cortical-surfaces-freesurfer/sub-06/scripts/recon-all.log

Thu Aug  8 10:53:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006
/opt/freesurfer/5.3.0/bin/recon-all
-i /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz -T2pial -subjid sub006 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subjid sub006
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Actual FREESURFER_HOME /opt/freesurfer/5.3.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    unlimited
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      unlimited
maxlocks     unlimited
maxsignal    16382 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:      99201692   96468108    2733584          0     177872   94401912
-/+ buffers/cache:    1888324   97313368
Swap:     25165780       3620   25162160

########################################
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: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-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: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-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: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:56-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 


 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:57-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:58-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-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: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-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: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:53:59-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: fkaule  Machine: snake5  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /opt/freesurfer/5.3.0/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/5.3.0/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
-cw256 option is now persistent (remove with -clean-cw256)
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/highres001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Thu Aug  8 10:54:17 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/sub006/anatomy/other/t2w001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Thu Aug  8 10:54:33 CEST 2013
Found 1 runs
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz --conform --cw256 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz --conform --cw256 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
Original Data has (0.699921, 0.666667, 0.666667) mm size and (274, 384, 384) 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/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Aug  8 10:55:14 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 10:58:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6592, pval=0.3663 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach_avi.log 

TalAviQA: 0.96493
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Aug  8 10:58:11 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
/opt/freesurfer/5.3.0/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
Thu Aug  8 10:58:11 CEST 2013
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.12861
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12861/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12861/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, -1.16415e-09, 1.86265e-09)
j_ras = (-1.86265e-09, 1.49012e-08, -1)
k_ras = (9.31323e-10, 1, -1.49012e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.12861/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Aug  8 10:58:14 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12861/0/
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:58:14] running:
  /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12861/0/ ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/nu1.imp

Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 25 
CV of field change: 0.000992595
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:58:53] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12861/nu0.mnc ./tmp.mri_nu_correct.mni.12861/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Thu Aug  8 10:59:01 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.12861/1/
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:59:01] running:
  /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12861/1/ ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
Number of iterations: 22 
CV of field change: 0.000982201
[fkaule@snake5:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/] [2013-08-08 10:59:39] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.12861/nu1.mnc ./tmp.mri_nu_correct.mni.12861/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12861/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.12861/ones.mgz 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule

input      ./tmp.mri_nu_correct.mni.12861/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/input.mean.dat 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.12861/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.12861/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.12861/ones.mgz --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/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.12861/ones.mgz --i ./tmp.mri_nu_correct.mni.12861/nu2.mnc --sum ./tmp.mri_nu_correct.mni.12861/sum.junk --avgwf ./tmp.mri_nu_correct.mni.12861/output.mean.dat 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.12861/ones.mgz
Loading ./tmp.mri_nu_correct.mni.12861/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.12861/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.12861/nu2.mnc ./tmp.mri_nu_correct.mni.12861/nu2.mnc mul .95246908919991135291
Saving result to './tmp.mri_nu_correct.mni.12861/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.12861/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.12861/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.12861/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.16415e-09, 1.86265e-09)
j_ras = (-1.86265e-09, 1.49012e-08, -1)
k_ras = (9.31323e-10, 1, -1.49012e-08)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 8 seconds.
mapping (12, 169) to ( 3, 110)
 
 
Thu Aug  8 11:00:31 CEST 2013
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Aug  8 11:00:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.130  -0.028   0.007   3.552;
 0.019   0.978   0.305  -29.156;
-0.010  -0.429   1.099  -5.547;
 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 = 19
Starting OpenSpline(): npoints = 19
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 108
gm peak at 48 (48), valley at 37 (37)
csf peak at 12, setting threshold to 36
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 49 (49), valley at 38 (38)
csf peak at 12, setting threshold to 36
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 52 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Aug  8 11:03:25 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/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/5.3.0/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=8.0
skull bounding box = (49, 0, 9) --> (203, 255, 206)
using (100, 85, 108) as brain centroid...
mean wm in atlas = 126, using box (81,53,84) --> (118, 116,132) to find MRI wm
before smoothing, mri peak at 110
after smoothing, mri peak at 110, scaling input intensities by 1.145
scaling channel 0 by 1.14545
initial log_p = -4.8
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.579503 @ (-9.091, 27.273, -9.091)
max log p =    -4.430745 @ (4.545, -4.545, -4.545)
max log p =    -4.333447 @ (2.273, 2.273, 2.273)
max log p =    -4.291113 @ (1.136, -3.409, 3.409)
max log p =    -4.289512 @ (0.568, 0.568, -0.568)
max log p =    -4.289512 @ (0.000, 0.000, 0.000)
Found translation: (-0.6, 22.2, -8.5): log p = -4.290
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.3 (thresh=-4.3)
 1.150   0.000   0.000  -19.518;
 0.000   1.111   0.298  -22.904;
 0.000  -0.220   0.821   33.748;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.150   0.000   0.000  -19.518;
 0.000   1.148   0.450  -36.545;
 0.000  -0.426   0.965   37.642;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.150   0.000   0.000  -19.518;
 0.000   1.148   0.450  -36.545;
 0.000  -0.426   0.965   37.642;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 1.150   0.000   0.000  -19.518;
 0.000   1.195   0.393  -36.297;
 0.000  -0.343   0.973   28.950;
 0.000   0.000   0.000   1.000;
****************************************
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)
 1.150   0.000   0.000  -19.518;
 0.000   1.195   0.393  -36.297;
 0.000  -0.343   0.973   28.950;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
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)
 1.152  -0.014  -0.022  -16.911;
 0.019   1.193   0.401  -40.410;
 0.019  -0.352   0.968   27.618;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.150  -0.014  -0.022  -16.577;
 0.019   1.196   0.402  -40.788;
 0.019  -0.351   0.967   27.711;
 0.000   0.000   0.000   1.000;
****************************************
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)
 1.150  -0.014  -0.022  -16.577;
 0.019   1.196   0.402  -40.788;
 0.019  -0.351   0.967   27.711;
 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
 1.14969  -0.01394  -0.02235  -16.57664;
 0.01903   1.19625   0.40165  -40.78821;
 0.01860  -0.35144   0.96652   27.71052;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.14969  -0.01394  -0.02235  -16.57664;
 0.01903   1.19625   0.40165  -40.78821;
 0.01860  -0.35144   0.96652   27.71052;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.150  -0.014  -0.022  -16.577;
 0.019   1.196   0.402  -40.788;
 0.019  -0.351   0.967   27.711;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.8)
transform before final EM align:
 1.150  -0.014  -0.022  -16.577;
 0.019   1.196   0.402  -40.788;
 0.019  -0.351   0.967   27.711;
 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
 1.14969  -0.01394  -0.02235  -16.57664;
 0.01903   1.19625   0.40165  -40.78821;
 0.01860  -0.35144   0.96652   27.71052;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.14969  -0.01394  -0.02235  -16.57664;
 0.01903   1.19625   0.40165  -40.78821;
 0.01860  -0.35144   0.96652   27.71052;
 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: 012: -log(p) =    4.4  tol 0.000000
final transform:
 1.150  -0.014  -0.022  -16.577;
 0.019   1.196   0.402  -40.788;
 0.019  -0.351   0.967   27.711;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 40 minutes and 23 seconds.

 mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/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=128 y=85 z=117 r=94
      first estimation of the main basin volume: 3486435 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        16 found in the rest of the brain 
      global maximum in x=147, y=83, z=76, Imax=255
      CSF=13, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 
      preflooding height equal to 10 percent
done.
Analyze...

      main basin size=20180669030 voxels, voxel volume =1.000 
                     = 20180669030 mmm3 = 20180668.416 cm3
done.
PostAnalyze...Basin Prior
 129 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=126,y=94, z=110, r=11272 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45874
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1031766979
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1091834324
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073225896
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082017464
    OTHER      CSF_MIN=1, CSF_intensity=2, CSF_MAX=24 , nb = 1069711904
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    4,      5,        24,   49
  after  analyzing :    4,      18,        25,   25
   RIGHT_CER   
  before analyzing :    4,      4,        19,   50
  after  analyzing :    4,      18,        25,   26
   LEFT_CER    
  before analyzing :    4,      4,        20,   51
  after  analyzing :    4,      18,        25,   26
  RIGHT_BRAIN  
  before analyzing :    4,      5,        24,   49
  after  analyzing :    4,      18,        25,   25
  LEFT_BRAIN   
  before analyzing :    4,      5,        24,   45
  after  analyzing :    4,      18,        25,   24
     OTHER     
  before analyzing :    24,      55,        79,   95
  after  analyzing :    24,      71,        79,   77
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...70 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.011
curvature mean = 74.901, std = 9.916

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 1.94, sigma = 3.55
      after  rotation: sse = 1.94, sigma = 3.55
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.15, its var is  3.63   
      before Erosion-Dilatation  0.50% 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...47 iterations

      mri_strip_skull: done peeling brain

Brain Size = 2061870 voxels, voxel volume = 1.000 mm3
           = 2061870 mmm3 = 2061.870 cm3


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

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Aug  8 11:44:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/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/5.3.0/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=20.0
skull bounding box = (58, 30, 25) --> (194, 179, 204)
using (103, 80, 115) as brain centroid...
mean wm in atlas = 107, using box (86,62,93) --> (119, 98,137) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 109, scaling input intensities by 0.982
scaling channel 0 by 0.981651
initial log_p = -4.5
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.122993 @ (-9.091, 27.273, -9.091)
max log p =    -3.901602 @ (4.545, -4.545, 4.545)
max log p =    -3.831934 @ (2.273, -2.273, -2.273)
max log p =    -3.790007 @ (-1.136, 1.136, -1.136)
max log p =    -3.768490 @ (0.568, -0.568, -0.568)
max log p =    -3.768490 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, 21.0, -8.5): log p = -3.768
****************************************
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)
 1.075   0.000   0.000  -12.565;
 0.000   1.028   0.275  -5.513;
 0.000  -0.236   0.883   27.980;
 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)
 1.075   0.000   0.000  -12.565;
 0.000   1.028   0.275  -5.513;
 0.000  -0.236   0.883   27.980;
 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=-3.3, old_max_log_p =-3.4 (thresh=-3.4)
 1.074   0.026   0.039  -17.352;
-0.034   1.038   0.307  -9.231;
-0.035  -0.266   0.856   40.123;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3)
 1.054   0.025   0.038  -14.649;
-0.034   1.038   0.307  -9.231;
-0.035  -0.266   0.856   40.123;
 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 =-3.3 (thresh=-3.3)
 1.057   0.021   0.022  -13.719;
-0.025   1.045   0.279  -8.970;
-0.018  -0.231   0.863   32.977;
 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)
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 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)
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 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
 1.05686   0.02056   0.02170  -13.71878;
-0.02464   1.04352   0.27875  -8.82042;
-0.01831  -0.23067   0.86304   32.97652;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 1.05686   0.02056   0.02170  -13.71878;
-0.02464   1.04352   0.27875  -8.82042;
-0.01831  -0.23067   0.86304   32.97652;
 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:
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.2 (old=-4.5)
transform before final EM align:
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 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
 1.05686   0.02056   0.02170  -13.71878;
-0.02464   1.04352   0.27875  -8.82042;
-0.01831  -0.23067   0.86304   32.97652;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 1.05686   0.02056   0.02170  -13.71878;
-0.02464   1.04352   0.27875  -8.82042;
-0.01831  -0.23067   0.86304   32.97652;
 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) =    3.9  tol 0.000000
final transform:
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 27 minutes and 20 seconds.
#--------------------------------------
#@# CA Normalize Thu Aug  8 12:11:40 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/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/5.3.0/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=20.0
skull bounding box = (57, 30, 25) --> (194, 179, 204)
using (103, 80, 115) as brain centroid...
mean wm in atlas = 107, using box (86,62,93) --> (119, 98,137) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 109, scaling input intensities by 0.982
scaling channel 0 by 0.981651
using 244171 sample points...
INFO: compute sample coordinates transform
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 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 (127, 33, 28) --> (190, 145, 210)
Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 160.0
0 of 71 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 33, 27) --> (129, 136, 211)
Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 160.0
0 of 72 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 118, 60) --> (175, 161, 119)
Left_Cerebellum_White_Matter: limiting intensities to 82.0 --> 160.0
0 of 19 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (84, 118, 56) --> (128, 159, 119)
Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 160.0
0 of 10 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (112, 106, 98) --> (143, 172, 131)
Brain_Stem: limiting intensities to 80.0 --> 160.0
0 of 12 (0.0%) samples deleted
using 184 total control points for intensity normalization...
bias field = 1.002 +- 0.050
0 of 184 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (127, 33, 28) --> (190, 145, 210)
Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 154.0
0 of 116 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 33, 27) --> (129, 136, 211)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 154.0
0 of 112 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 118, 60) --> (175, 161, 119)
Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 154.0
0 of 33 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (84, 118, 56) --> (128, 159, 119)
Right_Cerebellum_White_Matter: limiting intensities to 94.0 --> 154.0
21 of 44 (47.7%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (112, 106, 98) --> (143, 172, 131)
Brain_Stem: limiting intensities to 74.0 --> 154.0
0 of 74 (0.0%) samples deleted
using 379 total control points for intensity normalization...
bias field = 0.990 +- 0.054
0 of 358 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (127, 33, 28) --> (190, 145, 210)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 152.0
0 of 200 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 33, 27) --> (129, 136, 211)
Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 152.0
0 of 204 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 118, 60) --> (175, 161, 119)
Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 152.0
0 of 40 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (84, 118, 56) --> (128, 159, 119)
Right_Cerebellum_White_Matter: limiting intensities to 74.0 --> 152.0
0 of 42 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (112, 106, 98) --> (143, 172, 131)
Brain_Stem: limiting intensities to 70.0 --> 152.0
0 of 82 (0.0%) samples deleted
using 568 total control points for intensity normalization...
bias field = 1.010 +- 0.046
1 of 568 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 2 minutes and 3 seconds.
#--------------------------------------
#@# CA Reg Thu Aug  8 12:13:44 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3.0/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/5.3.0/average/RB_all_2008-03-26.gca'...
label assignment complete, 0 changed (0.00%)
det(m_affine) = 1.02 (predicted orig area = 7.8)
label assignment complete, 0 changed (0.00%)
freeing gibbs priors...done.
average std[0] = 5.0
**************** pass 1 of 1 ************************
setting smoothness coefficient to 0.039
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.920, neg=0, invalid=96777
0001: dt=129.472000, rms=0.826 (10.230%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.804 (2.702%), neg=0, invalid=96777
0003: dt=295.936000, rms=0.789 (1.859%), neg=0, invalid=96777
0004: dt=129.472000, rms=0.785 (0.456%), neg=0, invalid=96777
0005: dt=295.936000, rms=0.779 (0.775%), neg=0, invalid=96777
0006: dt=73.984000, rms=0.777 (0.346%), neg=0, invalid=96777
0007: dt=1479.680000, rms=0.765 (1.525%), neg=0, invalid=96777
0008: dt=92.480000, rms=0.762 (0.317%), neg=0, invalid=96777
0009: dt=443.904000, rms=0.759 (0.363%), neg=0, invalid=96777
0010: dt=55.488000, rms=0.758 (0.139%), neg=0, invalid=96777
0011: dt=55.488000, rms=0.758 (0.040%), neg=0, invalid=96777
0012: dt=55.488000, rms=0.758 (0.051%), neg=0, invalid=96777
0013: dt=55.488000, rms=0.757 (0.090%), neg=0, invalid=96777
0014: dt=55.488000, rms=0.756 (0.142%), neg=0, invalid=96777
0015: dt=55.488000, rms=0.755 (0.155%), neg=0, invalid=96777
0016: dt=55.488000, rms=0.754 (0.153%), neg=0, invalid=96777
0017: dt=55.488000, rms=0.752 (0.154%), neg=0, invalid=96777
0018: dt=55.488000, rms=0.751 (0.154%), neg=0, invalid=96777
0019: dt=55.488000, rms=0.750 (0.150%), neg=0, invalid=96777
0020: dt=55.488000, rms=0.749 (0.166%), neg=0, invalid=96777
0021: dt=55.488000, rms=0.748 (0.167%), neg=0, invalid=96777
0022: dt=55.488000, rms=0.747 (0.155%), neg=0, invalid=96777
0023: dt=55.488000, rms=0.746 (0.139%), neg=0, invalid=96777
0024: dt=55.488000, rms=0.745 (0.126%), neg=0, invalid=96777
0025: dt=55.488000, rms=0.744 (0.123%), neg=0, invalid=96777
0026: dt=55.488000, rms=0.743 (0.126%), neg=0, invalid=96777
0027: dt=55.488000, rms=0.742 (0.149%), neg=0, invalid=96777
0028: dt=55.488000, rms=0.741 (0.142%), neg=0, invalid=96777
0029: dt=55.488000, rms=0.740 (0.131%), neg=0, invalid=96777
0030: dt=55.488000, rms=0.739 (0.113%), neg=0, invalid=96777
0031: dt=55.488000, rms=0.738 (0.101%), neg=0, invalid=96777
0032: dt=517.888000, rms=0.737 (0.159%), neg=0, invalid=96777
0033: dt=27.744000, rms=0.737 (0.001%), neg=0, invalid=96777
0034: dt=27.744000, rms=0.737 (0.001%), neg=0, invalid=96777
0035: dt=27.744000, rms=0.737 (-0.011%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.737, neg=0, invalid=96777
0036: dt=92.480000, rms=0.736 (0.052%), neg=0, invalid=96777
0037: dt=369.920000, rms=0.735 (0.237%), neg=0, invalid=96777
0038: dt=32.368000, rms=0.735 (0.006%), neg=0, invalid=96777
0039: dt=32.368000, rms=0.735 (0.010%), neg=0, invalid=96777
0040: dt=32.368000, rms=0.735 (0.002%), neg=0, invalid=96777
0041: dt=32.368000, rms=0.735 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.739, neg=0, invalid=96777
0042: dt=145.152000, rms=0.722 (2.270%), neg=0, invalid=96777
0043: dt=124.416000, rms=0.716 (0.928%), neg=0, invalid=96777
0044: dt=36.288000, rms=0.708 (1.005%), neg=0, invalid=96777
0045: dt=20.736000, rms=0.707 (0.170%), neg=0, invalid=96777
0046: dt=20.736000, rms=0.706 (0.181%), neg=0, invalid=96777
0047: dt=20.736000, rms=0.704 (0.308%), neg=0, invalid=96777
0048: dt=20.736000, rms=0.701 (0.414%), neg=0, invalid=96777
0049: dt=20.736000, rms=0.697 (0.491%), neg=0, invalid=96777
0050: dt=20.736000, rms=0.694 (0.558%), neg=0, invalid=96777
0051: dt=20.736000, rms=0.689 (0.592%), neg=0, invalid=96777
0052: dt=20.736000, rms=0.685 (0.576%), neg=0, invalid=96777
0053: dt=20.736000, rms=0.682 (0.555%), neg=0, invalid=96777
0054: dt=20.736000, rms=0.678 (0.513%), neg=0, invalid=96777
0055: dt=20.736000, rms=0.675 (0.476%), neg=0, invalid=96777
0056: dt=20.736000, rms=0.672 (0.425%), neg=0, invalid=96777
0057: dt=20.736000, rms=0.670 (0.376%), neg=0, invalid=96777
0058: dt=20.736000, rms=0.667 (0.334%), neg=0, invalid=96777
0059: dt=20.736000, rms=0.665 (0.280%), neg=0, invalid=96777
0060: dt=20.736000, rms=0.664 (0.249%), neg=0, invalid=96777
0061: dt=20.736000, rms=0.662 (0.238%), neg=0, invalid=96777
0062: dt=20.736000, rms=0.661 (0.236%), neg=0, invalid=96777
0063: dt=20.736000, rms=0.659 (0.200%), neg=0, invalid=96777
0064: dt=20.736000, rms=0.658 (0.155%), neg=0, invalid=96777
0065: dt=20.736000, rms=0.658 (0.110%), neg=0, invalid=96777
0066: dt=20.736000, rms=0.657 (0.098%), neg=0, invalid=96777
0067: dt=145.152000, rms=0.656 (0.130%), neg=0, invalid=96777
0068: dt=6.480000, rms=0.656 (0.000%), neg=0, invalid=96777
0069: dt=6.480000, rms=0.656 (0.003%), neg=0, invalid=96777
0070: dt=6.480000, rms=0.656 (-0.011%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.656, neg=0, invalid=96777
0071: dt=15.552000, rms=0.656 (0.025%), neg=0, invalid=96777
0072: dt=20.736000, rms=0.656 (0.019%), neg=0, invalid=96777
0073: dt=20.736000, rms=0.656 (0.017%), neg=0, invalid=96777
0074: dt=20.736000, rms=0.656 (-0.005%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.681, neg=0, invalid=96777
0075: dt=7.157895, rms=0.681 (0.097%), neg=0, invalid=96777
0076: dt=2.800000, rms=0.681 (0.015%), neg=0, invalid=96777
0077: dt=2.800000, rms=0.681 (0.006%), neg=0, invalid=96777
0078: dt=2.800000, rms=0.681 (-0.022%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.681, neg=0, invalid=96777
0079: dt=0.000000, rms=0.681 (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=0.747, neg=0, invalid=96777
0080: dt=5.676259, rms=0.730 (2.311%), neg=0, invalid=96777
0081: dt=2.880000, rms=0.729 (0.101%), neg=0, invalid=96777
0082: dt=2.880000, rms=0.729 (-0.020%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.729, neg=0, invalid=96777
0083: dt=0.000000, rms=0.729 (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=0.798, neg=0, invalid=96777
0084: dt=0.877108, rms=0.795 (0.311%), neg=0, invalid=96777
0085: dt=2.204082, rms=0.790 (0.711%), neg=0, invalid=96777
0086: dt=1.280000, rms=0.788 (0.144%), neg=0, invalid=96777
0087: dt=1.280000, rms=0.787 (0.204%), neg=0, invalid=96777
0088: dt=1.280000, rms=0.786 (0.053%), neg=0, invalid=96777
0089: dt=1.280000, rms=0.786 (-0.358%), neg=0, invalid=96777
0090: dt=0.000000, rms=0.786 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.786, neg=0, invalid=96777
0091: dt=0.500000, rms=0.786 (0.058%), neg=0, invalid=96777
0092: dt=0.448000, rms=0.786 (0.007%), neg=0, invalid=96777
0093: dt=0.448000, rms=0.786 (-0.001%), 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=0.742, neg=0, invalid=96777
0094: dt=0.384000, rms=0.723 (2.622%), neg=0, invalid=96777
0095: dt=0.000000, rms=0.722 (0.005%), neg=0, invalid=96777
0096: dt=0.050000, rms=0.722 (-0.461%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.722, neg=0, invalid=96777
0097: dt=0.000000, rms=0.722 (0.000%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.07898 ( 6)
Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (2036 voxels, overlap=0.082)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2036 voxels, peak =  5), gca=9.6
gca peak = 0.14022 (22)
mri peak = 0.14083 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (1080 voxels, overlap=0.007)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1080 voxels, peak =  7), gca=8.8
gca peak = 0.24234 (100)
mri peak = 0.07527 (83)
Right_Pallidum (52): linear fit = 0.83 x + 0.0 (426 voxels, overlap=0.049)
Right_Pallidum (52): linear fit = 0.83 x + 0.0 (426 voxels, peak = 84), gca=83.5
gca peak = 0.19192 (97)
mri peak = 0.12903 (77)
Left_Pallidum (13): linear fit = 0.79 x + 0.0 (305 voxels, overlap=0.031)
Left_Pallidum (13): linear fit = 0.79 x + 0.0 (305 voxels, peak = 76), gca=76.1
gca peak = 0.24007 (63)
mri peak = 0.06263 (52)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (495 voxels, overlap=0.567)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (495 voxels, peak = 55), gca=55.1
gca peak = 0.29892 (64)
mri peak = 0.07822 (59)
Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (594 voxels, overlap=0.712)
Left_Hippocampus (17): linear fit = 0.90 x + 0.0 (594 voxels, peak = 58), gca=57.9
gca peak = 0.12541 (104)
mri peak = 0.09221 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76693 voxels, overlap=0.760)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (76693 voxels, peak = 108), gca=107.6
gca peak = 0.13686 (104)
mri peak = 0.08402 (106)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81954 voxels, overlap=0.713)
Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (81954 voxels, peak = 109), gca=108.7
gca peak = 0.11691 (63)
mri peak = 0.05463 (50)
Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (23299 voxels, overlap=0.013)
Left_Cerebral_Cortex (3): linear fit = 0.75 x + 0.0 (23299 voxels, peak = 47), gca=46.9
gca peak = 0.13270 (63)
mri peak = 0.06566 (52)
Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (23129 voxels, overlap=0.030)
Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (23129 voxels, peak = 49), gca=48.8
gca peak = 0.15182 (70)
mri peak = 0.08707 (61)
Right_Caudate (50): linear fit = 0.82 x + 0.0 (496 voxels, overlap=0.060)
Right_Caudate (50): linear fit = 0.82 x + 0.0 (496 voxels, peak = 58), gca=57.8
gca peak = 0.14251 (76)
mri peak = 0.07843 (62)
Left_Caudate (11): linear fit = 0.81 x + 0.0 (658 voxels, overlap=0.019)
Left_Caudate (11): linear fit = 0.81 x + 0.0 (658 voxels, peak = 61), gca=61.2
gca peak = 0.12116 (60)
mri peak = 0.04924 (52)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (8972 voxels, overlap=0.393)
Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (8972 voxels, peak = 51), gca=51.3
gca peak = 0.12723 (61)
mri peak = 0.03541 (54)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10365 voxels, overlap=0.602)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10365 voxels, peak = 56), gca=55.8
gca peak = 0.22684 (88)
mri peak = 0.07428 (89)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7794 voxels, overlap=0.948)
Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7794 voxels, peak = 90), gca=90.2
gca peak = 0.21067 (87)
mri peak = 0.07354 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (7053 voxels, overlap=0.965)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (7053 voxels, peak = 88), gca=88.3
gca peak = 0.25455 (62)
mri peak = 0.06376 (61)
Left_Amygdala (18): linear fit = 0.93 x + 0.0 (338 voxels, overlap=0.325)
Left_Amygdala (18): linear fit = 0.93 x + 0.0 (338 voxels, peak = 57), gca=57.4
gca peak = 0.39668 (62)
mri peak = 0.11341 (52)
Right_Amygdala (54): linear fit = 0.86 x + 0.0 (358 voxels, overlap=0.244)
Right_Amygdala (54): linear fit = 0.86 x + 0.0 (358 voxels, peak = 53), gca=53.0
gca peak = 0.10129 (93)
mri peak = 0.04493 (97)
Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6114 voxels, overlap=0.934)
Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6114 voxels, peak = 98), gca=98.1
gca peak = 0.12071 (89)
mri peak = 0.05059 (91)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4304 voxels, overlap=0.986)
Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (4304 voxels, peak = 91), gca=91.2
gca peak = 0.13716 (82)
mri peak = 0.04188 (73)
Left_Putamen (12): linear fit = 0.92 x + 0.0 (1836 voxels, overlap=0.536)
Left_Putamen (12): linear fit = 0.92 x + 0.0 (1836 voxels, peak = 75), gca=75.0
gca peak = 0.15214 (84)
mri peak = 0.05570 (69)
Right_Putamen (51): linear fit = 0.83 x + 0.0 (2150 voxels, overlap=0.023)
Right_Putamen (51): linear fit = 0.83 x + 0.0 (2150 voxels, peak = 70), gca=70.1
gca peak = 0.08983 (85)
mri peak = 0.07156 (87)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11745 voxels, overlap=0.778)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (11745 voxels, peak = 88), gca=88.0
gca peak = 0.11809 (92)
mri peak = 0.05832 (89)
Right_VentralDC (60): linear fit = 1.04 x + 0.0 (830 voxels, overlap=0.841)
Right_VentralDC (60): linear fit = 1.04 x + 0.0 (830 voxels, peak = 96), gca=96.1
gca peak = 0.12914 (94)
mri peak = 0.06610 (96)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (887 voxels, overlap=0.860)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (887 voxels, peak = 95), gca=95.4
gca peak = 0.21100 (36)
mri peak = 0.50000 (54)
Third_Ventricle (14): linear fit = 1.49 x + 0.0 (61 voxels, overlap=2.064)
Third_Ventricle (14): linear fit = 1.49 x + 0.0 (61 voxels, peak = 53), gca=53.5
gca peak = 0.13542 (27)
mri peak = 0.12434 (11)
Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (399 voxels, overlap=0.024)
Fourth_Ventricle (15): linear fit = 0.37 x + 0.0 (399 voxels, peak = 10), gca=9.9
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.21802 (40)
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 0.85 x + 0.0
estimating mean wm scale to be 1.04 x + 0.0
estimating mean csf scale to be 0.76 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=0.762, neg=0, invalid=96777
0098: dt=129.472000, rms=0.758 (0.578%), neg=0, invalid=96777
0099: dt=129.472000, rms=0.756 (0.302%), neg=0, invalid=96777
0100: dt=129.472000, rms=0.754 (0.225%), neg=0, invalid=96777
0101: dt=129.472000, rms=0.753 (0.132%), neg=0, invalid=96777
0102: dt=129.472000, rms=0.751 (0.185%), neg=0, invalid=96777
0103: dt=73.984000, rms=0.751 (0.046%), neg=0, invalid=96777
0104: dt=73.984000, rms=0.750 (0.088%), neg=0, invalid=96777
0105: dt=73.984000, rms=0.750 (0.119%), neg=0, invalid=96777
0106: dt=73.984000, rms=0.749 (0.130%), neg=0, invalid=96777
0107: dt=73.984000, rms=0.748 (0.132%), neg=0, invalid=96777
0108: dt=73.984000, rms=0.747 (0.149%), neg=0, invalid=96777
0109: dt=73.984000, rms=0.745 (0.142%), neg=0, invalid=96777
0110: dt=73.984000, rms=0.745 (0.119%), neg=0, invalid=96777
0111: dt=73.984000, rms=0.744 (0.094%), neg=0, invalid=96777
0112: dt=73.984000, rms=0.743 (0.092%), neg=0, invalid=96777
0113: dt=73.984000, rms=0.742 (0.112%), neg=0, invalid=96777
0114: dt=73.984000, rms=0.742 (0.092%), neg=0, invalid=96777
0115: dt=73.984000, rms=0.741 (0.084%), neg=0, invalid=96777
0116: dt=73.984000, rms=0.740 (0.079%), neg=0, invalid=96777
0117: dt=73.984000, rms=0.740 (0.070%), neg=0, invalid=96777
0118: dt=73.984000, rms=0.739 (0.078%), neg=0, invalid=96777
0119: dt=73.984000, rms=0.739 (0.084%), neg=0, invalid=96777
0120: dt=73.984000, rms=0.738 (0.076%), neg=0, invalid=96777
0121: dt=73.984000, rms=0.738 (0.077%), neg=0, invalid=96777
0122: dt=36.992000, rms=0.738 (0.009%), neg=0, invalid=96777
0123: dt=36.992000, rms=0.738 (0.007%), neg=0, invalid=96777
0124: dt=0.505750, rms=0.738 (0.000%), neg=0, invalid=96777
0125: dt=0.505750, rms=0.738 (0.000%), neg=0, invalid=96777
0126: dt=0.252875, rms=0.738 (0.000%), neg=0, invalid=96777
0127: dt=0.126438, rms=0.738 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.738, neg=0, invalid=96777
0128: dt=0.000000, rms=0.738 (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=0.738, neg=0, invalid=96777
0129: dt=0.000000, rms=0.738 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.738, neg=0, invalid=96777
0130: dt=0.000000, rms=0.738 (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=0.739, neg=0, invalid=96777
0131: dt=75.304540, rms=0.664 (10.116%), neg=0, invalid=96777
0132: dt=25.094225, rms=0.647 (2.551%), neg=0, invalid=96777
0133: dt=2.800000, rms=0.645 (0.371%), neg=0, invalid=96777
0134: dt=8.000000, rms=0.640 (0.722%), neg=0, invalid=96777
0135: dt=44.800000, rms=0.628 (1.826%), neg=0, invalid=96777
0136: dt=2.800000, rms=0.627 (0.187%), neg=0, invalid=96777
0137: dt=8.000000, rms=0.625 (0.339%), neg=0, invalid=96777
0138: dt=44.800000, rms=0.619 (1.042%), neg=0, invalid=96777
0139: dt=11.200000, rms=0.616 (0.356%), neg=0, invalid=96777
0140: dt=13.714286, rms=0.614 (0.336%), neg=0, invalid=96777
0141: dt=11.200000, rms=0.613 (0.213%), neg=0, invalid=96777
0142: dt=19.200000, rms=0.611 (0.301%), neg=0, invalid=96777
0143: dt=8.000000, rms=0.610 (0.229%), neg=0, invalid=96777
0144: dt=44.800000, rms=0.608 (0.358%), neg=0, invalid=96777
0145: dt=2.800000, rms=0.606 (0.255%), neg=0, invalid=96777
0146: dt=7.353535, rms=0.604 (0.294%), neg=0, invalid=96777
0147: dt=153.600000, rms=0.600 (0.650%), neg=0, invalid=96777
0148: dt=9.486339, rms=0.593 (1.163%), neg=0, invalid=96777
0149: dt=11.200000, rms=0.592 (0.300%), neg=0, invalid=96777
0150: dt=11.200000, rms=0.591 (0.129%), neg=0, invalid=96777
0151: dt=44.800000, rms=0.590 (0.185%), neg=0, invalid=96777
0152: dt=8.655738, rms=0.589 (0.166%), neg=0, invalid=96777
0153: dt=25.600000, rms=0.588 (0.103%), neg=0, invalid=96777
0154: dt=9.600000, rms=0.587 (0.113%), neg=0, invalid=96777
0155: dt=19.200000, rms=0.587 (0.077%), neg=0, invalid=96777
0156: dt=11.200000, rms=0.586 (0.093%), neg=0, invalid=96777
0157: dt=11.200000, rms=0.586 (0.070%), neg=0, invalid=96777
0158: dt=11.200000, rms=0.586 (0.068%), neg=0, invalid=96777
0159: dt=38.400000, rms=0.585 (0.117%), neg=0, invalid=96777
0160: dt=8.380952, rms=0.584 (0.122%), neg=0, invalid=96777
0161: dt=25.600000, rms=0.584 (0.089%), neg=0, invalid=96777
0162: dt=8.000000, rms=0.583 (0.084%), neg=0, invalid=96777
0163: dt=32.000000, rms=0.583 (0.090%), neg=0, invalid=96777
0164: dt=8.000000, rms=0.582 (0.095%), neg=0, invalid=96777
0165: dt=32.000000, rms=0.582 (0.100%), neg=0, invalid=96777
0166: dt=6.400000, rms=0.581 (0.065%), neg=0, invalid=96777
0167: dt=153.600000, rms=0.579 (0.438%), neg=0, invalid=96777
0168: dt=0.150000, rms=0.579 (0.002%), neg=0, invalid=96777
0169: dt=0.004687, rms=0.579 (0.001%), neg=0, invalid=96777
0170: dt=0.000586, rms=0.579 (0.000%), neg=0, invalid=96777
0171: dt=0.000293, rms=0.579 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.579, neg=0, invalid=96777
0172: dt=0.000488, rms=0.579 (0.000%), neg=0, invalid=96777
0173: dt=0.000000, rms=0.579 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.601, neg=0, invalid=96777
0174: dt=2.305085, rms=0.600 (0.105%), neg=0, invalid=96777
0175: dt=0.252000, rms=0.600 (0.015%), neg=0, invalid=96777
0176: dt=0.252000, rms=0.600 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.600, neg=0, invalid=96777
0177: dt=2.304000, rms=0.600 (0.051%), neg=0, invalid=96777
0178: dt=1.008000, rms=0.600 (0.011%), neg=0, invalid=96777
0179: dt=1.008000, rms=0.600 (-0.002%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.637, neg=0, invalid=96777
0180: dt=1.536313, rms=0.634 (0.516%), neg=0, invalid=96777
0181: dt=0.384000, rms=0.634 (0.013%), neg=0, invalid=96777
0182: dt=0.384000, rms=0.634 (-0.006%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.634, neg=0, invalid=96777
0183: dt=1.536000, rms=0.633 (0.203%), neg=0, invalid=96777
0184: dt=0.448000, rms=0.633 (0.015%), neg=0, invalid=96777
0185: dt=0.448000, rms=0.633 (-0.001%), 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=0.595, neg=0, invalid=96777
0186: dt=0.384000, rms=0.575 (3.369%), neg=0, invalid=96777
0187: dt=0.007000, rms=0.574 (0.014%), neg=0, invalid=96777
0188: dt=0.007000, rms=0.574 (0.019%), neg=0, invalid=96777
0189: dt=0.007000, rms=0.574 (0.036%), neg=0, invalid=96777
0190: dt=0.007000, rms=0.574 (0.053%), neg=0, invalid=96777
0191: dt=0.007000, rms=0.573 (0.064%), neg=0, invalid=96777
0192: dt=0.007000, rms=0.573 (0.075%), neg=0, invalid=96777
0193: dt=0.007000, rms=0.573 (0.085%), neg=0, invalid=96777
0194: dt=0.007000, rms=0.572 (0.094%), neg=0, invalid=96777
0195: dt=0.007000, rms=0.571 (0.099%), neg=0, invalid=96777
0196: dt=0.007000, rms=0.571 (0.102%), neg=0, invalid=96777
0197: dt=0.007000, rms=0.570 (0.106%), neg=0, invalid=96777
0198: dt=0.007000, rms=0.570 (0.107%), neg=0, invalid=96777
0199: dt=0.007000, rms=0.569 (0.111%), neg=0, invalid=96777
0200: dt=0.007000, rms=0.568 (0.110%), neg=0, invalid=96777
0201: dt=0.007000, rms=0.568 (0.108%), neg=0, invalid=96777
0202: dt=0.007000, rms=0.567 (0.107%), neg=0, invalid=96777
0203: dt=0.007000, rms=0.567 (0.104%), neg=0, invalid=96777
0204: dt=0.007000, rms=0.566 (0.101%), neg=0, invalid=96777
0205: dt=0.007000, rms=0.565 (0.096%), neg=0, invalid=96777
0206: dt=0.007000, rms=0.565 (0.093%), neg=0, invalid=96777
0207: dt=0.007000, rms=0.564 (0.090%), neg=0, invalid=96777
0208: dt=0.007000, rms=0.564 (0.086%), neg=0, invalid=96777
0209: dt=0.007000, rms=0.563 (0.080%), neg=0, invalid=96777
0210: dt=0.007000, rms=0.563 (0.078%), neg=0, invalid=96777
0211: dt=0.007000, rms=0.563 (0.074%), neg=0, invalid=96777
0212: dt=0.007000, rms=0.562 (0.068%), neg=0, invalid=96777
0213: dt=0.007000, rms=0.562 (0.063%), neg=0, invalid=96777
0214: dt=0.007000, rms=0.562 (0.058%), neg=0, invalid=96777
0215: dt=0.007000, rms=0.561 (0.057%), neg=0, invalid=96777
0216: dt=0.007000, rms=0.561 (0.053%), neg=0, invalid=96777
0217: dt=0.007000, rms=0.561 (0.046%), neg=0, invalid=96777
0218: dt=0.007000, rms=0.560 (0.043%), neg=0, invalid=96777
0219: dt=0.007000, rms=0.560 (0.041%), neg=0, invalid=96777
0220: dt=0.007000, rms=0.560 (0.039%), neg=0, invalid=96777
0221: dt=0.007000, rms=0.560 (0.035%), neg=0, invalid=96777
0222: dt=0.007000, rms=0.560 (0.035%), neg=0, invalid=96777
0223: dt=0.007000, rms=0.559 (0.026%), neg=0, invalid=96777
0224: dt=0.007000, rms=0.559 (0.026%), neg=0, invalid=96777
0225: dt=0.007000, rms=0.559 (0.027%), neg=0, invalid=96777
0226: dt=0.007000, rms=0.559 (0.021%), neg=0, invalid=96777
0227: dt=0.007000, rms=0.559 (0.019%), neg=0, invalid=96777
0228: dt=0.112000, rms=0.559 (0.011%), neg=0, invalid=96777
0229: dt=0.014000, rms=0.559 (0.005%), neg=0, invalid=96777
0230: dt=0.014000, rms=0.559 (0.003%), neg=0, invalid=96777
0231: dt=0.014000, rms=0.559 (0.005%), neg=0, invalid=96777
0232: dt=0.014000, rms=0.559 (0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.559, neg=0, invalid=96777
0233: dt=0.112000, rms=0.557 (0.316%), neg=0, invalid=96777
0234: dt=0.112000, rms=0.556 (0.244%), neg=0, invalid=96777
0235: dt=0.028000, rms=0.555 (0.042%), neg=0, invalid=96777
0236: dt=0.028000, rms=0.555 (0.044%), neg=0, invalid=96777
0237: dt=0.028000, rms=0.555 (0.080%), neg=0, invalid=96777
0238: dt=0.028000, rms=0.554 (0.109%), neg=0, invalid=96777
0239: dt=0.028000, rms=0.553 (0.129%), neg=0, invalid=96777
0240: dt=0.007000, rms=0.553 (0.004%), neg=0, invalid=96777
0241: dt=0.007000, rms=0.553 (0.007%), neg=0, invalid=96777
0242: dt=0.007000, rms=0.553 (0.008%), neg=0, invalid=96777
0243: dt=0.007000, rms=0.553 (0.015%), neg=0, invalid=96777
0244: dt=0.007000, rms=0.553 (0.021%), neg=0, invalid=96777
0245: dt=0.007000, rms=0.553 (0.020%), neg=0, invalid=96777
0246: dt=0.112000, rms=0.553 (0.075%), neg=0, invalid=96777
0247: dt=0.112000, rms=0.552 (0.061%), neg=0, invalid=96777
0248: dt=0.007000, rms=0.552 (-0.000%), neg=0, invalid=96777
0249: dt=0.007000, rms=0.552 (0.003%), neg=0, invalid=96777
0250: dt=0.007000, rms=0.552 (0.006%), neg=0, invalid=96777
0251: dt=0.003500, rms=0.552 (0.001%), neg=0, invalid=96777
0252: dt=0.003500, rms=0.552 (0.003%), neg=0, invalid=96777
0253: dt=0.003500, rms=0.552 (0.004%), neg=0, invalid=96777
0254: dt=0.003500, rms=0.552 (0.007%), neg=0, invalid=96777
0255: dt=0.003500, rms=0.552 (0.004%), 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=0.550, neg=0, invalid=96777
0256: dt=129.472000, rms=0.550 (0.028%), neg=0, invalid=96777
0257: dt=73.984000, rms=0.550 (0.007%), neg=0, invalid=96777
0258: dt=73.984000, rms=0.550 (0.002%), neg=0, invalid=96777
0259: dt=73.984000, rms=0.549 (0.011%), neg=0, invalid=96777
0260: dt=73.984000, rms=0.549 (0.007%), neg=0, invalid=96777
0261: dt=73.984000, rms=0.549 (0.005%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.549, neg=0, invalid=96777
0262: dt=129.472000, rms=0.549 (0.109%), neg=0, invalid=96777
0263: dt=129.472000, rms=0.549 (0.046%), neg=0, invalid=96777
0264: dt=129.472000, rms=0.548 (0.034%), neg=0, invalid=96777
0265: dt=129.472000, rms=0.548 (0.048%), neg=0, invalid=96777
0266: dt=129.472000, rms=0.548 (0.034%), neg=0, invalid=96777
0267: dt=129.472000, rms=0.548 (0.041%), neg=0, invalid=96777
0268: dt=129.472000, rms=0.548 (0.033%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.548, neg=0, invalid=96777
0269: dt=36.288000, rms=0.547 (0.166%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0270: dt=82.944000, rms=0.546 (0.143%), neg=0, invalid=96777
0271: dt=82.944000, rms=0.545 (0.066%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0272: dt=82.944000, rms=0.546 (-0.534%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.546, neg=0, invalid=96777
0273: dt=20.736000, rms=0.544 (0.254%), neg=0, invalid=96777
0274: dt=103.680000, rms=0.542 (0.336%), neg=0, invalid=96777
0275: dt=15.552000, rms=0.542 (0.142%), neg=0, invalid=96777
0276: dt=15.552000, rms=0.541 (0.034%), neg=0, invalid=96777
0277: dt=15.552000, rms=0.541 (0.057%), neg=0, invalid=96777
0278: dt=15.552000, rms=0.541 (0.072%), neg=0, invalid=96777
0279: dt=15.552000, rms=0.540 (0.086%), neg=0, invalid=96777
0280: dt=15.552000, rms=0.540 (0.105%), neg=0, invalid=96777
0281: dt=15.552000, rms=0.539 (0.100%), neg=0, invalid=96777
0282: dt=15.552000, rms=0.539 (0.097%), neg=0, invalid=96777
0283: dt=145.152000, rms=0.538 (0.078%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.538, neg=0, invalid=96777
iter 0, gcam->neg = 21
after 10 iterations, nbhd size=1, neg = 0
0284: dt=44.800000, rms=0.532 (1.138%), neg=0, invalid=96777
0285: dt=8.292683, rms=0.530 (0.463%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 13 iterations, nbhd size=2, neg = 0
0286: dt=25.600000, rms=0.528 (0.368%), neg=0, invalid=96777
0287: dt=6.400000, rms=0.526 (0.327%), neg=0, invalid=96777
iter 0, gcam->neg = 24
after 46 iterations, nbhd size=3, neg = 0
0288: dt=44.800000, rms=0.523 (0.503%), neg=0, invalid=96777
0289: dt=6.774194, rms=0.522 (0.250%), neg=0, invalid=96777
0290: dt=6.774194, rms=0.522 (0.105%), neg=0, invalid=96777
0291: dt=6.774194, rms=0.521 (0.123%), neg=0, invalid=96777
iter 0, gcam->neg = 7
after 37 iterations, nbhd size=4, neg = 0
0292: dt=6.774194, rms=0.520 (0.130%), neg=0, invalid=96777
0293: dt=6.774194, rms=0.519 (0.206%), neg=0, invalid=96777
0294: dt=6.774194, rms=0.518 (0.219%), neg=0, invalid=96777
0295: dt=6.774194, rms=0.517 (0.240%), neg=0, invalid=96777
0296: dt=6.774194, rms=0.516 (0.229%), neg=0, invalid=96777
0297: dt=6.774194, rms=0.514 (0.235%), neg=0, invalid=96777
0298: dt=6.774194, rms=0.513 (0.207%), neg=0, invalid=96777
0299: dt=6.774194, rms=0.512 (0.192%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 43 iterations, nbhd size=4, neg = 0
0300: dt=6.774194, rms=0.512 (0.146%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 1 iterations, nbhd size=0, neg = 0
0301: dt=6.774194, rms=0.511 (0.175%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0302: dt=6.774194, rms=0.510 (0.163%), neg=0, invalid=96777
0303: dt=6.774194, rms=0.509 (0.160%), neg=0, invalid=96777
0304: dt=6.774194, rms=0.508 (0.147%), neg=0, invalid=96777
0305: dt=6.774194, rms=0.508 (0.131%), neg=0, invalid=96777
0306: dt=6.774194, rms=0.507 (0.130%), neg=0, invalid=96777
0307: dt=6.774194, rms=0.506 (0.113%), neg=0, invalid=96777
0308: dt=6.774194, rms=0.506 (0.116%), neg=0, invalid=96777
0309: dt=6.774194, rms=0.505 (0.098%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 45 iterations, nbhd size=3, neg = 0
0310: dt=44.800000, rms=0.505 (-0.028%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.505, neg=0, invalid=96777
0311: dt=44.800000, rms=0.501 (0.785%), neg=0, invalid=96777
0312: dt=6.400000, rms=0.501 (0.066%), neg=0, invalid=96777
0313: dt=6.400000, rms=0.501 (0.060%), neg=0, invalid=96777
0314: dt=6.400000, rms=0.500 (0.091%), neg=0, invalid=96777
0315: dt=6.400000, rms=0.500 (0.095%), neg=0, invalid=96777
0316: dt=6.400000, rms=0.499 (0.092%), neg=0, invalid=96777
0317: dt=6.400000, rms=0.499 (0.090%), neg=0, invalid=96777
0318: dt=11.200000, rms=0.499 (0.052%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.506, neg=0, invalid=96777
iter 0, gcam->neg = 11
after 21 iterations, nbhd size=2, neg = 0
0319: dt=3.456000, rms=0.506 (0.081%), neg=0, invalid=96777
0320: dt=0.720000, rms=0.506 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.506, neg=0, invalid=96777
iter 0, gcam->neg = 12
after 3 iterations, nbhd size=0, neg = 0
0321: dt=1.826087, rms=0.506 (0.050%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 6 iterations, nbhd size=1, neg = 0
0322: dt=4.869565, rms=0.505 (0.128%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 5 iterations, nbhd size=1, neg = 0
0323: dt=4.032000, rms=0.505 (0.045%), neg=0, invalid=96777
iter 0, gcam->neg = 6
after 8 iterations, nbhd size=1, neg = 0
0324: dt=4.032000, rms=0.505 (0.031%), neg=0, invalid=96777
iter 0, gcam->neg = 36
after 9 iterations, nbhd size=1, neg = 0
0325: dt=4.032000, rms=0.505 (-0.033%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.513, neg=0, invalid=96777
0326: dt=0.000000, rms=0.513 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.513, neg=0, invalid=96777
0327: dt=0.000000, rms=0.513 (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=0.499, neg=0, invalid=96777
iter 0, gcam->neg = 1004
after 200 iterations, nbhd size=1, neg = 1
starting rms=0.006, neg=1, removing folds in lattice....
iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%)
---------- unfolding failed - restoring original position --------------------
0328: dt=2.029326, rms=0.499 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.499, neg=0, invalid=96777
iter 0, gcam->neg = 1336
after 43 iterations, nbhd size=1, neg = 0
0329: dt=2.183805, rms=0.427 (14.344%), neg=0, invalid=96777
0330: dt=0.000016, rms=0.427 (0.005%), neg=0, invalid=96777
0331: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
0332: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
0333: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
0334: dt=0.000016, rms=0.427 (0.000%), neg=0, invalid=96777
0335: dt=0.000050, rms=0.427 (0.000%), 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=0.399, neg=0, invalid=96777
0336: dt=0.000000, rms=0.400 (-0.319%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.400, neg=0, invalid=96777
0337: dt=32.368000, rms=0.400 (0.004%), neg=0, invalid=96777
0338: dt=8.092000, rms=0.400 (0.000%), neg=0, invalid=96777
0339: dt=8.092000, rms=0.400 (0.000%), neg=0, invalid=96777
0340: dt=8.092000, rms=0.400 (-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=0.401, neg=0, invalid=96777
0341: dt=0.000000, rms=0.401 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.401, neg=0, invalid=96777
0342: dt=25.920000, rms=0.400 (0.011%), neg=0, invalid=96777
0343: dt=9.072000, rms=0.400 (0.001%), neg=0, invalid=96777
0344: dt=9.072000, rms=0.400 (0.001%), neg=0, invalid=96777
0345: dt=9.072000, rms=0.400 (0.000%), neg=0, invalid=96777
0346: dt=9.072000, rms=0.400 (-0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.402, neg=0, invalid=96777
iter 0, gcam->neg = 5
after 200 iterations, nbhd size=3, neg = 1
starting rms=0.007, neg=1, removing folds in lattice....
iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.007 (0.000%)
---------- unfolding failed - restoring original position --------------------
0347: dt=6.400000, rms=0.402 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.402, neg=0, invalid=96777
iter 0, gcam->neg = 26
after 200 iterations, nbhd size=3, neg = 2
starting rms=0.008, neg=2, removing folds in lattice....
iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.008 (0.000%)
---------- unfolding failed - restoring original position --------------------
0348: dt=32.000000, rms=0.402 (0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.406, neg=0, invalid=96777
iter 0, gcam->neg = 41
after 200 iterations, nbhd size=2, neg = 1
starting rms=0.005, neg=1, removing folds in lattice....
iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.005 (0.000%)
---------- unfolding failed - restoring original position --------------------
0349: dt=3.456000, rms=0.406 (0.000%), 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 = 35
after 200 iterations, nbhd size=3, neg = 1
starting rms=0.004, neg=1, removing folds in lattice....
iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%)
---------- unfolding failed - restoring original position --------------------
0350: dt=4.032000, rms=0.406 (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=0.414, neg=0, invalid=96777
0351: dt=0.000000, rms=0.414 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.414, neg=0, invalid=96777
0352: dt=0.000000, rms=0.414 (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=0.400, neg=0, invalid=96777
iter 0, gcam->neg = 312
after 34 iterations, nbhd size=3, neg = 0
0353: dt=0.448000, rms=0.391 (2.148%), neg=0, invalid=96777
0354: dt=0.000027, rms=0.391 (0.002%), neg=0, invalid=96777
0355: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
0356: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
0357: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
0358: dt=0.000027, rms=0.391 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0359: dt=0.005000, rms=0.391 (0.002%), neg=0, invalid=96777
0360: dt=0.001250, rms=0.391 (0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.391, neg=0, invalid=96777
iter 0, gcam->neg = 12
after 14 iterations, nbhd size=2, neg = 0
0361: dt=0.028000, rms=0.391 (0.074%), neg=0, invalid=96777
0362: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0363: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0364: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0365: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0366: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0367: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0368: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0369: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0370: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0371: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0372: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0373: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0374: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0375: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0376: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0377: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0378: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0379: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0380: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0381: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0382: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0383: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0384: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0385: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0386: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0387: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0388: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0389: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0390: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0391: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0392: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0393: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
0394: dt=0.000008, rms=0.391 (0.000%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 3 hours, 46 minutes and 52 seconds.
#--------------------------------------
#@# CA Reg Inv Thu Aug  8 16:00:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

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

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z 
Inverting GCAM
Saving inverse 
#--------------------------------------
#@# Remove Neck Thu Aug  8 16:02:02 CEST 2013

 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz 

erasing everything more than 25 mm from possible brain
reading atlas '/opt/freesurfer/5.3.0/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...
10449376 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 31 seconds.
#--------------------------------------
#@# SkullLTA Thu Aug  8 16:03:33 CEST 2013

 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/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/5.3.0/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=9.0
skull bounding box = (43, 0, 0) --> (209, 205, 200)
using (98, 68, 100) as brain centroid...
mean wm in atlas = 126, using box (78,43,75) --> (118, 93,124) to find MRI wm
before smoothing, mri peak at 110
after smoothing, mri peak at 109, scaling input intensities by 1.156
scaling channel 0 by 1.15596
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.2 (thresh=-4.2)
 1.057   0.021   0.022  -13.719;
-0.026   1.122   0.300  -18.565;
-0.018  -0.231   0.863   32.977;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1)
 1.057   0.021   0.022  -13.719;
-0.026   1.122   0.300  -18.565;
-0.018  -0.231   0.863   32.977;
 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 =-4.1 (thresh=-4.1)
 1.037  -0.015   0.012  -6.714;
 0.009   1.080   0.289  -15.944;
-0.019  -0.235   0.879   31.607;
 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)
 1.037  -0.007  -0.017  -4.208;
 0.009   1.060   0.284  -15.249;
 0.016  -0.240   0.896   25.836;
 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)
 1.041  -0.007  -0.017  -3.726;
 0.009   1.047   0.312  -16.851;
 0.015  -0.275   0.887   30.695;
 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)
 1.042  -0.007  -0.017  -3.878;
 0.009   1.047   0.312  -16.851;
 0.015  -0.275   0.887   30.695;
 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
 1.04224  -0.00684  -0.01683  -3.87823;
 0.00940   1.04745   0.31168  -16.85081;
 0.01530  -0.27454   0.88693   30.69490;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.04224  -0.00684  -0.01683  -3.87823;
 0.00940   1.04745   0.31168  -16.85081;
 0.01530  -0.27454   0.88693   30.69490;
 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:
 1.042  -0.007  -0.017  -3.878;
 0.009   1.047   0.312  -16.851;
 0.015  -0.275   0.887   30.695;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.2)
transform before final EM align:
 1.042  -0.007  -0.017  -3.878;
 0.009   1.047   0.312  -16.851;
 0.015  -0.275   0.887   30.695;
 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
 1.04224  -0.00684  -0.01683  -3.87823;
 0.00940   1.04745   0.31168  -16.85081;
 0.01530  -0.27454   0.88693   30.69490;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.04224  -0.00684  -0.01683  -3.87823;
 0.00940   1.04745   0.31168  -16.85081;
 0.01530  -0.27454   0.88693   30.69490;
 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) =    4.4  tol 0.000000
final transform:
 1.042  -0.007  -0.017  -3.878;
 0.009   1.047   0.312  -16.851;
 0.015  -0.275   0.887   30.695;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 38 minutes and 18 seconds.
#--------------------------------------
#@# SubCort Seg Thu Aug  8 16:41:51 CEST 2013

 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 

sysname  Linux
hostname snake5
machine  x86_64

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri
mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/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/5.3.0/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/5.3.0/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 = 0.12487 ( 6)
Left_Lateral_Ventricle (4): linear fit = 0.19 x + 0.0 (899 voxels, overlap=0.007)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (899 voxels, peak =  5), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.13637 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.32 x + 0.0 (1122 voxels, overlap=0.008)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1122 voxels, peak =  6), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.08549 (89)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (505 voxels, overlap=0.058)
Right_Pallidum (52): linear fit = 0.88 x + 0.0 (505 voxels, peak = 86), gca=85.8
gca peak = 0.18160 (96)
mri peak = 0.09195 (85)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (350 voxels, overlap=0.051)
Left_Pallidum (13): linear fit = 0.88 x + 0.0 (350 voxels, peak = 84), gca=84.0
gca peak = 0.27536 (62)
mri peak = 0.08812 (57)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (595 voxels, overlap=0.440)
Right_Hippocampus (53): linear fit = 0.83 x + 0.0 (595 voxels, peak = 52), gca=51.8
gca peak = 0.32745 (63)
mri peak = 0.08194 (59)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (598 voxels, overlap=0.819)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (598 voxels, peak = 58), gca=58.3
gca peak = 0.08597 (105)
mri peak = 0.09455 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45864 voxels, overlap=0.701)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (45864 voxels, peak = 107), gca=106.6
gca peak = 0.09209 (106)
mri peak = 0.08356 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47371 voxels, overlap=0.613)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47371 voxels, peak = 110), gca=109.7
gca peak = 0.07826 (63)
mri peak = 0.05887 (52)
Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (17471 voxels, overlap=0.107)
Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (17471 voxels, peak = 48), gca=48.2
gca peak = 0.08598 (64)
mri peak = 0.07116 (52)
Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (16663 voxels, overlap=0.067)
Right_Cerebral_Cortex (42): linear fit = 0.75 x + 0.0 (16663 voxels, peak = 48), gca=48.3
gca peak = 0.24164 (71)
mri peak = 0.10545 (63)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (826 voxels, overlap=0.190)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (826 voxels, peak = 62), gca=62.1
gca peak = 0.18227 (75)
mri peak = 0.08061 (65)
Left_Caudate (11): linear fit = 0.86 x + 0.0 (1110 voxels, overlap=0.152)
Left_Caudate (11): linear fit = 0.86 x + 0.0 (1110 voxels, peak = 64), gca=64.1
gca peak = 0.10629 (62)
mri peak = 0.05314 (52)
Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (6613 voxels, overlap=0.861)
Left_Cerebellum_Cortex (8): linear fit = 0.88 x + 0.0 (6613 voxels, peak = 54), gca=54.2
gca peak = 0.11668 (59)
mri peak = 0.05021 (53)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (6203 voxels, overlap=0.768)
Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (6203 voxels, peak = 54), gca=54.0
gca peak = 0.17849 (88)
mri peak = 0.08202 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6058 voxels, overlap=0.980)
Left_Cerebellum_White_Matter (7): linear fit = 1.01 x + 0.0 (6058 voxels, peak = 89), gca=89.3
gca peak = 0.16819 (86)
mri peak = 0.07495 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6015 voxels, overlap=0.984)
Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (6015 voxels, peak = 87), gca=87.3
gca peak = 0.41688 (64)
mri peak = 0.08299 (56)
Left_Amygdala (18): linear fit = 0.86 x + 0.0 (264 voxels, overlap=0.768)
Left_Amygdala (18): linear fit = 0.86 x + 0.0 (264 voxels, peak = 55), gca=54.7
gca peak = 0.42394 (62)
mri peak = 0.10850 (52)
Right_Amygdala (54): linear fit = 0.86 x + 0.0 (224 voxels, overlap=0.627)
Right_Amygdala (54): linear fit = 0.86 x + 0.0 (224 voxels, peak = 53), gca=53.0
gca peak = 0.10041 (96)
mri peak = 0.05823 (91)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3976 voxels, overlap=0.996)
Left_Thalamus_Proper (10): linear fit = 0.99 x + 0.0 (3976 voxels, peak = 95), gca=94.6
gca peak = 0.13978 (88)
mri peak = 0.06134 (90)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, overlap=0.984)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, peak = 88), gca=87.6
gca peak = 0.08514 (81)
mri peak = 0.06002 (73)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1705 voxels, overlap=0.271)
Left_Putamen (12): linear fit = 0.87 x + 0.0 (1705 voxels, peak = 70), gca=70.1
gca peak = 0.09624 (82)
mri peak = 0.07704 (69)
Right_Putamen (51): linear fit = 0.85 x + 0.0 (1743 voxels, overlap=0.256)
Right_Putamen (51): linear fit = 0.85 x + 0.0 (1743 voxels, peak = 69), gca=69.3
gca peak = 0.07543 (88)
mri peak = 0.07082 (88)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (12039 voxels, overlap=0.765)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (12039 voxels, peak = 89), gca=89.3
gca peak = 0.12757 (95)
mri peak = 0.07129 (89)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1045 voxels, overlap=0.834)
Right_VentralDC (60): linear fit = 0.99 x + 0.0 (1045 voxels, peak = 94), gca=93.6
gca peak = 0.17004 (92)
mri peak = 0.06245 (97)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1262 voxels, overlap=0.899)
Left_VentralDC (28): linear fit = 1.03 x + 0.0 (1262 voxels, peak = 95), gca=95.2
gca peak = 0.21361 (36)
mri peak = 0.07715 (11)
gca peak = 0.26069 (23)
mri peak = 0.11330 (12)
Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (294 voxels, overlap=0.029)
Fourth_Ventricle (15): linear fit = 0.35 x + 0.0 (294 voxels, peak =  8), gca=8.2
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 0.83 x + 0.0
estimating mean wm scale to be 1.02 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 = 0.12487 ( 6)
Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (899 voxels, overlap=0.781)
Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (899 voxels, peak =  6), gca=5.8
gca peak = 0.29325 ( 9)
mri peak = 0.13637 ( 8)
Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1122 voxels, overlap=0.940)
Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1122 voxels, peak =  7), gca=7.1
gca peak = 0.27917 (88)
mri peak = 0.08549 (89)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (505 voxels, overlap=1.022)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (505 voxels, peak = 88), gca=88.0
gca peak = 0.18877 (84)
mri peak = 0.09195 (85)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (350 voxels, overlap=1.012)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (350 voxels, peak = 84), gca=83.6
gca peak = 0.32076 (52)
mri peak = 0.08812 (57)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (595 voxels, overlap=1.008)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (595 voxels, peak = 52), gca=52.0
gca peak = 0.30493 (58)
mri peak = 0.08194 (59)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (598 voxels, overlap=1.003)
Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (598 voxels, peak = 58), gca=58.0
gca peak = 0.08542 (107)
mri peak = 0.09455 (106)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45864 voxels, overlap=0.760)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45864 voxels, peak = 108), gca=107.5
gca peak = 0.08544 (110)
mri peak = 0.08356 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47371 voxels, overlap=0.744)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47371 voxels, peak = 110), gca=110.0
gca peak = 0.09987 (48)
mri peak = 0.05887 (52)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17471 voxels, overlap=0.995)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17471 voxels, peak = 48), gca=48.0
gca peak = 0.11781 (48)
mri peak = 0.07116 (52)
Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16663 voxels, overlap=0.995)
Right_Cerebral_Cortex (42): linear fit = 1.03 x + 0.0 (16663 voxels, peak = 50), gca=49.7
gca peak = 0.24215 (64)
mri peak = 0.10545 (63)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (826 voxels, overlap=1.006)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (826 voxels, peak = 63), gca=63.0
gca peak = 0.18458 (64)
mri peak = 0.08061 (65)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1110 voxels, overlap=1.000)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (1110 voxels, peak = 64), gca=64.0
gca peak = 0.12088 (53)
mri peak = 0.05314 (52)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (6613 voxels, overlap=0.995)
Left_Cerebellum_Cortex (8): linear fit = 1.04 x + 0.0 (6613 voxels, peak = 55), gca=55.4
gca peak = 0.12940 (55)
mri peak = 0.05021 (53)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6203 voxels, overlap=1.000)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (6203 voxels, peak = 54), gca=54.2
gca peak = 0.17397 (89)
mri peak = 0.08202 (90)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6058 voxels, overlap=0.992)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6058 voxels, peak = 89), gca=88.6
gca peak = 0.16063 (88)
mri peak = 0.07495 (87)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6015 voxels, overlap=0.997)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6015 voxels, peak = 88), gca=87.6
gca peak = 0.32010 (55)
mri peak = 0.08299 (56)
Left_Amygdala (18): linear fit = 1.07 x + 0.0 (264 voxels, overlap=1.020)
Left_Amygdala (18): linear fit = 1.07 x + 0.0 (264 voxels, peak = 59), gca=58.6
gca peak = 0.46062 (53)
mri peak = 0.10850 (52)
Right_Amygdala (54): linear fit = 1.07 x + 0.0 (224 voxels, overlap=1.023)
Right_Amygdala (54): linear fit = 1.07 x + 0.0 (224 voxels, peak = 56), gca=56.4
gca peak = 0.10422 (93)
mri peak = 0.05823 (91)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3976 voxels, overlap=0.979)
Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3976 voxels, peak = 94), gca=94.4
gca peak = 0.10935 (87)
mri peak = 0.06134 (90)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, overlap=0.992)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4124 voxels, peak = 87), gca=86.6
gca peak = 0.09481 (74)
mri peak = 0.06002 (73)
Left_Putamen (12): linear fit = 0.98 x + 0.0 (1705 voxels, overlap=1.002)
Left_Putamen (12): linear fit = 0.98 x + 0.0 (1705 voxels, peak = 72), gca=72.2
gca peak = 0.12360 (64)
mri peak = 0.07704 (69)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1743 voxels, overlap=0.997)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1743 voxels, peak = 63), gca=63.0
gca peak = 0.07465 (87)
mri peak = 0.07082 (88)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12039 voxels, overlap=0.799)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (12039 voxels, peak = 87), gca=86.6
gca peak = 0.14053 (93)
mri peak = 0.07129 (89)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1045 voxels, overlap=0.824)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1045 voxels, peak = 93), gca=92.5
gca peak = 0.15191 (95)
mri peak = 0.06245 (97)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1262 voxels, overlap=0.923)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1262 voxels, peak = 95), gca=95.5
gca peak = 0.35640 (14)
mri peak = 0.07715 (11)
gca peak = 0.33827 ( 9)
mri peak = 0.11330 (12)
Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (294 voxels, overlap=0.965)
Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (294 voxels, peak =  9), gca=9.5
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 = 0.51723 (60)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.62149 (62)
gca peak Left_choroid_plexus = 0.09108 (48)
gca peak Right_Inf_Lat_Vent = 0.30433 (27)
gca peak Right_Accumbens_area = 0.31102 (63)
gca peak Right_vessel = 0.29571 (59)
gca peak Right_choroid_plexus = 0.10219 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.14093 (84)
gca peak non_WM_hypointensities = 0.11402 (54)
gca peak Optic_Chiasm = 0.34849 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.03 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.79 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
14369 gm and wm labels changed (%10 to gray, %90 to white out of all changed labels)
331 hippocampal voxels changed.
12 amygdala voxels changed.
pass 1: 111271 changed. image ll: -2.298, PF=1.000
pass 2: 22081 changed. image ll: -2.296, PF=1.000
pass 3: 9319 changed.
pass 4: 4519 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 20 minutes and 23 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/cc_up.lta sub006 

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/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/norm.mgz
16109 voxels in left wm, 22492 in right wm, xrange [125, 130]
searching rotation angles z=[-8  6], y=[-5  9]

searching scale 1 Z rot -7.8  
searching scale 1 Z rot -7.6  
searching scale 1 Z rot -7.3  
searching scale 1 Z rot -7.1  
searching scale 1 Z rot -6.8  
searching scale 1 Z rot -6.6  
searching scale 1 Z rot -6.3  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.8  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 5.9  global minimum found at slice 127.6, rotations (1.66, -0.84)
final transformation (x=127.6, yr=1.660, zr=-0.844):
 0.999   0.015   0.029  -3.518;
-0.015   1.000  -0.000   47.929;
-0.029  -0.000   1.000   34.736;
 0.000   0.000   0.000   1.000;
updating x range to be [127, 130] in xformed coordinates
best xformed slice 129
cc center is found at 129 146 126
eigenvectors:
-0.001  -0.004   1.000;
-0.183  -0.983  -0.004;
 0.983  -0.183   0.000;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 0.6 minutes
#--------------------------------------
#@# Merge ASeg Thu Aug  8 17:02:53 CEST 2013

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Aug  8 17:02:53 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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...
4588 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 109
gm peak at 55 (55), valley at 30 (30)
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 56 (56), valley at 31 (31)
csf peak at 10, setting threshold to 40
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 30 seconds.
#--------------------------------------------
#@# Mask BFS Thu Aug  8 17:07:25 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1875800 voxels in mask (pct= 11.18)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Thu Aug  8 17:07:28 CEST 2013

 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 (108.0): 107.4 +- 4.6 [80.0 --> 125.0]
GM (66.0) : 65.4 +- 9.8 [30.0 --> 96.0]
setting bottom of white matter range to 75.2
setting top of gray matter range to 85.0
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...
7560 sparsely connected voxels removed...
thickening thin strands....
20 segments, 6169 filled
374 bright non-wm voxels segmented.
4405 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 0.69 minutes
reading wm segmentation from wm.seg.mgz...
45 voxels added to wm to prevent paths from MTL structures to cortex
1381 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 56233 voxels turned on, 47216 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+):  16 found -  16 modified     |    TOTAL:  16
pass   2 (xy+):   0 found -  16 modified     |    TOTAL:  16
pass   1 (xy-):  20 found -  20 modified     |    TOTAL:  36
pass   2 (xy-):   0 found -  20 modified     |    TOTAL:  36
pass   1 (yz+):  34 found -  34 modified     |    TOTAL:  70
pass   2 (yz+):   0 found -  34 modified     |    TOTAL:  70
pass   1 (yz-):  15 found -  15 modified     |    TOTAL:  85
pass   2 (yz-):   0 found -  15 modified     |    TOTAL:  85
pass   1 (xz+):  24 found -  24 modified     |    TOTAL: 109
pass   2 (xz+):   0 found -  24 modified     |    TOTAL: 109
pass   1 (xz-):  24 found -  24 modified     |    TOTAL: 133
pass   2 (xz-):   0 found -  24 modified     |    TOTAL: 133
Iteration Number : 1
pass   1 (+++):  25 found -  25 modified     |    TOTAL:  25
pass   2 (+++):   0 found -  25 modified     |    TOTAL:  25
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  35
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  35
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  45
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  45
pass   1 (+++):  19 found -  19 modified     |    TOTAL:  64
pass   2 (+++):   0 found -  19 modified     |    TOTAL:  64
Iteration Number : 1
pass   1 (++): 213 found - 213 modified     |    TOTAL: 213
pass   2 (++):   0 found - 213 modified     |    TOTAL: 213
pass   1 (+-): 173 found - 173 modified     |    TOTAL: 386
pass   2 (+-):   0 found - 173 modified     |    TOTAL: 386
pass   1 (--): 191 found - 191 modified     |    TOTAL: 577
pass   2 (--):   0 found - 191 modified     |    TOTAL: 577
pass   1 (-+): 190 found - 190 modified     |    TOTAL: 767
pass   2 (-+):   0 found - 190 modified     |    TOTAL: 767
Iteration Number : 2
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   5 found -   5 modified     |    TOTAL:   8
pass   2 (xy-):   0 found -   5 modified     |    TOTAL:   8
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   9
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   9
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:  10
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:  10
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  13
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  13
pass   1 (xz-):   4 found -   4 modified     |    TOTAL:  17
pass   2 (xz-):   0 found -   4 modified     |    TOTAL:  17
Iteration Number : 2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   2
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   4
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   4
pass   1 (+++):   2 found -   2 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   2 modified     |    TOTAL:   6
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   3
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   3
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   4
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 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 (--):   1 found -   1 modified     |    TOTAL:   1
pass   2 (--):   0 found -   1 modified     |    TOTAL:   1
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   1
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 5
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 995 (out of 667295: 0.149109)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Thu Aug  8 17:10:08 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.057   0.021   0.022  -13.719;
-0.025   1.044   0.279  -8.820;
-0.018  -0.231   0.863   32.977;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 914 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75)
no need to search
using seed (126, 115, 148), TAL = (2.0, 20.0, 13.0)
talairach voxel to voxel transform
 0.945  -0.022  -0.017   13.320;
 0.016   0.894  -0.289   17.639;
 0.024   0.238   1.081  -33.213;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (126,  115,  148) --> (2.0, 20.0, 13.0)
done.
writing output to filled.mgz...
filling took 1.0 minutes
talairach cc position changed to (2.00, 20.00, 13.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 20.00, 13.00) SRC: (110.41, 79.37, 156.83)
search lh wm seed point around talairach space (-16.00, 20.00, 13.00), SRC: (144.44, 79.94, 157.71)
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 Thu Aug  8 17:11:07 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

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


Iteration Number : 1
pass   1 (xy+):   2 found -   2 modified     |    TOTAL:   2
pass   2 (xy+):   0 found -   2 modified     |    TOTAL:   2
pass   1 (xy-):   3 found -   3 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   3 modified     |    TOTAL:   5
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   6
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   7
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   7
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   8
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   8
pass   1 (xz-):   1 found -   1 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   1 modified     |    TOTAL:   9
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (--):   2 found -   2 modified     |    TOTAL:   4
pass   2 (--):   0 found -   2 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
Iteration Number : 2
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz+):   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 = 14 (out of 319770: 0.004378)
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 30: 132 vertices, 158 faces
slice 40: 5154 vertices, 5422 faces
slice 50: 15090 vertices, 15484 faces
slice 60: 27343 vertices, 27780 faces
slice 70: 40146 vertices, 40596 faces
slice 80: 52914 vertices, 53297 faces
slice 90: 65174 vertices, 65598 faces
slice 100: 78142 vertices, 78578 faces
slice 110: 90088 vertices, 90497 faces
slice 120: 102254 vertices, 102675 faces
slice 130: 113707 vertices, 114156 faces
slice 140: 125465 vertices, 125866 faces
slice 150: 135787 vertices, 136156 faces
slice 160: 145524 vertices, 145859 faces
slice 170: 154037 vertices, 154323 faces
slice 180: 161662 vertices, 161914 faces
slice 190: 167381 vertices, 167600 faces
slice 200: 171832 vertices, 171986 faces
slice 210: 172752 vertices, 172782 faces
slice 220: 172752 vertices, 172782 faces
slice 230: 172752 vertices, 172782 faces
slice 240: 172752 vertices, 172782 faces
slice 250: 172752 vertices, 172782 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...
   172752 voxel in cpt #1: X=-30 [v=172752,e=518346,f=345564] located at (-26.980938, -19.630371, 40.472919)
For the whole surface: X=-30 [v=172752,e=518346,f=345564]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Aug  8 17:11:17 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 17:11:23 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
avg radius = 52.1 mm, total surface area = 91668 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=0.072 (target=0.015)   
step 010: RMS=0.052 (target=0.015)   
step 015: RMS=0.043 (target=0.015)   
step 020: RMS=0.036 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.028 (target=0.015)   
step 035: RMS=0.025 (target=0.015)   
step 040: RMS=0.022 (target=0.015)   
step 045: RMS=0.021 (target=0.015)   
step 050: RMS=0.020 (target=0.015)   
step 055: RMS=0.020 (target=0.015)   
step 060: RMS=0.019 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Thu Aug  8 17:12:06 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.88 +- 0.55 (0.00-->6.92) (max @ vno 79103 --> 79124)
face area 0.02 +- 0.03 (-0.34-->0.86)
scaling brain by 0.280...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.310, avgs=0
005/300: dt: 0.9000, rms radial error=176.051, avgs=0
010/300: dt: 0.9000, rms radial error=175.496, avgs=0
015/300: dt: 0.9000, rms radial error=174.766, avgs=0
020/300: dt: 0.9000, rms radial error=173.934, avgs=0
025/300: dt: 0.9000, rms radial error=173.044, avgs=0
030/300: dt: 0.9000, rms radial error=172.120, avgs=0
035/300: dt: 0.9000, rms radial error=171.178, avgs=0
040/300: dt: 0.9000, rms radial error=170.235, avgs=0
045/300: dt: 0.9000, rms radial error=169.288, avgs=0
050/300: dt: 0.9000, rms radial error=168.341, avgs=0
055/300: dt: 0.9000, rms radial error=167.397, avgs=0
060/300: dt: 0.9000, rms radial error=166.458, avgs=0
065/300: dt: 0.9000, rms radial error=165.528, avgs=0
070/300: dt: 0.9000, rms radial error=164.603, avgs=0
075/300: dt: 0.9000, rms radial error=163.682, avgs=0
080/300: dt: 0.9000, rms radial error=162.767, avgs=0
085/300: dt: 0.9000, rms radial error=161.856, avgs=0
090/300: dt: 0.9000, rms radial error=160.951, avgs=0
095/300: dt: 0.9000, rms radial error=160.050, avgs=0
100/300: dt: 0.9000, rms radial error=159.154, avgs=0
105/300: dt: 0.9000, rms radial error=158.264, avgs=0
110/300: dt: 0.9000, rms radial error=157.379, avgs=0
115/300: dt: 0.9000, rms radial error=156.499, avgs=0
120/300: dt: 0.9000, rms radial error=155.623, avgs=0
125/300: dt: 0.9000, rms radial error=154.752, avgs=0
130/300: dt: 0.9000, rms radial error=153.886, avgs=0
135/300: dt: 0.9000, rms radial error=153.024, avgs=0
140/300: dt: 0.9000, rms radial error=152.167, avgs=0
145/300: dt: 0.9000, rms radial error=151.315, avgs=0
150/300: dt: 0.9000, rms radial error=150.467, avgs=0
155/300: dt: 0.9000, rms radial error=149.624, avgs=0
160/300: dt: 0.9000, rms radial error=148.785, avgs=0
165/300: dt: 0.9000, rms radial error=147.951, avgs=0
170/300: dt: 0.9000, rms radial error=147.122, avgs=0
175/300: dt: 0.9000, rms radial error=146.296, avgs=0
180/300: dt: 0.9000, rms radial error=145.476, avgs=0
185/300: dt: 0.9000, rms radial error=144.660, avgs=0
190/300: dt: 0.9000, rms radial error=143.848, avgs=0
195/300: dt: 0.9000, rms radial error=143.041, avgs=0
200/300: dt: 0.9000, rms radial error=142.238, avgs=0
205/300: dt: 0.9000, rms radial error=141.439, avgs=0
210/300: dt: 0.9000, rms radial error=140.645, avgs=0
215/300: dt: 0.9000, rms radial error=139.855, avgs=0
220/300: dt: 0.9000, rms radial error=139.069, avgs=0
225/300: dt: 0.9000, rms radial error=138.288, avgs=0
230/300: dt: 0.9000, rms radial error=137.511, avgs=0
235/300: dt: 0.9000, rms radial error=136.738, avgs=0
240/300: dt: 0.9000, rms radial error=135.969, avgs=0
245/300: dt: 0.9000, rms radial error=135.205, avgs=0
250/300: dt: 0.9000, rms radial error=134.445, avgs=0
255/300: dt: 0.9000, rms radial error=133.689, avgs=0
260/300: dt: 0.9000, rms radial error=132.937, avgs=0
265/300: dt: 0.9000, rms radial error=132.190, avgs=0
270/300: dt: 0.9000, rms radial error=131.446, avgs=0
275/300: dt: 0.9000, rms radial error=130.707, avgs=0
280/300: dt: 0.9000, rms radial error=129.971, avgs=0
285/300: dt: 0.9000, rms radial error=129.240, avgs=0
290/300: dt: 0.9000, rms radial error=128.513, avgs=0
295/300: dt: 0.9000, rms radial error=127.790, avgs=0
300/300: dt: 0.9000, rms radial error=127.070, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20881.80
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 = 3776.48
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00000
epoch 3 (K=160.0), pass 1, starting sse = 442.44
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/10 = 0.00462
epoch 4 (K=640.0), pass 1, starting sse = 29.50
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.07/12 = 0.00571
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.10 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Thu Aug  8 17:18:15 CEST 2013

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


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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub006 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=-30 (nv=172752, nf=345564, ne=518346, g=16)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
2478 ambiguous faces found in tessellation
segmenting defects...
25 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 6 into 4
      -merging segment 8 into 7
      -merging segment 11 into 7
22 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.9378  (-4.9689)
      -vertex     loglikelihood: -6.7130  (-3.3565)
      -normal dot loglikelihood: -3.6670  (-3.6670)
      -quad curv  loglikelihood: -6.4196  (-3.2098)
      Total Loglikelihood : -26.7374

CORRECTING DEFECT 0 (vertices=10, convex hull=18)
After retessellation of defect 0, euler #=-21 (171201,512909,341687) : difference with theory (-19) = 2 

CORRECTING DEFECT 1 (vertices=90, convex hull=84)
After retessellation of defect 1, euler #=-20 (171220,513001,341761) : difference with theory (-18) = 2 

CORRECTING DEFECT 2 (vertices=101, convex hull=88)
After retessellation of defect 2, euler #=-19 (171241,513104,341844) : difference with theory (-17) = 2 

CORRECTING DEFECT 3 (vertices=33, convex hull=70)
After retessellation of defect 3, euler #=-18 (171262,513194,341914) : difference with theory (-16) = 2 

CORRECTING DEFECT 4 (vertices=228, convex hull=225)
After retessellation of defect 4, euler #=-16 (171280,513353,342057) : difference with theory (-15) = 1 

CORRECTING DEFECT 5 (vertices=213, convex hull=159)
After retessellation of defect 5, euler #=-15 (171315,513528,342198) : difference with theory (-14) = 1 

CORRECTING DEFECT 6 (vertices=342, convex hull=236)
After retessellation of defect 6, euler #=-12 (171346,513753,342395) : difference with theory (-13) = -1 

CORRECTING DEFECT 7 (vertices=6, convex hull=14)
After retessellation of defect 7, euler #=-11 (171346,513757,342400) : difference with theory (-12) = -1 

CORRECTING DEFECT 8 (vertices=26, convex hull=65)
After retessellation of defect 8, euler #=-10 (171361,513830,342459) : difference with theory (-11) = -1 

CORRECTING DEFECT 9 (vertices=47, convex hull=45)
After retessellation of defect 9, euler #=-10 (171374,513891,342507) : difference with theory (-10) = 0 

CORRECTING DEFECT 10 (vertices=25, convex hull=24)
After retessellation of defect 10, euler #=-9 (171378,513911,342524) : difference with theory (-9) = 0 

CORRECTING DEFECT 11 (vertices=57, convex hull=40)
After retessellation of defect 11, euler #=-8 (171384,513944,342552) : difference with theory (-8) = 0 

CORRECTING DEFECT 12 (vertices=21, convex hull=32)
After retessellation of defect 12, euler #=-7 (171388,513967,342572) : difference with theory (-7) = 0 

CORRECTING DEFECT 13 (vertices=12, convex hull=30)
After retessellation of defect 13, euler #=-6 (171393,513994,342595) : difference with theory (-6) = 0 

CORRECTING DEFECT 14 (vertices=51, convex hull=65)
After retessellation of defect 14, euler #=-5 (171408,514062,342649) : difference with theory (-5) = 0 

CORRECTING DEFECT 15 (vertices=70, convex hull=61)
After retessellation of defect 15, euler #=-4 (171415,514107,342688) : difference with theory (-4) = 0 

CORRECTING DEFECT 16 (vertices=23, convex hull=27)
After retessellation of defect 16, euler #=-3 (171421,514133,342709) : difference with theory (-3) = 0 

CORRECTING DEFECT 17 (vertices=9, convex hull=26)
After retessellation of defect 17, euler #=-2 (171424,514150,342724) : difference with theory (-2) = 0 

CORRECTING DEFECT 18 (vertices=55, convex hull=68)
After retessellation of defect 18, euler #=-1 (171437,514214,342776) : difference with theory (-1) = 0 

CORRECTING DEFECT 19 (vertices=34, convex hull=59)
After retessellation of defect 19, euler #=0 (171445,514261,342816) : difference with theory (0) = 0 

CORRECTING DEFECT 20 (vertices=45, convex hull=95)
After retessellation of defect 20, euler #=1 (171462,514349,342888) : difference with theory (1) = 0 

CORRECTING DEFECT 21 (vertices=49, convex hull=74)
After retessellation of defect 21, euler #=2 (171478,514428,342952) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.09-->11.19) (max @ vno 73397 --> 77073)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.23 (0.09-->11.19) (max @ vno 73397 --> 77073)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
81 mutations (34.6%), 153 crossovers (65.4%), 260 vertices were eliminated
building final representation...
1274 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=171478, nf=342952, ne=514428, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 29.8 minutes
0 defective edges
removing intersecting faces
000: 202 intersecting
001: 2 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 171478 - 514428 + 342952 = 2 --> 0 holes
      F =2V-4:          342952 = 342956-4 (0)
      2E=3F:            1028856 = 1028856 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 19 intersecting
001: 3 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Thu Aug  8 17:48:10 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub006 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/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
24515 bright wm thresholded.
438 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
computing class statistics...
border white:    318128 voxels (1.90%)
border gray      352780 voxels (2.10%)
WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 29.7 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->4.93) (max @ vno 73397 --> 77073)
face area 0.28 +- 0.12 (0.00-->4.07)
mean absolute distance = 0.66 +- 0.76
4605 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=106,    GM=57
mean inside = 93.4, mean outside = 67.5
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=71.0, 74 (74) missing vertices, mean dist 0.4 [0.5 (%28.2)->0.7 (%71.8))]
%73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 (0.11-->7.80) (max @ vno 77073 --> 73397)
face area 0.28 +- 0.13 (0.00-->6.15)
mean absolute distance = 0.33 +- 0.46
4148 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=10027942.0, rms=14.60
001: dt: 0.5000, sse=9368935.0, rms=10.566 (0.000%)
002: dt: 0.5000, sse=9359829.0, rms=8.174 (0.000%)
003: dt: 0.5000, sse=9455504.0, rms=6.630 (0.000%)
004: dt: 0.5000, sse=9669029.0, rms=5.705 (0.000%)
005: dt: 0.5000, sse=9780128.0, rms=5.172 (0.000%)
006: dt: 0.5000, sse=9891815.0, rms=4.903 (0.000%)
007: dt: 0.5000, sse=9901317.0, rms=4.749 (0.000%)
008: dt: 0.5000, sse=9908980.0, rms=4.663 (0.000%)
009: dt: 0.5000, sse=9865048.0, rms=4.605 (0.000%)
rms = 4.57, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9860651.0, rms=4.565 (0.000%)
011: dt: 0.2500, sse=6112863.0, rms=3.143 (0.000%)
012: dt: 0.2500, sse=5634209.5, rms=2.705 (0.000%)
013: dt: 0.2500, sse=5322691.0, rms=2.631 (0.000%)
014: dt: 0.2500, sse=5252264.5, rms=2.570 (0.000%)
rms = 2.56, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=5136448.5, rms=2.560 (0.000%)
016: dt: 0.1250, sse=4708750.5, rms=2.156 (0.000%)
017: dt: 0.1250, sse=4654870.0, rms=2.100 (0.000%)
rms = 2.09, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=4617372.5, rms=2.093 (0.000%)
positioning took 2.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=76.5, 49 (14) missing vertices, mean dist -0.2 [0.4 (%82.0)->0.2 (%18.0))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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 (0.09-->8.01) (max @ vno 77073 --> 73397)
face area 0.35 +- 0.17 (0.00-->8.31)
mean absolute distance = 0.21 +- 0.28
4675 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=6305146.5, rms=7.16
019: dt: 0.5000, sse=6108556.5, rms=4.764 (0.000%)
rms = 4.91, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=5510872.5, rms=3.535 (0.000%)
021: dt: 0.2500, sse=5267443.5, rms=2.833 (0.000%)
022: dt: 0.2500, sse=5214090.5, rms=2.299 (0.000%)
023: dt: 0.2500, sse=5223199.5, rms=2.220 (0.000%)
024: dt: 0.2500, sse=5142760.5, rms=2.063 (0.000%)
rms = 2.09, time step reduction 2 of 3 to 0.125...
025: dt: 0.1250, sse=5035590.5, rms=1.913 (0.000%)
026: dt: 0.1250, sse=4902379.0, rms=1.694 (0.000%)
rms = 1.65, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4851876.0, rms=1.651 (0.000%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 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=80.3, 35 (5) missing vertices, mean dist -0.1 [0.2 (%79.1)->0.2 (%20.9))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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 (0.10-->8.21) (max @ vno 77073 --> 73397)
face area 0.34 +- 0.16 (0.00-->8.32)
mean absolute distance = 0.15 +- 0.22
3223 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5480494.5, rms=4.80
028: dt: 0.5000, sse=5843610.0, rms=4.653 (0.000%)
029: dt: 0.5000, sse=6094991.5, rms=4.548 (0.000%)
rms = 4.91, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=5307931.5, rms=2.755 (0.000%)
031: dt: 0.2500, sse=5336993.5, rms=2.063 (0.000%)
rms = 2.07, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=5213570.5, rms=1.842 (0.000%)
033: dt: 0.1250, sse=5036277.0, rms=1.485 (0.000%)
034: dt: 0.1250, sse=4985887.5, rms=1.407 (0.000%)
rms = 1.41, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=4985887.5, rms=1.407 (0.004%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 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=81.4, 30 (4) missing vertices, mean dist -0.0 [0.2 (%59.5)->0.1 (%40.5))]
%93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=5031109.0, rms=1.92
rms = 3.04, time step reduction 1 of 3 to 0.250...
036: dt: 0.2500, sse=5082993.5, rms=1.249 (0.000%)
037: dt: 0.2500, sse=5214479.0, rms=1.069 (0.000%)
rms = 1.06, time step reduction 2 of 3 to 0.125...
038: dt: 0.2500, sse=5316066.5, rms=1.065 (0.000%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=5339791.5, rms=1.027 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
generating cortex label...
22 non-cortical segments detected
only using segment with 2212 vertices
erasing segment 1 (vno[0] = 73466)
erasing segment 2 (vno[0] = 78475)
erasing segment 3 (vno[0] = 100956)
erasing segment 4 (vno[0] = 112206)
erasing segment 5 (vno[0] = 122789)
erasing segment 6 (vno[0] = 123824)
erasing segment 7 (vno[0] = 123835)
erasing segment 8 (vno[0] = 123859)
erasing segment 9 (vno[0] = 124890)
erasing segment 10 (vno[0] = 127013)
erasing segment 11 (vno[0] = 127062)
erasing segment 12 (vno[0] = 127083)
erasing segment 13 (vno[0] = 128190)
erasing segment 14 (vno[0] = 129286)
erasing segment 15 (vno[0] = 131208)
erasing segment 16 (vno[0] = 131226)
erasing segment 17 (vno[0] = 132184)
erasing segment 18 (vno[0] = 133096)
erasing segment 19 (vno[0] = 133105)
erasing segment 20 (vno[0] = 133109)
erasing segment 21 (vno[0] = 134078)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397)
face area 0.34 +- 0.16 (0.00-->8.21)
refinement took 9.4 minutes
#--------------------------------------------
#@# Smooth2 lh Thu Aug  8 17:57:32 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 17:57:37 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

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

avg radius = 52.3 mm, total surface area = 105174 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.113 (target=0.015)   
step 005: RMS=0.078 (target=0.015)   
step 010: RMS=0.056 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.026 (target=0.015)   
step 035: RMS=0.022 (target=0.015)   
step 040: RMS=0.019 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
step 050: RMS=0.015 (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
242 vertices thresholded to be in k1 ~ [-0.25 0.92], k2 ~ [-0.17 0.07]
total integrated curvature = 0.488*4pi (6.130) --> 1 handles
ICI = 1.9, FI = 16.1, variation=257.292
156 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
128 vertices thresholded to be in [-0.13 0.17]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.026
done.

#-----------------------------------------
#@# Curvature Stats lh Thu Aug  8 18:00:26 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub006 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       [ sub006/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                      [ 311 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.410253
WARN:    S explicit min:                          0.000000	vertex = 12
#--------------------------------------------
#@# Sphere lh Thu Aug  8 18:00:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.262...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.43
pass 1: epoch 2 of 3 starting distance error %20.34
unfolding complete - removing small folds...
starting distance error %20.24
removing remaining folds...
final distance error %20.25
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.28 hours
#--------------------------------------------
#@# Surf Reg lh Thu Aug  8 19:17:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/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/5.3.0/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=snake, 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=snake, 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 = 0.579
curvature mean = 0.039, std = 0.935
curvature mean = 0.025, std = 0.829
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 379756.1, tmin=1.3897
  d=32.00 min @ (8.00, 8.00, 0.00) sse = 336884.5, tmin=2.7776
  d=16.00 min @ (0.00, -4.00, -4.00) sse = 296310.6, tmin=4.1916
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 287756.1, tmin=5.6632
  d=4.00 min @ (0.00, 0.00, 1.00) sse = 286234.4, tmin=7.1875
  d=2.00 min @ (0.50, 1.00, -0.50) sse = 285496.2, tmin=8.7121
  d=1.00 min @ (-0.25, -0.50, 0.25) sse = 285288.4, tmin=10.2292
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 285256.1, tmin=11.7381
tol=1.0e+00, sigma=0.5, host=snake, 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  11.74 min
curvature mean = 0.012, std = 0.938
curvature mean = 0.014, std = 0.924
curvature mean = 0.009, std = 0.948
curvature mean = 0.007, std = 0.963
curvature mean = 0.006, std = 0.946
curvature mean = 0.002, std = 0.983
2 Reading smoothwm
curvature mean = -0.022, std = 0.292
curvature mean = 0.004, std = 0.066
curvature mean = 0.073, std = 0.308
curvature mean = 0.004, std = 0.077
curvature mean = 0.035, std = 0.494
curvature mean = 0.004, std = 0.083
curvature mean = 0.020, std = 0.639
curvature mean = 0.004, std = 0.085
curvature mean = 0.006, std = 0.758
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Thu Aug  8 19:53:12 CEST 2013

 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 Thu Aug  8 19:53:15 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3.0/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/5.3.0/average/lh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/lh.avg_curv...
#-----------------------------------------
#@# Cortical Parc lh Thu Aug  8 19:53:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/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/5.3.0/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...
1813 labels changed using aseg
relabeling using gibbs priors...
000:   3786 changed, 171478 examined...
001:    799 changed, 15881 examined...
002:    222 changed, 4452 examined...
003:     84 changed, 1319 examined...
004:     34 changed, 498 examined...
005:     14 changed, 217 examined...
006:     11 changed, 85 examined...
007:      2 changed, 46 examined...
008:      0 changed, 11 examined...
244 labels changed using aseg
000: 145 total segments, 102 labels (377 vertices) changed
001: 43 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 58 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1900 vertices marked for relabeling...
1900 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 1 minutes and 18 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Thu Aug  8 19:54:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub006 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/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
24515 bright wm thresholded.
438 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
computing class statistics...
border white:    318128 voxels (1.90%)
border gray      352780 voxels (2.10%)
WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 29.7 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=57
mean inside = 93.4, mean outside = 67.5
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/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->4.93) (max @ vno 73397 --> 77073)
face area 0.28 +- 0.12 (0.00-->4.07)
mean absolute distance = 0.66 +- 0.77
4633 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 193 points - only 7.25% unknown
deleting segment 1 with 22 points - only 0.00% unknown
deleting segment 2 with 14 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 6 with 21 points - only 0.00% unknown
deleting segment 7 with 741 points - only 0.00% unknown
deleting segment 9 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 12 with 16 points - only 0.00% unknown
deleting segment 13 with 13 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
deleting segment 15 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
deleting segment 17 with 8 points - only 0.00% unknown
mean border=71.0, 74 (74) missing vertices, mean dist 0.4 [0.5 (%28.4)->0.7 (%71.6))]
%73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 (0.11-->7.80) (max @ vno 77073 --> 73397)
face area 0.28 +- 0.13 (0.00-->6.14)
mean absolute distance = 0.33 +- 0.46
4164 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=10060111.0, rms=14.57
001: dt: 0.5000, sse=9420631.0, rms=10.543 (0.000%)
002: dt: 0.5000, sse=9418131.0, rms=8.156 (0.000%)
003: dt: 0.5000, sse=9519878.0, rms=6.618 (0.000%)
004: dt: 0.5000, sse=9735789.0, rms=5.693 (0.000%)
005: dt: 0.5000, sse=9850333.0, rms=5.165 (0.000%)
006: dt: 0.5000, sse=9963383.0, rms=4.895 (0.000%)
007: dt: 0.5000, sse=9970060.0, rms=4.742 (0.000%)
008: dt: 0.5000, sse=9981884.0, rms=4.655 (0.000%)
009: dt: 0.5000, sse=9935452.0, rms=4.600 (0.000%)
rms = 4.56, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9933331.0, rms=4.559 (0.000%)
011: dt: 0.2500, sse=6159862.0, rms=3.139 (0.000%)
012: dt: 0.2500, sse=5673852.5, rms=2.701 (0.000%)
013: dt: 0.2500, sse=5361696.0, rms=2.628 (0.000%)
014: dt: 0.2500, sse=5288730.5, rms=2.568 (0.000%)
rms = 2.56, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=5172132.5, rms=2.558 (0.000%)
016: dt: 0.1250, sse=4745235.5, rms=2.156 (0.000%)
017: dt: 0.1250, sse=4692363.0, rms=2.101 (0.000%)
rms = 2.09, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=4655493.5, rms=2.095 (0.000%)
positioning took 2.9 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 244 points - only 8.61% unknown
deleting segment 1 with 22 points - only 0.00% unknown
deleting segment 2 with 17 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 5 with 19 points - only 0.00% unknown
deleting segment 7 with 8 points - only 0.00% unknown
deleting segment 8 with 660 points - only 0.00% unknown
deleting segment 9 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 15 with 16 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
deleting segment 17 with 6 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 18 with 3 points - only 0.00% unknown
mean border=76.5, 54 (14) missing vertices, mean dist -0.2 [0.4 (%82.0)->0.2 (%18.0))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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 (0.09-->8.01) (max @ vno 77073 --> 73397)
face area 0.35 +- 0.17 (0.00-->8.31)
mean absolute distance = 0.21 +- 0.28
4693 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=6350666.5, rms=7.15
019: dt: 0.5000, sse=6157726.0, rms=4.757 (0.000%)
rms = 4.90, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=5554555.0, rms=3.530 (0.000%)
021: dt: 0.2500, sse=5309827.0, rms=2.830 (0.000%)
022: dt: 0.2500, sse=5256700.5, rms=2.297 (0.000%)
023: dt: 0.2500, sse=5266794.0, rms=2.219 (0.000%)
024: dt: 0.2500, sse=5183961.0, rms=2.063 (0.000%)
rms = 2.09, time step reduction 2 of 3 to 0.125...
025: dt: 0.1250, sse=5076422.5, rms=1.914 (0.000%)
026: dt: 0.1250, sse=4942420.0, rms=1.695 (0.000%)
rms = 1.65, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4891604.5, rms=1.652 (0.000%)
positioning took 1.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 216 points - only 6.48% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 17 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 24 points - only 0.00% unknown
deleting segment 5 with 700 points - only 0.00% unknown
deleting segment 6 with 14 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 26 points - only 0.00% unknown
deleting segment 12 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 14 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
deleting segment 16 with 6 points - only 0.00% unknown
mean border=80.2, 36 (5) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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 +- 0.24 (0.10-->8.21) (max @ vno 77073 --> 73397)
face area 0.34 +- 0.16 (0.00-->8.31)
mean absolute distance = 0.15 +- 0.22
3263 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5522440.5, rms=4.79
028: dt: 0.5000, sse=5886809.0, rms=4.643 (0.000%)
029: dt: 0.5000, sse=6147410.0, rms=4.543 (0.000%)
rms = 4.91, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=5351452.0, rms=2.754 (0.000%)
031: dt: 0.2500, sse=5377083.0, rms=2.060 (0.000%)
rms = 2.07, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=5253498.0, rms=1.840 (0.000%)
033: dt: 0.1250, sse=5076645.5, rms=1.485 (0.000%)
034: dt: 0.1250, sse=5025209.0, rms=1.408 (0.000%)
rms = 1.41, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=5025209.0, rms=1.408 (0.004%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 215 points - only 5.58% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 17 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 3 with 1 points - only 0.00% unknown
deleting segment 4 with 22 points - only 0.00% unknown
deleting segment 5 with 707 points - only 0.00% unknown
deleting segment 6 with 14 points - only 0.00% unknown
deleting segment 7 with 5 points - only 0.00% unknown
deleting segment 8 with 35 points - only 0.00% unknown
deleting segment 9 with 20 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 11 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 12 with 3 points - only 0.00% unknown
deleting segment 13 with 7 points - only 0.00% unknown
mean border=81.3, 31 (4) missing vertices, mean dist -0.0 [0.2 (%59.4)->0.1 (%40.6))]
%93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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=5070727.0, rms=1.92
rms = 3.03, time step reduction 1 of 3 to 0.250...
036: dt: 0.2500, sse=5124402.0, rms=1.249 (0.000%)
037: dt: 0.2500, sse=5259710.5, rms=1.070 (0.000%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
038: dt: 0.2500, sse=5361433.0, rms=1.067 (0.000%)
rms = 1.03, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=5386527.0, rms=1.029 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=46.6, 37 (37) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))]
%14 local maxima, %62 large gradients and %20 min vals, 1854 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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=41829020.0, rms=34.18
001: dt: 0.5000, sse=29729242.0, rms=28.287 (0.000%)
002: dt: 0.5000, sse=21449460.0, rms=23.444 (0.000%)
003: dt: 0.5000, sse=15982869.0, rms=19.550 (0.000%)
004: dt: 0.5000, sse=12582245.0, rms=16.460 (0.000%)
005: dt: 0.5000, sse=10589562.0, rms=14.062 (0.000%)
006: dt: 0.5000, sse=9451943.0, rms=12.170 (0.000%)
007: dt: 0.5000, sse=8684540.0, rms=10.517 (0.000%)
008: dt: 0.5000, sse=8174177.5, rms=9.004 (0.000%)
009: dt: 0.5000, sse=7824750.5, rms=7.641 (0.000%)
010: dt: 0.5000, sse=7654596.5, rms=6.437 (0.000%)
011: dt: 0.5000, sse=7620808.5, rms=5.478 (0.000%)
012: dt: 0.5000, sse=7788831.0, rms=4.808 (0.000%)
013: dt: 0.5000, sse=7917054.5, rms=4.418 (0.000%)
014: dt: 0.5000, sse=8059843.5, rms=4.191 (0.000%)
015: dt: 0.5000, sse=8142026.5, rms=4.081 (0.000%)
016: dt: 0.5000, sse=8267752.0, rms=3.996 (0.000%)
rms = 3.95, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=8282918.5, rms=3.953 (0.000%)
018: dt: 0.2500, sse=5694765.5, rms=3.099 (0.000%)
019: dt: 0.2500, sse=5496246.0, rms=2.870 (0.000%)
rms = 2.84, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=5338956.0, rms=2.841 (0.000%)
021: dt: 0.1250, sse=5070952.5, rms=2.649 (0.000%)
rms = 2.62, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=5036784.5, rms=2.623 (0.000%)
positioning took 3.3 minutes
mean border=43.9, 753 (5) missing vertices, mean dist 0.2 [0.2 (%48.8)->0.6 (%51.2))]
%33 local maxima, %47 large gradients and %16 min vals, 476 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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=5913994.5, rms=5.00
023: dt: 0.5000, sse=6323110.0, rms=4.222 (0.000%)
024: dt: 0.5000, sse=8048154.5, rms=4.157 (0.000%)
rms = 4.14, time step reduction 1 of 3 to 0.250...
025: dt: 0.5000, sse=8038463.0, rms=4.141 (0.000%)
026: dt: 0.2500, sse=6275116.5, rms=3.104 (0.000%)
027: dt: 0.2500, sse=6170375.0, rms=2.796 (0.000%)
rms = 2.79, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=5969225.5, rms=2.793 (0.000%)
029: dt: 0.1250, sse=5720778.5, rms=2.553 (0.000%)
rms = 2.52, time step reduction 3 of 3 to 0.062...
030: dt: 0.1250, sse=5693824.5, rms=2.518 (0.000%)
positioning took 1.2 minutes
mean border=40.9, 885 (3) missing vertices, mean dist 0.1 [0.2 (%35.5)->0.4 (%64.5))]
%57 local maxima, %24 large gradients and %15 min vals, 602 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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=6194776.0, rms=4.52
031: dt: 0.5000, sse=6317909.0, rms=4.116 (0.000%)
rms = 4.10, time step reduction 1 of 3 to 0.250...
032: dt: 0.5000, sse=8341824.5, rms=4.101 (0.000%)
033: dt: 0.2500, sse=6203912.5, rms=3.015 (0.000%)
034: dt: 0.2500, sse=6381834.5, rms=2.697 (0.000%)
rms = 2.72, time step reduction 2 of 3 to 0.125...
035: dt: 0.1250, sse=6219413.0, rms=2.580 (0.000%)
036: dt: 0.1250, sse=5955520.5, rms=2.417 (0.000%)
rms = 2.39, time step reduction 3 of 3 to 0.062...
037: dt: 0.1250, sse=5891363.5, rms=2.393 (0.000%)
positioning took 1.2 minutes
mean border=39.4, 1880 (3) missing vertices, mean dist 0.1 [0.2 (%44.4)->0.3 (%55.6))]
%61 local maxima, %19 large gradients and %15 min vals, 422 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=5991562.0, rms=2.98
rms = 3.99, time step reduction 1 of 3 to 0.250...
038: dt: 0.2500, sse=5783776.5, rms=2.557 (0.000%)
039: dt: 0.2500, sse=5942419.5, rms=2.448 (0.000%)
rms = 2.42, time step reduction 2 of 3 to 0.125...
040: dt: 0.2500, sse=6016633.0, rms=2.420 (0.000%)
041: dt: 0.1250, sse=5899802.0, rms=2.287 (0.000%)
rms = 2.27, time step reduction 3 of 3 to 0.062...
042: dt: 0.1250, sse=5903649.5, rms=2.271 (0.000%)
positioning took 0.9 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area.pial
vertex spacing 1.01 +- 0.42 (0.07-->8.86) (max @ vno 77073 --> 73397)
face area 0.41 +- 0.31 (0.00-->9.50)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 171478 vertices processed
25000 of 171478 vertices processed
50000 of 171478 vertices processed
75000 of 171478 vertices processed
100000 of 171478 vertices processed
125000 of 171478 vertices processed
150000 of 171478 vertices processed
0 of 171478 vertices processed
25000 of 171478 vertices processed
50000 of 171478 vertices processed
75000 of 171478 vertices processed
100000 of 171478 vertices processed
125000 of 171478 vertices processed
150000 of 171478 vertices processed
thickness calculation complete, 240:598 truncations.
40441 vertices at 0 distance
120742 vertices at 1 distance
110846 vertices at 2 distance
42696 vertices at 3 distance
11082 vertices at 4 distance
2716 vertices at 5 distance
750 vertices at 6 distance
254 vertices at 7 distance
91 vertices at 8 distance
37 vertices at 9 distance
23 vertices at 10 distance
21 vertices at 11 distance
30 vertices at 12 distance
16 vertices at 13 distance
17 vertices at 14 distance
8 vertices at 15 distance
11 vertices at 16 distance
7 vertices at 17 distance
5 vertices at 18 distance
3 vertices at 19 distance
6 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.thickness
positioning took 17.8 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 20:12:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 20:12:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 pctsurfcon --s sub006 --lh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts/pctsurfcon.log
Thu Aug  8 20:12:24 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh --regheader sub006 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 133568
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh
Dim: 171478 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh --projfrac 0.3 --regheader sub006 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 153059
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh
Dim: 171478 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.2784/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.w-g.pct.mgh --annot sub006 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.w-g.pct.mgh --annot sub006 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
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/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.w-g.pct.mgh
Vertex Area is 0.667218 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    2087    1415.694
  2   1002            caudalanteriorcingulate    1419     970.881
  3   1003                caudalmiddlefrontal    3985    2657.052
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    2537    1656.748
  6   1006                         entorhinal     575     407.499
  7   1007                           fusiform    5408    3712.237
  8   1008                   inferiorparietal   10252    6776.328
  9   1009                   inferiortemporal    6684    4582.200
 10   1010                   isthmuscingulate    2348    1537.153
 11   1011                   lateraloccipital    9326    5996.407
 12   1012               lateralorbitofrontal    4511    3024.425
 13   1013                            lingual    4757    3296.165
 14   1014                medialorbitofrontal    3425    2281.483
 15   1015                     middletemporal    5998    4283.024
 16   1016                    parahippocampal    1042     727.525
 17   1017                        paracentral    2679    1757.445
 18   1018                    parsopercularis    3585    2399.116
 19   1019                      parsorbitalis    1202     794.842
 20   1020                   parstriangularis    2543    1678.600
 21   1021                      pericalcarine    2257    1504.341
 22   1022                        postcentral    7698    4989.887
 23   1023                 posteriorcingulate    2513    1640.895
 24   1024                         precentral    8936    5689.858
 25   1025                          precuneus    7701    5090.480
 26   1026           rostralanteriorcingulate    1900    1246.719
 27   1027               rostralmiddlefrontal   10703    7305.083
 28   1028                    superiorfrontal   15137   10291.527
 29   1029                   superiorparietal    9869    6443.312
 30   1030                   superiortemporal    6608    4488.436
 31   1031                      supramarginal    8389    5600.073
 32   1032                        frontalpole     380     252.491
 33   1033                       temporalpole     784     570.839
 34   1034                 transversetemporal     845     525.919
 35   1035                             insula    4256    2755.293

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Thu Aug  8 20:12:40 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

 2087   1416   3779  2.712 0.419     0.119     0.030       17     2.6  bankssts
 1419    971   3035  3.012 0.581     0.169     0.071       47     4.3  caudalanteriorcingulate
 3985   2657   7761  2.670 0.495     0.128     0.053       57     7.2  caudalmiddlefrontal
 2537   1657   3599  2.017 0.441     0.164     0.059       46     6.0  cuneus
  575    407   2153  3.663 0.827     0.139     0.047        7     1.2  entorhinal
 5408   3712  12135  2.805 0.544     0.142     0.048       98    11.7  fusiform
10252   6776  19259  2.508 0.468     0.131     0.041      141    16.7  inferiorparietal
 6684   4582  14149  2.623 0.632     0.145     0.057      128    15.2  inferiortemporal
 2348   1537   4343  2.576 0.845     0.155     0.063       53     5.6  isthmuscingulate
 9326   5996  15104  2.248 0.461     0.148     0.051      155    19.0  lateraloccipital
 4511   3024   9097  2.639 0.695     0.157     0.066      105    11.9  lateralorbitofrontal
 4757   3296   7854  2.170 0.578     0.158     0.071      113    12.2  lingual
 3425   2281   5652  2.116 0.698     0.146     0.071       96    10.7  medialorbitofrontal
 5998   4283  14011  2.662 0.629     0.152     0.059      139    13.7  middletemporal
 1042    728   2600  3.067 0.653     0.124     0.039       12     1.4  parahippocampal
 2679   1757   5234  2.613 0.525     0.111     0.026       22     3.1  paracentral
 3585   2399   7228  2.655 0.470     0.134     0.043       53     6.3  parsopercularis
 1202    795   2720  2.697 0.541     0.169     0.060       27     2.9  parsorbitalis
 2543   1679   4751  2.486 0.421     0.151     0.054       46     5.6  parstriangularis
 2257   1504   2742  1.906 0.387     0.132     0.050       28     5.0  pericalcarine
 7698   4990  12760  2.195 0.549     0.126     0.036      101    11.2  postcentral
 2513   1641   4838  2.709 0.659     0.164     0.080       58     6.6  posteriorcingulate
 8936   5690  17489  2.775 0.507     0.112     0.034       98    13.0  precentral
 7701   5090  14236  2.560 0.508     0.137     0.046      130    13.8  precuneus
 1900   1247   3957  2.678 0.653     0.157     0.079       62     5.0  rostralanteriorcingulate
10703   7305  19791  2.310 0.517     0.163     0.066      256    27.0  rostralmiddlefrontal
15137  10292  32166  2.685 0.544     0.136     0.042      221    25.9  superiorfrontal
 9869   6443  16255  2.281 0.451     0.129     0.038      126    15.1  superiorparietal
 6608   4488  15508  2.965 0.609     0.122     0.034       71     9.5  superiortemporal
 8389   5600  16613  2.619 0.501     0.144     0.052      152    17.3  supramarginal
  380    252    789  2.303 0.566     0.209     0.645       28    18.3  frontalpole
  784    571   2976  3.741 0.581     0.155     0.060       16     1.8  temporalpole
  845    526   1597  2.628 0.372     0.138     0.051       11     1.7  transversetemporal
 4256   2755   8840  3.098 0.688     0.123     0.054       69    10.1  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Aug  8 20:13:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/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/5.3.0/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...
11 labels changed using aseg
relabeling using gibbs priors...
000:  11640 changed, 171478 examined...
001:   2841 changed, 44597 examined...
002:    855 changed, 14481 examined...
003:    375 changed, 4767 examined...
004:    212 changed, 2161 examined...
005:     96 changed, 1161 examined...
006:     38 changed, 522 examined...
007:     23 changed, 235 examined...
008:     20 changed, 145 examined...
009:     11 changed, 106 examined...
010:      1 changed, 59 examined...
011:      2 changed, 7 examined...
012:      2 changed, 12 examined...
013:      0 changed, 6 examined...
2 labels changed using aseg
000: 336 total segments, 257 labels (3762 vertices) changed
001: 105 total segments, 26 labels (214 vertices) changed
002: 80 total segments, 1 labels (1 vertices) changed
003: 79 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 189 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1245 vertices marked for relabeling...
1245 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 30 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Thu Aug  8 20:14:46 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

 1737   1169   3047  2.147 0.633     0.169     0.069       40     4.7  G_and_S_frontomargin
 1889   1237   3422  2.383 0.506     0.146     0.060       37     5.6  G_and_S_occipital_inf
 1891   1142   3765  2.574 0.539     0.119     0.037       25     3.3  G_and_S_paracentral
 1824   1243   3729  2.567 0.490     0.150     0.044       29     3.4  G_and_S_subcentral
  852    595   1658  2.166 0.458     0.230     0.374       63    21.5  G_and_S_transv_frontopol
 3193   2148   6376  2.589 0.589     0.143     0.063       75     7.5  G_and_S_cingul-Ant
 2067   1418   4062  2.888 0.460     0.127     0.039       28     3.3  G_and_S_cingul-Mid-Ant
 1797   1207   3398  2.709 0.515     0.126     0.063       27     3.0  G_and_S_cingul-Mid-Post
 1115    716   2831  3.195 0.510     0.193     0.085       35     4.2  G_cingul-Post-dorsal
  480    305    916  2.558 0.883     0.143     0.063        8     1.1  G_cingul-Post-ventral
 2292   1503   3519  2.015 0.444     0.170     0.065       45     5.7  G_cuneus
 2154   1428   5200  2.809 0.457     0.149     0.055       42     4.7  G_front_inf-Opercular
  313    211    656  2.443 0.426     0.171     0.064        7     0.8  G_front_inf-Orbital
 1592   1049   3519  2.610 0.414     0.162     0.059       37     3.9  G_front_inf-Triangul
 5422   3699  12513  2.619 0.529     0.175     0.085      157    15.9  G_front_middle
10115   6825  23961  2.781 0.557     0.146     0.047      178    19.3  G_front_sup
  754    461   1743  3.266 0.456     0.125     0.062       10     1.6  G_Ins_lg_and_S_cent_ins
  991    620   2871  3.622 0.690     0.141     0.061       18     2.3  G_insular_short
 3173   2021   6460  2.548 0.391     0.157     0.056       67     7.1  G_occipital_middle
 1833   1159   3279  2.296 0.475     0.142     0.049       26     3.5  G_occipital_sup
 2350   1511   5812  2.918 0.528     0.149     0.046       51     4.5  G_oc-temp_lat-fusifor
 3136   2200   5725  2.155 0.589     0.177     0.089      100     9.4  G_oc-temp_med-Lingual
 1291    889   3727  3.273 0.717     0.126     0.038       14     2.0  G_oc-temp_med-Parahip
 3051   2056   7614  2.845 0.697     0.179     0.078       84    10.0  G_orbital
 4175   2737   9599  2.737 0.517     0.144     0.050       75     8.6  G_pariet_inf-Angular
 4269   2887   9859  2.740 0.498     0.151     0.057       87    10.1  G_pariet_inf-Supramar
 3559   2334   6755  2.376 0.491     0.142     0.044       58     6.3  G_parietal_sup
 3211   1999   6003  2.341 0.485     0.135     0.042       53     5.4  G_postcentral
 3609   2190   8796  3.010 0.455     0.120     0.037       53     6.0  G_precentral
 3348   2214   7711  2.720 0.504     0.152     0.053       82     6.8  G_precuneus
 1113    734   2205  2.191 0.714     0.202     0.127       61     6.5  G_rectus
  499    319    879  2.564 0.933     0.133     0.078       15     1.7  G_subcallosal
  670    412   1433  2.742 0.366     0.146     0.051       11     1.5  G_temp_sup-G_T_transv
 2497   1668   7760  3.253 0.579     0.144     0.044       37     4.5  G_temp_sup-Lateral
  850    595   2382  3.593 0.552     0.113     0.041        6     1.3  G_temp_sup-Plan_polar
 1029    709   2191  2.672 0.546     0.119     0.043       15     1.3  G_temp_sup-Plan_tempo
 3537   2418   9164  2.797 0.696     0.173     0.079      103    11.4  G_temporal_inf
 4024   2921  10745  2.734 0.616     0.174     0.076      123    11.6  G_temporal_middle
  445    291    651  2.189 0.373     0.138     0.045        6     0.8  Lat_Fis-ant-Horizont
  417    279    609  2.582 0.396     0.110     0.030        2     0.5  Lat_Fis-ant-Vertical
 1217    820   1624  2.434 0.379     0.131     0.044       14     2.0  Lat_Fis-post
 2975   1818   4538  2.099 0.443     0.153     0.059       61     7.2  Pole_occipital
 2014   1430   6654  3.368 0.775     0.149     0.053       34     4.4  Pole_temporal
 3300   2189   4297  2.155 0.608     0.128     0.049       37     6.8  S_calcarine
 3623   2425   4628  2.134 0.652     0.100     0.023       19     3.7  S_central
 1394    947   1970  2.403 0.452     0.108     0.028        8     1.6  S_cingul-Marginalis
  736    481   1165  2.690 0.531     0.096     0.026        4     0.8  S_circular_insula_ant
 1835   1226   3103  2.823 0.582     0.107     0.044       34     4.6  S_circular_insula_inf
 2151   1456   3355  2.669 0.461     0.113     0.029       14     2.7  S_circular_insula_sup
 1184    864   2131  2.609 0.442     0.110     0.026        8     1.3  S_collat_transv_ant
  375    259    522  2.041 0.343     0.146     0.036        4     0.6  S_collat_transv_post
 2928   1970   4637  2.352 0.440     0.133     0.039       37     4.8  S_front_inf
 2089   1431   3099  2.169 0.396     0.122     0.037       22     2.9  S_front_middle
 3628   2471   6259  2.484 0.415     0.115     0.034       38     4.8  S_front_sup
  500    332    659  2.292 0.414     0.095     0.022        2     0.5  S_interm_prim-Jensen
 4521   3004   6322  2.184 0.353     0.114     0.030       44     5.7  S_intrapariet_and_P_trans
 1742   1163   2282  2.165 0.391     0.141     0.043       21     2.9  S_oc_middle_and_Lunatus
 1724   1116   2290  2.197 0.364     0.123     0.030       16     2.2  S_oc_sup_and_transversal
  606    421    779  2.107 0.358     0.112     0.024        3     0.7  S_occipital_ant
 1021    720   1783  2.601 0.428     0.142     0.047       12     1.7  S_oc-temp_lat
 2070   1466   3358  2.587 0.489     0.122     0.032       17     2.8  S_oc-temp_med_and_Lingual
  590    389    855  2.173 0.415     0.150     0.051       12     1.1  S_orbital_lateral
  835    560   1291  2.274 0.784     0.129     0.058       17     1.7  S_orbital_med-olfact
 1564   1056   2608  2.381 0.579     0.147     0.051       29     2.9  S_orbital-H_Shaped
 2740   1773   3830  2.311 0.511     0.125     0.038       30     4.5  S_parieto_occipital
 2101   1369   2887  2.266 0.842     0.162     0.067       61     5.1  S_pericallosal
 3223   2146   4469  2.279 0.436     0.119     0.033       31     4.2  S_postcentral
 1958   1312   2909  2.481 0.365     0.104     0.026       13     2.0  S_precentral-inf-part
 1773   1189   2591  2.489 0.448     0.107     0.026       12     1.8  S_precentral-sup-part
 1103    736   1564  1.934 0.545     0.132     0.036       14     1.7  S_suborbital
 1655   1123   2824  2.467 0.449     0.138     0.043       22     2.8  S_subparietal
 2512   1717   3458  2.254 0.426     0.109     0.025       17     2.7  S_temporal_inf
 7563   5109  12889  2.542 0.414     0.118     0.034       82     9.9  S_temporal_sup
  525    349    851  2.728 0.377     0.130     0.034        6     0.8  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Thu Aug  8 20:15:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/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/5.3.0/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...
964 labels changed using aseg
relabeling using gibbs priors...
000:   3465 changed, 171478 examined...
001:    815 changed, 14674 examined...
002:    221 changed, 4418 examined...
003:     70 changed, 1306 examined...
004:     38 changed, 425 examined...
005:     18 changed, 227 examined...
006:      6 changed, 97 examined...
007:      2 changed, 32 examined...
008:      0 changed, 12 examined...
42 labels changed using aseg
000: 82 total segments, 49 labels (370 vertices) changed
001: 35 total segments, 2 labels (2 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 44 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1232 vertices marked for relabeling...
1232 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 1 minutes and 18 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Thu Aug  8 20:16:34 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

 2585   1747   5532  2.995 0.549     0.144     0.052       58     5.7  caudalanteriorcingulate
 4059   2709   7956  2.674 0.492     0.128     0.053       58     7.3  caudalmiddlefrontal
 3609   2359   5415  2.123 0.452     0.151     0.051       56     7.4  cuneus
  575    403   2011  3.578 0.875     0.137     0.045        7     1.1  entorhinal
 4848   3312  10143  2.752 0.513     0.139     0.046       85    10.2  fusiform
 9662   6365  18033  2.504 0.470     0.130     0.040      133    15.7  inferiorparietal
 6594   4535  15065  2.685 0.677     0.150     0.059      135    15.7  inferiortemporal
 2345   1531   4344  2.588 0.834     0.154     0.063       52     5.6  isthmuscingulate
 9684   6216  15672  2.248 0.461     0.148     0.052      162    19.8  lateraloccipital
 4809   3225   9957  2.622 0.741     0.161     0.071      118    13.4  lateralorbitofrontal
 4776   3307   7882  2.171 0.576     0.158     0.071      113    12.2  lingual
 2589   1731   4352  2.050 0.695     0.158     0.074       79     8.6  medialorbitofrontal
 8191   5793  18327  2.668 0.591     0.147     0.054      164    17.2  middletemporal
 1042    730   2607  3.066 0.657     0.123     0.039       12     1.3  parahippocampal
 3151   2067   6041  2.584 0.519     0.110     0.028       25     4.0  paracentral
 3200   2130   6516  2.700 0.441     0.136     0.045       48     5.9  parsopercularis
 1305    859   2436  2.388 0.499     0.142     0.045       19     2.4  parsorbitalis
 3386   2238   6226  2.480 0.464     0.151     0.053       61     7.2  parstriangularis
 2301   1527   2775  1.898 0.392     0.134     0.051       29     5.2  pericalcarine
 8522   5562  13931  2.198 0.542     0.126     0.035      108    12.2  postcentral
 2674   1757   5051  2.701 0.663     0.161     0.077       59     6.7  posteriorcingulate
 8839   5629  17249  2.772 0.514     0.113     0.033       97    12.5  precentral
 7312   4870  13848  2.573 0.516     0.139     0.047      128    13.3  precuneus
 2562   1677   4896  2.595 0.653     0.148     0.075       75     6.9  rostralanteriorcingulate
 7048   4770  13361  2.359 0.526     0.155     0.056      144    15.3  rostralmiddlefrontal
16629  11399  34844  2.585 0.556     0.148     0.065      332    51.8  superiorfrontal
 8053   5220  13213  2.290 0.444     0.128     0.037      103    12.1  superiorparietal
 9265   6276  21747  2.991 0.647     0.127     0.043      137    17.4  superiortemporal
 8092   5411  15950  2.613 0.505     0.143     0.051      140    16.7  supramarginal
  790    493   1526  2.627 0.360     0.140     0.052       11     1.6  transversetemporal
 3842   2501   8119  3.092 0.635     0.118     0.038       39     5.9  insula
#--------------------------------------------
#@# Tessellate rh Thu Aug  8 20:17:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

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


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

Total Number of Modified Voxels = 9 (out of 321357: 0.002801)
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 30: 847 vertices, 936 faces
slice 40: 6079 vertices, 6323 faces
slice 50: 15336 vertices, 15708 faces
slice 60: 26939 vertices, 27348 faces
slice 70: 39454 vertices, 39893 faces
slice 80: 51385 vertices, 51797 faces
slice 90: 63929 vertices, 64328 faces
slice 100: 77185 vertices, 77639 faces
slice 110: 88805 vertices, 89216 faces
slice 120: 100731 vertices, 101178 faces
slice 130: 112318 vertices, 112793 faces
slice 140: 124196 vertices, 124580 faces
slice 150: 134663 vertices, 135052 faces
slice 160: 143514 vertices, 143849 faces
slice 170: 152275 vertices, 152570 faces
slice 180: 159355 vertices, 159609 faces
slice 190: 165666 vertices, 165877 faces
slice 200: 170251 vertices, 170436 faces
slice 210: 171232 vertices, 171276 faces
slice 220: 171232 vertices, 171276 faces
slice 230: 171232 vertices, 171276 faces
slice 240: 171232 vertices, 171276 faces
slice 250: 171232 vertices, 171276 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...
   171232 voxel in cpt #1: X=-44 [v=171232,e=513828,f=342552] located at (28.968430, -19.361048, 41.754677)
For the whole surface: X=-44 [v=171232,e=513828,f=342552]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Thu Aug  8 20:17:11 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 20:17:17 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
avg radius = 51.7 mm, total surface area = 91178 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.8 minutes
Not saving sulc

step 000: RMS=0.098 (target=0.015)   
step 005: RMS=0.072 (target=0.015)   
step 010: RMS=0.052 (target=0.015)   
step 015: RMS=0.043 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.029 (target=0.015)   
step 035: RMS=0.026 (target=0.015)   
step 040: RMS=0.025 (target=0.015)   
step 045: RMS=0.023 (target=0.015)   
step 050: RMS=0.022 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Thu Aug  8 20:18:07 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.88 +- 0.54 (0.00-->6.40) (max @ vno 127943 --> 127944)
face area 0.02 +- 0.03 (-0.12-->0.57)
scaling brain by 0.274...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.945, avgs=0
005/300: dt: 0.9000, rms radial error=176.683, avgs=0
010/300: dt: 0.9000, rms radial error=176.120, avgs=0
015/300: dt: 0.9000, rms radial error=175.380, avgs=0
020/300: dt: 0.9000, rms radial error=174.537, avgs=0
025/300: dt: 0.9000, rms radial error=173.643, avgs=0
030/300: dt: 0.9000, rms radial error=172.720, avgs=0
035/300: dt: 0.9000, rms radial error=171.780, avgs=0
040/300: dt: 0.9000, rms radial error=170.832, avgs=0
045/300: dt: 0.9000, rms radial error=169.882, avgs=0
050/300: dt: 0.9000, rms radial error=168.932, avgs=0
055/300: dt: 0.9000, rms radial error=167.986, avgs=0
060/300: dt: 0.9000, rms radial error=167.043, avgs=0
065/300: dt: 0.9000, rms radial error=166.105, avgs=0
070/300: dt: 0.9000, rms radial error=165.172, avgs=0
075/300: dt: 0.9000, rms radial error=164.243, avgs=0
080/300: dt: 0.9000, rms radial error=163.320, avgs=0
085/300: dt: 0.9000, rms radial error=162.401, avgs=0
090/300: dt: 0.9000, rms radial error=161.488, avgs=0
095/300: dt: 0.9000, rms radial error=160.580, avgs=0
100/300: dt: 0.9000, rms radial error=159.678, avgs=0
105/300: dt: 0.9000, rms radial error=158.780, avgs=0
110/300: dt: 0.9000, rms radial error=157.888, avgs=0
115/300: dt: 0.9000, rms radial error=157.000, avgs=0
120/300: dt: 0.9000, rms radial error=156.118, avgs=0
125/300: dt: 0.9000, rms radial error=155.240, avgs=0
130/300: dt: 0.9000, rms radial error=154.367, avgs=0
135/300: dt: 0.9000, rms radial error=153.499, avgs=0
140/300: dt: 0.9000, rms radial error=152.636, avgs=0
145/300: dt: 0.9000, rms radial error=151.778, avgs=0
150/300: dt: 0.9000, rms radial error=150.924, avgs=0
155/300: dt: 0.9000, rms radial error=150.075, avgs=0
160/300: dt: 0.9000, rms radial error=149.230, avgs=0
165/300: dt: 0.9000, rms radial error=148.391, avgs=0
170/300: dt: 0.9000, rms radial error=147.555, avgs=0
175/300: dt: 0.9000, rms radial error=146.724, avgs=0
180/300: dt: 0.9000, rms radial error=145.898, avgs=0
185/300: dt: 0.9000, rms radial error=145.077, avgs=0
190/300: dt: 0.9000, rms radial error=144.260, avgs=0
195/300: dt: 0.9000, rms radial error=143.447, avgs=0
200/300: dt: 0.9000, rms radial error=142.639, avgs=0
205/300: dt: 0.9000, rms radial error=141.836, avgs=0
210/300: dt: 0.9000, rms radial error=141.037, avgs=0
215/300: dt: 0.9000, rms radial error=140.243, avgs=0
220/300: dt: 0.9000, rms radial error=139.453, avgs=0
225/300: dt: 0.9000, rms radial error=138.667, avgs=0
230/300: dt: 0.9000, rms radial error=137.887, avgs=0
235/300: dt: 0.9000, rms radial error=137.110, avgs=0
240/300: dt: 0.9000, rms radial error=136.338, avgs=0
245/300: dt: 0.9000, rms radial error=135.570, avgs=0
250/300: dt: 0.9000, rms radial error=134.806, avgs=0
255/300: dt: 0.9000, rms radial error=134.047, avgs=0
260/300: dt: 0.9000, rms radial error=133.292, avgs=0
265/300: dt: 0.9000, rms radial error=132.541, avgs=0
270/300: dt: 0.9000, rms radial error=131.794, avgs=0
275/300: dt: 0.9000, rms radial error=131.052, avgs=0
280/300: dt: 0.9000, rms radial error=130.314, avgs=0
285/300: dt: 0.9000, rms radial error=129.580, avgs=0
290/300: dt: 0.9000, rms radial error=128.850, avgs=0
295/300: dt: 0.9000, rms radial error=128.124, avgs=0
300/300: dt: 0.9000, rms radial error=127.402, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 20772.79
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00018
epoch 2 (K=40.0), pass 1, starting sse = 3745.31
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00001
epoch 3 (K=160.0), pass 1, starting sse = 451.40
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00515
epoch 4 (K=640.0), pass 1, starting sse = 32.44
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.10/13 = 0.00754
final writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.10 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology rh Thu Aug  8 20:24:21 CEST 2013

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


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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub006 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=-44 (nv=171232, nf=342552, ne=513828, g=23)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
3594 ambiguous faces found in tessellation
segmenting defects...
33 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
      -merging segment 14 into 11
32 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.9592  (-4.9796)
      -vertex     loglikelihood: -6.6689  (-3.3344)
      -normal dot loglikelihood: -3.6129  (-3.6129)
      -quad curv  loglikelihood: -6.2986  (-3.1493)
      Total Loglikelihood : -26.5396

CORRECTING DEFECT 0 (vertices=16, convex hull=50)
After retessellation of defect 0, euler #=-28 (169043,506286,337215) : difference with theory (-29) = -1 

CORRECTING DEFECT 1 (vertices=26, convex hull=56)
After retessellation of defect 1, euler #=-27 (169052,506335,337256) : difference with theory (-28) = -1 

CORRECTING DEFECT 2 (vertices=15, convex hull=21)
After retessellation of defect 2, euler #=-26 (169056,506351,337269) : difference with theory (-27) = -1 

CORRECTING DEFECT 3 (vertices=18, convex hull=49)
After retessellation of defect 3, euler #=-25 (169058,506377,337294) : difference with theory (-26) = -1 

CORRECTING DEFECT 4 (vertices=167, convex hull=117)
After retessellation of defect 4, euler #=-24 (169095,506537,337418) : difference with theory (-25) = -1 

CORRECTING DEFECT 5 (vertices=52, convex hull=78)
After retessellation of defect 5, euler #=-23 (169107,506605,337475) : difference with theory (-24) = -1 

CORRECTING DEFECT 6 (vertices=59, convex hull=81)
After retessellation of defect 6, euler #=-22 (169137,506726,337567) : difference with theory (-23) = -1 

CORRECTING DEFECT 7 (vertices=22, convex hull=30)
After retessellation of defect 7, euler #=-21 (169140,506744,337583) : difference with theory (-22) = -1 

CORRECTING DEFECT 8 (vertices=34, convex hull=84)
After retessellation of defect 8, euler #=-20 (169158,506832,337654) : difference with theory (-21) = -1 

CORRECTING DEFECT 9 (vertices=45, convex hull=80)
After retessellation of defect 9, euler #=-19 (169186,506948,337743) : difference with theory (-20) = -1 

CORRECTING DEFECT 10 (vertices=7, convex hull=22)
After retessellation of defect 10, euler #=-18 (169189,506961,337754) : difference with theory (-19) = -1 

CORRECTING DEFECT 11 (vertices=190, convex hull=202)
normal vector of length zero at vertex 169579 with 3 faces
normal vector of length zero at vertex 169579 with 3 faces
normal vector of length zero at vertex 169579 with 3 faces
normal vector of length zero at vertex 169579 with 3 faces
After retessellation of defect 11, euler #=-16 (169240,507210,337954) : difference with theory (-18) = -2 

CORRECTING DEFECT 12 (vertices=17, convex hull=33)
After retessellation of defect 12, euler #=-15 (169247,507241,337979) : difference with theory (-17) = -2 

CORRECTING DEFECT 13 (vertices=599, convex hull=272)
After retessellation of defect 13, euler #=-16 (169424,507944,338504) : difference with theory (-16) = 0 

CORRECTING DEFECT 14 (vertices=5, convex hull=15)
Warning - incorrect dp selected!!!!(-143.980131 >= -143.980132 ) 
After retessellation of defect 14, euler #=-15 (169425,507949,338509) : difference with theory (-15) = 0 

CORRECTING DEFECT 15 (vertices=9, convex hull=18)
After retessellation of defect 15, euler #=-14 (169428,507960,338518) : difference with theory (-14) = 0 

CORRECTING DEFECT 16 (vertices=11, convex hull=25)
After retessellation of defect 16, euler #=-13 (169431,507975,338531) : difference with theory (-13) = 0 

CORRECTING DEFECT 17 (vertices=60, convex hull=27)
Warning - incorrect dp selected!!!!(-76.716434 >= -76.716439 ) 
After retessellation of defect 17, euler #=-12 (169436,508000,338552) : difference with theory (-12) = 0 

CORRECTING DEFECT 18 (vertices=17, convex hull=36)
After retessellation of defect 18, euler #=-11 (169448,508048,338589) : difference with theory (-11) = 0 

CORRECTING DEFECT 19 (vertices=87, convex hull=39)
After retessellation of defect 19, euler #=-10 (169457,508089,338622) : difference with theory (-10) = 0 

CORRECTING DEFECT 20 (vertices=58, convex hull=50)
After retessellation of defect 20, euler #=-9 (169466,508136,338661) : difference with theory (-9) = 0 

CORRECTING DEFECT 21 (vertices=29, convex hull=51)
After retessellation of defect 21, euler #=-8 (169475,508186,338703) : difference with theory (-8) = 0 

CORRECTING DEFECT 22 (vertices=13, convex hull=28)
After retessellation of defect 22, euler #=-7 (169480,508210,338723) : difference with theory (-7) = 0 

CORRECTING DEFECT 23 (vertices=158, convex hull=52)
After retessellation of defect 23, euler #=-6 (169491,508263,338766) : difference with theory (-6) = 0 

CORRECTING DEFECT 24 (vertices=20, convex hull=71)
After retessellation of defect 24, euler #=-5 (169505,508330,338820) : difference with theory (-5) = 0 

CORRECTING DEFECT 25 (vertices=87, convex hull=60)
After retessellation of defect 25, euler #=-4 (169527,508423,338892) : difference with theory (-4) = 0 

CORRECTING DEFECT 26 (vertices=27, convex hull=26)
After retessellation of defect 26, euler #=-3 (169530,508440,338907) : difference with theory (-3) = 0 

CORRECTING DEFECT 27 (vertices=91, convex hull=77)
After retessellation of defect 27, euler #=-2 (169559,508562,339001) : difference with theory (-2) = 0 

CORRECTING DEFECT 28 (vertices=60, convex hull=64)
After retessellation of defect 28, euler #=-1 (169583,508657,339073) : difference with theory (-1) = 0 

CORRECTING DEFECT 29 (vertices=125, convex hull=102)
After retessellation of defect 29, euler #=0 (169619,508810,339191) : difference with theory (0) = 0 

CORRECTING DEFECT 30 (vertices=37, convex hull=50)
After retessellation of defect 30, euler #=1 (169631,508865,339235) : difference with theory (1) = 0 

CORRECTING DEFECT 31 (vertices=27, convex hull=60)
After retessellation of defect 31, euler #=2 (169645,508929,339286) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.07-->7.64) (max @ vno 43725 --> 169136)
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 (0.07-->7.64) (max @ vno 43725 --> 169136)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
106 mutations (34.8%), 199 crossovers (65.2%), 88 vertices were eliminated
building final representation...
1587 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=169645, nf=339286, ne=508929, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 22.0 minutes
0 defective edges
removing intersecting faces
000: 199 intersecting
001: 15 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 169645 - 508929 + 339286 = 2 --> 0 holes
      F =2V-4:          339286 = 339290-4 (0)
      2E=3F:            1017858 = 1017858 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 30 intersecting
001: 2 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Thu Aug  8 20:46:30 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub006 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/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
25014 bright wm thresholded.
438 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
computing class statistics...
border white:    318128 voxels (1.90%)
border gray      352780 voxels (2.10%)
WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0]
GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70)
setting MAX_BORDER_WHITE to 116.3 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 30.2 (was 40)
setting MAX_GRAY to 95.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->5.00) (max @ vno 43725 --> 169070)
face area 0.28 +- 0.12 (0.00-->2.22)
mean absolute distance = 0.65 +- 0.73
5203 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=106,    GM=57
mean inside = 93.6, mean outside = 67.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
mean border=71.2, 19 (19) missing vertices, mean dist 0.4 [0.4 (%28.5)->0.7 (%71.5))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 (0.07-->4.98) (max @ vno 43725 --> 169070)
face area 0.28 +- 0.13 (0.00-->1.95)
mean absolute distance = 0.33 +- 0.46
4503 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=9990156.0, rms=14.65
001: dt: 0.5000, sse=9387922.0, rms=10.573 (0.000%)
002: dt: 0.5000, sse=9285183.0, rms=8.140 (0.000%)
003: dt: 0.5000, sse=9331436.0, rms=6.565 (0.000%)
004: dt: 0.5000, sse=9548231.0, rms=5.626 (0.000%)
005: dt: 0.5000, sse=9633569.0, rms=5.075 (0.000%)
006: dt: 0.5000, sse=9750143.0, rms=4.811 (0.000%)
007: dt: 0.5000, sse=9731474.0, rms=4.648 (0.000%)
008: dt: 0.5000, sse=9764969.0, rms=4.577 (0.000%)
009: dt: 0.5000, sse=9673746.0, rms=4.507 (0.000%)
rms = 4.48, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9707184.0, rms=4.482 (0.000%)
011: dt: 0.2500, sse=5934601.0, rms=3.033 (0.000%)
012: dt: 0.2500, sse=5435345.0, rms=2.562 (0.000%)
013: dt: 0.2500, sse=5103281.0, rms=2.468 (0.000%)
014: dt: 0.2500, sse=5028657.0, rms=2.377 (0.000%)
rms = 2.36, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4909786.0, rms=2.356 (0.000%)
016: dt: 0.1250, sse=4550146.5, rms=1.988 (0.000%)
017: dt: 0.1250, sse=4497600.0, rms=1.937 (0.000%)
rms = 1.93, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=4465426.5, rms=1.931 (0.000%)
positioning took 2.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=76.9, 33 (1) missing vertices, mean dist -0.3 [0.3 (%83.0)->0.2 (%17.0))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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 (0.12-->4.65) (max @ vno 43725 --> 169070)
face area 0.35 +- 0.16 (0.00-->2.52)
mean absolute distance = 0.20 +- 0.27
5040 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=6179281.5, rms=7.16
019: dt: 0.5000, sse=5953634.5, rms=4.656 (0.000%)
rms = 4.88, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=5379315.0, rms=3.448 (0.000%)
021: dt: 0.2500, sse=5148878.5, rms=2.750 (0.000%)
022: dt: 0.2500, sse=5075867.5, rms=2.213 (0.000%)
023: dt: 0.2500, sse=5088533.5, rms=2.122 (0.000%)
024: dt: 0.2500, sse=5003672.0, rms=1.957 (0.000%)
rms = 1.98, time step reduction 2 of 3 to 0.125...
025: dt: 0.1250, sse=4903640.0, rms=1.819 (0.000%)
026: dt: 0.1250, sse=4778593.0, rms=1.615 (0.000%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4730548.0, rms=1.577 (0.000%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=80.6, 28 (0) missing vertices, mean dist -0.1 [0.2 (%79.0)->0.2 (%21.0))]
%91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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 +- 0.24 (0.08-->4.51) (max @ vno 43725 --> 169070)
face area 0.34 +- 0.16 (0.00-->2.53)
mean absolute distance = 0.15 +- 0.21
2777 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5347951.5, rms=4.74
028: dt: 0.5000, sse=5737506.5, rms=4.523 (0.000%)
rms = 4.52, time step reduction 1 of 3 to 0.250...
029: dt: 0.5000, sse=5971399.0, rms=4.523 (0.000%)
030: dt: 0.2500, sse=5333414.5, rms=2.476 (0.000%)
031: dt: 0.2500, sse=5356994.5, rms=2.198 (0.000%)
032: dt: 0.2500, sse=5267410.5, rms=2.040 (0.000%)
rms = 2.08, time step reduction 2 of 3 to 0.125...
033: dt: 0.1250, sse=5128239.5, rms=1.809 (0.000%)
034: dt: 0.1250, sse=4969164.0, rms=1.449 (0.000%)
035: dt: 0.1250, sse=4908489.5, rms=1.381 (0.000%)
rms = 1.39, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=4908489.5, rms=1.381 (0.005%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=81.6, 37 (0) missing vertices, mean dist -0.0 [0.1 (%59.5)->0.1 (%40.5))]
%93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=4953128.5, rms=1.90
rms = 3.03, time step reduction 1 of 3 to 0.250...
037: dt: 0.2500, sse=5013320.5, rms=1.213 (0.000%)
038: dt: 0.2500, sse=5143698.0, rms=1.045 (0.000%)
rms = 1.04, time step reduction 2 of 3 to 0.125...
039: dt: 0.2500, sse=5229137.5, rms=1.042 (0.000%)
rms = 1.01, time step reduction 3 of 3 to 0.062...
040: dt: 0.1250, sse=5254944.5, rms=1.006 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
generating cortex label...
13 non-cortical segments detected
only using segment with 1951 vertices
erasing segment 1 (vno[0] = 107042)
erasing segment 2 (vno[0] = 111864)
erasing segment 3 (vno[0] = 116863)
erasing segment 4 (vno[0] = 120328)
erasing segment 5 (vno[0] = 121221)
erasing segment 6 (vno[0] = 122277)
erasing segment 7 (vno[0] = 122408)
erasing segment 8 (vno[0] = 123167)
erasing segment 9 (vno[0] = 123288)
erasing segment 10 (vno[0] = 124218)
erasing segment 11 (vno[0] = 130353)
erasing segment 12 (vno[0] = 133485)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area
vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
face area 0.34 +- 0.15 (0.00-->2.54)
refinement took 9.5 minutes
#--------------------------------------------
#@# Smooth2 rh Thu Aug  8 20:56:00 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 20:56:06 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

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

avg radius = 51.9 mm, total surface area = 104232 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.112 (target=0.015)   
step 005: RMS=0.078 (target=0.015)   
step 010: RMS=0.055 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.026 (target=0.015)   
step 035: RMS=0.022 (target=0.015)   
step 040: RMS=0.019 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
inflation complete.
inflation took 0.7 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
200 vertices thresholded to be in k1 ~ [-0.41 0.19], k2 ~ [-0.13 0.06]
total integrated curvature = 0.492*4pi (6.177) --> 1 handles
ICI = 2.0, FI = 17.8, variation=283.367
152 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
164 vertices thresholded to be in [-0.19 0.10]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.027
done.

#-----------------------------------------
#@# Curvature Stats rh Thu Aug  8 20:59:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub006 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       [ sub006/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                      [ 322 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.893362
WARN:    S explicit min:                          0.000000	vertex = 407
#--------------------------------------------
#@# Sphere rh Thu Aug  8 20:59:06 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 0.258...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=snake, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.34
pass 1: epoch 2 of 3 starting distance error %20.31
unfolding complete - removing small folds...
starting distance error %20.25
removing remaining folds...
final distance error %20.26
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.19 hours
#--------------------------------------------
#@# Surf Reg rh Thu Aug  8 22:10:14 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/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/5.3.0/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=snake, 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=snake, 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 = 0.581
curvature mean = 0.025, std = 0.936
curvature mean = 0.025, std = 0.831
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 349579.9, tmin=3.3531
  d=16.00 min @ (4.00, 4.00, 0.00) sse = 342747.6, tmin=5.0340
  d=8.00 min @ (-2.00, -2.00, 0.00) sse = 331556.2, tmin=6.7395
  d=4.00 min @ (1.00, 0.00, 0.00) sse = 329772.9, tmin=8.4627
  d=2.00 min @ (0.00, 0.00, 0.50) sse = 329564.4, tmin=10.2497
  d=1.00 min @ (0.00, 0.00, -0.25) sse = 329553.1, tmin=11.9913
  d=0.50 min @ (-0.12, 0.00, 0.12) sse = 329507.0, tmin=13.7184
tol=1.0e+00, sigma=0.5, host=snake, 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  13.72 min
curvature mean = 0.010, std = 0.925
curvature mean = 0.013, std = 0.923
curvature mean = 0.006, std = 0.928
curvature mean = 0.006, std = 0.963
curvature mean = 0.004, std = 0.925
curvature mean = 0.002, std = 0.983
2 Reading smoothwm
curvature mean = -0.023, std = 0.286
curvature mean = 0.006, std = 0.068
curvature mean = 0.070, std = 0.322
curvature mean = 0.006, std = 0.081
curvature mean = 0.035, std = 0.514
curvature mean = 0.006, std = 0.086
curvature mean = 0.018, std = 0.663
curvature mean = 0.007, std = 0.089
curvature mean = 0.006, std = 0.778
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
#--------------------------------------------
#@# Jacobian white rh Thu Aug  8 22:55:50 CEST 2013

 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 Thu Aug  8 22:55:55 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mrisp_paint -a 5 /opt/freesurfer/5.3.0/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/5.3.0/average/rh.average.curvature.filled.buckner40.tif...
writing curvature file to ../surf/rh.avg_curv...
#-----------------------------------------
#@# Cortical Parc rh Thu Aug  8 22:56:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/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/5.3.0/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...
1364 labels changed using aseg
relabeling using gibbs priors...
000:   3470 changed, 169645 examined...
001:    819 changed, 14646 examined...
002:    187 changed, 4571 examined...
003:     61 changed, 1116 examined...
004:     21 changed, 387 examined...
005:      5 changed, 124 examined...
006:      1 changed, 32 examined...
007:      0 changed, 7 examined...
218 labels changed using aseg
000: 119 total segments, 80 labels (484 vertices) changed
001: 43 total segments, 4 labels (5 vertices) changed
002: 39 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 50 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1942 vertices marked for relabeling...
1942 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 19 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Thu Aug  8 22:57:19 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub006 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/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
25014 bright wm thresholded.
438 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
computing class statistics...
border white:    318128 voxels (1.90%)
border gray      352780 voxels (2.10%)
WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0]
GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70)
setting MAX_BORDER_WHITE to 116.3 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 30.2 (was 40)
setting MAX_GRAY to 95.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=57
mean inside = 93.6, mean outside = 67.7
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/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.02-->5.00) (max @ vno 43725 --> 169070)
face area 0.28 +- 0.12 (0.00-->2.22)
mean absolute distance = 0.65 +- 0.73
5230 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 2 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 380 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 11 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 2 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
mean border=71.2, 19 (19) missing vertices, mean dist 0.4 [0.4 (%28.5)->0.7 (%71.5))]
%74 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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 (0.07-->4.98) (max @ vno 43725 --> 169070)
face area 0.28 +- 0.13 (0.00-->1.95)
mean absolute distance = 0.33 +- 0.46
4530 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=10003488.0, rms=14.64
001: dt: 0.5000, sse=9404758.0, rms=10.567 (0.000%)
002: dt: 0.5000, sse=9304696.0, rms=8.135 (0.000%)
003: dt: 0.5000, sse=9350051.0, rms=6.560 (0.000%)
004: dt: 0.5000, sse=9569986.0, rms=5.622 (0.000%)
005: dt: 0.5000, sse=9656816.0, rms=5.072 (0.000%)
006: dt: 0.5000, sse=9776060.0, rms=4.808 (0.000%)
007: dt: 0.5000, sse=9756018.0, rms=4.646 (0.000%)
008: dt: 0.5000, sse=9792059.0, rms=4.575 (0.000%)
009: dt: 0.5000, sse=9700319.0, rms=4.505 (0.000%)
rms = 4.48, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9735061.0, rms=4.481 (0.000%)
011: dt: 0.2500, sse=5951123.0, rms=3.033 (0.000%)
012: dt: 0.2500, sse=5449661.5, rms=2.563 (0.000%)
013: dt: 0.2500, sse=5117837.0, rms=2.469 (0.000%)
014: dt: 0.2500, sse=5043594.0, rms=2.378 (0.000%)
rms = 2.36, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4924040.5, rms=2.357 (0.000%)
016: dt: 0.1250, sse=4564908.5, rms=1.990 (0.000%)
017: dt: 0.1250, sse=4512501.0, rms=1.939 (0.000%)
rms = 1.93, time step reduction 3 of 3 to 0.062...
018: dt: 0.1250, sse=4479939.0, rms=1.934 (0.000%)
positioning took 3.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 points - only 0.00% unknown
deleting segment 1 with 5 points - only 0.00% unknown
deleting segment 2 with 255 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 3 with 3 points - only 0.00% unknown
deleting segment 4 with 11 points - only 0.00% unknown
deleting segment 5 with 25 points - only 44.00% unknown
removing 2 vertex label from ripped group
deleting segment 6 with 2 points - only 0.00% unknown
deleting segment 7 with 19 points - only 0.00% unknown
deleting segment 8 with 8 points - only 0.00% unknown
mean border=76.8, 33 (1) missing vertices, mean dist -0.3 [0.3 (%82.9)->0.2 (%17.1))]
%85 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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 (0.12-->4.65) (max @ vno 43725 --> 169070)
face area 0.35 +- 0.16 (0.00-->2.52)
mean absolute distance = 0.21 +- 0.27
5067 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=6199635.0, rms=7.16
019: dt: 0.5000, sse=5973438.0, rms=4.652 (0.000%)
rms = 4.88, time step reduction 1 of 3 to 0.250...
020: dt: 0.2500, sse=5397965.5, rms=3.445 (0.000%)
021: dt: 0.2500, sse=5167652.5, rms=2.749 (0.000%)
022: dt: 0.2500, sse=5093224.0, rms=2.213 (0.000%)
023: dt: 0.2500, sse=5106467.0, rms=2.123 (0.000%)
024: dt: 0.2500, sse=5020157.5, rms=1.958 (0.000%)
rms = 1.98, time step reduction 2 of 3 to 0.125...
025: dt: 0.1250, sse=4920171.0, rms=1.820 (0.000%)
026: dt: 0.1250, sse=4796014.0, rms=1.617 (0.000%)
rms = 1.58, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=4747594.5, rms=1.580 (0.000%)
positioning took 1.5 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 points - only 0.00% unknown
deleting segment 1 with 10 points - only 0.00% unknown
deleting segment 2 with 12 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 300 points - only 0.00% unknown
deleting segment 5 with 5 points - only 0.00% unknown
deleting segment 6 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 7 with 4 points - only 0.00% unknown
deleting segment 8 with 31 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
mean border=80.5, 27 (0) missing vertices, mean dist -0.1 [0.2 (%78.9)->0.2 (%21.1))]
%92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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 +- 0.24 (0.06-->4.57) (max @ vno 43725 --> 169070)
face area 0.34 +- 0.16 (0.00-->2.52)
mean absolute distance = 0.15 +- 0.21
2870 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5364998.0, rms=4.74
028: dt: 0.5000, sse=5754745.0, rms=4.519 (0.000%)
rms = 4.52, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=5142845.0, rms=2.842 (0.000%)
030: dt: 0.2500, sse=4988408.0, rms=2.323 (0.000%)
031: dt: 0.2500, sse=5072433.0, rms=1.909 (0.000%)
rms = 1.99, time step reduction 2 of 3 to 0.125...
032: dt: 0.1250, sse=4977359.5, rms=1.707 (0.000%)
033: dt: 0.1250, sse=4858171.0, rms=1.407 (0.000%)
034: dt: 0.1250, sse=4822910.0, rms=1.357 (0.000%)
rms = 1.37, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=4822910.0, rms=1.357 (0.010%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 20 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 16 points - only 0.00% unknown
deleting segment 3 with 7 points - only 0.00% unknown
deleting segment 4 with 12 points - only 0.00% unknown
deleting segment 5 with 280 points - only 0.00% unknown
deleting segment 6 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 10 with 4 points - only 0.00% unknown
deleting segment 11 with 30 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 points - only 0.00% unknown
deleting segment 14 with 12 points - only 0.00% unknown
mean border=81.6, 31 (0) missing vertices, mean dist -0.0 [0.1 (%59.4)->0.1 (%40.6))]
%93 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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=4869947.5, rms=1.89
rms = 2.97, time step reduction 1 of 3 to 0.250...
036: dt: 0.2500, sse=4939095.5, rms=1.211 (0.000%)
037: dt: 0.2500, sse=5076491.0, rms=1.035 (0.000%)
rms = 1.04, time step reduction 2 of 3 to 0.125...
rms = 1.02, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=5079325.0, rms=1.016 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
mean border=46.6, 53 (53) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))]
%14 local maxima, %62 large gradients and %20 min vals, 1777 gradients ignored
tol=1.0e-04, sigma=2.0, host=snake, 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=42034216.0, rms=34.46
001: dt: 0.5000, sse=29884576.0, rms=28.534 (0.000%)
002: dt: 0.5000, sse=21492024.0, rms=23.613 (0.000%)
003: dt: 0.5000, sse=15902650.0, rms=19.644 (0.000%)
004: dt: 0.5000, sse=12446432.0, rms=16.501 (0.000%)
005: dt: 0.5000, sse=10397814.0, rms=14.072 (0.000%)
006: dt: 0.5000, sse=9310842.0, rms=12.188 (0.000%)
007: dt: 0.5000, sse=8615309.0, rms=10.572 (0.000%)
008: dt: 0.5000, sse=8150395.5, rms=9.098 (0.000%)
009: dt: 0.5000, sse=7844656.5, rms=7.741 (0.000%)
010: dt: 0.5000, sse=7717932.0, rms=6.564 (0.000%)
011: dt: 0.5000, sse=7694301.5, rms=5.626 (0.000%)
012: dt: 0.5000, sse=7799948.5, rms=4.951 (0.000%)
013: dt: 0.5000, sse=7930760.0, rms=4.514 (0.000%)
014: dt: 0.5000, sse=8099019.5, rms=4.289 (0.000%)
015: dt: 0.5000, sse=8210826.0, rms=4.154 (0.000%)
016: dt: 0.5000, sse=8267964.5, rms=4.070 (0.000%)
rms = 4.02, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=8310543.5, rms=4.022 (0.000%)
018: dt: 0.2500, sse=5667292.0, rms=3.160 (0.000%)
019: dt: 0.2500, sse=5442487.5, rms=2.929 (0.000%)
rms = 2.90, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=5284241.5, rms=2.899 (0.000%)
021: dt: 0.1250, sse=5025618.5, rms=2.716 (0.000%)
rms = 2.69, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=4989413.5, rms=2.691 (0.000%)
positioning took 3.2 minutes
mean border=44.0, 754 (9) missing vertices, mean dist 0.2 [0.2 (%48.6)->0.5 (%51.4))]
%34 local maxima, %46 large gradients and %16 min vals, 421 gradients ignored
tol=1.0e-04, sigma=1.0, host=snake, 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=5811038.0, rms=4.88
023: dt: 0.5000, sse=6232976.0, rms=4.133 (0.000%)
rms = 4.11, time step reduction 1 of 3 to 0.250...
024: dt: 0.5000, sse=7965109.0, rms=4.112 (0.000%)
025: dt: 0.2500, sse=6002721.5, rms=3.127 (0.000%)
026: dt: 0.2500, sse=6037564.5, rms=2.869 (0.000%)
rms = 2.85, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=5879275.5, rms=2.848 (0.000%)
028: dt: 0.1250, sse=5651194.0, rms=2.628 (0.000%)
rms = 2.59, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=5624315.5, rms=2.588 (0.000%)
positioning took 1.0 minutes
mean border=41.2, 917 (8) missing vertices, mean dist 0.1 [0.2 (%36.6)->0.4 (%63.4))]
%57 local maxima, %23 large gradients and %16 min vals, 581 gradients ignored
tol=1.0e-04, sigma=0.5, host=snake, 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=6056351.0, rms=4.36
030: dt: 0.5000, sse=6282195.0, rms=4.138 (0.000%)
rms = 4.13, time step reduction 1 of 3 to 0.250...
031: dt: 0.5000, sse=8222272.0, rms=4.128 (0.000%)
032: dt: 0.2500, sse=6136946.0, rms=3.043 (0.000%)
033: dt: 0.2500, sse=6323475.5, rms=2.712 (0.000%)
rms = 2.74, time step reduction 2 of 3 to 0.125...
034: dt: 0.1250, sse=6165397.5, rms=2.598 (0.000%)
035: dt: 0.1250, sse=5898154.0, rms=2.439 (0.000%)
rms = 2.41, time step reduction 3 of 3 to 0.062...
036: dt: 0.1250, sse=5838201.0, rms=2.414 (0.000%)
positioning took 1.1 minutes
mean border=39.9, 1803 (5) missing vertices, mean dist 0.1 [0.2 (%45.1)->0.3 (%54.9))]
%61 local maxima, %18 large gradients and %16 min vals, 419 gradients ignored
tol=1.0e-04, sigma=0.2, host=snake, 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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=5926427.0, rms=2.93
rms = 3.94, time step reduction 1 of 3 to 0.250...
037: dt: 0.2500, sse=5730611.5, rms=2.536 (0.000%)
038: dt: 0.2500, sse=5896865.0, rms=2.457 (0.000%)
rms = 2.44, time step reduction 2 of 3 to 0.125...
039: dt: 0.2500, sse=5980395.5, rms=2.440 (0.000%)
040: dt: 0.1250, sse=5854210.5, rms=2.301 (0.000%)
rms = 2.28, time step reduction 3 of 3 to 0.062...
041: dt: 0.1250, sse=5855223.5, rms=2.279 (0.000%)
positioning took 0.9 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area.pial
vertex spacing 1.01 +- 0.42 (0.05-->8.48) (max @ vno 120578 --> 119429)
face area 0.41 +- 0.30 (0.00-->9.41)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 169645 vertices processed
25000 of 169645 vertices processed
50000 of 169645 vertices processed
75000 of 169645 vertices processed
100000 of 169645 vertices processed
125000 of 169645 vertices processed
150000 of 169645 vertices processed
0 of 169645 vertices processed
25000 of 169645 vertices processed
50000 of 169645 vertices processed
75000 of 169645 vertices processed
100000 of 169645 vertices processed
125000 of 169645 vertices processed
150000 of 169645 vertices processed
thickness calculation complete, 164:643 truncations.
40505 vertices at 0 distance
121379 vertices at 1 distance
109370 vertices at 2 distance
40989 vertices at 3 distance
10693 vertices at 4 distance
2358 vertices at 5 distance
619 vertices at 6 distance
204 vertices at 7 distance
91 vertices at 8 distance
51 vertices at 9 distance
32 vertices at 10 distance
31 vertices at 11 distance
28 vertices at 12 distance
16 vertices at 13 distance
8 vertices at 14 distance
7 vertices at 15 distance
8 vertices at 16 distance
9 vertices at 17 distance
9 vertices at 18 distance
3 vertices at 19 distance
8 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.thickness
positioning took 18.1 minutes
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 23:15:26 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 Thu Aug  8 23:15:30 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 pctsurfcon --s sub006 --rh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts/pctsurfcon.log
Thu Aug  8 23:15:31 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh --regheader sub006 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 132232
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh
Dim: 169645 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh --projfrac 0.3 --regheader sub006 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 151597
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh
Dim: 169645 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/tmp.pctsurfcon.18021/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.w-g.pct.mgh --annot sub006 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.w-g.pct.mgh --annot sub006 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.w-g.pct.mgh
Vertex Area is 0.667852 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1610    1110.019
  2   2002            caudalanteriorcingulate    1502    1063.116
  3   2003                caudalmiddlefrontal    3799    2611.014
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2768    1817.631
  6   2006                         entorhinal     486     368.606
  7   2007                           fusiform    6320    4272.622
  8   2008                   inferiorparietal   11478    7683.567
  9   2009                   inferiortemporal    5811    3928.208
 10   2010                   isthmuscingulate    1736    1132.247
 11   2011                   lateraloccipital    9606    6132.968
 12   2012               lateralorbitofrontal    4897    3264.001
 13   2013                            lingual    4996    3427.336
 14   2014                medialorbitofrontal    2949    1973.371
 15   2015                     middletemporal    5856    4037.792
 16   2016                    parahippocampal    1110     765.764
 17   2017                        paracentral    3361    2175.972
 18   2018                    parsopercularis    2097    1417.664
 19   2019                      parsorbitalis    1361     918.504
 20   2020                   parstriangularis    2784    1843.752
 21   2021                      pericalcarine    2638    1805.453
 22   2022                        postcentral    7713    4966.229
 23   2023                 posteriorcingulate    2503    1716.131
 24   2024                         precentral    9841    6472.066
 25   2025                          precuneus    7647    5166.704
 26   2026           rostralanteriorcingulate    1460     975.283
 27   2027               rostralmiddlefrontal   11762    8062.871
 28   2028                    superiorfrontal   13951    9490.628
 29   2029                   superiorparietal    9841    6412.687
 30   2030                   superiortemporal    6693    4451.472
 31   2031                      supramarginal    6577    4376.953
 32   2032                        frontalpole     559     379.694
 33   2033                       temporalpole     754     536.237
 34   2034                 transversetemporal     591     366.553
 35   2035                             insula    3899    2599.391

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Thu Aug  8 23:15:51 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

 1610   1110   3092  2.880 0.441     0.118     0.027       14     1.8  bankssts
 1502   1063   3240  2.787 0.712     0.158     0.065       39     4.7  caudalanteriorcingulate
 3799   2611   7981  2.728 0.455     0.130     0.037       48     5.9  caudalmiddlefrontal
 2768   1818   4177  2.055 0.434     0.164     0.058       49     6.7  cuneus
  486    369   1741  3.642 0.638     0.143     0.050        4     1.0  entorhinal
 6320   4273  13576  2.664 0.580     0.145     0.079      180    12.5  fusiform
11478   7684  21958  2.515 0.527     0.142     0.045      186    19.9  inferiorparietal
 5811   3928  11520  2.455 0.710     0.149     0.063      125    14.8  inferiortemporal
 1736   1132   3208  2.529 0.808     0.156     0.075       36     4.4  isthmuscingulate
 9606   6133  15622  2.211 0.468     0.143     0.051      169    19.6  lateraloccipital
 4897   3264   9898  2.687 0.698     0.149     0.061       89    12.1  lateralorbitofrontal
 4996   3427   7828  2.146 0.516     0.158     0.072       92    11.8  lingual
 2949   1973   5355  2.358 0.590     0.167     0.083      100    10.2  medialorbitofrontal
 5856   4038  14461  2.879 0.637     0.135     0.044       98    10.1  middletemporal
 1110    766   2406  2.744 0.618     0.138     0.053       15     2.4  parahippocampal
 3361   2176   6071  2.540 0.533     0.122     0.033       33     4.6  paracentral
 2097   1418   4645  2.841 0.438     0.124     0.036       23     3.0  parsopercularis
 1361    919   3215  2.716 0.485     0.163     0.064       30     2.9  parsorbitalis
 2784   1844   5152  2.508 0.388     0.132     0.040       40     4.6  parstriangularis
 2638   1805   3496  2.021 0.392     0.129     0.036       28     3.7  pericalcarine
 7713   4966  12208  2.182 0.563     0.117     0.033       79    11.3  postcentral
 2503   1716   4944  2.554 0.696     0.154     0.051       53     4.9  posteriorcingulate
 9841   6472  19598  2.729 0.564     0.117     0.033       99    13.4  precentral
 7647   5167  13732  2.451 0.543     0.140     0.048      122    14.8  precuneus
 1460    975   3341  2.920 0.624     0.149     0.087       31     3.1  rostralanteriorcingulate
11762   8063  22493  2.393 0.525     0.161     0.066      289    28.9  rostralmiddlefrontal
13951   9491  30200  2.750 0.524     0.139     0.043      210    24.0  superiorfrontal
 9841   6413  16008  2.237 0.447     0.130     0.039      135    14.9  superiorparietal
 6693   4451  15382  2.996 0.615     0.119     0.035       70     9.9  superiortemporal
 6577   4377  12969  2.637 0.492     0.140     0.043      103    11.1  supramarginal
  559    380   1318  2.561 0.551     0.194     0.074       16     1.7  frontalpole
  754    536   2343  3.120 0.936     0.182     0.106       25     3.5  temporalpole
  591    367   1191  2.796 0.341     0.131     0.038        7     0.9  transversetemporal
 3899   2599   8105  2.984 0.698     0.133     0.059       84     9.1  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Aug  8 23:16:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/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/5.3.0/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...
2 labels changed using aseg
relabeling using gibbs priors...
000:  11829 changed, 169645 examined...
001:   2876 changed, 45320 examined...
002:    908 changed, 14566 examined...
003:    403 changed, 5107 examined...
004:    203 changed, 2193 examined...
005:    109 changed, 1151 examined...
006:     64 changed, 629 examined...
007:     35 changed, 326 examined...
008:     13 changed, 174 examined...
009:     10 changed, 84 examined...
010:     10 changed, 57 examined...
011:      6 changed, 57 examined...
012:      2 changed, 30 examined...
013:      1 changed, 8 examined...
014:      2 changed, 8 examined...
015:      3 changed, 9 examined...
016:      0 changed, 12 examined...
1 labels changed using aseg
000: 351 total segments, 269 labels (3338 vertices) changed
001: 109 total segments, 27 labels (122 vertices) changed
002: 84 total segments, 2 labels (21 vertices) changed
003: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 135 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1158 vertices marked for relabeling...
1158 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 31 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Thu Aug  8 23:17:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

 1199    831   2236  2.263 0.468     0.185     0.089       42     3.8  G_and_S_frontomargin
 1656   1085   3232  2.411 0.561     0.147     0.044       25     3.0  G_and_S_occipital_inf
 1833   1157   3543  2.487 0.591     0.119     0.041       18     3.7  G_and_S_paracentral
 1730   1138   3512  2.629 0.514     0.132     0.038       23     2.8  G_and_S_subcentral
 1574   1073   3401  2.415 0.579     0.206     0.107       59     6.1  G_and_S_transv_frontopol
 3773   2524   7296  2.687 0.520     0.128     0.054       50     6.3  G_and_S_cingul-Ant
 2081   1483   4625  2.905 0.459     0.135     0.037       32     3.2  G_and_S_cingul-Mid-Ant
 2469   1657   4938  2.706 0.500     0.134     0.038       31     4.1  G_and_S_cingul-Mid-Post
  863    584   2251  3.051 0.438     0.181     0.072       26     2.3  G_cingul-Post-dorsal
  426    278   1075  2.945 0.541     0.204     0.149       16     2.2  G_cingul-Post-ventral
 2491   1657   3713  1.996 0.442     0.167     0.061       46     6.1  G_cuneus
 1211    820   3408  3.060 0.352     0.137     0.042       17     2.0  G_front_inf-Opercular
  464    303   1078  2.642 0.402     0.154     0.051       11     1.0  G_front_inf-Orbital
 1099    738   2650  2.725 0.312     0.157     0.055       24     2.5  G_front_inf-Triangul
 5717   3978  14339  2.705 0.517     0.173     0.066      161    14.7  G_front_middle
 9273   6277  22609  2.836 0.538     0.154     0.054      196    19.9  G_front_sup
  766    497   1955  3.323 0.626     0.145     0.085       39     1.9  G_Ins_lg_and_S_cent_ins
  898    609   2528  3.344 0.578     0.152     0.062       17     2.4  G_insular_short
 3590   2264   7000  2.455 0.437     0.156     0.058       75     8.1  G_occipital_middle
 2027   1268   3514  2.267 0.434     0.139     0.056       40     3.5  G_occipital_sup
 2729   1779   6586  2.830 0.523     0.158     0.057       56     6.5  G_oc-temp_lat-fusifor
 3008   2064   5328  2.206 0.566     0.179     0.091       73     8.7  G_oc-temp_med-Lingual
 1454   1014   4481  3.391 0.722     0.156     0.067       23     3.8  G_oc-temp_med-Parahip
 3246   2159   8014  2.839 0.695     0.173     0.075       85    10.3  G_orbital
 4420   2968  10700  2.695 0.605     0.158     0.054       99     9.2  G_pariet_inf-Angular
 3492   2323   8005  2.740 0.473     0.154     0.050       75     6.4  G_pariet_inf-Supramar
 3233   2099   5997  2.299 0.434     0.138     0.039       54     5.1  G_parietal_sup
 2762   1703   5058  2.335 0.456     0.127     0.035       35     4.0  G_postcentral
 3697   2341   9230  3.045 0.461     0.123     0.037       49     5.1  G_precentral
 2940   1987   6751  2.638 0.507     0.147     0.048       59     5.8  G_precuneus
  579    403   1267  2.267 0.664     0.240     0.160       43     3.6  G_rectus
  606    405   1196  2.541 0.870     0.105     0.053        8     1.5  G_subcallosal
  480    291   1063  2.951 0.375     0.145     0.042        7     0.8  G_temp_sup-G_T_transv
 2298   1478   6917  3.322 0.515     0.143     0.047       39     4.6  G_temp_sup-Lateral
 1009    687   2589  3.153 0.703     0.122     0.052       19     2.6  G_temp_sup-Plan_polar
  984    699   2168  2.802 0.487     0.117     0.026        7     1.1  G_temp_sup-Plan_tempo
 3150   2099   7184  2.523 0.821     0.175     0.086       98    11.3  G_temporal_inf
 3362   2298  10004  3.092 0.602     0.152     0.058       78     7.5  G_temporal_middle
  578    380    899  2.421 0.401     0.102     0.021        4     0.6  Lat_Fis-ant-Horizont
  219    155    373  2.633 0.479     0.096     0.026        1     0.2  Lat_Fis-ant-Vertical
 1656   1102   2440  2.483 0.510     0.115     0.032       11     2.2  Lat_Fis-post
 4572   2897   6639  1.997 0.418     0.151     0.059       90    11.4  Pole_occipital
 1950   1380   5551  3.005 0.687     0.171     0.083       53     6.3  Pole_temporal
 3051   2090   4282  2.247 0.565     0.133     0.047       37     5.4  S_calcarine
 3677   2459   4755  2.107 0.705     0.107     0.030       24     4.8  S_central
 1698   1147   2501  2.310 0.454     0.125     0.038       19     2.4  S_cingul-Marginalis
  676    456   1194  2.725 0.553     0.104     0.024        3     0.7  S_circular_insula_ant
 1466    971   2401  2.737 0.553     0.092     0.029        7     2.0  S_circular_insula_inf
 1747   1163   2622  2.591 0.404     0.105     0.027       10     2.0  S_circular_insula_sup
 1340    951   2179  2.361 0.483     0.115     0.030       12     1.8  S_collat_transv_ant
  815    538   1150  2.232 0.371     0.126     0.037        7     1.2  S_collat_transv_post
 2327   1584   3739  2.319 0.444     0.128     0.040       33     3.6  S_front_inf
 3348   2232   4732  2.214 0.404     0.129     0.039       42     5.2  S_front_middle
 2969   2074   5133  2.543 0.406     0.123     0.035       30     4.0  S_front_sup
 1000    675   1282  2.163 0.386     0.112     0.025        6     1.1  S_interm_prim-Jensen
 4107   2757   5883  2.263 0.439     0.128     0.042       49     6.0  S_intrapariet_and_P_trans
 1628   1102   2199  2.127 0.382     0.135     0.032       15     2.2  S_oc_middle_and_Lunatus
 1504    995   1987  2.046 0.379     0.107     0.023       11     1.4  S_oc_sup_and_transversal
  915    608   1478  2.392 0.444     0.109     0.028       10     0.9  S_occipital_ant
 1119    769   1819  2.321 0.494     0.135     0.211       93     1.8  S_oc-temp_lat
 2333   1622   3685  2.414 0.386     0.108     0.028       15     2.5  S_oc-temp_med_and_Lingual
  710    472    890  2.150 0.320     0.132     0.054        6     1.1  S_orbital_lateral
  850    599   1306  2.320 0.791     0.115     0.042        9     0.9  S_orbital_med-olfact
 1944   1290   3332  2.539 0.512     0.151     0.054       30     4.1  S_orbital-H_Shaped
 3147   2075   4465  2.272 0.501     0.131     0.038       34     5.0  S_parieto_occipital
 2093   1368   2621  2.156 0.865     0.149     0.067       46     6.1  S_pericallosal
 2900   1919   4031  2.196 0.436     0.114     0.031       25     3.8  S_postcentral
 1963   1307   3068  2.637 0.367     0.117     0.029       17     2.4  S_precentral-inf-part
 2345   1586   3589  2.362 0.419     0.102     0.024       15     2.4  S_precentral-sup-part
  402    265    542  2.059 0.517     0.165     0.055        7     0.9  S_suborbital
 1593   1093   2476  2.302 0.331     0.128     0.037       18     2.4  S_subparietal
 1807   1233   2434  2.221 0.531     0.107     0.023       11     1.8  S_temporal_inf
 7570   5149  12736  2.654 0.511     0.118     0.030       68     9.3  S_temporal_sup
  348    237    629  2.852 0.431     0.132     0.031        3     0.5  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Thu Aug  8 23:18:25 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub006 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/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/5.3.0/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...
951 labels changed using aseg
relabeling using gibbs priors...
000:   3255 changed, 169645 examined...
001:    750 changed, 13958 examined...
002:    161 changed, 4001 examined...
003:     62 changed, 952 examined...
004:     22 changed, 367 examined...
005:     10 changed, 126 examined...
006:      7 changed, 61 examined...
007:      4 changed, 45 examined...
008:      3 changed, 24 examined...
009:      1 changed, 19 examined...
010:      1 changed, 7 examined...
011:      1 changed, 9 examined...
012:      2 changed, 5 examined...
013:      3 changed, 10 examined...
014:      2 changed, 13 examined...
015:      2 changed, 14 examined...
016:      2 changed, 14 examined...
017:      2 changed, 13 examined...
018:      2 changed, 10 examined...
019:      2 changed, 15 examined...
020:      4 changed, 14 examined...
021:      1 changed, 16 examined...
022:      2 changed, 7 examined...
023:      3 changed, 8 examined...
024:      2 changed, 15 examined...
025:      2 changed, 11 examined...
026:      3 changed, 14 examined...
027:      0 changed, 11 examined...
132 labels changed using aseg
000: 70 total segments, 37 labels (189 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 46 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1079 vertices marked for relabeling...
1079 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 18 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Thu Aug  8 23:19:43 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 sub006 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

 1508   1064   3233  2.777 0.723     0.158     0.065       39     4.7  caudalanteriorcingulate
 4034   2755   8209  2.711 0.452     0.128     0.037       49     6.1  caudalmiddlefrontal
 3476   2303   5187  2.072 0.415     0.156     0.052       55     7.6  cuneus
  483    370   1752  3.672 0.631     0.145     0.051        5     1.0  entorhinal
 5673   3810  12223  2.695 0.566     0.144     0.081      167    11.1  fusiform
10541   7050  20164  2.500 0.531     0.141     0.045      168    18.0  inferiorparietal
 6462   4380  12924  2.462 0.705     0.150     0.063      143    16.3  inferiortemporal
 1799   1173   3268  2.510 0.806     0.153     0.073       36     4.4  isthmuscingulate
10121   6449  16464  2.214 0.467     0.143     0.051      178    20.5  lateraloccipital
 5262   3516  10471  2.630 0.714     0.160     0.068      111    14.6  lateralorbitofrontal
 5011   3441   7881  2.148 0.516     0.157     0.071       91    11.7  lingual
 2424   1646   4749  2.355 0.694     0.177     0.094       94     9.7  medialorbitofrontal
 7140   4914  16799  2.874 0.616     0.133     0.042      111    11.9  middletemporal
 1098    757   2352  2.708 0.609     0.138     0.052       15     2.3  parahippocampal
 3515   2296   6431  2.539 0.529     0.124     0.033       35     4.8  paracentral
 2144   1457   4679  2.827 0.437     0.122     0.035       23     3.1  parsopercularis
 1472    990   3219  2.642 0.492     0.144     0.056       26     2.7  parsorbitalis
 2990   1979   5362  2.466 0.416     0.134     0.040       42     5.2  parstriangularis
 2641   1806   3515  2.027 0.390     0.131     0.038       29     3.9  pericalcarine
 8196   5292  12923  2.180 0.562     0.117     0.034       84    11.9  postcentral
 2669   1825   5537  2.622 0.691     0.155     0.052       56     5.5  posteriorcingulate
 9377   6146  19002  2.753 0.561     0.119     0.034       97    13.1  precentral
 7636   5155  13856  2.451 0.547     0.140     0.048      123    14.7  precuneus
 1666   1103   3530  2.825 0.635     0.148     0.081       33     3.5  rostralanteriorcingulate
 7457   5068  14428  2.450 0.508     0.155     0.058      162    16.6  rostralmiddlefrontal
18386  12561  38768  2.659 0.543     0.145     0.050      335    34.9  superiorfrontal
 8370   5453  13730  2.253 0.453     0.131     0.040      118    12.9  superiorparietal
 8815   5906  20569  2.989 0.636     0.127     0.043      119    16.5  superiortemporal
 6446   4301  12618  2.630 0.491     0.141     0.043      103    10.8  supramarginal
  584    361   1177  2.802 0.333     0.131     0.038        7     0.9  transversetemporal
 3560   2397   7458  2.959 0.675     0.130     0.052       68     7.1  insula
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 23:20:09 CEST 2013

 bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.log
Thu Aug  8 23:20:09 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
FREESURFER_HOME /opt/freesurfer/5.3.0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii...
fslregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fslregister.log

Thu Aug  8 23:20:14 CEST 2013
--s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake5
Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.16415e-09, 1.86265e-09)
j_ras = (-1.86265e-09, 1.49012e-08, -1)
k_ras = (9.31323e-10, 1, -1.49012e-08)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311076
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 --s sub006 --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
Ttarg: --------------------
-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;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.889;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 0.999  -0.041  -0.029  -0.000;
 0.023  -0.128   0.992  -0.000;
-0.044  -0.991  -0.127   0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.041  -0.029  -0.000;
 0.023  -0.128   0.992  -0.000;
-0.044  -0.991  -0.127   0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub006
RegMat ---------------------------
 0.999  -0.041  -0.029  -0.000;
 0.023  -0.128   0.992  -0.000;
-0.044  -0.991  -0.127   0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311076, ref det = -1
Thu Aug  8 23:20:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0
Thu Aug  8 23:24:44 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.999  -0.042  -0.020   40.136;
-0.025  -0.120  -0.992   274.192;
 0.039   0.992  -0.121   12.050;
 0.000   0.000   0.000   1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
Ttarg: --------------------
-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;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.889;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -0.311076, ref det = -1
---- Input registration matrix (computed) --------
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub006
RegMat ---------------------------
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 23:20:14 CEST 2013 
Ended   at Thu Aug  8 23:31:25 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat
subject sub006
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1376052073
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   0.990036
 1  -25.0 -25.0  25.0   1.013869
 2  -25.0  25.0 -25.0   1.045360
 3  -25.0  25.0  25.0   1.003149
 4   25.0 -25.0 -25.0   1.023281
 5   25.0 -25.0  25.0   1.006686
 6   25.0  25.0 -25.0   1.010024
 7   25.0  25.0  25.0   1.048604
REL:  8  0.322576    8.141011  1.017626 rel = 0.316989 
Initial costs ----------------
Number of surface hits 3238
WM  Intensity    61.7561 +/-  11.7398
Ctx Intensity    77.7046 +/-  15.1309
Pct Contrast     22.3549 +/-  23.0208
Cost   0.3226
RelCost   0.3170

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9854   0.9854  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9791   0.9791  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9606   0.9606  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9556   0.9556  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8671   0.8671  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8189   0.8189  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.7643   0.7643  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.6566   0.6566  0.0
   283   0.0000  -4.0000   0.0000   0.0000   0.0000   0.0000      0.6078   0.6078  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3226   0.3226  0.0
Brute Force --------------------------
Min cost was 0.322576
Number of iterations   729
Search time 2.528000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
  10 -0.006  0.000  0.000  0.000  0.000  0.000   0.3225513539
  11 -0.005  0.000  0.000  0.000  0.000  0.000   0.3225499366
  15 -0.005 -1.618  0.000  0.000  0.000  0.000   0.1223710691
  20 -0.005 -1.431  0.000  0.000  0.000  0.000   0.1196453081
  21 -0.005 -1.460  0.000  0.000  0.000  0.000   0.1190840389
  22 -0.005 -1.491  0.000  0.000  0.000  0.000   0.1184857389
  24 -0.005 -1.500  0.000  0.000  0.000  0.000   0.1184697786
  25 -0.005 -1.498  0.000  0.000  0.000  0.000   0.1184583008
  26 -0.005 -1.496  0.000  0.000  0.000  0.000   0.1184563610
  29 -0.005 -1.496  1.000  0.000  0.000  0.000   0.1170204377
  33 -0.005 -1.496  0.618  0.000  0.000  0.000   0.0877717013
  35 -0.005 -1.496  0.524  0.000  0.000  0.000   0.0860064007
  36 -0.005 -1.496  0.509  0.000  0.000  0.000   0.0859274583
  38 -0.005 -1.496  0.507  0.000  0.000  0.000   0.0859264095
  48 -0.005 -1.496  0.507 -0.064  0.000  0.000   0.0855856668
  49 -0.005 -1.496  0.507 -0.038  0.000  0.000   0.0849571324
  59 -0.005 -1.496  0.507 -0.038 -0.082  0.000   0.0845974589
  60 -0.005 -1.496  0.507 -0.038 -0.052  0.000   0.0843965611
  61 -0.005 -1.496  0.507 -0.038 -0.051  0.000   0.0843894536
  62 -0.005 -1.496  0.507 -0.038 -0.032  0.000   0.0843761775
  63 -0.005 -1.496  0.507 -0.038 -0.040  0.000   0.0843609554
  64 -0.005 -1.496  0.507 -0.038 -0.039  0.000   0.0843584762
  65 -0.005 -1.496  0.507 -0.038 -0.037  0.000   0.0843576955
  74 -0.005 -1.496  0.507 -0.038 -0.037  0.119   0.0818356881
  76 -0.005 -1.496  0.507 -0.038 -0.037  0.104   0.0817269000
  79 -0.005 -1.496  0.507 -0.038 -0.037  0.098   0.0817165227
  89  0.062 -1.496  0.507 -0.038 -0.037  0.098   0.0784200867
  91  0.079 -1.496  0.507 -0.038 -0.037  0.098   0.0783580601
  92  0.076 -1.496  0.507 -0.038 -0.037  0.098   0.0783375078
  93  0.074 -1.496  0.507 -0.038 -0.037  0.098   0.0783332821
 102  0.074 -1.500  0.507 -0.038 -0.037  0.098   0.0782613848
 104  0.074 -1.532  0.507 -0.038 -0.037  0.098   0.0782124181
 105  0.074 -1.518  0.507 -0.038 -0.037  0.098   0.0781260750
 106  0.074 -1.519  0.507 -0.038 -0.037  0.098   0.0781256759
 114  0.074 -1.519  0.518 -0.038 -0.037  0.098   0.0780031421
 116  0.074 -1.519  0.528 -0.038 -0.037  0.098   0.0779685306
 117  0.074 -1.519  0.530 -0.038 -0.037  0.098   0.0779660198
 128  0.074 -1.519  0.530 -0.079 -0.037  0.098   0.0775032375
 129  0.074 -1.519  0.530 -0.070 -0.037  0.098   0.0773934281
 130  0.074 -1.519  0.530 -0.066 -0.037  0.098   0.0773850494
 140  0.074 -1.519  0.530 -0.066 -0.045  0.098   0.0772513331
 142  0.074 -1.519  0.530 -0.066 -0.049  0.098   0.0772355263
 151  0.074 -1.519  0.530 -0.066 -0.049  0.153   0.0768815185
 152  0.074 -1.519  0.530 -0.066 -0.049  0.144   0.0767667536
 153  0.074 -1.519  0.530 -0.066 -0.049  0.133   0.0767352155
 154  0.074 -1.519  0.530 -0.066 -0.049  0.136   0.0767350124
 156  0.074 -1.519  0.530 -0.066 -0.049  0.135   0.0767345098
 157  0.153 -1.542  0.554 -0.094 -0.061  0.171   0.0757315281
 165  0.156 -1.543  0.555 -0.096 -0.062  0.173   0.0757278872
 166  0.160 -1.544  0.556 -0.097 -0.062  0.175   0.0757259927
 169  0.160 -1.544  0.556 -0.097 -0.062  0.175   0.0757256658
 177  0.160 -1.544  0.556 -0.097 -0.062  0.204   0.0755171844
 179  0.160 -1.544  0.556 -0.097 -0.062  0.196   0.0755028243
 181  0.160 -1.544  0.556 -0.097 -0.062  0.199   0.0754996383
 190  0.160 -1.513  0.556 -0.097 -0.062  0.199   0.0746624075
 191  0.160 -1.464  0.556 -0.097 -0.062  0.199   0.0746055559
 193  0.160 -1.487  0.556 -0.097 -0.062  0.199   0.0744588357
 195  0.160 -1.489  0.556 -0.097 -0.062  0.199   0.0744576947
 206  0.160 -1.489  0.566 -0.097 -0.062  0.199   0.0743555643
 207  0.160 -1.489  0.571 -0.097 -0.062  0.199   0.0743416053
 219  0.160 -1.489  0.571 -0.102 -0.062  0.199   0.0743244867
 229  0.160 -1.489  0.571 -0.102 -0.054  0.199   0.0742840259
 232  0.160 -1.489  0.571 -0.102 -0.055  0.199   0.0742834399
 239  0.190 -1.498  0.580 -0.112 -0.059  0.213   0.0741403009
 242  0.209 -1.503  0.586 -0.119 -0.062  0.221   0.0741398050
 244  0.209 -1.503  0.586 -0.119 -0.062  0.221   0.0741395840
 247  0.211 -1.504  0.586 -0.120 -0.063  0.222   0.0741395027
 248  0.210 -1.503  0.586 -0.120 -0.062  0.222   0.0741393948
 249  0.210 -1.503  0.586 -0.120 -0.062  0.222   0.0741393463
 259  0.210 -1.503  0.586 -0.120 -0.062  0.233   0.0738855742
 261  0.210 -1.503  0.586 -0.120 -0.062  0.248   0.0737759217
 262  0.210 -1.503  0.586 -0.120 -0.062  0.246   0.0737721810
 273  0.210 -1.490  0.586 -0.120 -0.062  0.246   0.0736963995
 285  0.210 -1.490  0.587 -0.120 -0.062  0.246   0.0736915133
 286  0.210 -1.490  0.592 -0.120 -0.062  0.246   0.0736834938
 288  0.210 -1.490  0.591 -0.120 -0.062  0.246   0.0736833623
 298  0.210 -1.490  0.591 -0.111 -0.062  0.246   0.0735968226
 300  0.210 -1.490  0.591 -0.107 -0.062  0.246   0.0735963327
 302  0.210 -1.490  0.591 -0.108 -0.062  0.246   0.0735944569
 303  0.210 -1.490  0.591 -0.109 -0.062  0.246   0.0735940538
 311  0.210 -1.490  0.591 -0.109 -0.070  0.246   0.0735228430
 312  0.210 -1.490  0.591 -0.109 -0.074  0.246   0.0735080376
 315  0.210 -1.490  0.591 -0.109 -0.075  0.246   0.0735077031
 321  0.240 -1.498  0.599 -0.120 -0.080  0.260   0.0734949468
 322  0.226 -1.494  0.595 -0.115 -0.078  0.254   0.0734300529
 324  0.228 -1.495  0.596 -0.116 -0.078  0.255   0.0734286940
 327  0.228 -1.495  0.596 -0.116 -0.078  0.255   0.0734286205
 338  0.228 -1.495  0.596 -0.116 -0.078  0.253   0.0734281123
 348  0.228 -1.479  0.596 -0.116 -0.078  0.253   0.0734006223
 349  0.228 -1.482  0.596 -0.116 -0.078  0.253   0.0733844990
 350  0.228 -1.486  0.596 -0.116 -0.078  0.253   0.0733790100
 362  0.228 -1.486  0.592 -0.116 -0.078  0.253   0.0733697099
 364  0.228 -1.486  0.593 -0.116 -0.078  0.253   0.0733696556
 374  0.228 -1.486  0.593 -0.110 -0.078  0.253   0.0733206040
 376  0.228 -1.486  0.593 -0.105 -0.078  0.253   0.0733125478
 377  0.228 -1.486  0.593 -0.107 -0.078  0.253   0.0733110118
 387  0.228 -1.486  0.593 -0.107 -0.083  0.253   0.0732951888
 396  0.232 -1.487  0.595 -0.108 -0.083  0.255   0.0732732502
 397  0.237 -1.488  0.596 -0.110 -0.084  0.257   0.0732630673
 398  0.238 -1.488  0.596 -0.110 -0.084  0.258   0.0732627839
 399  0.238 -1.488  0.596 -0.110 -0.084  0.257   0.0732624241
 403  0.247 -1.482  0.597 -0.104 -0.090  0.260   0.0732474931
 437  0.238 -1.483  0.592 -0.110 -0.084  0.259   0.0732438122
 439  0.238 -1.483  0.590 -0.110 -0.084  0.259   0.0732404503
 449  0.238 -1.483  0.590 -0.108 -0.084  0.259   0.0732309201
 451  0.238 -1.483  0.590 -0.105 -0.084  0.259   0.0732277520
 452  0.238 -1.483  0.590 -0.106 -0.084  0.259   0.0732268628
 462  0.238 -1.483  0.590 -0.106 -0.083  0.259   0.0732261879
 471  0.241 -1.484  0.590 -0.107 -0.084  0.260   0.0732203038
 472  0.242 -1.484  0.591 -0.108 -0.084  0.260   0.0732202274
 481  0.245 -1.480  0.585 -0.105 -0.083  0.263   0.0732121668
 527  0.242 -1.483  0.588 -0.105 -0.084  0.260   0.0732108126
 547  0.243 -1.483  0.589 -0.106 -0.084  0.261   0.0732097022
 549  0.243 -1.483  0.589 -0.106 -0.084  0.261   0.0732096414
 551  0.244 -1.482  0.587 -0.104 -0.084  0.262   0.0732042478
 556  0.245 -1.481  0.586 -0.103 -0.084  0.262   0.0732030385
 559  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732029930
 561  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732029320
 562  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732029164
 564  0.245 -1.481  0.585 -0.103 -0.084  0.262   0.0732028100
 577  0.245 -1.481  0.585 -0.103 -0.084  0.264   0.0732018670
Powell done niters = 7
Computing relative cost
 0  -25.0 -25.0 -25.0   1.013482
 1  -25.0 -25.0  25.0   1.015559
 2  -25.0  25.0 -25.0   1.034208
 3  -25.0  25.0  25.0   1.000666
 4   25.0 -25.0 -25.0   1.034182
 5   25.0 -25.0  25.0   0.991798
 6   25.0  25.0 -25.0   1.006023
 7   25.0  25.0  25.0   1.034180
REL:  8  0.073202    8.130098  1.016262 rel = 0.0720305 
Number of iterations     7
Min cost was 0.073202
Number of FunctionCalls   641
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 2.591000 sec
Parameters at optimum (transmm)  0.24532 -1.48124  0.58539
Parameters at optimum (rotdeg) -0.10298 -0.08425  0.26413 
Final costs ----------------
Number of surface hits 3238
WM  Intensity    60.0746 +/-  10.5131
Ctx Intensity    78.1624 +/-  10.7433
Pct Contrast     26.4330 +/-  15.2985
Cost   0.0732
RelCost   0.3170
Reg at min cost was 
 0.999  -0.037  -0.029   0.250;
 0.024  -0.123   0.992  -0.175;
-0.040  -0.992  -0.122  -0.347;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat, type = 14 
Original Reg 
 0.999  -0.039  -0.025   0.009;
 0.020  -0.121   0.992   1.308;
-0.042  -0.992  -0.120  -0.930;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000  -0.002   0.004  -0.241;
-0.005   0.002   0.000   1.483;
-0.001  -0.000   0.002  -0.583;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 1.655014
Computing change in rh position
Surface RMS Diff (mm) 1.549561 1.872015
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat
subject sub006
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1376539157
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.037  -0.029   0.250;
 0.024  -0.123   0.992  -0.175;
-0.040  -0.992  -0.122  -0.347;
 0.000   0.000   0.000   1.000;

Loading mov
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   1.000144
 1  -25.0 -25.0  25.0   1.011963
 2  -25.0  25.0 -25.0   1.028762
 3  -25.0  25.0  25.0   1.017444
 4   25.0 -25.0 -25.0   1.023030
 5   25.0 -25.0  25.0   1.003200
 6   25.0  25.0 -25.0   1.006099
 7   25.0  25.0  25.0   1.018704
REL:  8  0.074000    8.109344  1.013668 rel = 0.0730019 
Initial costs ----------------
Number of surface hits 323295
WM  Intensity    60.0945 +/-  10.4129
Ctx Intensity    78.3960 +/-  10.7337
Pct Contrast     26.6644 +/-  15.2882
Cost   0.0740
RelCost   0.0730

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.0884   0.0884  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.0860   0.0860  0.0
     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.0824   0.0824  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.0789   0.0789  0.0
    21  -0.1000  -0.1000  -0.1000   0.1000   0.0000  -0.1000      0.0775   0.0775  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.0762   0.0762  0.0
   120  -0.1000   0.0000   0.0000   0.0000   0.0000  -0.1000      0.0755   0.0755  0.0
   121  -0.1000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0755   0.0755  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0732   0.0732  0.0
Brute Force --------------------------
Min cost was 0.073202
Number of iterations   729
Search time 2.842000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
   7 -0.011  0.000  0.000  0.000  0.000  0.000   0.0739579968
   8 -0.023  0.000  0.000  0.000  0.000  0.000   0.0739393766
  10 -0.024  0.000  0.000  0.000  0.000  0.000   0.0739391684
  18 -0.024  0.068  0.000  0.000  0.000  0.000   0.0736410288
  19 -0.024  0.054  0.000  0.000  0.000  0.000   0.0736210929
  28 -0.024  0.054  0.144  0.000  0.000  0.000   0.0712034427
  29 -0.024  0.054  0.145  0.000  0.000  0.000   0.0712014029
  30 -0.024  0.054  0.154  0.000  0.000  0.000   0.0711957153
  32 -0.024  0.054  0.152  0.000  0.000  0.000   0.0711948811
  42 -0.024  0.054  0.152  0.003  0.000  0.000   0.0711937157
  51 -0.024  0.054  0.152  0.003 -0.021  0.000   0.0710840807
  52 -0.024  0.054  0.152  0.003 -0.028  0.000   0.0710745386
  55 -0.024  0.054  0.152  0.003 -0.029  0.000   0.0710742340
  63 -0.024  0.054  0.152  0.003 -0.029  0.003   0.0710718816
  65 -0.024  0.054  0.152  0.003 -0.029  0.005   0.0710714752
  66 -0.024  0.054  0.152  0.003 -0.029  0.006   0.0710712416
  77 -0.013  0.054  0.152  0.003 -0.029  0.006   0.0710605916
  87 -0.013  0.055  0.152  0.003 -0.029  0.006   0.0710605245
  96 -0.013  0.055  0.154  0.003 -0.029  0.006   0.0710602217
 106 -0.013  0.055  0.154  0.004 -0.029  0.006   0.0710595122
 115 -0.013  0.055  0.154  0.004 -0.031  0.006   0.0710593576
 124 -0.013  0.055  0.154  0.004 -0.031  0.010   0.0710563353
 126 -0.013  0.055  0.154  0.004 -0.031  0.011   0.0710561702
 127 -0.013  0.055  0.154  0.004 -0.031  0.012   0.0710560869
 130 -0.003  0.056  0.156  0.006 -0.032  0.018   0.0710552827
 136 -0.007  0.056  0.155  0.005 -0.032  0.016   0.0710535106
 137 -0.008  0.056  0.155  0.005 -0.031  0.015   0.0710534580
 138 -0.008  0.056  0.155  0.005 -0.031  0.016   0.0710533858
 162 -0.008  0.057  0.155  0.005 -0.031  0.016   0.0710532018
 171 -0.008  0.057  0.152  0.005 -0.031  0.016   0.0710519125
 198 -0.006  0.057  0.153  0.005 -0.032  0.016   0.0710517517
 199 -0.006  0.057  0.153  0.005 -0.032  0.016   0.0710517061
 200 -0.007  0.057  0.152  0.005 -0.032  0.016   0.0710517012
 203 -0.007  0.057  0.152  0.005 -0.032  0.016   0.0710516797
 217 -0.007  0.057  0.152  0.005 -0.032  0.017   0.0710516335
 270 -0.007  0.057  0.152  0.005 -0.032  0.017   0.0710516217
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.000527
 1  -25.0 -25.0  25.0   1.012389
 2  -25.0  25.0 -25.0   1.028572
 3  -25.0  25.0  25.0   1.018441
 4   25.0 -25.0 -25.0   1.022629
 5   25.0 -25.0  25.0   1.001609
 6   25.0  25.0 -25.0   1.005235
 7   25.0  25.0  25.0   1.020102
REL:  8  0.071052    8.109503  1.013688 rel = 0.0700922 
Number of iterations     4
Min cost was 0.071052
Number of FunctionCalls   333
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 51.287000 sec
Parameters at optimum (transmm) -0.00683  0.05697  0.15243
Parameters at optimum (rotdeg)  0.00519 -0.03151  0.01697 
Final costs ----------------
Number of surface hits 323295
WM  Intensity    60.0684 +/-  10.3946
Ctx Intensity    78.3842 +/-  10.7444
Pct Contrast     26.6871 +/-  15.2674
Cost   0.0711
RelCost   0.0730
Reg at min cost was 
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.999  -0.037  -0.029   0.250;
 0.024  -0.123   0.992  -0.175;
-0.040  -0.992  -0.122  -0.347;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000  -0.001   0.000   0.007;
-0.000  -0.000  -0.000  -0.057;
-0.001   0.000  -0.000  -0.153;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.153461
Computing change in rh position
Surface RMS Diff (mm) 0.170445 0.209095
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz
Ttarg: --------------------
-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;
INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.889;
 0.000   0.000   0.667  -128.000;
 0.000  -0.667   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub006
RegMat ---------------------------
 0.999  -0.036  -0.029   0.243;
 0.025  -0.123   0.992  -0.118;
-0.040  -0.992  -0.122  -0.195;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000  -0.005   0.001  -0.130;
 0.005   1.000   0.005  -0.080;
-0.001  -0.005   1.000   0.196;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699  -0.026  -0.016   40.677;
-0.021  -0.081  -0.661   273.305;
 0.025   0.661  -0.082   13.122;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 23:20:09 CEST 2013 
Ended   at Thu Aug  8 23:33:28 CEST 2013
BBR-Run-Time-Sec 799
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz 

mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998757, 0.0408089, 0.02861)
j_ras = (0.0441177, 0.99097, 0.126615)
k_ras = (0.0231846, -0.12772, 0.991539)
INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading extra input line subject sub006
reading extra input line fscale 0.150000
reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz...
INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.000  -0.005   0.001  -0.129;
 0.005   1.000   0.005  -0.080;
-0.001  -0.005   1.000   0.196;
 0.000   0.000   0.000   1.000;
---------------------------------
Applying LTAtransformInterp (resample_type 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz...

 mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz 

using segmentation for initial intensity normalization
using Gaussian smoothing of bias field, sigma=4.000
reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz...
computing distance transform
computing distance transform
computing nonmaximum suppression
14582 non wm control points removed
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
smoothing bias field
writing normalized volume to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/T2.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub006 lh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
refining pial surfaces placement using T2 volume ../mri/T2
using white starting white location...
using woT2.pial starting pial locations...
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/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
24515 bright wm thresholded.
438 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.orig...
computing class statistics...
border white:    318128 voxels (1.90%)
border gray      352780 voxels (2.10%)
WM (93.0): 93.8 +- 10.2 [70.0 --> 110.0]
GM (75.0) : 73.0 +- 13.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 43.3 (was 70)
setting MAX_BORDER_WHITE to 116.2 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 29.7 (was 40)
setting MAX_GRAY to 95.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.2 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 16.0 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=57
mean inside = 93.4, mean outside = 67.5
smoothing surface for 5 iterations...
reading initial white vertex positions from white...
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/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.03-->8.22) (max @ vno 73397 --> 77073)
face area 0.33 +- 0.16 (0.00-->8.17)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 205 points - only 10.24% unknown
deleting segment 2 with 22 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 7 with 21 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 742 points - only 0.00% unknown
deleting segment 11 with 12 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
deleting segment 15 with 38 points - only 0.00% unknown
deleting segment 16 with 15 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 17 with 4 points - only 0.00% unknown
deleting segment 18 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 19 with 3 points - only 0.00% unknown
deleting segment 20 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=2.0, host=snake, 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 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397)
face area 0.33 +- 0.16 (0.00-->8.17)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5338815.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.34, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
001: dt: 0.1250, sse=5338815.5, rms=0.000 (1.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 205 points - only 10.24% unknown
deleting segment 2 with 22 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 21 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 742 points - only 0.00% unknown
deleting segment 8 with 12 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 38 points - only 0.00% unknown
deleting segment 11 with 15 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
deleting segment 15 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397)
face area 0.33 +- 0.16 (0.00-->8.17)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5338815.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.34, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
002: dt: 0.1250, sse=5338815.5, rms=0.000 (1.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 205 points - only 10.24% unknown
deleting segment 2 with 22 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 21 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 742 points - only 0.00% unknown
deleting segment 8 with 12 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 38 points - only 0.00% unknown
deleting segment 11 with 15 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
deleting segment 15 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.25 (0.09-->8.22) (max @ vno 77073 --> 73397)
face area 0.33 +- 0.16 (0.00-->8.17)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5338815.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.34, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
003: dt: 0.1250, sse=5338815.5, rms=0.000 (1.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 205 points - only 10.24% unknown
deleting segment 2 with 22 points - only 0.00% unknown
deleting segment 3 with 12 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 4 with 1 points - only 0.00% unknown
deleting segment 5 with 21 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 7 with 742 points - only 0.00% unknown
deleting segment 8 with 12 points - only 0.00% unknown
deleting segment 9 with 5 points - only 0.00% unknown
deleting segment 10 with 38 points - only 0.00% unknown
deleting segment 11 with 15 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 12 with 4 points - only 0.00% unknown
deleting segment 13 with 5 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 14 with 3 points - only 0.00% unknown
deleting segment 15 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=0.2, host=snake, 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=5338815.5, rms=0.00
rms = 1.34, time step reduction 1 of 3 to 0.250...
rms = 0.34, time step reduction 2 of 3 to 0.125...
rms = 0.04, time step reduction 3 of 3 to 0.062...
004: dt: 0.1250, sse=5338815.5, rms=0.000 (1.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from woT2.pial...
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [101.60 232.40], gm=167.00+-21.80, and vertices in regions > 156.1
56865 surface locations found to contain inconsistent values (3318 in, 53547 out)
tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=585899.2, rms=0.24
001: dt: 0.5000, sse=552557.2, rms=0.233 (0.000%)
002: dt: 0.5000, sse=532313.9, rms=0.218 (0.000%)
003: dt: 0.5000, sse=520637.5, rms=0.207 (0.000%)
004: dt: 0.5000, sse=511675.7, rms=0.198 (0.000%)
005: dt: 0.5000, sse=505424.5, rms=0.189 (0.000%)
006: dt: 0.5000, sse=500991.1, rms=0.182 (0.000%)
007: dt: 0.5000, sse=498248.5, rms=0.175 (0.000%)
008: dt: 0.5000, sse=496290.6, rms=0.170 (0.000%)
009: dt: 0.5000, sse=494632.1, rms=0.165 (0.000%)
010: dt: 0.5000, sse=493524.8, rms=0.161 (0.000%)
011: dt: 0.5000, sse=492451.7, rms=0.158 (0.000%)
012: dt: 0.5000, sse=491455.6, rms=0.155 (0.000%)
013: dt: 0.5000, sse=490763.1, rms=0.153 (0.000%)
014: dt: 0.5000, sse=489956.1, rms=0.151 (0.000%)
015: dt: 0.5000, sse=489047.1, rms=0.149 (0.000%)
016: dt: 0.5000, sse=487979.8, rms=0.148 (0.000%)
017: dt: 0.5000, sse=486870.7, rms=0.146 (0.000%)
018: dt: 0.5000, sse=485633.1, rms=0.145 (0.000%)
019: dt: 0.5000, sse=484633.0, rms=0.145 (0.000%)
020: dt: 0.5000, sse=483442.2, rms=0.144 (0.000%)
021: dt: 0.5000, sse=482316.2, rms=0.144 (0.000%)
022: dt: 0.5000, sse=480975.9, rms=0.143 (0.000%)
023: dt: 0.5000, sse=479811.6, rms=0.143 (0.000%)
024: dt: 0.5000, sse=478604.6, rms=0.143 (0.000%)
025: dt: 0.5000, sse=477404.8, rms=0.143 (0.000%)
026: dt: 0.5000, sse=476307.0, rms=0.143 (0.000%)
027: dt: 0.5000, sse=475251.8, rms=0.143 (0.000%)
028: dt: 0.5000, sse=474003.1, rms=0.143 (0.000%)
029: dt: 0.5000, sse=472755.9, rms=0.144 (0.000%)
030: dt: 0.5000, sse=472009.8, rms=0.144 (0.000%)
positioning took 4.9 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [102.80 231.20], gm=167.00+-21.40, and vertices in regions > 156.3
45313 surface locations found to contain inconsistent values (2095 in, 43218 out)
tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=49324.5, rms=0.13
031: dt: 0.5000, sse=49042.9, rms=0.124 (0.000%)
032: dt: 0.5000, sse=50265.4, rms=0.113 (0.000%)
033: dt: 0.5000, sse=51683.0, rms=0.105 (0.000%)
034: dt: 0.5000, sse=52895.4, rms=0.100 (0.000%)
035: dt: 0.5000, sse=53878.7, rms=0.095 (0.000%)
036: dt: 0.5000, sse=54822.2, rms=0.090 (0.000%)
037: dt: 0.5000, sse=55703.8, rms=0.085 (0.000%)
038: dt: 0.5000, sse=56564.3, rms=0.081 (0.000%)
039: dt: 0.5000, sse=57430.5, rms=0.077 (0.000%)
040: dt: 0.5000, sse=58277.3, rms=0.074 (0.000%)
041: dt: 0.5000, sse=59050.3, rms=0.071 (0.000%)
042: dt: 0.5000, sse=59801.1, rms=0.067 (0.000%)
043: dt: 0.5000, sse=60506.4, rms=0.065 (0.000%)
044: dt: 0.5000, sse=61189.5, rms=0.062 (0.000%)
045: dt: 0.5000, sse=61814.1, rms=0.060 (0.000%)
046: dt: 0.5000, sse=62407.8, rms=0.058 (0.000%)
047: dt: 0.5000, sse=62950.9, rms=0.055 (0.000%)
048: dt: 0.5000, sse=63444.4, rms=0.054 (0.000%)
049: dt: 0.5000, sse=63930.4, rms=0.052 (0.000%)
050: dt: 0.5000, sse=64379.0, rms=0.050 (0.000%)
051: dt: 0.5000, sse=64806.3, rms=0.049 (0.000%)
052: dt: 0.5000, sse=65179.3, rms=0.048 (0.000%)
053: dt: 0.5000, sse=65511.7, rms=0.046 (0.000%)
054: dt: 0.5000, sse=65844.9, rms=0.045 (0.000%)
055: dt: 0.5000, sse=66145.9, rms=0.044 (0.000%)
056: dt: 0.5000, sse=66411.4, rms=0.043 (0.000%)
057: dt: 0.5000, sse=66612.0, rms=0.042 (0.000%)
058: dt: 0.5000, sse=66851.4, rms=0.042 (0.000%)
059: dt: 0.5000, sse=67050.4, rms=0.041 (0.000%)
060: dt: 0.5000, sse=67243.6, rms=0.040 (0.000%)
positioning took 5.2 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [63.40 268.60], gm=166.00+-34.20, and vertices in regions > 148.9
37661 surface locations found to contain inconsistent values (5 in, 37656 out)
tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=12155.9, rms=0.18
061: dt: 0.5000, sse=11530.2, rms=0.171 (0.000%)
062: dt: 0.5000, sse=10624.7, rms=0.153 (0.000%)
063: dt: 0.5000, sse=9952.6, rms=0.136 (0.000%)
064: dt: 0.5000, sse=9473.3, rms=0.121 (0.000%)
065: dt: 0.5000, sse=9178.2, rms=0.108 (0.000%)
066: dt: 0.5000, sse=9013.4, rms=0.098 (0.000%)
067: dt: 0.5000, sse=8920.9, rms=0.089 (0.000%)
068: dt: 0.5000, sse=8868.3, rms=0.083 (0.000%)
069: dt: 0.5000, sse=8861.6, rms=0.076 (0.000%)
070: dt: 0.5000, sse=8896.1, rms=0.071 (0.000%)
071: dt: 0.5000, sse=8960.4, rms=0.066 (0.000%)
072: dt: 0.5000, sse=9027.7, rms=0.062 (0.000%)
073: dt: 0.5000, sse=9092.5, rms=0.058 (0.000%)
074: dt: 0.5000, sse=9157.8, rms=0.054 (0.000%)
075: dt: 0.5000, sse=9223.9, rms=0.051 (0.000%)
076: dt: 0.5000, sse=9287.0, rms=0.048 (0.000%)
077: dt: 0.5000, sse=9349.0, rms=0.046 (0.000%)
078: dt: 0.5000, sse=9409.1, rms=0.044 (0.000%)
079: dt: 0.5000, sse=9464.9, rms=0.042 (0.000%)
080: dt: 0.5000, sse=9518.9, rms=0.040 (0.000%)
081: dt: 0.5000, sse=9571.4, rms=0.038 (0.000%)
082: dt: 0.5000, sse=9617.6, rms=0.037 (0.000%)
083: dt: 0.5000, sse=9662.5, rms=0.036 (0.000%)
084: dt: 0.5000, sse=9702.4, rms=0.035 (0.000%)
085: dt: 0.5000, sse=9738.6, rms=0.034 (0.000%)
086: dt: 0.5000, sse=9772.5, rms=0.033 (0.000%)
087: dt: 0.5000, sse=9803.9, rms=0.032 (0.000%)
088: dt: 0.5000, sse=9831.5, rms=0.032 (0.000%)
089: dt: 0.5000, sse=9856.0, rms=0.031 (0.000%)
090: dt: 0.5000, sse=9878.5, rms=0.031 (0.000%)
positioning took 4.7 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [71.20 260.80], gm=166.00+-31.60, and vertices in regions > 150.2
10453 surface locations found to contain inconsistent values (10 in, 10443 out)
tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000
mom=0.00, dt=0.50
writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=1900.5, rms=0.07
091: dt: 0.5000, sse=1866.7, rms=0.073 (0.000%)
092: dt: 0.5000, sse=1715.0, rms=0.067 (0.000%)
093: dt: 0.5000, sse=1589.9, rms=0.061 (0.000%)
094: dt: 0.5000, sse=1487.0, rms=0.056 (0.000%)
095: dt: 0.5000, sse=1408.0, rms=0.051 (0.000%)
096: dt: 0.5000, sse=1353.5, rms=0.048 (0.000%)
097: dt: 0.5000, sse=1316.5, rms=0.045 (0.000%)
098: dt: 0.5000, sse=1289.3, rms=0.043 (0.000%)
099: dt: 0.5000, sse=1264.8, rms=0.041 (0.000%)
100: dt: 0.5000, sse=1240.9, rms=0.039 (0.000%)
101: dt: 0.5000, sse=1219.6, rms=0.037 (0.000%)
102: dt: 0.5000, sse=1202.6, rms=0.035 (0.000%)
103: dt: 0.5000, sse=1188.9, rms=0.034 (0.000%)
104: dt: 0.5000, sse=1178.0, rms=0.033 (0.000%)
105: dt: 0.5000, sse=1169.0, rms=0.031 (0.000%)
106: dt: 0.5000, sse=1161.6, rms=0.030 (0.000%)
107: dt: 0.5000, sse=1155.5, rms=0.030 (0.000%)
108: dt: 0.5000, sse=1150.6, rms=0.029 (0.000%)
109: dt: 0.5000, sse=1147.0, rms=0.028 (0.000%)
110: dt: 0.5000, sse=1144.2, rms=0.028 (0.000%)
111: dt: 0.5000, sse=1141.2, rms=0.027 (0.000%)
112: dt: 0.5000, sse=1139.7, rms=0.027 (0.000%)
113: dt: 0.5000, sse=1138.0, rms=0.027 (0.000%)
114: dt: 0.5000, sse=1136.9, rms=0.026 (0.000%)
115: dt: 0.5000, sse=1135.8, rms=0.026 (0.000%)
116: dt: 0.5000, sse=1134.9, rms=0.026 (0.000%)
117: dt: 0.5000, sse=1134.2, rms=0.026 (0.000%)
118: dt: 0.5000, sse=1134.0, rms=0.026 (0.000%)
119: dt: 0.5000, sse=1133.7, rms=0.026 (0.000%)
120: dt: 0.5000, sse=1133.2, rms=0.026 (0.000%)
positioning took 4.8 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.area.pial
vertex spacing 1.04 +- 0.45 (0.06-->8.89) (max @ vno 77073 --> 73397)
face area 0.42 +- 0.33 (0.00-->7.81)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 171478 vertices processed
25000 of 171478 vertices processed
50000 of 171478 vertices processed
75000 of 171478 vertices processed
100000 of 171478 vertices processed
125000 of 171478 vertices processed
150000 of 171478 vertices processed
0 of 171478 vertices processed
25000 of 171478 vertices processed
50000 of 171478 vertices processed
75000 of 171478 vertices processed
100000 of 171478 vertices processed
125000 of 171478 vertices processed
150000 of 171478 vertices processed
thickness calculation complete, 260:847 truncations.
38131 vertices at 0 distance
119330 vertices at 1 distance
110616 vertices at 2 distance
44684 vertices at 3 distance
12417 vertices at 4 distance
3184 vertices at 5 distance
956 vertices at 6 distance
315 vertices at 7 distance
114 vertices at 8 distance
39 vertices at 9 distance
30 vertices at 10 distance
19 vertices at 11 distance
18 vertices at 12 distance
25 vertices at 13 distance
17 vertices at 14 distance
9 vertices at 15 distance
11 vertices at 16 distance
7 vertices at 17 distance
3 vertices at 18 distance
6 vertices at 19 distance
9 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.thickness
positioning took 24.3 minutes
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub006 rh 

-white NOWRITE indicates that white, curv, area, and cortex.label files will not be written...
refining pial surfaces placement using T2 volume ../mri/T2
using white starting white location...
using woT2.pial starting pial locations...
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/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
25014 bright wm thresholded.
438 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.orig...
computing class statistics...
border white:    318128 voxels (1.90%)
border gray      352780 voxels (2.10%)
WM (93.0): 93.7 +- 10.3 [70.0 --> 110.0]
GM (75.0) : 73.1 +- 13.4 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 43.6 (was 70)
setting MAX_BORDER_WHITE to 116.3 (was 105)
setting MIN_BORDER_WHITE to 57.0 (was 85)
setting MAX_CSF to 30.2 (was 40)
setting MAX_GRAY to 95.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 50.3 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 16.8 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=57
mean inside = 93.6, mean outside = 67.7
smoothing surface for 5 iterations...
reading initial white vertex positions from white...
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/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.25 (0.03-->4.47) (max @ vno 43725 --> 169070)
face area 0.33 +- 0.15 (0.00-->2.53)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 4 with 2 points - only 0.00% unknown
deleting segment 5 with 16 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 9 with 3 points - only 0.00% unknown
deleting segment 10 with 12 points - only 0.00% unknown
deleting segment 11 with 355 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 15 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 16 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 17 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 18 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 19 with 1 points - only 0.00% unknown
deleting segment 20 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=2.0, host=snake, 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 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
face area 0.33 +- 0.15 (0.00-->2.53)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5232412.5, rms=0.00
rms = 1.52, time step reduction 1 of 3 to 0.250...
rms = 0.40, time step reduction 2 of 3 to 0.125...
rms = 0.05, time step reduction 3 of 3 to 0.062...
001: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 12 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 12 points - only 0.00% unknown
deleting segment 9 with 355 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
deleting segment 17 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=1.0, host=snake, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
face area 0.33 +- 0.15 (0.00-->2.53)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5232412.5, rms=0.00
rms = 1.51, time step reduction 1 of 3 to 0.250...
rms = 0.40, time step reduction 2 of 3 to 0.125...
rms = 0.05, time step reduction 3 of 3 to 0.062...
002: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 12 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 12 points - only 0.00% unknown
deleting segment 9 with 355 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
deleting segment 17 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=0.5, host=snake, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.09-->4.47) (max @ vno 43725 --> 169070)
face area 0.33 +- 0.15 (0.00-->2.53)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5232412.5, rms=0.00
rms = 1.52, time step reduction 1 of 3 to 0.250...
rms = 0.40, time step reduction 2 of 3 to 0.125...
rms = 0.05, time step reduction 3 of 3 to 0.062...
003: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 1 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 4 with 16 points - only 0.00% unknown
deleting segment 5 with 7 points - only 0.00% unknown
deleting segment 6 with 12 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 12 points - only 0.00% unknown
deleting segment 9 with 355 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 11 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 14 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 16 with 1 points - only 0.00% unknown
deleting segment 17 with 8 points - only 0.00% unknown
tol=1.0e-04, sigma=0.2, host=snake, 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=5232412.5, rms=0.00
rms = 1.51, time step reduction 1 of 3 to 0.250...
rms = 0.40, time step reduction 2 of 3 to 0.125...
rms = 0.05, time step reduction 3 of 3 to 0.062...
004: dt: 0.1250, sse=5232412.5, rms=0.000 (1.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 1 vertex label from ripped group
removing 2 vertex label from ripped group
smoothing surface for 5 iterations...
reading initial pial vertex positions from woT2.pial...
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [120.90 215.10], gm=168.00+-15.70, and vertices in regions > 160.1
66741 surface locations found to contain inconsistent values (16077 in, 50664 out)
tol=1.0e-04, sigma=2.0, host=snake, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 1.000
averaging target values for 5 iterations...
000: dt: 0.0000, sse=583937.5, rms=0.31
001: dt: 0.5000, sse=551291.9, rms=0.299 (0.000%)
002: dt: 0.5000, sse=531946.6, rms=0.285 (0.000%)
003: dt: 0.5000, sse=521613.3, rms=0.273 (0.000%)
004: dt: 0.5000, sse=513313.1, rms=0.264 (0.000%)
005: dt: 0.5000, sse=507816.8, rms=0.255 (0.000%)
006: dt: 0.5000, sse=504162.0, rms=0.247 (0.000%)
007: dt: 0.5000, sse=502088.8, rms=0.240 (0.000%)
008: dt: 0.5000, sse=500069.7, rms=0.234 (0.000%)
009: dt: 0.5000, sse=498060.4, rms=0.228 (0.000%)
010: dt: 0.5000, sse=497946.9, rms=0.223 (0.000%)
011: dt: 0.5000, sse=496109.5, rms=0.218 (0.000%)
012: dt: 0.5000, sse=495622.3, rms=0.214 (0.000%)
013: dt: 0.5000, sse=494527.0, rms=0.210 (0.000%)
014: dt: 0.5000, sse=493889.6, rms=0.206 (0.000%)
015: dt: 0.5000, sse=492955.4, rms=0.203 (0.000%)
016: dt: 0.5000, sse=491788.3, rms=0.200 (0.000%)
017: dt: 0.5000, sse=491022.9, rms=0.197 (0.000%)
018: dt: 0.5000, sse=490132.5, rms=0.194 (0.000%)
019: dt: 0.5000, sse=489833.7, rms=0.191 (0.000%)
020: dt: 0.5000, sse=488871.8, rms=0.189 (0.000%)
021: dt: 0.5000, sse=487999.1, rms=0.187 (0.000%)
022: dt: 0.5000, sse=487343.7, rms=0.185 (0.000%)
023: dt: 0.5000, sse=486283.6, rms=0.183 (0.000%)
024: dt: 0.5000, sse=485447.2, rms=0.181 (0.000%)
025: dt: 0.5000, sse=484462.7, rms=0.179 (0.000%)
026: dt: 0.5000, sse=483647.3, rms=0.178 (0.000%)
027: dt: 0.5000, sse=483251.5, rms=0.176 (0.000%)
028: dt: 0.5000, sse=482651.1, rms=0.175 (0.000%)
029: dt: 0.5000, sse=481343.0, rms=0.174 (0.000%)
030: dt: 0.5000, sse=480459.8, rms=0.173 (0.000%)
positioning took 5.0 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [76.30 255.70], gm=166.00+-29.90, and vertices in regions > 151.0
49970 surface locations found to contain inconsistent values (100 in, 49870 out)
tol=1.0e-04, sigma=1.0, host=snake, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.500
averaging target values for 5 iterations...
000: dt: 0.0000, sse=54304.9, rms=0.21
031: dt: 0.5000, sse=53312.4, rms=0.196 (0.000%)
032: dt: 0.5000, sse=52236.9, rms=0.177 (0.000%)
033: dt: 0.5000, sse=51999.8, rms=0.161 (0.000%)
034: dt: 0.5000, sse=52344.8, rms=0.147 (0.000%)
035: dt: 0.5000, sse=53118.3, rms=0.135 (0.000%)
036: dt: 0.5000, sse=53940.3, rms=0.125 (0.000%)
037: dt: 0.5000, sse=54820.1, rms=0.116 (0.000%)
038: dt: 0.5000, sse=55713.6, rms=0.108 (0.000%)
039: dt: 0.5000, sse=56747.7, rms=0.102 (0.000%)
040: dt: 0.5000, sse=57823.4, rms=0.096 (0.000%)
041: dt: 0.5000, sse=58912.9, rms=0.091 (0.000%)
042: dt: 0.5000, sse=60000.9, rms=0.086 (0.000%)
043: dt: 0.5000, sse=61020.5, rms=0.082 (0.000%)
044: dt: 0.5000, sse=61998.4, rms=0.078 (0.000%)
045: dt: 0.5000, sse=62877.1, rms=0.075 (0.000%)
046: dt: 0.5000, sse=63736.4, rms=0.072 (0.000%)
047: dt: 0.5000, sse=64541.3, rms=0.069 (0.000%)
048: dt: 0.5000, sse=65293.5, rms=0.066 (0.000%)
049: dt: 0.5000, sse=65989.3, rms=0.064 (0.000%)
050: dt: 0.5000, sse=66664.4, rms=0.062 (0.000%)
051: dt: 0.5000, sse=67276.1, rms=0.060 (0.000%)
052: dt: 0.5000, sse=67850.1, rms=0.058 (0.000%)
053: dt: 0.5000, sse=68409.1, rms=0.056 (0.000%)
054: dt: 0.5000, sse=68891.1, rms=0.054 (0.000%)
055: dt: 0.5000, sse=69357.8, rms=0.053 (0.000%)
056: dt: 0.5000, sse=69782.3, rms=0.051 (0.000%)
057: dt: 0.5000, sse=70202.2, rms=0.050 (0.000%)
058: dt: 0.5000, sse=70580.1, rms=0.049 (0.000%)
059: dt: 0.5000, sse=70922.8, rms=0.047 (0.000%)
060: dt: 0.5000, sse=71252.9, rms=0.046 (0.000%)
positioning took 4.6 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [114.00 222.00], gm=168.00+-18.00, and vertices in regions > 159.0
37039 surface locations found to contain inconsistent values (15337 in, 21702 out)
tol=1.0e-04, sigma=0.5, host=snake, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
averaging target values for 5 iterations...
000: dt: 0.0000, sse=10268.8, rms=0.14
061: dt: 0.5000, sse=10068.2, rms=0.135 (0.000%)
062: dt: 0.5000, sse=9596.7, rms=0.125 (0.000%)
063: dt: 0.5000, sse=9328.5, rms=0.118 (0.000%)
064: dt: 0.5000, sse=9147.7, rms=0.111 (0.000%)
065: dt: 0.5000, sse=9011.6, rms=0.106 (0.000%)
066: dt: 0.5000, sse=8905.1, rms=0.101 (0.000%)
067: dt: 0.5000, sse=8808.3, rms=0.097 (0.000%)
068: dt: 0.5000, sse=8732.1, rms=0.093 (0.000%)
069: dt: 0.5000, sse=8673.0, rms=0.089 (0.000%)
070: dt: 0.5000, sse=8628.8, rms=0.085 (0.000%)
071: dt: 0.5000, sse=8600.9, rms=0.081 (0.000%)
072: dt: 0.5000, sse=8578.6, rms=0.077 (0.000%)
073: dt: 0.5000, sse=8558.2, rms=0.074 (0.000%)
074: dt: 0.5000, sse=8545.4, rms=0.071 (0.000%)
075: dt: 0.5000, sse=8538.6, rms=0.068 (0.000%)
076: dt: 0.5000, sse=8539.4, rms=0.065 (0.000%)
077: dt: 0.5000, sse=8544.7, rms=0.062 (0.000%)
078: dt: 0.5000, sse=8548.4, rms=0.060 (0.000%)
079: dt: 0.5000, sse=8557.6, rms=0.058 (0.000%)
080: dt: 0.5000, sse=8572.7, rms=0.055 (0.000%)
081: dt: 0.5000, sse=8582.5, rms=0.053 (0.000%)
082: dt: 0.5000, sse=8600.0, rms=0.051 (0.000%)
083: dt: 0.5000, sse=8613.9, rms=0.049 (0.000%)
084: dt: 0.5000, sse=8633.2, rms=0.048 (0.000%)
085: dt: 0.5000, sse=8649.9, rms=0.046 (0.000%)
086: dt: 0.5000, sse=8660.2, rms=0.045 (0.000%)
087: dt: 0.5000, sse=8676.0, rms=0.043 (0.000%)
088: dt: 0.5000, sse=8688.7, rms=0.042 (0.000%)
089: dt: 0.5000, sse=8703.5, rms=0.041 (0.000%)
090: dt: 0.5000, sse=8719.0, rms=0.040 (0.000%)
positioning took 4.6 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [91.20 244.80], gm=168.00+-25.60, and vertices in regions > 155.2
13872 surface locations found to contain inconsistent values (48 in, 13824 out)
tol=1.0e-04, sigma=0.2, host=snake, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000
mom=0.00, dt=0.50
writing pial surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=2027.1, rms=0.09
091: dt: 0.5000, sse=1969.7, rms=0.083 (0.000%)
092: dt: 0.5000, sse=1765.6, rms=0.075 (0.000%)
093: dt: 0.5000, sse=1605.0, rms=0.068 (0.000%)
094: dt: 0.5000, sse=1477.9, rms=0.061 (0.000%)
095: dt: 0.5000, sse=1383.8, rms=0.056 (0.000%)
096: dt: 0.5000, sse=1322.9, rms=0.052 (0.000%)
097: dt: 0.5000, sse=1277.8, rms=0.049 (0.000%)
098: dt: 0.5000, sse=1243.1, rms=0.046 (0.000%)
099: dt: 0.5000, sse=1214.2, rms=0.044 (0.000%)
100: dt: 0.5000, sse=1186.9, rms=0.042 (0.000%)
101: dt: 0.5000, sse=1165.8, rms=0.040 (0.000%)
102: dt: 0.5000, sse=1148.6, rms=0.038 (0.000%)
103: dt: 0.5000, sse=1134.2, rms=0.036 (0.000%)
104: dt: 0.5000, sse=1122.8, rms=0.035 (0.000%)
105: dt: 0.5000, sse=1113.8, rms=0.034 (0.000%)
106: dt: 0.5000, sse=1107.0, rms=0.033 (0.000%)
107: dt: 0.5000, sse=1101.6, rms=0.032 (0.000%)
108: dt: 0.5000, sse=1096.5, rms=0.031 (0.000%)
109: dt: 0.5000, sse=1092.6, rms=0.031 (0.000%)
110: dt: 0.5000, sse=1089.5, rms=0.030 (0.000%)
111: dt: 0.5000, sse=1087.5, rms=0.030 (0.000%)
112: dt: 0.5000, sse=1084.6, rms=0.030 (0.000%)
113: dt: 0.5000, sse=1082.9, rms=0.029 (0.000%)
114: dt: 0.5000, sse=1081.3, rms=0.029 (0.000%)
115: dt: 0.5000, sse=1079.9, rms=0.029 (0.000%)
116: dt: 0.5000, sse=1079.9, rms=0.029 (0.000%)
117: dt: 0.5000, sse=1079.1, rms=0.029 (0.000%)
118: dt: 0.5000, sse=1079.3, rms=0.028 (0.000%)
119: dt: 0.5000, sse=1078.9, rms=0.028 (0.000%)
120: dt: 0.5000, sse=1078.6, rms=0.028 (0.000%)
positioning took 4.6 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.area.pial
vertex spacing 1.04 +- 0.45 (0.09-->8.56) (max @ vno 120578 --> 119429)
face area 0.42 +- 0.32 (0.00-->9.00)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 169645 vertices processed
25000 of 169645 vertices processed
50000 of 169645 vertices processed
75000 of 169645 vertices processed
100000 of 169645 vertices processed
125000 of 169645 vertices processed
150000 of 169645 vertices processed
0 of 169645 vertices processed
25000 of 169645 vertices processed
50000 of 169645 vertices processed
75000 of 169645 vertices processed
100000 of 169645 vertices processed
125000 of 169645 vertices processed
150000 of 169645 vertices processed
thickness calculation complete, 257:851 truncations.
39532 vertices at 0 distance
119234 vertices at 1 distance
109115 vertices at 2 distance
42502 vertices at 3 distance
11691 vertices at 4 distance
2940 vertices at 5 distance
812 vertices at 6 distance
270 vertices at 7 distance
102 vertices at 8 distance
56 vertices at 9 distance
41 vertices at 10 distance
34 vertices at 11 distance
23 vertices at 12 distance
18 vertices at 13 distance
13 vertices at 14 distance
12 vertices at 15 distance
11 vertices at 16 distance
10 vertices at 17 distance
12 vertices at 18 distance
6 vertices at 19 distance
10 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.thickness
positioning took 23.5 minutes
#--------------------------------------------
#@# Surf Volume lh Fri Aug  9 00:23:44 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 ]
#--------------------------------------------
#@# Surf Volume rh Fri Aug  9 00:23:45 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 ]
#--------------------------------------------
#@# Cortical ribbon mask Fri Aug  9 00:23:45 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub006 

SUBJECTS_DIR is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
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 = 10
writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Fri Aug  9 00:58:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 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/5.3.0/ASegStatsLUT.txt --subject sub006 


$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/5.3.0/ASegStatsLUT.txt --subject sub006 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1428534 mm^3    (det: 1.363710 )
Computing euler number
orig.nofix lheno =  -30, rheno = -44
orig.nofix lhholes =   16, rhholes = 23
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 336212.563 332461.000  diff= 3751.6  pctdiff= 1.116
rhCtxGM: 328476.300 325187.000  diff= 3289.3  pctdiff= 1.001
lhCtxWM: 277850.585 277588.500  diff=  262.1  pctdiff= 0.094
rhCtxWM: 278985.206 278975.500  diff=    9.7  pctdiff= 0.003
SubCortGMVol  73421.000
SupraTentVol  1315795.655 (1307464.000) diff=8331.655 pctdiff=0.633
SupraTentVolNotVent  1296172.655 (1287841.000) diff=8331.655 pctdiff=0.643
BrainSegVol  1456908.000 (1453971.000) diff=2937.000 pctdiff=0.202
BrainSegVolNotVent  1433208.000 (1440132.655) diff=-6924.655 pctdiff=-0.483
BrainSegVolNotVent  1433208.000
CerebellumVol 144979.000
VentChorVol   19623.000
3rd4th5thCSF   4077.000
CSFVol  1172.000, OptChiasmVol   356.000
MaskVol 1955327.000
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    7330    7330.012
  4     5                  Left-Inf-Lat-Vent     485     485.404
  5     7       Left-Cerebellum-White-Matter   19126   19126.078
  6     8             Left-Cerebellum-Cortex   54076   54075.738
  7    10               Left-Thalamus-Proper    9801    9800.789
  8    11                       Left-Caudate    4593    4592.850
  9    12                       Left-Putamen    6882    6882.185
 10    13                      Left-Pallidum    2582    2581.743
 11    14                      3rd-Ventricle    1031    1030.534
 12    15                      4th-Ventricle    2076    2076.042
 13    16                         Brain-Stem   28015   28015.285
 14    17                   Left-Hippocampus    4356    4355.679
 15    18                      Left-Amygdala    1830    1830.003
 16    24                                CSF    1168    1167.957
 17    26                Left-Accumbens-area    1138    1137.688
 18    28                     Left-VentralDC    4830    4829.687
 19    30                        Left-vessel      89      88.732
 20    31                Left-choroid-plexus    1089    1088.721
 23    43            Right-Lateral-Ventricle    8169    8168.733
 24    44                 Right-Inf-Lat-Vent     835     834.640
 25    46      Right-Cerebellum-White-Matter   19688   19687.779
 26    47            Right-Cerebellum-Cortex   54426   54426.105
 27    49              Right-Thalamus-Proper    8898    8898.092
 28    50                      Right-Caudate    5030    5030.434
 29    51                      Right-Putamen    6987    6987.416
 30    52                     Right-Pallidum    2747    2746.605
 31    53                  Right-Hippocampus    4251    4250.944
 32    54                     Right-Amygdala    1875    1875.328
 33    58               Right-Accumbens-area     902     901.986
 34    60                    Right-VentralDC    4849    4848.833
 35    62                       Right-vessel      98      97.882
 36    63               Right-choroid-plexus    1666    1665.774
 37    72                      5th-Ventricle       0       0.000
 38    77                 WM-hypointensities    1291    1290.874
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities      30      29.574
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     360     359.910
 45   251                       CC_Posterior     733     732.649
 46   252                   CC_Mid_Posterior     381     380.823
 47   253                         CC_Central     374     373.556
 48   254                    CC_Mid_Anterior     392     392.228
 49   255                        CC_Anterior     867     866.925

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Fri Aug  9 01:02:15 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 mri_aparc2aseg --s sub006 --volmask 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub006
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/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 = 655708
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 mri_aparc2aseg --s sub006 --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub006
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/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 = 655708
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Fri Aug  9 01:08:27 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 mri_aparc2aseg --s sub006 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub006
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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/forrest_gump/openfmri.org/freesurfer/sub006/mri/ribbon.mgz
Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 9139 vertices from left hemi
Ripped 8689 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/forrest_gump/openfmri.org/freesurfer/sub006/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 = 1211345
Used brute-force search on 255 voxels
Fixing Parahip LH WM
  Found 14 clusters
     0 k 7.000000
     1 k 2.000000
     2 k 1.000000
     3 k 2.000000
     4 k 3.000000
     5 k 1.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1.000000
     9 k 1.000000
     10 k 1.000000
     11 k 1683.000000
     12 k 36.000000
     13 k 2.000000
Fixing Parahip RH WM
  Found 4 clusters
     0 k 1757.000000
     1 k 1.000000
     2 k 8.000000
     3 k 1.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006

 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 sub006 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/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 sub006 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname snake5
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1428534 mm^3    (det: 1.363710 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 336212.563 332461.000  diff= 3751.6  pctdiff= 1.116
rhCtxGM: 328476.300 325187.000  diff= 3289.3  pctdiff= 1.001
lhCtxWM: 277850.585 277588.500  diff=  262.1  pctdiff= 0.094
rhCtxWM: 278985.206 278975.500  diff=    9.7  pctdiff= 0.003
SubCortGMVol  73421.000
SupraTentVol  1315795.655 (1307464.000) diff=8331.655 pctdiff=0.633
SupraTentVolNotVent  1296172.655 (1287841.000) diff=8331.655 pctdiff=0.643
BrainSegVol  1456908.000 (1453971.000) diff=2937.000 pctdiff=0.202
BrainSegVolNotVent  1433208.000 (1440132.655) diff=-6924.655 pctdiff=-0.483
BrainSegVolNotVent  1433208.000
CerebellumVol 144979.000
VentChorVol   19623.000
3rd4th5thCSF   4077.000
CSFVol  1172.000, OptChiasmVol   356.000
MaskVol 1955327.000
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    4418    4417.723
  2   3002      wm-lh-caudalanteriorcingulate    3864    3864.340
  3   3003          wm-lh-caudalmiddlefrontal    7755    7755.121
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    2922    2922.244
  6   3006                   wm-lh-entorhinal     866     865.680
  7   3007                     wm-lh-fusiform    7879    7879.229
  8   3008             wm-lh-inferiorparietal   13874   13874.421
  9   3009             wm-lh-inferiortemporal    8577    8576.690
 10   3010             wm-lh-isthmuscingulate    5079    5079.076
 11   3011             wm-lh-lateraloccipital   11434   11433.657
 12   3012         wm-lh-lateralorbitofrontal    7590    7590.018
 13   3013                      wm-lh-lingual    5167    5166.894
 14   3014          wm-lh-medialorbitofrontal    4050    4049.541
 15   3015               wm-lh-middletemporal    6849    6848.841
 16   3016              wm-lh-parahippocampal    1745    1745.474
 17   3017                  wm-lh-paracentral    4994    4993.876
 18   3018              wm-lh-parsopercularis    5347    5347.052
 19   3019                wm-lh-parsorbitalis    1058    1058.097
 20   3020             wm-lh-parstriangularis    3877    3876.976
 21   3021                wm-lh-pericalcarine    3776    3775.736
 22   3022                  wm-lh-postcentral    9375    9375.486
 23   3023           wm-lh-posteriorcingulate    5697    5696.546
 24   3024                   wm-lh-precentral   15315   15314.828
 25   3025                    wm-lh-precuneus   12411   12410.523
 26   3026     wm-lh-rostralanteriorcingulate    3254    3253.774
 27   3027         wm-lh-rostralmiddlefrontal   14948   14948.436
 28   3028              wm-lh-superiorfrontal   24509   24508.672
 29   3029             wm-lh-superiorparietal   14397   14396.718
 30   3030             wm-lh-superiortemporal    8630    8630.139
 31   3031                wm-lh-supramarginal   12144   12143.636
 32   3032                  wm-lh-frontalpole     242     241.895
 33   3033                 wm-lh-temporalpole     663     662.969
 34   3034           wm-lh-transversetemporal     896     895.882
 35   3035                       wm-lh-insula   11996   11995.933
 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    3372    3371.896
120   4002      wm-rh-caudalanteriorcingulate    3721    3721.009
121   4003          wm-rh-caudalmiddlefrontal    7093    7092.917
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2876    2875.500
124   4006                   wm-rh-entorhinal     742     741.779
125   4007                     wm-rh-fusiform    8916    8916.202
126   4008             wm-rh-inferiorparietal   16859   16858.648
127   4009             wm-rh-inferiortemporal    6662    6662.298
128   4010             wm-rh-isthmuscingulate    3680    3679.761
129   4011             wm-rh-lateraloccipital   11668   11668.020
130   4012         wm-rh-lateralorbitofrontal    8058    8058.475
131   4013                      wm-rh-lingual    5615    5615.262
132   4014          wm-rh-medialorbitofrontal    4398    4398.331
133   4015               wm-rh-middletemporal    7127    7127.338
134   4016              wm-rh-parahippocampal    1785    1785.232
135   4017                  wm-rh-paracentral    7082    7082.070
136   4018              wm-rh-parsopercularis    3396    3396.415
137   4019                wm-rh-parsorbitalis    1044    1044.153
138   4020             wm-rh-parstriangularis    4546    4545.789
139   4021                wm-rh-pericalcarine    4072    4071.632
140   4022                  wm-rh-postcentral    9982    9982.438
141   4023           wm-rh-posteriorcingulate    5548    5548.213
142   4024                   wm-rh-precentral   17896   17895.854
143   4025                    wm-rh-precuneus   12276   12276.496
144   4026     wm-rh-rostralanteriorcingulate    2472    2471.522
145   4027         wm-rh-rostralmiddlefrontal   17153   17153.137
146   4028              wm-rh-superiorfrontal   22915   22914.824
147   4029             wm-rh-superiorparietal   13379   13379.062
148   4030             wm-rh-superiortemporal    8384    8383.724
149   4031                wm-rh-supramarginal   10440   10439.874
150   4032                  wm-rh-frontalpole     371     370.807
151   4033                 wm-rh-temporalpole     824     823.720
152   4034           wm-rh-transversetemporal     747     746.819
153   4035                       wm-rh-insula   10663   10662.812
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   35030   35030.414
237   5002       Right-UnsegmentedWhiteMatter   35614   35613.559
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/forrest_gump/openfmri.org/freesurfer/sub006/label
#--------------------------------------------
#@# BA Labels lh Fri Aug  9 01:20:29 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub006 --trglabel ./lh.BA1.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 550
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4679
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub006 --trglabel ./lh.BA2.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 965
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8874
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub006 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 323
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4400
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub006 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 716
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6699
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub006 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 915
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6699
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub006 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 541
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4611
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub006 --trglabel ./lh.BA6.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 3216
Checking for and removing duplicates
Writing label file ./lh.BA6.label 16805
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub006 --trglabel ./lh.BA44.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 1125
Checking for and removing duplicates
Writing label file ./lh.BA44.label 5306
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub006 --trglabel ./lh.BA45.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 1858
Checking for and removing duplicates
Writing label file ./lh.BA45.label 5280
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub006 --trglabel ./lh.V1.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 1794
Checking for and removing duplicates
Writing label file ./lh.V1.label 6435
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub006 --trglabel ./lh.V2.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 3925
Checking for and removing duplicates
Writing label file ./lh.V2.label 12039
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub006 --trglabel ./lh.MT.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 721
Checking for and removing duplicates
Writing label file ./lh.MT.label 2739
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub006 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 133
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1332
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub006 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 194
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1208
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub006 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 273
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2365
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub006 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1567
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub006 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 338
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2334
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub006 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 414
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2733
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub006 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 203
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1752
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub006 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 1544
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 8579
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub006 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 610
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2522
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub006 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 787
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1938
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub006 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 1254
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 4659
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub006 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 1742
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 5076
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub006 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 171478
Number of reverse mapping hits = 105
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 618
mri_label2label: Done


 mris_label2annot --s sub006 --hemi lh --ctab /opt/freesurfer/5.3.0/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/5.3.0/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/forrest_gump/openfmri.org/freesurfer/sub006/label
cmdline mris_label2annot --s sub006 --hemi lh --ctab /opt/freesurfer/5.3.0/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 snake5
machine  x86_64
user     fkaule

subject sub006
hemi    lh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 119564 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.BA.annot

 mris_label2annot --s sub006 --hemi lh --ctab /opt/freesurfer/5.3.0/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/5.3.0/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/forrest_gump/openfmri.org/freesurfer/sub006/label
cmdline mris_label2annot --s sub006 --hemi lh --ctab /opt/freesurfer/5.3.0/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 snake5
machine  x86_64
user     fkaule

subject sub006
hemi    lh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 141481 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub006 lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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

 1378    807   3306  2.741 0.426     0.156     0.056       31     2.8  BA1
 4430   2985   8490  2.575 0.472     0.126     0.036       51     6.3  BA2
 1063    731   1176  2.100 0.429     0.124     0.032        7     1.4  BA3a
 2986   1952   4892  2.120 0.531     0.115     0.030       33     3.7  BA3b
 2212   1327   5542  3.143 0.534     0.108     0.037       33     3.8  BA4a
 1633    990   3294  3.204 0.511     0.087     0.028       10     2.2  BA4p
12933   8663  33247  2.976 0.590     0.127     0.036      155    19.9  BA6
 3462   2296   7744  2.848 0.477     0.131     0.040       50     5.7  BA44
 4517   2998   9386  2.593 0.519     0.150     0.052       81     9.7  BA45
 4068   2705   6033  2.041 0.453     0.143     0.060       70     9.9  V1
 9771   6406  15502  2.210 0.529     0.161     0.069      215    26.7  V2
 2425   1628   4352  2.448 0.436     0.141     0.044       34     4.1  MT
 1036    740   3633  3.547 0.666     0.143     0.047       15     2.2  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub006 lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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

  916    498   2199  2.777 0.451     0.161     0.063       24     2.2  BA1
 1751   1201   3672  2.621 0.441     0.118     0.029       18     2.0  BA2
  888    608    917  2.063 0.437     0.127     0.032        6     1.3  BA3a
 1918   1249   2800  1.992 0.439     0.095     0.021       13     1.6  BA3b
 2123   1298   5281  3.195 0.550     0.096     0.024       18     2.4  BA4a
 1272    785   2439  3.106 0.523     0.090     0.027        9     1.4  BA4p
 7237   4829  18409  2.940 0.595     0.124     0.034       86    10.7  BA6
 2322   1552   5408  2.887 0.475     0.137     0.042       35     3.9  BA44
 1901   1245   4596  2.785 0.482     0.168     0.066       48     5.2  BA45
 4307   2867   6459  2.040 0.454     0.144     0.061       78    10.5  V1
 4819   3198   6972  2.041 0.499     0.172     0.078      116    14.3  V2
  543    373    907  2.204 0.405     0.120     0.027        5     0.6  MT
#--------------------------------------------
#@# BA Labels rh Fri Aug  9 01:25:46 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub006 --trglabel ./rh.BA1.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 497
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4459
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub006 --trglabel ./rh.BA2.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 818
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7505
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub006 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 367
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4347
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub006 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 564
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 5086
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub006 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1117
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6864
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub006 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 565
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 5038
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub006 --trglabel ./rh.BA6.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 2990
Checking for and removing duplicates
Writing label file ./rh.BA6.label 15246
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub006 --trglabel ./rh.BA44.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1139
Checking for and removing duplicates
Writing label file ./rh.BA44.label 8051
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub006 --trglabel ./rh.BA45.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1562
Checking for and removing duplicates
Writing label file ./rh.BA45.label 6917
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub006 --trglabel ./rh.V1.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 2392
Checking for and removing duplicates
Writing label file ./rh.V1.label 7119
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub006 --trglabel ./rh.V2.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 4535
Checking for and removing duplicates
Writing label file ./rh.V2.label 12551
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub006 --trglabel ./rh.MT.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1008
Checking for and removing duplicates
Writing label file ./rh.MT.label 2940
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub006 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 79
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 831
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub006 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 160
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 1036
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub006 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 317
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 3005
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub006 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 98
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1796
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub006 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 332
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2515
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub006 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 177
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1565
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub006 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 218
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1707
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub006 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1884
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 8843
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub006 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 161
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1173
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub006 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 215
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1393
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub006 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1582
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 4814
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub006 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 1924
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 5361
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub006 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface 


srclabel = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label
srcsubject = fsaverage
trgsubject = sub006
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/forrest_gump/openfmri.org/freesurfer
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 169645
Number of reverse mapping hits = 157
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 425
mri_label2label: Done


 mris_label2annot --s sub006 --hemi rh --ctab /opt/freesurfer/5.3.0/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/5.3.0/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/forrest_gump/openfmri.org/freesurfer/sub006/label
cmdline mris_label2annot --s sub006 --hemi rh --ctab /opt/freesurfer/5.3.0/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 snake5
machine  x86_64
user     fkaule

subject sub006
hemi    rh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 118049 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.BA.annot

 mris_label2annot --s sub006 --hemi rh --ctab /opt/freesurfer/5.3.0/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/5.3.0/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/forrest_gump/openfmri.org/freesurfer/sub006/label
cmdline mris_label2annot --s sub006 --hemi rh --ctab /opt/freesurfer/5.3.0/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 snake5
machine  x86_64
user     fkaule

subject sub006
hemi    rh
SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 141116 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub006 rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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

 1105    660   2688  2.770 0.422     0.143     0.040       17     1.9  BA1
 3922   2579   6929  2.511 0.470     0.110     0.028       34     4.6  BA2
 1273    831   1327  2.040 0.505     0.122     0.035       10     1.8  BA3a
 2457   1582   3835  2.036 0.491     0.112     0.036       23     4.3  BA3b
 2087   1284   4635  2.870 0.719     0.107     0.029       18     2.8  BA4a
 1453    941   2898  2.968 0.584     0.105     0.030        9     1.9  BA4p
11589   7829  29107  2.978 0.623     0.125     0.035      133    16.2  BA6
 4073   2738   8712  2.858 0.456     0.123     0.032       43     5.7  BA44
 5202   3488  11692  2.693 0.482     0.145     0.051       92    10.0  BA45
 4782   3197   7009  2.051 0.442     0.146     0.059       93    12.0  V1
10170   6679  16461  2.231 0.498     0.155     0.063      177    21.8  V2
 2839   1860   4901  2.463 0.467     0.135     0.040       41     4.5  MT
  644    476   1946  3.377 0.629     0.144     0.047        7     1.3  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub006 rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
INFO: assuming MGZ format for volumes.
reading colortable from annotation file...
colortable with 14 entries read (originally /opt/freesurfer/5.3.0/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

  789    452   1909  2.817 0.358     0.137     0.041       12     1.2  BA1
 2254   1479   4014  2.489 0.475     0.103     0.024       16     2.4  BA2
 1075    699   1063  2.043 0.493     0.123     0.036        7     1.6  BA3a
 2021   1352   2836  1.912 0.421     0.102     0.024       14     2.1  BA3b
 1150    712   2500  2.590 0.737     0.118     0.033       12     1.4  BA4a
 1226    784   2518  3.157 0.527     0.104     0.030        8     1.6  BA4p
 7764   5223  18944  2.911 0.643     0.125     0.035       91    10.9  BA6
  954    667   2456  2.956 0.493     0.135     0.038       13     1.6  BA44
 1186    821   3175  2.892 0.374     0.142     0.049       21     2.2  BA45
 4570   3064   6629  2.052 0.441     0.143     0.057       84    11.5  V1
 5134   3415   7778  2.088 0.498     0.171     0.075      100    12.6  V2
  406    245    837  2.678 0.306     0.149     0.048        8     0.8  MT
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Fri Aug  9 01:31:00 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub006 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject sub006.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 1003 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub006 lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

  368    242   1509  3.742 0.513     0.126     0.051        5     0.9  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Fri Aug  9 01:31:17 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub006 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject sub006.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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 789 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub006 rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/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

  283    193    947  3.346 0.579     0.139     0.039        3     0.5  ./rh.entorhinal_exvivo.label

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

Started at Thu Aug 8 10:53:55 CEST 2013 
Ended   at Fri Aug 9 01:31:34 CEST 2013
#@#%# recon-all-run-time-hours 14.627
recon-all -s sub006 finished without error at Fri Aug  9 01:31:34 CEST 2013