083.0, rms=4.389 (0.000%)
rms = 4.35, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8398626.0, rms=4.350 (0.000%)
010: dt: 0.2500, sse=5226592.0, rms=2.936 (0.000%)
011: dt: 0.2500, sse=4744113.5, rms=2.481 (0.000%)
012: dt: 0.2500, sse=4452875.5, rms=2.378 (0.000%)
013: dt: 0.2500, sse=4380480.5, rms=2.282 (0.000%)
rms = 2.25, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4282299.5, rms=2.252 (0.000%)
015: dt: 0.1250, sse=4022300.5, rms=1.944 (0.000%)
rms = 1.90, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=3976102.0, rms=1.901 (0.000%)
positioning took 1.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=77.4, 58 (21) missing vertices, mean dist -0.2 [0.3 (%77.3)->0.2 (%22.7))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=medus, 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 0.91 +- 0.25 (0.07-->7.25) (max @ vno 64618 --> 66904)
face area 0.35 +- 0.17 (0.00-->6.68)
mean absolute distance = 0.22 +- 0.32
3176 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5037330.5, rms=6.05
017: dt: 0.5000, sse=5307208.5, rms=4.201 (0.000%)
rms = 4.49, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=4785868.5, rms=3.078 (0.000%)
019: dt: 0.2500, sse=4581481.0, rms=2.445 (0.000%)
020: dt: 0.2500, sse=4504135.0, rms=2.056 (0.000%)
021: dt: 0.2500, sse=4482594.5, rms=1.977 (0.000%)
022: dt: 0.2500, sse=4424060.0, rms=1.880 (0.000%)
rms = 1.86, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=4439866.5, rms=1.863 (0.000%)
024: dt: 0.1250, sse=4275351.0, rms=1.616 (0.000%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=4238247.5, rms=1.583 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=80.5, 59 (11) missing vertices, mean dist -0.1 [0.2 (%76.1)->0.2 (%23.9))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=medus, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.04-->7.27) (max @ vno 64618 --> 66904)
face area 0.34 +- 0.16 (0.00-->6.65)
mean absolute distance = 0.17 +- 0.27
3480 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4597967.0, rms=4.04
rms = 4.02, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=5057836.5, rms=4.018 (0.000%)
027: dt: 0.2500, sse=4399944.5, rms=2.370 (0.000%)
028: dt: 0.2500, sse=4549107.0, rms=1.805 (0.000%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
029: dt: 0.1250, sse=4458342.0, rms=1.637 (0.000%)
030: dt: 0.1250, sse=4330668.0, rms=1.397 (0.000%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=4286808.0, rms=1.359 (0.000%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=81.5, 61 (11) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
%91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=medus, 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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=4314666.0, rms=1.79
rms = 2.63, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4392036.0, rms=1.218 (0.000%)
033: dt: 0.2500, sse=4530349.0, rms=1.060 (0.000%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
rms = 1.04, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=4528386.0, rms=1.044 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
generating cortex label...
23 non-cortical segments detected
only using segment with 2609 vertices
erasing segment 1 (vno[0] = 74722)
erasing segment 2 (vno[0] = 74753)
erasing segment 3 (vno[0] = 77070)
erasing segment 4 (vno[0] = 95787)
erasing segment 5 (vno[0] = 95799)
erasing segment 6 (vno[0] = 108818)
erasing segment 7 (vno[0] = 109816)
erasing segment 8 (vno[0] = 110719)
erasing segment 9 (vno[0] = 111777)
erasing segment 10 (vno[0] = 112783)
erasing segment 11 (vno[0] = 113102)
erasing segment 12 (vno[0] = 113765)
erasing segment 13 (vno[0] = 113777)
erasing segment 14 (vno[0] = 114038)
erasing segment 15 (vno[0] = 114691)
erasing segment 16 (vno[0] = 115000)
erasing segment 17 (vno[0] = 115969)
erasing segment 18 (vno[0] = 116591)
erasing segment 19 (vno[0] = 117497)
erasing segment 20 (vno[0] = 118336)
erasing segment 21 (vno[0] = 118343)
erasing segment 22 (vno[0] = 118350)
writing cortex label to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.cortex.label...
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.area
vertex spacing 0.90 +- 0.25 (0.06-->7.24) (max @ vno 64618 --> 66904)
face area 0.34 +- 0.16 (0.00-->6.65)
refinement took 6.6 minutes
#--------------------------------------------
#@# Smooth2 rh Fri Jun 20 18:56:55 CEST 2014

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

/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
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...
#--------------------------------------------
#@# Inflation2 rh Fri Jun 20 18:56:59 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated 

avg radius = 47.7 mm, total surface area = 89976 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.114 (target=0.015)   
step 005: RMS=0.079 (target=0.015)   
step 010: RMS=0.056 (target=0.015)   
step 015: RMS=0.046 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
step 050: RMS=0.015 (target=0.015)   
inflation complete.
inflation took 0.5 minutes

 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated 

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
254 vertices thresholded to be in k1 ~ [-0.22 0.47], k2 ~ [-0.09 0.07]
total integrated curvature = 0.483*4pi (6.067) --> 1 handles
ICI = 1.8, FI = 13.9, variation=228.243
136 vertices thresholded to be in [-0.01 0.01]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
147 vertices thresholded to be in [-0.12 0.23]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.028
done.

#-----------------------------------------
#@# Curvature Stats rh Fri Jun 20 18:59:16 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm surface_3T 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   [ surface_3T/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                      [ 291 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.371244
WARN:    S explicit min:                          0.000000	vertex = 419
#--------------------------------------------
#@# Sphere rh Fri Jun 20 18:59:21 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
scaling brain by 0.288...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=medus, 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 %19.20
pass 1: epoch 2 of 3 starting distance error %19.15
unfolding complete - removing small folds...
starting distance error %19.09
removing remaining folds...
final distance error %19.10
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.93 hours
#--------------------------------------------
#@# Surf Reg rh Fri Jun 20 19:54:54 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 

using smoothwm curvature for final alignment
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading surface from ../surf/rh.sphere...
reading template parameterization from /opt/freesurfer/5.3/average/rh.average.curvature.filled.buckner40.tif...
MRISregister() -------
max_passes = 4 
min_degrees = 0.500000 
max_degrees = 64.000000 
nangles = 8 
tol=5.0e-01, sigma=0.0, host=medus, 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=medus, 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 = 0.589
curvature mean = 0.021, std = 0.939
curvature mean = 0.021, std = 0.853
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 401754.0, tmin=1.0912
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 321420.4, tmin=2.1879
  d=16.00 min @ (0.00, 0.00, -4.00) sse = 303020.8, tmin=3.2941
  d=8.00 min @ (-2.00, -2.00, 0.00) sse = 298494.3, tmin=4.4253
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 296507.2, tmin=5.7886
  d=2.00 min @ (0.00, 0.00, 0.50) sse = 296349.0, tmin=7.1591
  d=1.00 min @ (0.00, 0.25, -0.25) sse = 296304.0, tmin=8.5467
  d=0.50 min @ (0.00, -0.12, 0.12) sse = 296271.2, tmin=9.9311
tol=1.0e+00, sigma=0.5, host=medus, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
MRISrigidBodyAlignGlobal() done   9.93 min
curvature mean = -0.001, std = 0.936
curvature mean = 0.011, std = 0.934
curvature mean = -0.007, std = 0.940
curvature mean = 0.005, std = 0.970
curvature mean = -0.009, std = 0.938
curvature mean = 0.001, std = 0.987
2 Reading smoothwm
curvature mean = -0.021, std = 0.278
curvature mean = 0.004, std = 0.070
curvature mean = 0.063, std = 0.341
curvature mean = 0.005, std = 0.082
curvature mean = 0.030, std = 0.544
curvature mean = 0.005, std = 0.089
curvature mean = 0.016, std = 0.690
curvature mean = 0.006, std = 0.091
curvature mean = 0.005, std = 0.802
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Fri Jun 20 20:27:31 CEST 2014

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

reading surface from ../surf/rh.white...
writing curvature file ../surf/rh.jacobian_white
#--------------------------------------------
#@# AvgCurv rh Fri Jun 20 20:27:34 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3/average/rh.average.curvature.filled.buckner40.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 /opt/freesurfer/5.3/average/rh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/rh.avg_curv...
#-----------------------------------------
#@# Cortical Parc rh Fri Jun 20 20:27:36 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 surface_3T rh ../surf/rh.sphere.reg /opt/freesurfer/5.3/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file....
average std = 0.7   using min determinant for regularization = 0.006
0 singular and 311 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1308 labels changed using aseg
relabeling using gibbs priors...
000:   3084 changed, 145997 examined...
001:    765 changed, 13195 examined...
002:    188 changed, 4206 examined...
003:     57 changed, 1094 examined...
004:     17 changed, 337 examined...
005:      7 changed, 92 examined...
006:      2 changed, 36 examined...
007:      0 changed, 15 examined...
155 labels changed using aseg
000: 102 total segments, 65 labels (383 vertices) changed
001: 40 total segments, 3 labels (3 vertices) changed
002: 37 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 35 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1093 vertices marked for relabeling...
1093 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 11 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Fri Jun 20 20:28:47 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs surface_3T rh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/filled.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
18488 bright wm thresholded.
490 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.orig...
computing class statistics...
border white:    270110 voxels (1.61%)
border gray      299704 voxels (1.79%)
WM (93.0): 93.9 +- 9.5 [70.0 --> 110.0]
GM (77.0) : 74.5 +- 13.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 45.5 (was 70)
setting MAX_BORDER_WHITE to 114.5 (was 105)
setting MIN_BORDER_WHITE to 59.0 (was 85)
setting MAX_CSF to 32.0 (was 40)
setting MAX_GRAY to 95.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 52.2 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 18.5 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=59
mean inside = 93.1, mean outside = 68.9
smoothing surface for 5 iterations...
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->5.29) (max @ vno 64618 --> 66904)
face area 0.28 +- 0.12 (0.00-->5.08)
mean absolute distance = 0.68 +- 0.82
4053 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 1 with 254 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
deleting segment 5 with 36 points - only 0.00% unknown
deleting segment 6 with 261 points - only 0.00% unknown
deleting segment 7 with 9 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 66 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=73.2, 86 (84) missing vertices, mean dist 0.3 [0.5 (%32.7)->0.8 (%67.3))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=medus, 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 0.92 +- 0.26 (0.03-->7.17) (max @ vno 64618 --> 66904)
face area 0.28 +- 0.13 (0.00-->5.04)
mean absolute distance = 0.32 +- 0.51
3492 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8146196.0, rms=14.05
001: dt: 0.5000, sse=7816017.5, rms=10.154 (0.000%)
002: dt: 0.5000, sse=7936990.5, rms=7.808 (0.000%)
003: dt: 0.5000, sse=8005154.5, rms=6.276 (0.000%)
004: dt: 0.5000, sse=8204565.5, rms=5.339 (0.000%)
005: dt: 0.5000, sse=8304326.0, rms=4.839 (0.000%)
006: dt: 0.5000, sse=8430206.0, rms=4.590 (0.000%)
007: dt: 0.5000, sse=8432160.0, rms=4.464 (0.000%)
008: dt: 0.5000, sse=8453079.0, rms=4.385 (0.000%)
rms = 4.35, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8435763.0, rms=4.347 (0.000%)
010: dt: 0.2500, sse=5246974.5, rms=2.934 (0.000%)
011: dt: 0.2500, sse=4761203.5, rms=2.479 (0.000%)
012: dt: 0.2500, sse=4468708.0, rms=2.376 (0.000%)
013: dt: 0.2500, sse=4396245.5, rms=2.281 (0.000%)
rms = 2.25, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4298295.5, rms=2.250 (0.000%)
015: dt: 0.1250, sse=4038471.2, rms=1.943 (0.000%)
rms = 1.90, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=3992142.8, rms=1.901 (0.000%)
positioning took 1.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 276 points - only 0.00% unknown
deleting segment 3 with 30 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
deleting segment 6 with 70 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 106 points - only 0.00% unknown
deleting segment 9 with 15 points - only 0.00% unknown
deleting segment 10 with 30 points - only 0.00% unknown
deleting segment 11 with 18 points - only 0.00% unknown
mean border=77.4, 61 (21) missing vertices, mean dist -0.2 [0.3 (%77.2)->0.2 (%22.8))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=medus, 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 0.91 +- 0.25 (0.07-->7.25) (max @ vno 64618 --> 66904)
face area 0.35 +- 0.17 (0.00-->6.68)
mean absolute distance = 0.22 +- 0.32
3200 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5056183.5, rms=6.04
017: dt: 0.5000, sse=5331028.5, rms=4.195 (0.000%)
rms = 4.48, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=4807997.5, rms=3.074 (0.000%)
019: dt: 0.2500, sse=4604233.0, rms=2.442 (0.000%)
020: dt: 0.2500, sse=4525152.0, rms=2.055 (0.000%)
021: dt: 0.2500, sse=4504441.5, rms=1.976 (0.000%)
022: dt: 0.2500, sse=4446913.5, rms=1.879 (0.000%)
rms = 1.86, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=4463340.5, rms=1.862 (0.000%)
024: dt: 0.1250, sse=4298733.0, rms=1.617 (0.000%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=4262124.5, rms=1.584 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 265 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
deleting segment 2 with 29 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 74 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 3 points - only 0.00% unknown
deleting segment 6 with 119 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 7 with 3 points - only 0.00% unknown
deleting segment 8 with 19 points - only 0.00% unknown
deleting segment 9 with 34 points - only 0.00% unknown
deleting segment 10 with 18 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
mean border=80.5, 62 (11) missing vertices, mean dist -0.1 [0.2 (%76.0)->0.2 (%24.0))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=medus, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.90 +- 0.25 (0.04-->7.27) (max @ vno 64618 --> 66904)
face area 0.34 +- 0.16 (0.00-->6.65)
mean absolute distance = 0.17 +- 0.27
3488 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4622218.0, rms=4.03
rms = 4.01, time step reduction 1 of 3 to 0.250...
026: dt: 0.5000, sse=5084939.0, rms=4.013 (0.000%)
027: dt: 0.2500, sse=4428615.0, rms=2.368 (0.000%)
028: dt: 0.2500, sse=4576717.0, rms=1.805 (0.000%)
rms = 1.87, time step reduction 2 of 3 to 0.125...
029: dt: 0.1250, sse=4485739.0, rms=1.638 (0.000%)
030: dt: 0.1250, sse=4357545.0, rms=1.399 (0.000%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=4313183.5, rms=1.361 (0.000%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 264 points - only 0.00% unknown
deleting segment 1 with 31 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 204 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 60 points - only 0.00% unknown
deleting segment 7 with 18 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
mean border=81.5, 67 (11) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))]
%92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=medus, 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
repositioning cortical surface to gray/csf boundary.
smoothing T1 volume with sigma = 2.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4341436.0, rms=1.80
rms = 2.62, time step reduction 1 of 3 to 0.250...
032: dt: 0.2500, sse=4420162.0, rms=1.221 (0.000%)
033: dt: 0.2500, sse=4562045.0, rms=1.061 (0.000%)
rms = 1.09, time step reduction 2 of 3 to 0.125...
rms = 1.05, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=4560240.5, rms=1.046 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
deleting segment 2 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
smoothing surface for 5 iterations...
mean border=48.3, 71 (71) missing vertices, mean dist 1.6 [0.1 (%0.0)->2.3 (%100.0))]
%13 local maxima, %53 large gradients and %30 min vals, 2300 gradients ignored
tol=1.0e-04, sigma=2.0, host=medus, 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=32958704.0, rms=32.79
001: dt: 0.5000, sse=23680530.0, rms=27.251 (0.000%)
002: dt: 0.5000, sse=17171844.0, rms=22.604 (0.000%)
003: dt: 0.5000, sse=12818902.0, rms=18.837 (0.000%)
004: dt: 0.5000, sse=10123144.0, rms=15.845 (0.000%)
005: dt: 0.5000, sse=8550346.0, rms=13.509 (0.000%)
006: dt: 0.5000, sse=7652005.5, rms=11.664 (0.000%)
007: dt: 0.5000, sse=7119855.0, rms=10.113 (0.000%)
008: dt: 0.5000, sse=6800549.5, rms=8.694 (0.000%)
009: dt: 0.5000, sse=6613534.0, rms=7.422 (0.000%)
010: dt: 0.5000, sse=6565245.0, rms=6.282 (0.000%)
011: dt: 0.5000, sse=6626222.0, rms=5.392 (0.000%)
012: dt: 0.5000, sse=6717546.0, rms=4.719 (0.000%)
013: dt: 0.5000, sse=6917868.0, rms=4.402 (0.000%)
014: dt: 0.5000, sse=7016898.5, rms=4.211 (0.000%)
rms = 4.18, time step reduction 1 of 3 to 0.250...
015: dt: 0.5000, sse=7113707.0, rms=4.181 (0.000%)
016: dt: 0.2500, sse=4989565.5, rms=3.460 (0.000%)
017: dt: 0.2500, sse=4821522.5, rms=3.276 (0.000%)
rms = 3.25, time step reduction 2 of 3 to 0.125...
018: dt: 0.2500, sse=4724076.5, rms=3.252 (0.000%)
019: dt: 0.1250, sse=4467756.5, rms=3.070 (0.000%)
rms = 3.04, time step reduction 3 of 3 to 0.062...
020: dt: 0.1250, sse=4449238.0, rms=3.035 (0.000%)
positioning took 2.4 minutes
mean border=46.4, 1118 (7) missing vertices, mean dist 0.1 [0.2 (%50.9)->0.6 (%49.1))]
%26 local maxima, %43 large gradients and %26 min vals, 610 gradients ignored
tol=1.0e-04, sigma=1.0, host=medus, 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=5029953.5, rms=4.70
021: dt: 0.5000, sse=5390519.0, rms=4.056 (0.000%)
022: dt: 0.5000, sse=6897392.5, rms=3.967 (0.000%)
rms = 4.02, time step reduction 1 of 3 to 0.250...
023: dt: 0.2500, sse=5689430.5, rms=3.263 (0.000%)
024: dt: 0.2500, sse=5207588.0, rms=2.991 (0.000%)
rms = 2.94, time step reduction 2 of 3 to 0.125...
025: dt: 0.2500, sse=5170370.5, rms=2.941 (0.000%)
026: dt: 0.1250, sse=4923171.5, rms=2.749 (0.000%)
rms = 2.72, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4897771.5, rms=2.717 (0.000%)
positioning took 0.9 minutes
mean border=44.1, 1228 (2) missing vertices, mean dist 0.1 [0.2 (%39.4)->0.4 (%60.6))]
%45 local maxima, %24 large gradients and %26 min vals, 797 gradients ignored
tol=1.0e-04, sigma=0.5, host=medus, 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=5192193.5, rms=4.13
028: dt: 0.5000, sse=5493247.0, rms=3.979 (0.000%)
rms = 3.96, time step reduction 1 of 3 to 0.250...
029: dt: 0.5000, sse=7237624.5, rms=3.960 (0.000%)
030: dt: 0.2500, sse=5424686.0, rms=3.105 (0.000%)
031: dt: 0.2500, sse=5561674.0, rms=2.862 (0.000%)
rms = 2.88, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=5434358.0, rms=2.761 (0.000%)
033: dt: 0.1250, sse=5219937.0, rms=2.619 (0.000%)
rms = 2.59, time step reduction 3 of 3 to 0.062...
034: dt: 0.1250, sse=5178588.5, rms=2.594 (0.000%)
positioning took 0.9 minutes
mean border=42.9, 2682 (1) missing vertices, mean dist 0.1 [0.2 (%44.8)->0.3 (%55.2))]
%50 local maxima, %19 large gradients and %25 min vals, 642 gradients ignored
tol=1.0e-04, sigma=0.2, host=medus, 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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=5250245.5, rms=3.04
rms = 3.80, time step reduction 1 of 3 to 0.250...
035: dt: 0.2500, sse=5090942.0, rms=2.726 (0.000%)
036: dt: 0.2500, sse=5248290.5, rms=2.644 (0.000%)
rms = 2.65, time step reduction 2 of 3 to 0.125...
rms = 2.60, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=5193707.5, rms=2.601 (0.000%)
positioning took 0.5 minutes
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.area.pial
vertex spacing 1.00 +- 0.41 (0.08-->7.64) (max @ vno 64618 --> 66904)
face area 0.40 +- 0.29 (0.00-->10.55)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 145997 vertices processed
25000 of 145997 vertices processed
50000 of 145997 vertices processed
75000 of 145997 vertices processed
100000 of 145997 vertices processed
125000 of 145997 vertices processed
0 of 145997 vertices processed
25000 of 145997 vertices processed
50000 of 145997 vertices processed
75000 of 145997 vertices processed
100000 of 145997 vertices processed
125000 of 145997 vertices processed
thickness calculation complete, 153:427 truncations.
35290 vertices at 0 distance
105907 vertices at 1 distance
92472 vertices at 2 distance
33153 vertices at 3 distance
9134 vertices at 4 distance
2577 vertices at 5 distance
730 vertices at 6 distance
220 vertices at 7 distance
117 vertices at 8 distance
68 vertices at 9 distance
35 vertices at 10 distance
26 vertices at 11 distance
23 vertices at 12 distance
17 vertices at 13 distance
27 vertices at 14 distance
15 vertices at 15 distance
13 vertices at 16 distance
9 vertices at 17 distance
4 vertices at 18 distance
2 vertices at 19 distance
5 vertices at 20 distance
writing curvature file /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.thickness
positioning took 12.3 minutes
#--------------------------------------------
#@# Surf Volume rh Fri Jun 20 20:41:08 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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_calc -o rh.volume rh.area.mid mul rh.thickness 

Saving result to 'rh.volume' (type = MRI_CURV_FILE)                       [ ok ]
#-----------------------------------------
#@# WM/GM Contrast rh Fri Jun 20 20:41:08 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 pctsurfcon --s surface_3T --rh-only 

Log file is /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts/pctsurfcon.log
Fri Jun 20 20:41:08 CEST 2014
setenv SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
cd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts
/opt/freesurfer/5.3/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.57-3 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3
mri_vol2surf --mov /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.51760/rh.wm.mgh --regheader surface_3T --cortex
srcvol = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjDist = -1
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.cortex.label
Reading surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 = 114149
Masking with /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.cortex.label
Writing to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.51760/rh.wm.mgh
Dim: 145997 1 1
mri_vol2surf --mov /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.51760/rh.gm.mgh --projfrac 0.3 --regheader surface_3T --cortex
srcvol = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/rawavg.mgz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
ProjFrac = 0.3
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.cortex.label
Reading surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 = 130040
Masking with /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.cortex.label
Writing to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.51760/rh.gm.mgh
Dim: 145997 1 1
mri_concat /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.51760/rh.wm.mgh /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/tmp.pctsurfcon.51760/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.w-g.pct.mgh --annot surface_3T rh aparc --sum /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/stats/rh.w-g.pct.stats --snr

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd 
cmdline mri_segstats --in /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.w-g.pct.mgh --annot surface_3T rh aparc --sum /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
Constructing seg from annotation

Reading annotation
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Seg base 2000
Loading /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.w-g.pct.mgh
Vertex Area is 0.672071 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1541    1062.988
  2   2002            caudalanteriorcingulate    1298     859.597
  3   2003                caudalmiddlefrontal    3359    2220.368
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2203    1471.972
  6   2006                         entorhinal     443     335.258
  7   2007                           fusiform    5018    3417.207
  8   2008                   inferiorparietal    8955    6167.594
  9   2009                   inferiortemporal    4419    3032.289
 10   2010                   isthmuscingulate    1886    1247.059
 11   2011                   lateraloccipital    8708    5808.687
 12   2012               lateralorbitofrontal    3955    2663.297
 13   2013                            lingual    5258    3618.418
 14   2014                medialorbitofrontal    2618    1665.297
 15   2015                     middletemporal    5663    3878.483
 16   2016                    parahippocampal    1215     827.283
 17   2017                        paracentral    2109    1391.729
 18   2018                    parsopercularis    2044    1392.898
 19   2019                      parsorbitalis    1300     889.057
 20   2020                   parstriangularis    2085    1408.225
 21   2021                      pericalcarine    2463    1732.740
 22   2022                        postcentral    7665    5047.090
 23   2023                 posteriorcingulate    2064    1360.777
 24   2024                         precentral    7869    5028.319
 25   2025                          precuneus    7287    4858.169
 26   2026           rostralanteriorcingulate     942     614.596
 27   2027               rostralmiddlefrontal   10207    6908.767
 28   2028                    superiorfrontal   11002    7464.743
 29   2029                   superiorparietal    7662    4972.452
 30   2030                   superiortemporal    5887    4006.620
 31   2031                      supramarginal    5277    3543.648
 32   2032                        frontalpole     330     247.269
 33   2033                       temporalpole     531     395.624
 34   2034                 transversetemporal     528     342.580
 35   2035                             insula    3189    2117.040

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Fri Jun 20 20:41:19 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab surface_3T rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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

 1541   1063   2687  2.644 0.413     0.103     0.023       10     1.4  bankssts
 1298    860   2162  2.338 0.674     0.149     0.043       24     2.3  caudalanteriorcingulate
 3359   2220   6002  2.420 0.473     0.117     0.039       44     6.3  caudalmiddlefrontal
 2203   1472   3082  1.962 0.507     0.171     0.064       46     5.4  cuneus
  443    335   1191  2.950 0.816     0.149     0.072        9     1.3  entorhinal
 5018   3417   9954  2.535 0.563     0.153     0.059      145    12.5  fusiform
 8955   6168  16323  2.303 0.470     0.146     0.048      156    17.5  inferiorparietal
 4419   3032   7730  2.151 0.675     0.150     0.058       92    10.5  inferiortemporal
 1886   1247   3156  2.354 0.764     0.157     0.065       37     5.1  isthmuscingulate
 8708   5809  13822  2.274 0.434     0.162     0.073      346    19.6  lateraloccipital
 3955   2663   7990  2.595 0.626     0.156     0.066       99    10.6  lateralorbitofrontal
 5258   3618   7401  1.976 0.554     0.174     0.081      108    17.2  lingual
 2618   1665   3889  1.987 0.653     0.147     0.065       62     6.9  medialorbitofrontal
 5663   3878  13355  2.769 0.666     0.144     0.048       96    10.9  middletemporal
 1215    827   2117  2.332 0.597     0.124     0.044       16     2.1  parahippocampal
 2109   1392   3834  2.595 0.509     0.120     0.030       19     2.7  paracentral
 2044   1393   3717  2.543 0.381     0.135     0.039       27     3.2  parsopercularis
 1300    889   2938  2.598 0.563     0.158     0.053       26     2.9  parsorbitalis
 2085   1408   3818  2.408 0.404     0.130     0.037       25     3.0  parstriangularis
 2463   1733   2890  1.843 0.400     0.149     0.053       29     5.3  pericalcarine
 7665   5047  11881  2.076 0.536     0.130     0.048      106    12.3  postcentral
 2064   1361   3781  2.555 0.664     0.153     0.057       36     4.7  posteriorcingulate
 7869   5028  14927  2.684 0.526     0.115     0.089      229    18.7  precentral
 7287   4858  12326  2.395 0.499     0.139     0.046      111    12.8  precuneus
  942    615   1806  2.590 0.562     0.155     0.061       20     1.9  rostralanteriorcingulate
10207   6909  18190  2.326 0.459     0.142     0.044      167    18.7  rostralmiddlefrontal
11002   7465  22308  2.642 0.519     0.136     0.040      145    18.3  superiorfrontal
 7662   4972  11694  2.147 0.412     0.133     0.038      103    11.6  superiorparietal
 5887   4007  13036  2.827 0.575     0.129     0.039       74     9.4  superiortemporal
 5277   3544   9948  2.553 0.486     0.142     0.047       81     9.9  supramarginal
  330    247    819  2.395 0.464     0.217     0.067       12     1.1  frontalpole
  531    396   2064  3.924 0.662     0.183     0.069       12     1.4  temporalpole
  528    343    937  2.531 0.317     0.140     0.043        7     1.0  transversetemporal
 3189   2117   6143  2.892 0.620     0.143     0.079      105     7.8  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Fri Jun 20 20:41:47 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 surface_3T rh ../surf/rh.sphere.reg /opt/freesurfer/5.3/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3/average/rh.destrieux.simple.2009-07-29.gcs...
reading color table from GCSA file....
average std = 1.9 0.2   using min determinant for regularization = 0.000
0 singular and 851 ill-conditioned covariance matrices regularized
input 1: CURVATURE FILE, flags 0, avgs 0, name sulc
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
25 labels changed using aseg
relabeling using gibbs priors...
000:  10175 changed, 145997 examined...
001:   2419 changed, 38912 examined...
002:    731 changed, 12436 examined...
003:    320 changed, 4082 examined...
004:    119 changed, 1760 examined...
005:     69 changed, 711 examined...
006:     32 changed, 396 examined...
007:     17 changed, 185 examined...
008:     14 changed, 99 examined...
009:      3 changed, 64 examined...
010:      1 changed, 22 examined...
011:      1 changed, 10 examined...
012:      0 changed, 6 examined...
12 labels changed using aseg
000: 306 total segments, 226 labels (2577 vertices) changed
001: 105 total segments, 25 labels (152 vertices) changed
002: 82 total segments, 2 labels (2 vertices) changed
003: 80 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 165 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
618 vertices marked for relabeling...
618 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 22 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Fri Jun 20 20:43:09 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_anatomical_stats -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 surface_3T rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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

  939    643   1658  2.147 0.507     0.154     0.045       21     1.7  G_and_S_frontomargin
 1485   1007   2668  2.309 0.442     0.150     0.053       28     3.1  G_and_S_occipital_inf
 1349    847   2401  2.389 0.554     0.121     0.034       13     1.9  G_and_S_paracentral
 1587   1069   3182  2.603 0.390     0.156     0.063       30     3.3  G_and_S_subcentral
  960    671   2041  2.384 0.472     0.183     0.066       26     2.6  G_and_S_transv_frontopol
 2676   1817   5070  2.542 0.579     0.134     0.042       35     4.4  G_and_S_cingul-Ant
 1823   1178   3506  2.804 0.412     0.128     0.041       23     3.1  G_and_S_cingul-Mid-Ant
 1620   1092   3110  2.758 0.389     0.141     0.051       21     3.3  G_and_S_cingul-Mid-Post
  655    417   1606  2.886 0.478     0.180     0.074       20     1.8  G_cingul-Post-dorsal
  508    333   1026  2.548 0.775     0.170     0.085       12     2.2  G_cingul-Post-ventral
 1975   1390   2727  1.808 0.429     0.178     0.068       43     5.4  G_cuneus
 1229    837   2794  2.604 0.391     0.150     0.050       23     2.5  G_front_inf-Opercular
  351    229    958  2.841 0.373     0.161     0.049        7     0.8  G_front_inf-Orbital
  945    634   2247  2.682 0.318     0.166     0.055       19     2.0  G_front_inf-Triangul
 5168   3438  11064  2.497 0.484     0.148     0.053      106    12.0  G_front_middle
 7407   4946  16604  2.688 0.561     0.148     0.047      128    14.4  G_front_sup
  570    389   1266  2.992 0.439     0.141     0.046        9     1.0  G_Ins_lg_and_S_cent_ins
  635    419   1783  3.409 0.639     0.191     0.116       22     2.7  G_insular_short
 2303   1579   4473  2.374 0.447     0.177     0.063       56     6.2  G_occipital_middle
 2210   1449   3832  2.223 0.401     0.148     0.086       76     4.0  G_occipital_sup
 2238   1487   5217  2.734 0.518     0.158     0.065       98     6.3  G_oc-temp_lat-fusifor
 3291   2273   4896  1.913 0.562     0.185     0.083       77    11.8  G_oc-temp_med-Lingual
 1008    645   2096  2.632 0.732     0.150     0.142       72     3.7  G_oc-temp_med-Parahip
 3019   2036   7308  2.694 0.678     0.172     0.071       85     9.0  G_orbital
 3732   2593   8216  2.492 0.528     0.165     0.060       84     9.1  G_pariet_inf-Angular
 2628   1746   5713  2.670 0.454     0.155     0.051       52     5.4  G_pariet_inf-Supramar
 2120   1356   3682  2.197 0.433     0.141     0.042       34     3.4  G_parietal_sup
 2890   1876   5083  2.149 0.502     0.137     0.059       48     5.0  G_postcentral
 3003   1788   7092  2.970 0.475     0.116     0.160      134    12.1  G_precentral
 3604   2385   7178  2.471 0.435     0.148     0.050       66     7.1  G_precuneus
  685    417   1099  2.033 0.633     0.198     0.111       29     3.3  G_rectus
  293    190    518  2.404 0.891     0.111     0.071        7     0.5  G_subcallosal
  405    257    742  2.465 0.310     0.131     0.043        6     0.7  G_temp_sup-G_T_transv
 1927   1319   5582  3.026 0.489     0.158     0.057       39     4.6  G_temp_sup-Lateral
  817    552   2179  3.415 0.643     0.116     0.032        7     1.1  G_temp_sup-Plan_polar
  935    649   1850  2.565 0.436     0.121     0.025        9     1.0  G_temp_sup-Plan_tempo
 2218   1557   4313  2.095 0.689     0.177     0.079       65     7.2  G_temporal_inf
 3541   2423   9724  2.935 0.602     0.154     0.055       72     7.8  G_temporal_middle
  499    337    663  2.183 0.294     0.084     0.016        2     0.3  Lat_Fis-ant-Horizont
  247    167    407  2.727 0.431     0.123     0.025        2     0.3  Lat_Fis-ant-Vertical
 1333    914   1956  2.515 0.371     0.115     0.030       11     1.6  Lat_Fis-post
 3532   2336   5305  2.129 0.500     0.182     0.095      222     9.9  Pole_occipital
 1673   1189   5042  2.979 0.919     0.184     0.084       50     5.2  Pole_temporal
 3580   2407   4439  2.026 0.565     0.150     0.063       58     8.6  S_calcarine
 3138   2097   3712  1.999 0.629     0.109     0.051       73     4.6  S_central
 1088    751   1690  2.452 0.420     0.106     0.021        6     1.0  S_cingul-Marginalis
  613    412   1150  2.987 0.498     0.124     0.035        5     0.9  S_circular_insula_ant
 1116    749   1721  2.493 0.463     0.091     0.022        6     1.0  S_circular_insula_inf
 1766   1181   2609  2.528 0.477     0.117     0.029       13     2.2  S_circular_insula_sup
  872    619   1437  2.364 0.613     0.126     0.037       10     1.4  S_collat_transv_ant
  806    535   1069  2.302 0.420     0.153     0.053       12     1.7  S_collat_transv_post
 2357   1608   3570  2.258 0.323     0.125     0.036       28     3.9  S_front_inf
 2843   1905   3815  2.178 0.367     0.119     0.033       28     3.6  S_front_middle
 2645   1829   4172  2.340 0.433     0.114     0.029       20     3.2  S_front_sup
  498    321    621  2.309 0.406     0.142     0.050        6     1.1  S_interm_prim-Jensen
 2478   1651   3256  2.119 0.384     0.136     0.044       33     4.2  S_intrapariet_and_P_trans
 1515   1023   2146  2.285 0.372     0.137     0.041       18     2.5  S_oc_middle_and_Lunatus
 1463    959   2265  2.229 0.348     0.139     0.036       20     2.2  S_oc_sup_and_transversal
 1008    690   1470  2.302 0.361     0.123     0.035        9     1.5  S_occipital_ant
  995    682   1341  1.954 0.416     0.129     0.042       12     1.8  S_oc-temp_lat
 2322   1630   3558  2.419 0.492     0.126     0.037       22     3.2  S_oc-temp_med_and_Lingual
  428    289    567  2.163 0.323     0.129     0.036        4     0.6  S_orbital_lateral
  444    305    694  2.159 0.683     0.116     0.030        3     0.6  S_orbital_med-olfact
 1605   1097   2659  2.403 0.480     0.151     0.062       38     4.0  S_orbital-H_Shaped
 2321   1525   3117  2.203 0.482     0.131     0.039       28     3.6  S_parieto_occipital
 1894   1230   1890  1.868 0.659     0.148     0.047       30     3.4  S_pericallosal
 3610   2333   4452  2.076 0.437     0.111     0.032       32     4.4  S_postcentral
 1548   1084   2259  2.238 0.366     0.104     0.021       10     1.4  S_precentral-inf-part
 1432    983   2089  2.496 0.370     0.107     0.029       11     1.6  S_precentral-sup-part
  338    224    305  1.325 0.200     0.107     0.023        2     0.4  S_suborbital
 1609   1111   2379  2.351 0.478     0.132     0.039       17     2.4  S_subparietal
 1250    841   1709  2.151 0.656     0.117     0.031        9     1.7  S_temporal_inf
 7134   4875  11495  2.468 0.529     0.117     0.030       66     8.7  S_temporal_sup
  231    178    385  2.550 0.363     0.167     0.032        2     0.4  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Fri Jun 20 20:43:40 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 surface_3T rh ../surf/rh.sphere.reg /opt/freesurfer/5.3/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot 

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading atlas from /opt/freesurfer/5.3/average/rh.DKTatlas40.gcs...
reading color table from GCSA file....
average std = 0.9   using min determinant for regularization = 0.008
0 singular and 237 ill-conditioned covariance matrices regularized
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
labeling surface...
1320 labels changed using aseg
relabeling using gibbs priors...
000:   2922 changed, 145997 examined...
001:    717 changed, 12442 examined...
002:    192 changed, 3834 examined...
003:     59 changed, 1093 examined...
004:     26 changed, 359 examined...
005:     15 changed, 159 examined...
006:     19 changed, 91 examined...
007:      6 changed, 80 examined...
008:      4 changed, 32 examined...
009:      6 changed, 29 examined...
010:      7 changed, 30 examined...
011:      4 changed, 31 examined...
012:      5 changed, 18 examined...
013:      5 changed, 21 examined...
014:      2 changed, 22 examined...
015:      4 changed, 14 examined...
016:      1 changed, 19 examined...
017:      1 changed, 7 examined...
018:      1 changed, 7 examined...
019:      1 changed, 7 examined...
020:      2 changed, 7 examined...
021:      0 changed, 11 examined...
173 labels changed using aseg
000: 71 total segments, 38 labels (200 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 41 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
636 vertices marked for relabeling...
636 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 11 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Fri Jun 20 20:44:51 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/scripts

 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab surface_3T rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness.
reading colortable from annotation file...
colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt)
Saving annotation colortable ../label/aparc.annot.DKTatlas40.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

 1371    901   2357  2.382 0.694     0.149     0.043       25     2.5  caudalanteriorcingulate
 3389   2246   6023  2.443 0.480     0.119     0.040       45     6.4  caudalmiddlefrontal
 2817   1882   3973  1.978 0.481     0.158     0.057       52     6.2  cuneus
  430    316   1153  2.979 0.819     0.149     0.073        9     1.3  entorhinal
 4422   3013   8746  2.555 0.556     0.148     0.054      127    10.3  fusiform
 8489   5866  15636  2.309 0.474     0.148     0.049      149    17.0  inferiorparietal
 4962   3417   8915  2.180 0.676     0.153     0.062      109    12.4  inferiortemporal
 1889   1251   3177  2.353 0.765     0.157     0.066       38     5.1  isthmuscingulate
 9080   6059  14452  2.271 0.433     0.163     0.073      355    20.6  lateraloccipital
 4341   2928   8773  2.519 0.639     0.163     0.083      167    12.9  lateralorbitofrontal
 5267   3631   7434  1.976 0.554     0.174     0.082      108    17.2  lingual
 1900   1191   2883  1.953 0.705     0.158     0.075       55     5.8  medialorbitofrontal
 6746   4619  15281  2.753 0.629     0.139     0.044      105    12.0  middletemporal
 1133    775   1990  2.343 0.596     0.123     0.044       14     1.9  parahippocampal
 2223   1463   4157  2.619 0.535     0.119     0.030       20     2.9  paracentral
 2165   1481   3959  2.541 0.374     0.136     0.039       30     3.4  parsopercularis
 1422    969   3143  2.610 0.520     0.140     0.043       20     2.6  parsorbitalis
 2121   1413   3754  2.396 0.413     0.135     0.039       27     3.3  parstriangularis
 2421   1690   2821  1.848 0.401     0.149     0.053       29     5.2  pericalcarine
 8334   5480  12858  2.083 0.531     0.130     0.048      117    13.4  postcentral
 2156   1419   3908  2.564 0.653     0.153     0.056       38     4.8  posteriorcingulate
 7650   4875  14444  2.669 0.529     0.115     0.090      225    18.6  precentral
 7294   4865  12402  2.396 0.497     0.141     0.046      114    13.0  precuneus
 1073    704   1905  2.453 0.602     0.153     0.058       21     2.1  rostralanteriorcingulate
 6949   4718  12426  2.342 0.448     0.140     0.043      110    12.7  rostralmiddlefrontal
14544   9888  28602  2.554 0.527     0.138     0.042      208    24.9  superiorfrontal
 6441   4176   9905  2.170 0.415     0.134     0.039       86     9.9  superiorparietal
 7480   5116  16905  2.869 0.651     0.132     0.040       96    12.4  superiortemporal
 4841   3229   8906  2.520 0.494     0.136     0.045       69     8.3  supramarginal
  533    345    941  2.529 0.317     0.139     0.043        7     1.0  transversetemporal
 3097   2075   6089  2.930 0.591     0.139     0.055       49     6.4  insula
#--------------------------------------------
#@# Cortical ribbon mask Fri Jun 20 20:45:19 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon surface_3T 

SUBJECTS_DIR is /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
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 = 33
writing volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Fri Jun 20 21:01:29 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 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 /opt/freesurfer/5.3/ASegStatsLUT.txt --subject surface_3T 


$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 /opt/freesurfer/5.3/ASegStatsLUT.txt --subject surface_3T 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
atlas_icv (eTIV) = 1085507 mm^3    (det: 1.794650 )
Computing euler number
orig.nofix lheno =  -26, rheno = -28
orig.nofix lhholes =   14, rhholes = 15
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 242777.741 242849.000  diff=  -71.3  pctdiff=-0.029
rhCtxGM: 245333.130 245148.000  diff=  185.1  pctdiff= 0.075
lhCtxWM: 249301.032 248906.000  diff=  395.0  pctdiff= 0.158
rhCtxWM: 250322.862 251168.000  diff= -845.1  pctdiff=-0.338
SubCortGMVol  64160.000
SupraTentVol  1064229.765 (1063422.000) diff=807.765 pctdiff=0.076
SupraTentVolNotVent  1053174.765 (1052367.000) diff=807.765 pctdiff=0.077
BrainSegVol  1198232.000 (1196906.000) diff=1326.000 pctdiff=0.111
BrainSegVolNotVent  1184960.000 (1184318.765) diff=641.235 pctdiff=0.054
BrainSegVolNotVent  1184960.000
CerebellumVol 132288.000
VentChorVol   11055.000
3rd4th5thCSF   2217.000
CSFVol   901.000, OptChiasmVol   295.000
MaskVol 1566392.000
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
  3     4             Left-Lateral-Ventricle    3522    3521.550
  4     5                  Left-Inf-Lat-Vent     406     405.917
  5     7       Left-Cerebellum-White-Matter   18142   18142.318
  6     8             Left-Cerebellum-Cortex   48435   48435.062
  7    10               Left-Thalamus-Proper    7779    7778.864
  8    11                       Left-Caudate    4051    4051.495
  9    12                       Left-Putamen    6047    6047.163
 10    13                      Left-Pallidum    1752    1752.170
 11    14                      3rd-Ventricle     568     568.376
 12    15                      4th-Ventricle     980     980.326
 13    16                         Brain-Stem   24600   24599.863
 14    17                   Left-Hippocampus    4143    4142.793
 15    18                      Left-Amygdala    1617    1617.442
 16    24                                CSF     954     954.152
 17    26                Left-Accumbens-area     949     948.765
 18    28                     Left-VentralDC    4792    4791.649
 19    30                        Left-vessel      60      59.794
 20    31                Left-choroid-plexus    1324    1323.781
 23    43            Right-Lateral-Ventricle    3110    3110.017
 24    44                 Right-Inf-Lat-Vent    1354    1353.711
 25    46      Right-Cerebellum-White-Matter   18985   18985.104
 26    47            Right-Cerebellum-Cortex   49712   49711.672
 27    49              Right-Thalamus-Proper    7513    7512.680
 28    50                      Right-Caudate    4381    4381.314
 29    51                      Right-Putamen    5742    5742.247
 30    52                     Right-Pallidum    2058    2058.061
 31    53                  Right-Hippocampus    4006    4006.481
 32    54                     Right-Amygdala    2129    2129.092
 33    58               Right-Accumbens-area     605     604.734
 34    60                    Right-VentralDC    4794    4793.971
 35    62                       Right-vessel      76      76.346
 36    63               Right-choroid-plexus    1612    1611.935
 37    72                      5th-Ventricle       2       1.713
 38    77                 WM-hypointensities    1936    1935.870
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities       8       8.198
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     293     293.342
 45   251                       CC_Posterior    1191    1190.913
 46   252                   CC_Mid_Posterior     512     512.326
 47   253                         CC_Central     536     535.922
 48   254                    CC_Mid_Anterior     590     589.932
 49   255                        CC_Anterior    1039    1038.759

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Fri Jun 20 21:04:47 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 mri_aparc2aseg --s surface_3T --volmask 

SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
subject surface_3T
outvol /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial

Loading lh annotations from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial

Loading rh annotations from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

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 = 484991
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aparc+aseg.mgz
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 mri_aparc2aseg --s surface_3T --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
subject surface_3T
outvol /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial

Loading lh annotations from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)

Reading rh white surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial

Loading rh annotations from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.aparc.a2009s.annot
reading colortable from annotation file...
colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

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 = 484991
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Fri Jun 20 21:08:09 CEST 2014
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 mri_aparc2aseg --s surface_3T --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 

SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
subject surface_3T
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial

Loading lh annotations from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial

Loading rh annotations from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/ribbon.mgz
Loading filled from /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 8742 vertices from left hemi
Ripped 9017 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 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/aparc+aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

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 = 983892
Used brute-force search on 1387 voxels
Fixing Parahip LH WM
  Found 14 clusters
     0 k 1.000000
     1 k 1591.000000
     2 k 1.000000
     3 k 3.000000
     4 k 1.000000
     5 k 2.000000
     6 k 3.000000
     7 k 1.000000
     8 k 62.000000
     9 k 2.000000
     10 k 1.000000
     11 k 1.000000
     12 k 1.000000
     13 k 1.000000
Fixing Parahip RH WM
  Found 13 clusters
     0 k 1.000000
     1 k 3.000000
     2 k 1.000000
     3 k 1824.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 2.000000
     8 k 4.000000
     9 k 1.000000
     10 k 55.000000
     11 k 1.000000
     12 k 1.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T

 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 surface_3T --surf-wm-vol --ctab /opt/freesurfer/5.3/WMParcStatsLUT.txt --etiv 


$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 surface_3T --surf-wm-vol --ctab /opt/freesurfer/5.3/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname medusa
machine  x86_64
user     spark
UseRobust  0
atlas_icv (eTIV) = 1085507 mm^3    (det: 1.794650 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 242777.741 242849.000  diff=  -71.3  pctdiff=-0.029
rhCtxGM: 245333.130 245148.000  diff=  185.1  pctdiff= 0.075
lhCtxWM: 249301.032 248906.000  diff=  395.0  pctdiff= 0.158
rhCtxWM: 250322.862 251168.000  diff= -845.1  pctdiff=-0.338
SubCortGMVol  64160.000
SupraTentVol  1064229.765 (1063422.000) diff=807.765 pctdiff=0.076
SupraTentVolNotVent  1053174.765 (1052367.000) diff=807.765 pctdiff=0.077
BrainSegVol  1198232.000 (1196906.000) diff=1326.000 pctdiff=0.111
BrainSegVolNotVent  1184960.000 (1184318.765) diff=641.235 pctdiff=0.054
BrainSegVolNotVent  1184960.000
CerebellumVol 132288.000
VentChorVol   11055.000
3rd4th5thCSF   2217.000
CSFVol   901.000, OptChiasmVol   295.000
MaskVol 1566392.000
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
  0   3000                      wm-lh-unknown       0       0.000
  1   3001                     wm-lh-bankssts    3479    3479.084
  2   3002      wm-lh-caudalanteriorcingulate    3099    3098.694
  3   3003          wm-lh-caudalmiddlefrontal    7061    7061.189
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    3101    3101.239
  6   3006                   wm-lh-entorhinal     869     869.005
  7   3007                     wm-lh-fusiform    7381    7381.418
  8   3008             wm-lh-inferiorparietal    9508    9508.226
  9   3009             wm-lh-inferiortemporal    6948    6947.563
 10   3010             wm-lh-isthmuscingulate    4300    4299.927
 11   3011             wm-lh-lateraloccipital    9855    9855.441
 12   3012         wm-lh-lateralorbitofrontal    6632    6632.318
 13   3013                      wm-lh-lingual    6163    6162.532
 14   3014          wm-lh-medialorbitofrontal    3250    3250.120
 15   3015               wm-lh-middletemporal    5879    5879.457
 16   3016              wm-lh-parahippocampal    1626    1625.658
 17   3017                  wm-lh-paracentral    3742    3741.693
 18   3018              wm-lh-parsopercularis    3697    3697.381
 19   3019                wm-lh-parsorbitalis     971     971.308
 20   3020             wm-lh-parstriangularis    3505    3505.456
 21   3021                wm-lh-pericalcarine    3527    3526.815
 22   3022                  wm-lh-postcentral    7088    7087.515
 23   3023           wm-lh-posteriorcingulate    5000    5000.267
 24   3024                   wm-lh-precentral   13247   13247.066
 25   3025                    wm-lh-precuneus    9914    9913.850
 26   3026     wm-lh-rostralanteriorcingulate    2556    2556.438
 27   3027         wm-lh-rostralmiddlefrontal   13097   13097.314
 28   3028              wm-lh-superiorfrontal   20047   20047.096
 29   3029             wm-lh-superiorparietal   13381   13380.821
 30   3030             wm-lh-superiortemporal    8890    8890.255
 31   3031                wm-lh-supramarginal   10364   10363.562
 32   3032                  wm-lh-frontalpole     154     154.182
 33   3033                 wm-lh-temporalpole     606     605.545
 34   3034           wm-lh-transversetemporal     947     946.927
 35   3035                       wm-lh-insula    8510    8510.410
 36   3100                      wm-lh-Unknown       0       0.000
 37   3101              wm-lh-Corpus_callosum       0       0.000
 38   3102  wm-lh-G_and_S_Insula_ONLY_AVERAGE       0       0.000
 39   3103          wm-lh-G_cingulate-Isthmus       0       0.000
 40   3104        wm-lh-G_cingulate-Main_part       0       0.000
 41   3105                     wm-lh-G_cuneus       0       0.000
 42   3106  wm-lh-G_frontal_inf-Opercular_part       0       0.000
 43   3107   wm-lh-G_frontal_inf-Orbital_part       0       0.000
 44   3108  wm-lh-G_frontal_inf-Triangular_part       0       0.000
 45   3109             wm-lh-G_frontal_middle       0       0.000
 46   3110           wm-lh-G_frontal_superior       0       0.000
 47   3111             wm-lh-G_frontomarginal       0       0.000
 48   3112               wm-lh-G_insular_long       0       0.000
 49   3113              wm-lh-G_insular_short       0       0.000
 50   3114   wm-lh-G_and_S_occipital_inferior       0       0.000
 51   3115           wm-lh-G_occipital_middle       0       0.000
 52   3116         wm-lh-G_occipital_superior       0       0.000
 53   3117  wm-lh-G_occipit-temp_lat-Or_fusiform       0       0.000
 54   3118  wm-lh-G_occipit-temp_med-Lingual_part       0       0.000
 55   3119  wm-lh-G_occipit-temp_med-Parahippocampal_part       0       0.000
 56   3120                    wm-lh-G_orbital       0       0.000
 57   3121                wm-lh-G_paracentral       0       0.000
 58   3122  wm-lh-G_parietal_inferior-Angular_part       0       0.000
 59   3123  wm-lh-G_parietal_inferior-Supramarginal_part       0       0.000
 60   3124          wm-lh-G_parietal_superior       0       0.000
 61   3125                wm-lh-G_postcentral       0       0.000
 62   3126                 wm-lh-G_precentral       0       0.000
 63   3127                  wm-lh-G_precuneus       0       0.000
 64   3128                     wm-lh-G_rectus       0       0.000
 65   3129                wm-lh-G_subcallosal       0       0.000
 66   3130                 wm-lh-G_subcentral       0       0.000
 67   3131          wm-lh-G_temporal_inferior       0       0.000
 68   3132            wm-lh-G_temporal_middle       0       0.000
 69   3133  wm-lh-G_temp_sup-G_temp_transv_and_interm_S       0       0.000
 70   3134    wm-lh-G_temp_sup-Lateral_aspect       0       0.000
 71   3135     wm-lh-G_temp_sup-Planum_polare       0       0.000
 72   3136  wm-lh-G_temp_sup-Planum_tempolare       0       0.000
 73   3137  wm-lh-G_and_S_transverse_frontopolar       0       0.000
 74   3138  wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal       0       0.000
 75   3139  wm-lh-Lat_Fissure-ant_sgt-ramus_vertical       0       0.000
 76   3140         wm-lh-Lat_Fissure-post_sgt       0       0.000
 77   3141                  wm-lh-Medial_wall       0       0.000
 78   3142               wm-lh-Pole_occipital       0       0.000
 79   3143                wm-lh-Pole_temporal       0       0.000
 80   3144                  wm-lh-S_calcarine       0       0.000
 81   3145                    wm-lh-S_central       0       0.000
 82   3146             wm-lh-S_central_insula       0       0.000
 83   3147  wm-lh-S_cingulate-Main_part_and_Intracingulate       0       0.000
 84   3148  wm-lh-S_cingulate-Marginalis_part       0       0.000
 85   3149   wm-lh-S_circular_insula_anterior       0       0.000
 86   3150   wm-lh-S_circular_insula_inferior       0       0.000
 87   3151   wm-lh-S_circular_insula_superior       0       0.000
 88   3152  wm-lh-S_collateral_transverse_ant       0       0.000
 89   3153  wm-lh-S_collateral_transverse_post       0       0.000
 90   3154           wm-lh-S_frontal_inferior       0       0.000
 91   3155             wm-lh-S_frontal_middle       0       0.000
 92   3156           wm-lh-S_frontal_superior       0       0.000
 93   3157             wm-lh-S_frontomarginal       0       0.000
 94   3158  wm-lh-S_intermedius_primus-Jensen       0       0.000
 95   3159  wm-lh-S_intraparietal-and_Parietal_transverse       0       0.000
 96   3160         wm-lh-S_occipital_anterior       0       0.000
 97   3161  wm-lh-S_occipital_middle_and_Lunatus       0       0.000
 98   3162  wm-lh-S_occipital_superior_and_transversalis       0       0.000
 99   3163  wm-lh-S_occipito-temporal_lateral       0       0.000
100   3164  wm-lh-S_occipito-temporal_medial_and_S_Lingual       0       0.000
101   3165          wm-lh-S_orbital-H_shapped       0       0.000
102   3166            wm-lh-S_orbital_lateral       0       0.000
103   3167  wm-lh-S_orbital_medial-Or_olfactory       0       0.000
104   3168                wm-lh-S_paracentral       0       0.000
105   3169          wm-lh-S_parieto_occipital       0       0.000
106   3170               wm-lh-S_pericallosal       0       0.000
107   3171                wm-lh-S_postcentral       0       0.000
108   3172   wm-lh-S_precentral-Inferior-part       0       0.000
109   3173   wm-lh-S_precentral-Superior-part       0       0.000
110   3174             wm-lh-S_subcentral_ant       0       0.000
111   3175            wm-lh-S_subcentral_post       0       0.000
112   3176                 wm-lh-S_suborbital       0       0.000
113   3177                wm-lh-S_subparietal       0       0.000
114   3178             wm-lh-S_supracingulate       0       0.000
115   3179          wm-lh-S_temporal_inferior       0       0.000
116   3180          wm-lh-S_temporal_superior       0       0.000
117   3181        wm-lh-S_temporal_transverse       0       0.000
118   4000                      wm-rh-unknown       0       0.000
119   4001                     wm-rh-bankssts    3628    3627.951
120   4002      wm-rh-caudalanteriorcingulate    3317    3317.321
121   4003          wm-rh-caudalmiddlefrontal    5536    5535.634
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2181    2181.081
124   4006                   wm-rh-entorhinal     629     629.352
125   4007                     wm-rh-fusiform    6259    6259.126
126   4008             wm-rh-inferiorparietal   12315   12315.320
127   4009             wm-rh-inferiortemporal    5923    5923.266
128   4010             wm-rh-isthmuscingulate    4184    4183.918
129   4011             wm-rh-lateraloccipital   11692   11691.983
130   4012         wm-rh-lateralorbitofrontal    6688    6688.436
131   4013                      wm-rh-lingual    6691    6691.479
132   4014          wm-rh-medialorbitofrontal    3781    3780.510
133   4015               wm-rh-middletemporal    6769    6769.413
134   4016              wm-rh-parahippocampal    1841    1840.813
135   4017                  wm-rh-paracentral    4534    4534.311
136   4018              wm-rh-parsopercularis    3801    3801.266
137   4019                wm-rh-parsorbitalis    1260    1260.301
138   4020             wm-rh-parstriangularis    3393    3392.845
139   4021                wm-rh-pericalcarine    3445    3445.135
140   4022                  wm-rh-postcentral    9418    9417.538
141   4023           wm-rh-posteriorcingulate    4449    4448.532
142   4024                   wm-rh-precentral   14028   14027.633
143   4025                    wm-rh-precuneus   11354   11354.092
144   4026     wm-rh-rostralanteriorcingulate    1953    1953.033
145   4027         wm-rh-rostralmiddlefrontal   14428   14427.503
146   4028              wm-rh-superiorfrontal   18893   18893.096
147   4029             wm-rh-superiorparietal   11250   11250.444
148   4030             wm-rh-superiortemporal    7626    7625.889
149   4031                wm-rh-supramarginal    8312    8311.766
150   4032                  wm-rh-frontalpole     230     229.547
151   4033                 wm-rh-temporalpole     677     676.701
152   4034           wm-rh-transversetemporal     770     770.007
153   4035                       wm-rh-insula    8671    8671.061
154   4100                      wm-rh-Unknown       0       0.000
155   4101              wm-rh-Corpus_callosum       0       0.000
156   4102  wm-rh-G_and_S_Insula_ONLY_AVERAGE       0       0.000
157   4103          wm-rh-G_cingulate-Isthmus       0       0.000
158   4104        wm-rh-G_cingulate-Main_part       0       0.000
159   4105                     wm-rh-G_cuneus       0       0.000
160   4106  wm-rh-G_frontal_inf-Opercular_part       0       0.000
161   4107   wm-rh-G_frontal_inf-Orbital_part       0       0.000
162   4108  wm-rh-G_frontal_inf-Triangular_part       0       0.000
163   4109             wm-rh-G_frontal_middle       0       0.000
164   4110           wm-rh-G_frontal_superior       0       0.000
165   4111             wm-rh-G_frontomarginal       0       0.000
166   4112               wm-rh-G_insular_long       0       0.000
167   4113              wm-rh-G_insular_short       0       0.000
168   4114   wm-rh-G_and_S_occipital_inferior       0       0.000
169   4115           wm-rh-G_occipital_middle       0       0.000
170   4116         wm-rh-G_occipital_superior       0       0.000
171   4117  wm-rh-G_occipit-temp_lat-Or_fusiform       0       0.000
172   4118  wm-rh-G_occipit-temp_med-Lingual_part       0       0.000
173   4119  wm-rh-G_occipit-temp_med-Parahippocampal_part       0       0.000
174   4120                    wm-rh-G_orbital       0       0.000
175   4121                wm-rh-G_paracentral       0       0.000
176   4122  wm-rh-G_parietal_inferior-Angular_part       0       0.000
177   4123  wm-rh-G_parietal_inferior-Supramarginal_part       0       0.000
178   4124          wm-rh-G_parietal_superior       0       0.000
179   4125                wm-rh-G_postcentral       0       0.000
180   4126                 wm-rh-G_precentral       0       0.000
181   4127                  wm-rh-G_precuneus       0       0.000
182   4128                     wm-rh-G_rectus       0       0.000
183   4129                wm-rh-G_subcallosal       0       0.000
184   4130                 wm-rh-G_subcentral       0       0.000
185   4131          wm-rh-G_temporal_inferior       0       0.000
186   4132            wm-rh-G_temporal_middle       0       0.000
187   4133  wm-rh-G_temp_sup-G_temp_transv_and_interm_S       0       0.000
188   4134    wm-rh-G_temp_sup-Lateral_aspect       0       0.000
189   4135     wm-rh-G_temp_sup-Planum_polare       0       0.000
190   4136  wm-rh-G_temp_sup-Planum_tempolare       0       0.000
191   4137  wm-rh-G_and_S_transverse_frontopolar       0       0.000
192   4138  wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal       0       0.000
193   4139  wm-rh-Lat_Fissure-ant_sgt-ramus_vertical       0       0.000
194   4140         wm-rh-Lat_Fissure-post_sgt       0       0.000
195   4141                  wm-rh-Medial_wall       0       0.000
196   4142               wm-rh-Pole_occipital       0       0.000
197   4143                wm-rh-Pole_temporal       0       0.000
198   4144                  wm-rh-S_calcarine       0       0.000
199   4145                    wm-rh-S_central       0       0.000
200   4146             wm-rh-S_central_insula       0       0.000
201   4147  wm-rh-S_cingulate-Main_part_and_Intracingulate       0       0.000
202   4148  wm-rh-S_cingulate-Marginalis_part       0       0.000
203   4149   wm-rh-S_circular_insula_anterior       0       0.000
204   4150   wm-rh-S_circular_insula_inferior       0       0.000
205   4151   wm-rh-S_circular_insula_superior       0       0.000
206   4152  wm-rh-S_collateral_transverse_ant       0       0.000
207   4153  wm-rh-S_collateral_transverse_post       0       0.000
208   4154           wm-rh-S_frontal_inferior       0       0.000
209   4155             wm-rh-S_frontal_middle       0       0.000
210   4156           wm-rh-S_frontal_superior       0       0.000
211   4157             wm-rh-S_frontomarginal       0       0.000
212   4158  wm-rh-S_intermedius_primus-Jensen       0       0.000
213   4159  wm-rh-S_intraparietal-and_Parietal_transverse       0       0.000
214   4160         wm-rh-S_occipital_anterior       0       0.000
215   4161  wm-rh-S_occipital_middle_and_Lunatus       0       0.000
216   4162  wm-rh-S_occipital_superior_and_transversalis       0       0.000
217   4163  wm-rh-S_occipito-temporal_lateral       0       0.000
218   4164  wm-rh-S_occipito-temporal_medial_and_S_Lingual       0       0.000
219   4165          wm-rh-S_orbital-H_shapped       0       0.000
220   4166            wm-rh-S_orbital_lateral       0       0.000
221   4167  wm-rh-S_orbital_medial-Or_olfactory       0       0.000
222   4168                wm-rh-S_paracentral       0       0.000
223   4169          wm-rh-S_parieto_occipital       0       0.000
224   4170               wm-rh-S_pericallosal       0       0.000
225   4171                wm-rh-S_postcentral       0       0.000
226   4172   wm-rh-S_precentral-Inferior-part       0       0.000
227   4173   wm-rh-S_precentral-Superior-part       0       0.000
228   4174             wm-rh-S_subcentral_ant       0       0.000
229   4175            wm-rh-S_subcentral_post       0       0.000
230   4176                 wm-rh-S_suborbital       0       0.000
231   4177                wm-rh-S_subparietal       0       0.000
232   4178             wm-rh-S_supracingulate       0       0.000
233   4179          wm-rh-S_temporal_inferior       0       0.000
234   4180          wm-rh-S_temporal_superior       0       0.000
235   4181        wm-rh-S_temporal_transverse       0       0.000
236   5001        Left-UnsegmentedWhiteMatter   37400   37400.066
237   5002       Right-UnsegmentedWhiteMatter   38929   38929.238
238   13100                      wm_lh_Unknown       0       0.000
239   13101         wm_lh_G_and_S_frontomargin       0       0.000
240   13102        wm_lh_G_and_S_occipital_inf       0       0.000
241   13103          wm_lh_G_and_S_paracentral       0       0.000
242   13104           wm_lh_G_and_S_subcentral       0       0.000
243   13105     wm_lh_G_and_S_transv_frontopol       0       0.000
244   13106           wm_lh_G_and_S_cingul-Ant       0       0.000
245   13107       wm_lh_G_and_S_cingul-Mid-Ant       0       0.000
246   13108      wm_lh_G_and_S_cingul-Mid-Post       0       0.000
247   13109         wm_lh_G_cingul-Post-dorsal       0       0.000
248   13110        wm_lh_G_cingul-Post-ventral       0       0.000
249   13111                     wm_lh_G_cuneus       0       0.000
250   13112        wm_lh_G_front_inf-Opercular       0       0.000
251   13113          wm_lh_G_front_inf-Orbital       0       0.000
252   13114         wm_lh_G_front_inf-Triangul       0       0.000
253   13115               wm_lh_G_front_middle       0       0.000
254   13116                  wm_lh_G_front_sup       0       0.000
255   13117      wm_lh_G_Ins_lg_and_S_cent_ins       0       0.000
256   13118              wm_lh_G_insular_short       0       0.000
257   13119           wm_lh_G_occipital_middle       0       0.000
258   13120              wm_lh_G_occipital_sup       0       0.000
259   13121        wm_lh_G_oc-temp_lat-fusifor       0       0.000
260   13122        wm_lh_G_oc-temp_med-Lingual       0       0.000
261   13123        wm_lh_G_oc-temp_med-Parahip       0       0.000
262   13124                    wm_lh_G_orbital       0       0.000
263   13125         wm_lh_G_pariet_inf-Angular       0       0.000
264   13126        wm_lh_G_pariet_inf-Supramar       0       0.000
265   13127               wm_lh_G_parietal_sup       0       0.000
266   13128                wm_lh_G_postcentral       0       0.000
267   13129                 wm_lh_G_precentral       0       0.000
268   13130                  wm_lh_G_precuneus       0       0.000
269   13131                     wm_lh_G_rectus       0       0.000
270   13132                wm_lh_G_subcallosal       0       0.000
271   13133        wm_lh_G_temp_sup-G_T_transv       0       0.000
272   13134           wm_lh_G_temp_sup-Lateral       0       0.000
273   13135        wm_lh_G_temp_sup-Plan_polar       0       0.000
274   13136        wm_lh_G_temp_sup-Plan_tempo       0       0.000
275   13137               wm_lh_G_temporal_inf       0       0.000
276   13138            wm_lh_G_temporal_middle       0       0.000
277   13139         wm_lh_Lat_Fis-ant-Horizont       0       0.000
278   13140         wm_lh_Lat_Fis-ant-Vertical       0       0.000
279   13141                 wm_lh_Lat_Fis-post       0       0.000
280   13142                  wm_lh_Medial_wall       0       0.000
281   13143               wm_lh_Pole_occipital       0       0.000
282   13144                wm_lh_Pole_temporal       0       0.000
283   13145                  wm_lh_S_calcarine       0       0.000
284   13146                    wm_lh_S_central       0       0.000
285   13147          wm_lh_S_cingul-Marginalis       0       0.000
286   13148        wm_lh_S_circular_insula_ant       0       0.000
287   13149        wm_lh_S_circular_insula_inf       0       0.000
288   13150        wm_lh_S_circular_insula_sup       0       0.000
289   13151          wm_lh_S_collat_transv_ant       0       0.000
290   13152         wm_lh_S_collat_transv_post       0       0.000
291   13153                  wm_lh_S_front_inf       0       0.000
292   13154               wm_lh_S_front_middle       0       0.000
293   13155                  wm_lh_S_front_sup       0       0.000
294   13156         wm_lh_S_interm_prim-Jensen       0       0.000
295   13157    wm_lh_S_intrapariet_and_P_trans       0       0.000
296   13158      wm_lh_S_oc_middle_and_Lunatus       0       0.000
297   13159     wm_lh_S_oc_sup_and_transversal       0       0.000
298   13160              wm_lh_S_occipital_ant       0       0.000
299   13161                wm_lh_S_oc-temp_lat       0       0.000
300   13162    wm_lh_S_oc-temp_med_and_Lingual       0       0.000
301   13163            wm_lh_S_orbital_lateral       0       0.000
302   13164         wm_lh_S_orbital_med-olfact       0       0.000
303   13165           wm_lh_S_orbital-H_Shaped       0       0.000
304   13166          wm_lh_S_parieto_occipital       0       0.000
305   13167               wm_lh_S_pericallosal       0       0.000
306   13168                wm_lh_S_postcentral       0       0.000
307   13169        wm_lh_S_precentral-inf-part       0       0.000
308   13170        wm_lh_S_precentral-sup-part       0       0.000
309   13171                 wm_lh_S_suborbital       0       0.000
310   13172                wm_lh_S_subparietal       0       0.000
311   13173               wm_lh_S_temporal_inf       0       0.000
312   13174               wm_lh_S_temporal_sup       0       0.000
313   13175        wm_lh_S_temporal_transverse       0       0.000
314   14100                      wm_rh_Unknown       0       0.000
315   14101         wm_rh_G_and_S_frontomargin       0       0.000
316   14102        wm_rh_G_and_S_occipital_inf       0       0.000
317   14103          wm_rh_G_and_S_paracentral       0       0.000
318   14104           wm_rh_G_and_S_subcentral       0       0.000
319   14105     wm_rh_G_and_S_transv_frontopol       0       0.000
320   14106           wm_rh_G_and_S_cingul-Ant       0       0.000
321   14107       wm_rh_G_and_S_cingul-Mid-Ant       0       0.000
322   14108      wm_rh_G_and_S_cingul-Mid-Post       0       0.000
323   14109         wm_rh_G_cingul-Post-dorsal       0       0.000
324   14110        wm_rh_G_cingul-Post-ventral       0       0.000
325   14111                     wm_rh_G_cuneus       0       0.000
326   14112        wm_rh_G_front_inf-Opercular       0       0.000
327   14113          wm_rh_G_front_inf-Orbital       0       0.000
328   14114         wm_rh_G_front_inf-Triangul       0       0.000
329   14115               wm_rh_G_front_middle       0       0.000
330   14116                  wm_rh_G_front_sup       0       0.000
331   14117      wm_rh_G_Ins_lg_and_S_cent_ins       0       0.000
332   14118              wm_rh_G_insular_short       0       0.000
333   14119           wm_rh_G_occipital_middle       0       0.000
334   14120              wm_rh_G_occipital_sup       0       0.000
335   14121        wm_rh_G_oc-temp_lat-fusifor       0       0.000
336   14122        wm_rh_G_oc-temp_med-Lingual       0       0.000
337   14123        wm_rh_G_oc-temp_med-Parahip       0       0.000
338   14124                    wm_rh_G_orbital       0       0.000
339   14125         wm_rh_G_pariet_inf-Angular       0       0.000
340   14126        wm_rh_G_pariet_inf-Supramar       0       0.000
341   14127               wm_rh_G_parietal_sup       0       0.000
342   14128                wm_rh_G_postcentral       0       0.000
343   14129                 wm_rh_G_precentral       0       0.000
344   14130                  wm_rh_G_precuneus       0       0.000
345   14131                     wm_rh_G_rectus       0       0.000
346   14132                wm_rh_G_subcallosal       0       0.000
347   14133        wm_rh_G_temp_sup-G_T_transv       0       0.000
348   14134           wm_rh_G_temp_sup-Lateral       0       0.000
349   14135        wm_rh_G_temp_sup-Plan_polar       0       0.000
350   14136        wm_rh_G_temp_sup-Plan_tempo       0       0.000
351   14137               wm_rh_G_temporal_inf       0       0.000
352   14138            wm_rh_G_temporal_middle       0       0.000
353   14139         wm_rh_Lat_Fis-ant-Horizont       0       0.000
354   14140         wm_rh_Lat_Fis-ant-Vertical       0       0.000
355   14141                 wm_rh_Lat_Fis-post       0       0.000
356   14142                  wm_rh_Medial_wall       0       0.000
357   14143               wm_rh_Pole_occipital       0       0.000
358   14144                wm_rh_Pole_temporal       0       0.000
359   14145                  wm_rh_S_calcarine       0       0.000
360   14146                    wm_rh_S_central       0       0.000
361   14147          wm_rh_S_cingul-Marginalis       0       0.000
362   14148        wm_rh_S_circular_insula_ant       0       0.000
363   14149        wm_rh_S_circular_insula_inf       0       0.000
364   14150        wm_rh_S_circular_insula_sup       0       0.000
365   14151          wm_rh_S_collat_transv_ant       0       0.000
366   14152         wm_rh_S_collat_transv_post       0       0.000
367   14153                  wm_rh_S_front_inf       0       0.000
368   14154               wm_rh_S_front_middle       0       0.000
369   14155                  wm_rh_S_front_sup       0       0.000
370   14156         wm_rh_S_interm_prim-Jensen       0       0.000
371   14157    wm_rh_S_intrapariet_and_P_trans       0       0.000
372   14158      wm_rh_S_oc_middle_and_Lunatus       0       0.000
373   14159     wm_rh_S_oc_sup_and_transversal       0       0.000
374   14160              wm_rh_S_occipital_ant       0       0.000
375   14161                wm_rh_S_oc-temp_lat       0       0.000
376   14162    wm_rh_S_oc-temp_med_and_Lingual       0       0.000
377   14163            wm_rh_S_orbital_lateral       0       0.000
378   14164         wm_rh_S_orbital_med-olfact       0       0.000
379   14165           wm_rh_S_orbital-H_Shaped       0       0.000
380   14166          wm_rh_S_parieto_occipital       0       0.000
381   14167               wm_rh_S_pericallosal       0       0.000
382   14168                wm_rh_S_postcentral       0       0.000
383   14169        wm_rh_S_precentral-inf-part       0       0.000
384   14170        wm_rh_S_precentral-sup-part       0       0.000
385   14171                 wm_rh_S_suborbital       0       0.000
386   14172                wm_rh_S_subparietal       0       0.000
387   14173               wm_rh_S_temporal_inf       0       0.000
388   14174               wm_rh_S_temporal_sup       0       0.000
389   14175        wm_rh_S_temporal_transverse       0       0.000

Reporting on  70 segmentations
mri_segstats done
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label
#--------------------------------------------
#@# BA Labels lh Fri Jun 20 21:20:47 CEST 2014
INFO: fsaverage subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to fsaverage subject...

 cd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy; ln -s /opt/freesurfer/5.3/subjects/fsaverage; cd - 


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA1.label --trgsubject surface_3T --trglabel ./lh.BA1.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 280
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4409
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA2.label --trgsubject surface_3T --trglabel ./lh.BA2.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA2.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 643
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8552
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3a.label --trgsubject surface_3T --trglabel ./lh.BA3a.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3a.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA3a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 148
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4225
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3b.label --trgsubject surface_3T --trglabel ./lh.BA3b.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3b.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA3b.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 466
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6449
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4a.label --trgsubject surface_3T --trglabel ./lh.BA4a.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4a.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA4a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 533
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6317
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4p.label --trgsubject surface_3T --trglabel ./lh.BA4p.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4p.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA4p.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 284
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4354
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA6.label --trgsubject surface_3T --trglabel ./lh.BA6.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA6.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA6.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 1507
Checking for and removing duplicates
Writing label file ./lh.BA6.label 15096
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA44.label --trgsubject surface_3T --trglabel ./lh.BA44.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA44.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA44.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 372
Checking for and removing duplicates
Writing label file ./lh.BA44.label 4553
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA45.label --trgsubject surface_3T --trglabel ./lh.BA45.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA45.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA45.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 1331
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4753
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V1.label --trgsubject surface_3T --trglabel ./lh.V1.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V1.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.V1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 2012
Checking for and removing duplicates
Writing label file ./lh.V1.label 6653
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V2.label --trgsubject surface_3T --trglabel ./lh.V2.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V2.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.V2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 3789
Checking for and removing duplicates
Writing label file ./lh.V2.label 11903
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.MT.label --trgsubject surface_3T --trglabel ./lh.MT.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.MT.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.MT.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 525
Checking for and removing duplicates
Writing label file ./lh.MT.label 2543
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.perirhinal.label --trgsubject surface_3T --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.perirhinal.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.perirhinal.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 128
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1327
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA1.thresh.label --trgsubject surface_3T --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 71
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1085
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA2.thresh.label --trgsubject surface_3T --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 134
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2226
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3a.thresh.label --trgsubject surface_3T --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA3a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 32
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1536
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3b.thresh.label --trgsubject surface_3T --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA3b.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 188
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2184
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4a.thresh.label --trgsubject surface_3T --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA4a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 308
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2627
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4p.thresh.label --trgsubject surface_3T --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA4p.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 64
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1613
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA6.thresh.label --trgsubject surface_3T --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA6.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 651
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 7686
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA44.thresh.label --trgsubject surface_3T --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA44.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 125
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2037
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA45.thresh.label --trgsubject surface_3T --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.BA45.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 635
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1786
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V1.thresh.label --trgsubject surface_3T --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V1.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.V1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 1447
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 4852
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V2.thresh.label --trgsubject surface_3T --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.V2.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.V2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 1708
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 5042
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.MT.thresh.label --trgsubject surface_3T --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/lh.MT.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./lh.MT.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 144053
Number of reverse mapping hits = 102
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 615
mri_label2label: Done


 mris_label2annot --s surface_3T --hemi lh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label
cmdline mris_label2annot --s surface_3T --hemi lh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose 
sysname  Linux
hostname medusa
machine  x86_64
user     spark

subject surface_3T
hemi    lh
SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
ColorTable /opt/freesurfer/5.3/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
13 16422433 perirhinal
Mapping unhit to unknown
Found 99228 unhit vertices
Writing annot to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.BA.annot

 mris_label2annot --s surface_3T --hemi lh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label
cmdline mris_label2annot --s surface_3T --hemi lh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname medusa
machine  x86_64
user     spark

subject surface_3T
hemi    lh
SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
ColorTable /opt/freesurfer/5.3/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
Mapping unhit to unknown
Found 118153 unhit vertices
Writing annot to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab surface_3T lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

 1074    615   1822  2.225 0.400     0.142     0.048       17     2.1  BA1
 4128   2692   6445  2.265 0.422     0.126     0.034       47     5.5  BA2
  970    674    974  1.865 0.406     0.140     0.039        9     1.7  BA3a
 2672   1738   3586  1.867 0.598     0.122     0.038       33     4.2  BA3b
 1879   1004   3669  3.009 0.623     0.106     0.046       28     4.1  BA4a
 1255    859   2175  2.661 0.545     0.097     0.030        6     1.5  BA4p
 9918   6553  21284  2.759 0.520     0.126     0.037      111    15.3  BA6
 2120   1407   3868  2.521 0.460     0.124     0.035       26     3.0  BA44
 4008   2693   7483  2.428 0.470     0.132     0.036       50     6.0  BA45
 4238   2854   5279  1.744 0.478     0.153     0.068       77    10.3  V1
 9391   6382  13556  2.030 0.563     0.179     0.083      247    28.8  V2
 2191   1467   3836  2.434 0.541     0.146     0.048       41     4.5  MT
  981    703   2551  3.030 0.943     0.131     0.044       11     1.6  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab surface_3T lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

  725    385   1204  2.257 0.435     0.147     0.056       13     1.7  BA1
 1532    986   2514  2.280 0.350     0.114     0.030       15     1.8  BA2
  836    569    764  1.816 0.363     0.148     0.043        8     1.6  BA3a
 1619   1075   1753  1.544 0.330     0.108     0.030       14     2.1  BA3b
 1833    996   3639  3.043 0.591     0.099     0.041       23     3.6  BA4a
  981    698   1616  2.526 0.485     0.102     0.032        5     1.3  BA4p
 5578   3578  11803  2.773 0.545     0.124     0.037       62     8.7  BA6
 1332    894   2491  2.479 0.460     0.135     0.041       21     2.2  BA44
 1725   1116   3735  2.624 0.362     0.147     0.044       29     3.2  BA45
 4519   3046   5767  1.769 0.478     0.154     0.069       82    11.2  V1
 4677   3206   6129  1.932 0.571     0.188     0.095      120    14.8  V2
  543    369    914  2.486 0.510     0.131     0.034        7     0.7  MT
#--------------------------------------------
#@# BA Labels rh Fri Jun 20 21:24:59 CEST 2014

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA1.label --trgsubject surface_3T --trglabel ./rh.BA1.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA1.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 584
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4546
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA2.label --trgsubject surface_3T --trglabel ./rh.BA2.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA2.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 1003
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7690
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3a.label --trgsubject surface_3T --trglabel ./rh.BA3a.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3a.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA3a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 229
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4209
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3b.label --trgsubject surface_3T --trglabel ./rh.BA3b.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3b.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA3b.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 404
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 4926
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4a.label --trgsubject surface_3T --trglabel ./rh.BA4a.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4a.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA4a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 398
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6145
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4p.label --trgsubject surface_3T --trglabel ./rh.BA4p.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4p.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA4p.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 257
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4730
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA6.label --trgsubject surface_3T --trglabel ./rh.BA6.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA6.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA6.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 1139
Checking for and removing duplicates
Writing label file ./rh.BA6.label 13395
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA44.label --trgsubject surface_3T --trglabel ./rh.BA44.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA44.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA44.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 954
Checking for and removing duplicates
Writing label file ./rh.BA44.label 7866
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA45.label --trgsubject surface_3T --trglabel ./rh.BA45.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA45.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA45.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 1077
Checking for and removing duplicates
Writing label file ./rh.BA45.label 6432
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V1.label --trgsubject surface_3T --trglabel ./rh.V1.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V1.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.V1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 2118
Checking for and removing duplicates
Writing label file ./rh.V1.label 6845
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V2.label --trgsubject surface_3T --trglabel ./rh.V2.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V2.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.V2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 3947
Checking for and removing duplicates
Writing label file ./rh.V2.label 11963
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.MT.label --trgsubject surface_3T --trglabel ./rh.MT.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.MT.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.MT.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 732
Checking for and removing duplicates
Writing label file ./rh.MT.label 2664
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.perirhinal.label --trgsubject surface_3T --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.perirhinal.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.perirhinal.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 81
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 833
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA1.thresh.label --trgsubject surface_3T --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 202
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 1078
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA2.thresh.label --trgsubject surface_3T --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 475
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 3163
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3a.thresh.label --trgsubject surface_3T --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA3a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 39
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1737
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3b.thresh.label --trgsubject surface_3T --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA3b.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 207
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2390
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4a.thresh.label --trgsubject surface_3T --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA4a.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 84
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1472
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4p.thresh.label --trgsubject surface_3T --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA4p.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 141
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1630
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA6.thresh.label --trgsubject surface_3T --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA6.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 603
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 7562
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA44.thresh.label --trgsubject surface_3T --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA44.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 87
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1099
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA45.thresh.label --trgsubject surface_3T --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.BA45.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 131
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1309
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V1.thresh.label --trgsubject surface_3T --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V1.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.V1.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 1404
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 4636
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V2.thresh.label --trgsubject surface_3T --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.V2.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.V2.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 1773
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 5210
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.MT.thresh.label --trgsubject surface_3T --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/label/rh.MT.thresh.label
srcsubject = fsaverage
trgsubject = surface_3T
trglabel = ./rh.MT.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    /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
FREESURFER_HOME /opt/freesurfer/5.3
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white
Reading target registration 
 /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/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 145997
Number of reverse mapping hits = 106
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 374
mri_label2label: Done


 mris_label2annot --s surface_3T --hemi rh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label
cmdline mris_label2annot --s surface_3T --hemi rh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose 
sysname  Linux
hostname medusa
machine  x86_64
user     spark

subject surface_3T
hemi    rh
SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
ColorTable /opt/freesurfer/5.3/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
13 16422433 perirhinal
Mapping unhit to unknown
Found 100347 unhit vertices
Writing annot to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.BA.annot

 mris_label2annot --s surface_3T --hemi rh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 

Reading ctab /opt/freesurfer/5.3/average/colortable_BA.txt
Number of ctab entries 14

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label
cmdline mris_label2annot --s surface_3T --hemi rh --ctab /opt/freesurfer/5.3/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 
sysname  Linux
hostname medusa
machine  x86_64
user     spark

subject surface_3T
hemi    rh
SUBJECTS_DIR /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy
ColorTable /opt/freesurfer/5.3/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.orig
 1 1530880 BA1
 2 16749699 BA2
 3 16711680 BA3a
 4 3368703 BA3b
 5 1376196 BA4a
 6 13382655 BA4p
 7 10036737 BA6
 8 2490521 BA44
 9 39283 BA45
10 3993 V1
11 8508928 V2
12 10027163 MT
Mapping unhit to unknown
Found 120961 unhit vertices
Writing annot to /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab surface_3T rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

 1192    737   2186  2.287 0.471     0.142     0.086       24     2.3  BA1
 4285   2792   6061  2.085 0.423     0.113     0.032       43     5.3  BA2
 1027    674    959  1.881 0.358     0.135     0.040        8     1.8  BA3a
 2183   1459   2931  1.726 0.538     0.118     0.044       23     3.1  BA3b
 1488    891   3191  2.957 0.486     0.108     0.258      102     7.4  BA4a
 1292    833   2105  2.652 0.447     0.115     0.112       76     4.4  BA4p
 8478   5616  18104  2.772 0.493     0.121     0.035       88    12.1  BA6
 3983   2738   7380  2.496 0.393     0.131     0.036       49     6.0  BA44
 4417   2983   8624  2.451 0.459     0.142     0.043       67     8.0  BA45
 4535   3187   5672  1.803 0.508     0.174     0.084      133    13.7  V1
 9670   6486  13864  2.066 0.504     0.169     0.080      330    25.2  V2
 2465   1680   3821  2.334 0.350     0.142     0.046       36     4.7  MT
  635    436   1690  2.837 0.858     0.132     0.059        9     1.6  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab surface_3T rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3/average/colortable_BA.txt)
Saving annotation colortable ./BA.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

  862    509   1534  2.254 0.469     0.151     0.105       21     1.8  BA1
 2638   1728   4002  2.141 0.395     0.118     0.037       30     3.7  BA2
  880    569    766  1.873 0.373     0.133     0.040        7     1.5  BA3a
 1787   1236   2134  1.576 0.425     0.107     0.028       12     2.1  BA3b
  861    483   1811  3.080 0.478     0.116     0.118       29     6.7  BA4a
 1066    686   1731  2.696 0.490     0.112     0.073       22     4.1  BA4p
 5423   3543  11745  2.814 0.496     0.122     0.036       60     7.8  BA6
  815    575   1689  2.478 0.350     0.145     0.049       14     1.6  BA44
 1035    689   2314  2.640 0.346     0.159     0.053       19     2.0  BA45
 4327   3057   5349  1.801 0.498     0.169     0.072       73    12.5  V1
 4989   3362   7073  1.994 0.555     0.185     0.083      116    16.5  V2
  353    231    668  2.435 0.332     0.179     0.080       10     1.2  MT
/home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Fri Jun 20 21:29:12 CEST 2014
INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to lh.EC_average subject...

 cd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy; ln -s /opt/freesurfer/5.3/subjects/lh.EC_average; cd - 


 mris_spherical_average -erode 1 -orig white -t 0.4 -o surface_3T label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject surface_3T.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.sphere.reg...
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
only 1 subject - copying statistics...
writing label with 939 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label surface_3T lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/lh.white...
INFO: assuming MGZ format for volumes.

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

  373    226   1033  2.656 0.976     0.129     0.056        6     0.8  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Fri Jun 20 21:29:30 CEST 2014
INFO: rh.EC_average subject does not exist in SUBJECTS_DIR
INFO: Creating symlink to rh.EC_average subject...

 cd /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy; ln -s /opt/freesurfer/5.3/subjects/rh.EC_average; cd - 


 mris_spherical_average -erode 1 -orig white -t 0.4 -o surface_3T label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject surface_3T.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.sphere.reg...
eroding label 1 times before writing
thresholding label stat at 0.400 before writing
only 1 subject - copying statistics...
writing label with 877 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label surface_3T rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/mri/wm.mgz...
reading input surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
reading input pial surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.pial...
reading input white surface /home/data/exppsy/spark/Field_Strength_Comparison/data/sub001/anatomy/surface_3T/surf/rh.white...
INFO: assuming MGZ format for volumes.

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

  311    194    813  2.828 0.843     0.127     0.610       21     4.2  ./rh.entorhinal_exvivo.label

#------------------------------------------

Started at Fri Jun 20 09:58:54 CEST 2014 
Ended   at Fri Jun 20 21:29:49 CEST 2014
#@#%# recon-all-run-time-hours 11.515
recon-all -s surface_3T finished without error at Fri Jun 20 21:29:49 CEST 2014



New invocation of recon-all 



Sa 29. Nov 08:20:19 CET 2014
/home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021
/opt/freesurfer/5.3/bin/recon-all
-s sub021 -hippo-subfields
subjid sub021
setenv SUBJECTS_DIR /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer
FREESURFER_HOME /opt/freesurfer/5.3
Actual FREESURFER_HOME /opt/freesurfer/5.3
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u3 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    8000000 kbytes
vmemoryuse   18000000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      500 
maxlocks     unlimited
maxsignal    2067069 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:     264664496  248739956   15924540          0    1309724  208846396
-/+ buffers/cache:   38583836  226080660
Swap:    293227320      10104  293217216

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:19-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:20-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:21-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:22-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:23-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:24-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:24-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:25-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:25-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:25-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:25-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:25-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:26-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:26-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:26-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:27-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:27-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:27-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:28-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:28-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:20:28-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /opt/freesurfer/5.3/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /opt/freesurfer/5.3/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# Hippocampal Subfields processing Sa 29. Nov 08:20:28 CET 2014

 mkdir -p /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults

 kvlSegmentHippocampalSubfields.sh sub021 left /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults 




New invocation of recon-all 



Sa 29. Nov 08:57:45 CET 2014
/home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021
/opt/freesurfer/5.3/bin/recon-all
-s sub021 -hippo-subfields
subjid sub021
setenv SUBJECTS_DIR /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer
FREESURFER_HOME /opt/freesurfer/5.3
Actual FREESURFER_HOME /opt/freesurfer/5.3
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux medusa 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u3 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    8000000 kbytes
vmemoryuse   18000000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      500 
maxlocks     unlimited
maxsignal    2067069 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:     264664496  249343616   15320880          0    1309832  209180672
-/+ buffers/cache:   38853112  225811384
Swap:    293227320      10104  293217216

########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:45-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:46-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

ProgramName: mri_robust_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

ProgramName: mri_robust_template  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2014/11/29-07:57:48-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $  User: spark  Machine: medusa  Platform: Linux  PlatformVersion: 3.2.0-4-amd64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /opt/freesurfer/5.3/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /opt/freesurfer/5.3/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################

 kvlSegmentHippocampalSubfields.sh sub021 right /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults 


 cp /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults/sub021/left/segmentationWithoutPartialVolumingLog/posterior_left* /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/mri 


 cp /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults/sub021/left/segmentationWithoutPartialVolumingLog/posterior_Left* /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/mri 


 cp /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults/sub021/right/segmentationWithoutPartialVolumingLog/posterior_right* /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/mri 


 cp /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults/sub021/right/segmentationWithoutPartialVolumingLog/posterior_Right* /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/mri 


 rm -rf /home/data/exppsy/Field_Strength_Comparison/analysis/Freesurfer/sub021/tmp/subfieldResults 


#------------------------------------------

Started at Sa 29. Nov 08:20:19 CET 2014 
Ended   at Sa 29. Nov 10:52:24 CET 2014
#@#%# recon-all-run-time-hours 2,535
recon-all -s sub021 finished without error at Sa 29. Nov 10:52:24 CET 2014