cortical-surfaces-freesurfer/sub-16/scripts/recon-all.log

Thu Aug  8 10:54:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016
/opt/freesurfer/5.3.0/bin/recon-all
-i /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz -cw256 -all -T2 /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz -T2pial -subjid sub016 -sd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subjid sub016
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 snake6 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   96978996    2222696          0     118440   94733872
-/+ buffers/cache:    2126684   97075008
Swap:     25165780       2780   25163000

########################################
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: 2013/08/08-08:54:16-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: snake6  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: 2013/08/08-08:54:17-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: snake6  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: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:17-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: snake6  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: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:18-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:19-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  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: 2013/08/08-08:54:20-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: snake6  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: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  Platform: Linux  PlatformVersion: 2.6.32-5-amd64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/08/08-08:54:20-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: snake6  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/sub016

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/001.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/anatomy/highres001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999248, 0.0307568, 0.0236215)
j_ras = (0.0317878, 0.9985, 0.0445881)
k_ras = (0.0222147, -0.0453054, 0.998726)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Thu Aug  8 10:54:37 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub016/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/anatomy/other/t2w001.nii.gz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999248, 0.0307568, 0.0236215)
j_ras = (0.0317878, 0.9985, 0.0445881)
k_ras = (0.0222147, -0.0453054, 0.998726)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Thu Aug  8 10:54:53 CEST 2013
Found 1 runs
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz 

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz --conform --cw256 

mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999248, 0.0307568, 0.0236215)
j_ras = (0.0317878, 0.9985, 0.0445881)
k_ras = (0.0222147, -0.0453054, 0.998726)
Original Data has (0.699898, 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/sub016/mri/orig.mgz...

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu Aug  8 10:55:33 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 10:58:41 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7652, pval=0.6675 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach_avi.log 

TalAviQA: 0.96776
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Thu Aug  8 10:58:42 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/sub016/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 snake6 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux
Thu Aug  8 10:58:42 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.25504
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25504/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.25504/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, 1.86265e-09, 3.72529e-09)
j_ras = (1.86265e-09, 0, -1)
k_ras = (-1.97906e-09, 1, -3.72529e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.25504/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Thu Aug  8 10:58:46 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.25504/0/
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:58:46] 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.25504/0/ ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/nu1.imp

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Number of iterations: 50 
CV of field change: 0.00127909
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:59:52] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25504/nu0.mnc ./tmp.mri_nu_correct.mni.25504/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
--------------------------------------------------------
Iteration 2 Thu Aug  8 10:59:59 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.25504/1/
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 10:59:59] 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.25504/1/ ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/nu2.imp

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Number of iterations: 36 
CV of field change: 0.000992739
[fkaule@snake6:/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/] [2013-08-08 11:00:35] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.25504/nu1.mnc ./tmp.mri_nu_correct.mni.25504/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25504/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/sub016/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.25504/ones.mgz 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule

input      ./tmp.mri_nu_correct.mni.25504/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/input.mean.dat 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.25504/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.25504/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.25504/ones.mgz --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/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.25504/ones.mgz --i ./tmp.mri_nu_correct.mni.25504/nu2.mnc --sum ./tmp.mri_nu_correct.mni.25504/sum.junk --avgwf ./tmp.mri_nu_correct.mni.25504/output.mean.dat 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.25504/ones.mgz
Loading ./tmp.mri_nu_correct.mni.25504/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.25504/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.25504/nu2.mnc ./tmp.mri_nu_correct.mni.25504/nu2.mnc mul .91902004648487725472
Saving result to './tmp.mri_nu_correct.mni.25504/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.25504/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.25504/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.25504/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86264e-09, 3.72529e-09)
j_ras = (1.86265e-09, 0, -1)
k_ras = (-1.97906e-09, 1, -3.72529e-09)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 7 seconds.
mapping (11, 145) to ( 3, 110)
 
 
Thu Aug  8 11:01:18 CEST 2013
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Thu Aug  8 11:01:19 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri

 mri_normalize -g 1 nu.mgz T1.mgz 

using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
 1.058  -0.012  -0.029   2.523;
 0.001   1.053   0.291  -44.522;
 0.050  -0.333   1.154  -5.882;
 0.000   0.000   0.000   1.000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 18
Starting OpenSpline(): npoints = 18
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 108
gm peak at 56 (56), valley at 38 (38)
csf peak at 28, setting threshold to 46
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 57 (57), valley at 37 (37)
csf peak at 28, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 2 minutes and 46 seconds.
#--------------------------------------------
#@# Skull Stripping Thu Aug  8 11:04:06 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=10.0
skull bounding box = (48, 13, 15) --> (205, 255, 204)
using (100, 94, 110) as brain centroid...
mean wm in atlas = 126, using box (81,64,87) --> (119, 123,133) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 108, scaling input intensities by 1.167
scaling channel 0 by 1.16667
initial log_p = -4.7
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.486263 @ (-9.091, 27.273, -9.091)
max log p =    -4.316039 @ (4.545, -4.545, -4.545)
max log p =    -4.208757 @ (2.273, -2.273, 6.818)
max log p =    -4.208757 @ (0.000, 0.000, 0.000)
max log p =    -4.208757 @ (0.000, 0.000, 0.000)
max log p =    -4.208757 @ (0.000, 0.000, 0.000)
Found translation: (-2.3, 20.5, -6.8): log p = -4.209
****************************************
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)
 1.000   0.000   0.000  -2.273;
 0.000   1.194   0.320  -35.195;
 0.000  -0.239   0.893   29.301;
 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)
 1.000   0.000   0.000  -2.273;
 0.000   1.194   0.320  -35.195;
 0.000  -0.239   0.893   29.301;
 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)
 0.962  -0.003   0.027  -0.106;
-0.002   1.201   0.292  -28.668;
-0.037  -0.210   0.955   24.058;
 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)
 0.962  -0.003   0.027  -0.106;
-0.002   1.201   0.292  -28.668;
-0.037  -0.210   0.955   24.058;
 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)
 0.966  -0.003   0.027  -0.575;
-0.002   1.198   0.291  -28.306;
-0.037  -0.210   0.958   24.199;
 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)
 0.966  -0.003   0.027  -0.575;
-0.002   1.203   0.292  -28.832;
-0.037  -0.210   0.957   24.295;
 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)
 0.966  -0.003   0.027  -0.575;
-0.002   1.205   0.292  -29.183;
-0.037  -0.210   0.956   24.391;
 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)
 0.966  -0.003   0.027  -0.575;
-0.002   1.205   0.292  -29.183;
-0.037  -0.210   0.956   24.391;
 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
 0.96553  -0.00330   0.02692  -0.57520;
-0.00214   1.20541   0.29238  -29.18299;
-0.03709  -0.20989   0.95579   24.39078;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 0.96553  -0.00330   0.02692  -0.57520;
-0.00214   1.20541   0.29238  -29.18299;
-0.03709  -0.20989   0.95579   24.39078;
 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: 010: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.966  -0.003   0.027  -0.575;
-0.002   1.205   0.292  -29.183;
-0.037  -0.210   0.956   24.391;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.7)
transform before final EM align:
 0.966  -0.003   0.027  -0.575;
-0.002   1.205   0.292  -29.183;
-0.037  -0.210   0.956   24.391;
 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
 0.96553  -0.00330   0.02692  -0.57520;
-0.00214   1.20541   0.29238  -29.18299;
-0.03709  -0.20989   0.95579   24.39078;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 0.96553  -0.00330   0.02692  -0.57520;
-0.00214   1.20541   0.29238  -29.18299;
-0.03709  -0.20989   0.95579   24.39078;
 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:
 0.966  -0.003   0.027  -0.575;
-0.002   1.205   0.292  -29.183;
-0.037  -0.210   0.956   24.391;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull.lta...
registration took 40 minutes and 24 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=86 z=118 r=96
      first estimation of the main basin volume: 3810863 voxels
      Looking for seedpoints 
        2 found in the cerebellum 
        18 found in the rest of the brain 
      global maximum in x=165, y=88, z=85, 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=22582056777 voxels, voxel volume =1.000 
                     = 22582056777 mmm3 = 22582056.960 cm3
done.
PostAnalyze...Basin Prior
 214 basins merged thanks to atlas 
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template 

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

      second estimation of the COG coord: x=127,y=97, z=111, r=9970 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45424
  RIGHT_CER    CSF_MIN=1, CSF_intensity=2, CSF_MAX=12 , nb = -1033853503
  LEFT_CER     CSF_MIN=1, CSF_intensity=2, CSF_MAX=5 , nb = 1101477547
 RIGHT_BRAIN   CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1079460279
 LEFT_BRAIN    CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1082319012
    OTHER      CSF_MIN=0, CSF_intensity=9, CSF_MAX=32 , nb = 1066689784
   
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL     
  before analyzing :    4,      6,        36,   57
  after  analyzing :    4,      26,        36,   33
   RIGHT_CER   
  before analyzing :    12,      20,        39,   61
  after  analyzing :    12,      32,        39,   39
   LEFT_CER    
  before analyzing :    5,      7,        36,   70
  after  analyzing :    5,      26,        36,   37
  RIGHT_BRAIN  
  before analyzing :    4,      6,        35,   56
  after  analyzing :    4,      25,        35,   32
  LEFT_BRAIN   
  before analyzing :    4,      6,        36,   57
  after  analyzing :    4,      26,        36,   33
     OTHER     
  before analyzing :    32,      66,        80,   89
  after  analyzing :    32,      75,        80,   78
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...66 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.011
curvature mean = 73.306, std = 8.785

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 2.07, sigma = 3.40
      after  rotation: sse = 2.07, sigma = 3.40
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  2.13, its var is  2.71   
      before Erosion-Dilatation  0.01% 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...52 iterations

      mri_strip_skull: done peeling brain

Brain Size = 1932674 voxels, voxel volume = 1.000 mm3
           = 1932674 mmm3 = 1932.674 cm3


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

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Thu Aug  8 11:45:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=22.0
skull bounding box = (56, 37, 33) --> (198, 176, 203)
using (103, 83, 118) as brain centroid...
mean wm in atlas = 107, using box (86,66,97) --> (120, 100,138) to find MRI wm
before smoothing, mri peak at 106
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.5
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.052590 @ (-9.091, 27.273, -9.091)
max log p =    -3.920415 @ (4.545, -4.545, 4.545)
max log p =    -3.806407 @ (2.273, 2.273, -6.818)
max log p =    -3.742288 @ (1.136, -3.409, 3.409)
max log p =    -3.716874 @ (-1.705, -1.705, -0.568)
max log p =    -3.716874 @ (0.000, 0.000, 0.000)
Found translation: (-2.8, 19.9, -8.5): log p = -3.717
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7)
 1.000   0.000   0.000  -2.841;
 0.000   1.050   0.156  -2.858;
 0.000  -0.112   0.997   2.922;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6)
 1.000   0.000   0.000  -2.841;
 0.000   1.050   0.156  -2.858;
 0.000  -0.112   0.997   2.922;
 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=-3.5, old_max_log_p =-3.6 (thresh=-3.6)
 0.998  -0.045   0.052  -3.782;
 0.036   1.092   0.268  -20.552;
-0.063  -0.199   0.940   28.185;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.5 (thresh=-3.5)
 0.980  -0.039   0.020   3.232;
 0.039   1.119   0.241  -22.394;
-0.030  -0.167   0.967   15.950;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 0.980  -0.039   0.020   3.232;
 0.039   1.119   0.241  -22.394;
-0.030  -0.167   0.967   15.950;
 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=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 0.981  -0.039   0.020   2.619;
 0.039   1.121   0.242  -23.193;
-0.030  -0.167   0.963   16.264;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 0.983  -0.021   0.024   0.151;
 0.022   1.119   0.249  -21.700;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 7 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 8 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 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
 0.98311  -0.02089   0.02425   0.15113;
 0.02232   1.11629   0.24862  -21.37015;
-0.02989  -0.17573   0.96035   17.53523;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2772
Quasinewton: input matrix
 0.98311  -0.02089   0.02425   0.15113;
 0.02232   1.11629   0.24862  -21.37015;
-0.02989  -0.17573   0.96035   17.53523;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.4 (old=-4.5)
transform before final EM align:
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 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
 0.98311  -0.02089   0.02425   0.15113;
 0.02232   1.11629   0.24862  -21.37015;
-0.02989  -0.17573   0.96035   17.53523;
 0.00000   0.00000   0.00000   1.00000;
nsamples 312841
Quasinewton: input matrix
 0.98311  -0.02089   0.02425   0.15113;
 0.02232   1.11629   0.24862  -21.37015;
-0.02989  -0.17573   0.96035   17.53523;
 0.00000   0.00000   0.00000   1.00000;
dfp_em_step_func: 012: -log(p) = 3.9
after pass:transform: ( 0.98, -0.02, 0.02, 0.15)
                      ( 0.02, 1.12, 0.25, -21.37)
                      ( -0.03, -0.18, 0.96, 17.54)
 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 TOLERANCESpass 2 through quasi-newton minimization...
 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: 014: -log(p) =    3.9  tol 0.000000
final transform:
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 34 minutes and 25 seconds.
#--------------------------------------
#@# CA Normalize Thu Aug  8 12:19:24 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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=22.0
skull bounding box = (56, 37, 33) --> (198, 176, 203)
using (103, 83, 118) as brain centroid...
mean wm in atlas = 107, using box (86,66,97) --> (120, 100,138) to find MRI wm
before smoothing, mri peak at 106
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
using 244171 sample points...
INFO: compute sample coordinates transform
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 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, 38, 35) --> (195, 141, 204)
Left_Cerebral_White_Matter: limiting intensities to 106.0 --> 177.0
0 of 11 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (62, 39, 34) --> (128, 139, 203)
Right_Cerebral_White_Matter: limiting intensities to 101.0 --> 177.0
0 of 8 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 118, 63) --> (180, 157, 117)
Left_Cerebellum_White_Matter: limiting intensities to 91.0 --> 177.0
0 of 7 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (82, 118, 59) --> (129, 158, 117)
Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 177.0
2 of 7 (28.6%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (111, 108, 97) --> (144, 170, 128)
Brain_Stem: limiting intensities to 79.0 --> 177.0
0 of 13 (0.0%) samples deleted
using 46 total control points for intensity normalization...
bias field = 0.956 +- 0.064
0 of 44 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (127, 38, 35) --> (195, 141, 204)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 169.0
0 of 91 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (62, 39, 34) --> (128, 139, 203)
Right_Cerebral_White_Matter: limiting intensities to 99.0 --> 169.0
0 of 103 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 118, 63) --> (180, 157, 117)
Left_Cerebellum_White_Matter: limiting intensities to 99.0 --> 169.0
26 of 39 (66.7%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (82, 118, 59) --> (129, 158, 117)
Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 169.0
0 of 35 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (111, 108, 97) --> (144, 170, 128)
Brain_Stem: limiting intensities to 89.0 --> 169.0
28 of 58 (48.3%) samples deleted
using 326 total control points for intensity normalization...
bias field = 0.957 +- 0.070
0 of 272 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (127, 38, 35) --> (195, 141, 204)
Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 154.0
3 of 220 (1.4%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (62, 39, 34) --> (128, 139, 203)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 154.0
0 of 222 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 118, 63) --> (180, 157, 117)
Left_Cerebellum_White_Matter: limiting intensities to 75.0 --> 154.0
0 of 41 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (82, 118, 59) --> (129, 158, 117)
Right_Cerebellum_White_Matter: limiting intensities to 81.0 --> 154.0
3 of 38 (7.9%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (111, 108, 97) --> (144, 170, 128)
Brain_Stem: limiting intensities to 64.0 --> 154.0
0 of 58 (0.0%) samples deleted
using 579 total control points for intensity normalization...
bias field = 1.027 +- 0.060
0 of 573 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 12:21:28 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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) = 1.10 (predicted orig area = 7.3)
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=0.863, neg=0, invalid=96777
0001: dt=129.472000, rms=0.793 (8.133%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.779 (1.805%), neg=0, invalid=96777
0003: dt=129.472000, rms=0.765 (1.709%), neg=0, invalid=96777
0004: dt=110.976000, rms=0.761 (0.564%), neg=0, invalid=96777
0005: dt=129.472000, rms=0.754 (0.867%), neg=0, invalid=96777
0006: dt=92.480000, rms=0.752 (0.262%), neg=0, invalid=96777
0007: dt=369.920000, rms=0.745 (1.036%), neg=0, invalid=96777
0008: dt=55.488000, rms=0.742 (0.371%), neg=0, invalid=96777
0009: dt=129.472000, rms=0.740 (0.210%), neg=0, invalid=96777
0010: dt=129.472000, rms=0.738 (0.377%), neg=0, invalid=96777
0011: dt=129.472000, rms=0.734 (0.468%), neg=0, invalid=96777
0012: dt=129.472000, rms=0.731 (0.457%), neg=0, invalid=96777
0013: dt=129.472000, rms=0.726 (0.656%), neg=0, invalid=96777
0014: dt=129.472000, rms=0.721 (0.643%), neg=0, invalid=96777
0015: dt=129.472000, rms=0.718 (0.499%), neg=0, invalid=96777
0016: dt=129.472000, rms=0.715 (0.405%), neg=0, invalid=96777
0017: dt=129.472000, rms=0.712 (0.450%), neg=0, invalid=96777
0018: dt=129.472000, rms=0.709 (0.398%), neg=0, invalid=96777
0019: dt=129.472000, rms=0.707 (0.305%), neg=0, invalid=96777
0020: dt=129.472000, rms=0.705 (0.276%), neg=0, invalid=96777
0021: dt=129.472000, rms=0.703 (0.283%), neg=0, invalid=96777
0022: dt=129.472000, rms=0.701 (0.246%), neg=0, invalid=96777
0023: dt=129.472000, rms=0.699 (0.222%), neg=0, invalid=96777
0024: dt=129.472000, rms=0.698 (0.223%), neg=0, invalid=96777
0025: dt=129.472000, rms=0.696 (0.235%), neg=0, invalid=96777
0026: dt=129.472000, rms=0.694 (0.254%), neg=0, invalid=96777
0027: dt=129.472000, rms=0.693 (0.228%), neg=0, invalid=96777
0028: dt=129.472000, rms=0.691 (0.190%), neg=0, invalid=96777
0029: dt=129.472000, rms=0.690 (0.216%), neg=0, invalid=96777
0030: dt=129.472000, rms=0.689 (0.202%), neg=0, invalid=96777
0031: dt=129.472000, rms=0.687 (0.192%), neg=0, invalid=96777
0032: dt=129.472000, rms=0.686 (0.154%), neg=0, invalid=96777
0033: dt=129.472000, rms=0.685 (0.132%), neg=0, invalid=96777
0034: dt=129.472000, rms=0.684 (0.162%), neg=0, invalid=96777
0035: dt=129.472000, rms=0.683 (0.136%), neg=0, invalid=96777
0036: dt=129.472000, rms=0.683 (0.108%), neg=0, invalid=96777
0037: dt=129.472000, rms=0.682 (0.141%), neg=0, invalid=96777
0038: dt=129.472000, rms=0.680 (0.167%), neg=0, invalid=96777
0039: dt=129.472000, rms=0.679 (0.143%), neg=0, invalid=96777
0040: dt=129.472000, rms=0.679 (0.109%), neg=0, invalid=96777
0041: dt=129.472000, rms=0.678 (0.150%), neg=0, invalid=96777
0042: dt=129.472000, rms=0.677 (0.167%), neg=0, invalid=96777
0043: dt=129.472000, rms=0.676 (0.107%), neg=0, invalid=96777
0044: dt=129.472000, rms=0.675 (0.065%), neg=0, invalid=96777
0045: dt=295.936000, rms=0.675 (0.069%), neg=0, invalid=96777
0046: dt=4.624000, rms=0.675 (-0.006%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.675, neg=0, invalid=96777
0047: dt=27.744000, rms=0.675 (0.009%), neg=0, invalid=96777
0048: dt=18.496000, rms=0.675 (0.005%), neg=0, invalid=96777
0049: dt=18.496000, rms=0.675 (0.006%), neg=0, invalid=96777
0050: dt=18.496000, rms=0.675 (0.001%), neg=0, invalid=96777
0051: dt=18.496000, rms=0.675 (-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=0.684, neg=0, invalid=96777
0052: dt=331.776000, rms=0.666 (2.583%), neg=0, invalid=96777
0053: dt=36.288000, rms=0.663 (0.424%), neg=0, invalid=96777
0054: dt=145.152000, rms=0.656 (1.150%), neg=0, invalid=96777
0055: dt=20.736000, rms=0.654 (0.263%), neg=0, invalid=96777
0056: dt=36.288000, rms=0.653 (0.116%), neg=0, invalid=96777
0057: dt=36.288000, rms=0.652 (0.227%), neg=0, invalid=96777
0058: dt=36.288000, rms=0.650 (0.299%), neg=0, invalid=96777
0059: dt=36.288000, rms=0.647 (0.341%), neg=0, invalid=96777
0060: dt=36.288000, rms=0.645 (0.435%), neg=0, invalid=96777
0061: dt=36.288000, rms=0.641 (0.555%), neg=0, invalid=96777
0062: dt=36.288000, rms=0.637 (0.575%), neg=0, invalid=96777
0063: dt=36.288000, rms=0.634 (0.491%), neg=0, invalid=96777
0064: dt=36.288000, rms=0.631 (0.437%), neg=0, invalid=96777
0065: dt=36.288000, rms=0.629 (0.393%), neg=0, invalid=96777
0066: dt=36.288000, rms=0.626 (0.403%), neg=0, invalid=96777
0067: dt=36.288000, rms=0.624 (0.368%), neg=0, invalid=96777
0068: dt=36.288000, rms=0.622 (0.297%), neg=0, invalid=96777
0069: dt=36.288000, rms=0.621 (0.261%), neg=0, invalid=96777
0070: dt=36.288000, rms=0.619 (0.301%), neg=0, invalid=96777
0071: dt=36.288000, rms=0.617 (0.291%), neg=0, invalid=96777
0072: dt=36.288000, rms=0.615 (0.239%), neg=0, invalid=96777
0073: dt=36.288000, rms=0.614 (0.186%), neg=0, invalid=96777
0074: dt=36.288000, rms=0.613 (0.163%), neg=0, invalid=96777
0075: dt=36.288000, rms=0.612 (0.169%), neg=0, invalid=96777
0076: dt=36.288000, rms=0.611 (0.149%), neg=0, invalid=96777
0077: dt=36.288000, rms=0.611 (0.104%), neg=0, invalid=96777
0078: dt=36.288000, rms=0.610 (0.063%), neg=0, invalid=96777
0079: dt=145.152000, rms=0.610 (0.082%), neg=0, invalid=96777
0080: dt=0.000000, rms=0.610 (-0.005%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.610, neg=0, invalid=96777
0081: dt=15.552000, rms=0.610 (0.015%), neg=0, invalid=96777
0082: dt=31.104000, rms=0.610 (0.019%), neg=0, invalid=96777
0083: dt=25.920000, rms=0.610 (0.013%), neg=0, invalid=96777
0084: dt=25.920000, rms=0.610 (-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=0.640, neg=0, invalid=96777
0085: dt=2.800000, rms=0.640 (0.023%), neg=0, invalid=96777
0086: dt=0.700000, rms=0.640 (0.001%), neg=0, invalid=96777
0087: dt=0.700000, rms=0.640 (0.001%), neg=0, invalid=96777
0088: dt=0.700000, rms=0.640 (-0.003%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.640, neg=0, invalid=96777
0089: dt=0.000000, rms=0.640 (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=0.725, neg=0, invalid=96777
0090: dt=5.393665, rms=0.700 (3.417%), neg=0, invalid=96777
0091: dt=3.456000, rms=0.699 (0.216%), neg=0, invalid=96777
0092: dt=3.456000, rms=0.699 (-0.021%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.699, neg=0, invalid=96777
0093: dt=0.000000, rms=0.699 (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=0.774, neg=0, invalid=96777
0094: dt=1.290672, rms=0.768 (0.749%), neg=0, invalid=96777
0095: dt=1.536000, rms=0.760 (0.999%), neg=0, invalid=96777
0096: dt=0.816964, rms=0.759 (0.172%), neg=0, invalid=96777
0097: dt=0.816964, rms=0.758 (0.146%), neg=0, invalid=96777
0098: dt=0.816964, rms=0.757 (0.157%), neg=0, invalid=96777
0099: dt=0.816964, rms=0.757 (0.021%), neg=0, invalid=96777
0100: dt=0.816964, rms=0.757 (-0.282%), neg=0, invalid=96777
0101: dt=1.024000, rms=0.757 (0.018%), neg=0, invalid=96777
0102: dt=1.792000, rms=0.756 (0.071%), neg=0, invalid=96777
0103: dt=0.384000, rms=0.756 (0.005%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.756, neg=0, invalid=96777
0104: dt=1.166667, rms=0.755 (0.103%), neg=0, invalid=96777
0105: dt=0.000000, rms=0.755 (0.003%), neg=0, invalid=96777
0106: dt=0.100000, rms=0.755 (-0.004%), 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=0.719, neg=0, invalid=96777
0107: dt=0.155548, rms=0.711 (1.144%), neg=0, invalid=96777
0108: dt=0.000000, rms=0.711 (0.002%), neg=0, invalid=96777
0109: dt=0.050000, rms=0.711 (-0.029%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.711, neg=0, invalid=96777
0110: dt=0.278195, rms=0.709 (0.339%), neg=0, invalid=96777
0111: dt=0.081926, rms=0.708 (0.125%), neg=0, invalid=96777
0112: dt=0.081926, rms=0.708 (0.024%), neg=0, invalid=96777
0113: dt=0.081926, rms=0.707 (0.049%), neg=0, invalid=96777
0114: dt=0.081926, rms=0.707 (0.086%), neg=0, invalid=96777
0115: dt=0.081926, rms=0.706 (0.117%), neg=0, invalid=96777
0116: dt=0.081926, rms=0.705 (0.125%), neg=0, invalid=96777
0117: dt=0.081926, rms=0.704 (0.115%), neg=0, invalid=96777
0118: dt=0.081926, rms=0.703 (0.098%), neg=0, invalid=96777
0119: dt=0.000000, rms=0.703 (-0.000%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.12699 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (1441 voxels, overlap=0.154)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1441 voxels, peak =  7), gca=9.6
gca peak = 0.14022 (22)
mri peak = 0.16230 (10)
Right_Lateral_Ventricle (43): linear fit = 0.28 x + 0.0 (1121 voxels, overlap=0.005)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1121 voxels, peak =  6), gca=8.8
gca peak = 0.24234 (100)
mri peak = 0.10576 (78)
Right_Pallidum (52): linear fit = 0.81 x + 0.0 (420 voxels, overlap=0.039)
Right_Pallidum (52): linear fit = 0.81 x + 0.0 (420 voxels, peak = 80), gca=80.5
gca peak = 0.19192 (97)
mri peak = 0.12456 (75)
Left_Pallidum (13): linear fit = 0.77 x + 0.0 (275 voxels, overlap=0.036)
Left_Pallidum (13): linear fit = 0.77 x + 0.0 (275 voxels, peak = 75), gca=75.2
gca peak = 0.24007 (63)
mri peak = 0.06338 (56)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (563 voxels, overlap=0.562)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (563 voxels, peak = 55), gca=55.1
gca peak = 0.29892 (64)
mri peak = 0.08085 (61)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (753 voxels, overlap=0.931)
Left_Hippocampus (17): linear fit = 0.93 x + 0.0 (753 voxels, peak = 59), gca=59.2
gca peak = 0.12541 (104)
mri peak = 0.06872 (105)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (71044 voxels, overlap=0.897)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (71044 voxels, peak = 106), gca=105.6
gca peak = 0.13686 (104)
mri peak = 0.07761 (105)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73417 voxels, overlap=0.866)
Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (73417 voxels, peak = 106), gca=105.6
gca peak = 0.11691 (63)
mri peak = 0.05348 (55)
Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (24106 voxels, overlap=0.379)
Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (24106 voxels, peak = 53), gca=53.2
gca peak = 0.13270 (63)
mri peak = 0.05168 (54)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (24760 voxels, overlap=0.382)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (24760 voxels, peak = 52), gca=52.0
gca peak = 0.15182 (70)
mri peak = 0.08942 (63)
Right_Caudate (50): linear fit = 0.86 x + 0.0 (569 voxels, overlap=0.135)
Right_Caudate (50): linear fit = 0.86 x + 0.0 (569 voxels, peak = 60), gca=59.9
gca peak = 0.14251 (76)
mri peak = 0.08017 (63)
Left_Caudate (11): linear fit = 0.79 x + 0.0 (718 voxels, overlap=0.017)
Left_Caudate (11): linear fit = 0.79 x + 0.0 (718 voxels, peak = 60), gca=59.7
gca peak = 0.12116 (60)
mri peak = 0.04645 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10675 voxels, overlap=0.948)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (10675 voxels, peak = 62), gca=61.5
gca peak = 0.12723 (61)
mri peak = 0.05533 (58)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (12758 voxels, overlap=0.986)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (12758 voxels, peak = 60), gca=60.1
gca peak = 0.22684 (88)
mri peak = 0.05304 (94)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7086 voxels, overlap=0.844)
Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (7086 voxels, peak = 95), gca=95.5
gca peak = 0.21067 (87)
mri peak = 0.06032 (89)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6944 voxels, overlap=0.924)
Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6944 voxels, peak = 94), gca=93.5
gca peak = 0.25455 (62)
mri peak = 0.09078 (58)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (357 voxels, overlap=0.846)
Left_Amygdala (18): linear fit = 0.88 x + 0.0 (357 voxels, peak = 54), gca=54.2
gca peak = 0.39668 (62)
mri peak = 0.10542 (57)
Right_Amygdala (54): linear fit = 0.90 x + 0.0 (359 voxels, overlap=0.771)
Right_Amygdala (54): linear fit = 0.90 x + 0.0 (359 voxels, peak = 56), gca=56.1
gca peak = 0.10129 (93)
mri peak = 0.05544 (88)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5742 voxels, overlap=0.918)
Left_Thalamus_Proper (10): linear fit = 0.94 x + 0.0 (5742 voxels, peak = 88), gca=87.9
gca peak = 0.12071 (89)
mri peak = 0.06385 (80)
Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4190 voxels, overlap=0.796)
Right_Thalamus_Proper (49): linear fit = 0.94 x + 0.0 (4190 voxels, peak = 83), gca=83.2
gca peak = 0.13716 (82)
mri peak = 0.06132 (70)
Left_Putamen (12): linear fit = 0.85 x + 0.0 (2017 voxels, overlap=0.082)
Left_Putamen (12): linear fit = 0.85 x + 0.0 (2017 voxels, peak = 69), gca=69.3
gca peak = 0.15214 (84)
mri peak = 0.06152 (68)
Right_Putamen (51): linear fit = 0.81 x + 0.0 (2255 voxels, overlap=0.096)
Right_Putamen (51): linear fit = 0.81 x + 0.0 (2255 voxels, peak = 68), gca=67.6
gca peak = 0.08983 (85)
mri peak = 0.07352 (88)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (12104 voxels, overlap=0.777)
Brain_Stem (16): linear fit = 1.03 x + 0.0 (12104 voxels, peak = 88), gca=88.0
gca peak = 0.11809 (92)
mri peak = 0.07851 (92)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (922 voxels, overlap=0.901)
Right_VentralDC (60): linear fit = 0.96 x + 0.0 (922 voxels, peak = 89), gca=88.8
gca peak = 0.12914 (94)
mri peak = 0.07596 (87)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1094 voxels, overlap=0.925)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (1094 voxels, peak = 90), gca=89.8
gca peak = 0.21100 (36)
mri peak = 0.15915 (55)
Third_Ventricle (14): linear fit = 1.50 x + 0.0 (68 voxels, overlap=0.039)
Third_Ventricle (14): linear fit = 1.50 x + 0.0 (68 voxels, peak = 54), gca=53.8
gca peak = 0.13542 (27)
mri peak = 0.12095 ( 8)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (239 voxels, overlap=0.022)
Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (239 voxels, peak =  9), gca=8.8
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 0.88 x + 0.0
estimating mean wm scale to be 1.01 x + 0.0
estimating mean csf scale to be 0.77 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=0.731, neg=0, invalid=96777
0120: dt=129.472000, rms=0.722 (1.153%), neg=0, invalid=96777
0121: dt=295.936000, rms=0.717 (0.792%), neg=0, invalid=96777
0122: dt=110.976000, rms=0.715 (0.267%), neg=0, invalid=96777
0123: dt=129.472000, rms=0.713 (0.248%), neg=0, invalid=96777
0124: dt=129.472000, rms=0.712 (0.150%), neg=0, invalid=96777
0125: dt=129.472000, rms=0.711 (0.163%), neg=0, invalid=96777
0126: dt=110.976000, rms=0.710 (0.112%), neg=0, invalid=96777
0127: dt=129.472000, rms=0.709 (0.126%), neg=0, invalid=96777
0128: dt=129.472000, rms=0.708 (0.083%), neg=0, invalid=96777
0129: dt=129.472000, rms=0.708 (0.110%), neg=0, invalid=96777
0130: dt=110.976000, rms=0.707 (0.074%), neg=0, invalid=96777
0131: dt=129.472000, rms=0.707 (0.093%), neg=0, invalid=96777
0132: dt=129.472000, rms=0.706 (0.069%), neg=0, invalid=96777
0133: dt=129.472000, rms=0.705 (0.080%), neg=0, invalid=96777
0134: dt=129.472000, rms=0.705 (0.064%), neg=0, invalid=96777
0135: dt=129.472000, rms=0.704 (0.075%), neg=0, invalid=96777
0136: dt=110.976000, rms=0.704 (0.047%), neg=0, invalid=96777
0137: dt=110.976000, rms=0.704 (0.063%), neg=0, invalid=96777
0138: dt=110.976000, rms=0.703 (0.085%), neg=0, invalid=96777
0139: dt=110.976000, rms=0.702 (0.118%), neg=0, invalid=96777
0140: dt=110.976000, rms=0.701 (0.121%), neg=0, invalid=96777
0141: dt=110.976000, rms=0.700 (0.158%), neg=0, invalid=96777
0142: dt=110.976000, rms=0.699 (0.145%), neg=0, invalid=96777
0143: dt=110.976000, rms=0.698 (0.165%), neg=0, invalid=96777
0144: dt=110.976000, rms=0.697 (0.131%), neg=0, invalid=96777
0145: dt=110.976000, rms=0.696 (0.130%), neg=0, invalid=96777
0146: dt=110.976000, rms=0.696 (0.090%), neg=0, invalid=96777
0147: dt=110.976000, rms=0.695 (0.109%), neg=0, invalid=96777
0148: dt=110.976000, rms=0.694 (0.080%), neg=0, invalid=96777
0149: dt=110.976000, rms=0.694 (0.105%), neg=0, invalid=96777
0150: dt=110.976000, rms=0.693 (0.091%), neg=0, invalid=96777
0151: dt=110.976000, rms=0.692 (0.097%), neg=0, invalid=96777
0152: dt=110.976000, rms=0.692 (0.103%), neg=0, invalid=96777
0153: dt=110.976000, rms=0.691 (0.083%), neg=0, invalid=96777
0154: dt=110.976000, rms=0.690 (0.102%), neg=0, invalid=96777
0155: dt=110.976000, rms=0.690 (0.095%), neg=0, invalid=96777
0156: dt=110.976000, rms=0.689 (0.096%), neg=0, invalid=96777
0157: dt=110.976000, rms=0.688 (0.082%), neg=0, invalid=96777
0158: dt=110.976000, rms=0.688 (0.100%), neg=0, invalid=96777
0159: dt=110.976000, rms=0.687 (0.096%), neg=0, invalid=96777
0160: dt=110.976000, rms=0.686 (0.099%), neg=0, invalid=96777
0161: dt=110.976000, rms=0.686 (0.078%), neg=0, invalid=96777
0162: dt=110.976000, rms=0.685 (0.106%), neg=0, invalid=96777
0163: dt=110.976000, rms=0.685 (0.095%), neg=0, invalid=96777
0164: dt=110.976000, rms=0.684 (0.079%), neg=0, invalid=96777
0165: dt=110.976000, rms=0.684 (0.067%), neg=0, invalid=96777
0166: dt=110.976000, rms=0.683 (0.090%), neg=0, invalid=96777
0167: dt=110.976000, rms=0.682 (0.079%), neg=0, invalid=96777
0168: dt=110.976000, rms=0.682 (0.068%), neg=0, invalid=96777
0169: dt=110.976000, rms=0.682 (0.057%), neg=0, invalid=96777
0170: dt=110.976000, rms=0.681 (0.069%), neg=0, invalid=96777
0171: dt=110.976000, rms=0.680 (0.084%), neg=0, invalid=96777
0172: dt=110.976000, rms=0.680 (0.073%), neg=0, invalid=96777
0173: dt=110.976000, rms=0.680 (0.059%), neg=0, invalid=96777
0174: dt=110.976000, rms=0.679 (0.049%), neg=0, invalid=96777
0175: dt=110.976000, rms=0.679 (0.062%), neg=0, invalid=96777
0176: dt=110.976000, rms=0.678 (0.065%), neg=0, invalid=96777
0177: dt=110.976000, rms=0.678 (0.054%), neg=0, invalid=96777
0178: dt=110.976000, rms=0.678 (0.040%), neg=0, invalid=96777
0179: dt=110.976000, rms=0.677 (0.054%), neg=0, invalid=96777
0180: dt=110.976000, rms=0.677 (0.055%), neg=0, invalid=96777
0181: dt=110.976000, rms=0.677 (0.059%), neg=0, invalid=96777
0182: dt=110.976000, rms=0.676 (0.048%), neg=0, invalid=96777
0183: dt=110.976000, rms=0.676 (0.044%), neg=0, invalid=96777
0184: dt=110.976000, rms=0.676 (0.037%), neg=0, invalid=96777
0185: dt=110.976000, rms=0.676 (0.027%), neg=0, invalid=96777
0186: dt=110.976000, rms=0.675 (0.037%), neg=0, invalid=96777
0187: dt=110.976000, rms=0.675 (0.038%), neg=0, invalid=96777
0188: dt=110.976000, rms=0.675 (0.052%), neg=0, invalid=96777
0189: dt=110.976000, rms=0.674 (0.042%), neg=0, invalid=96777
0190: dt=110.976000, rms=0.674 (0.028%), neg=0, invalid=96777
0191: dt=110.976000, rms=0.674 (0.029%), neg=0, invalid=96777
0192: dt=110.976000, rms=0.674 (0.031%), neg=0, invalid=96777
0193: dt=110.976000, rms=0.674 (0.033%), neg=0, invalid=96777
0194: dt=110.976000, rms=0.673 (0.036%), neg=0, invalid=96777
0195: dt=110.976000, rms=0.673 (0.032%), neg=0, invalid=96777
0196: dt=110.976000, rms=0.673 (0.022%), neg=0, invalid=96777
0197: dt=110.976000, rms=0.673 (0.020%), neg=0, invalid=96777
0198: dt=517.888000, rms=0.673 (0.045%), neg=0, invalid=96777
0199: dt=27.744000, rms=0.673 (0.003%), neg=0, invalid=96777
0200: dt=27.744000, rms=0.673 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.673, neg=0, invalid=96777
0201: dt=73.984000, rms=0.672 (0.035%), neg=0, invalid=96777
0202: dt=129.472000, rms=0.672 (0.056%), neg=0, invalid=96777
0203: dt=517.888000, rms=0.671 (0.128%), neg=0, invalid=96777
0204: dt=221.952000, rms=0.671 (0.070%), neg=0, invalid=96777
0205: dt=92.480000, rms=0.670 (0.019%), neg=0, invalid=96777
0206: dt=92.480000, rms=0.670 (0.015%), neg=0, invalid=96777
0207: dt=92.480000, rms=0.670 (0.019%), neg=0, invalid=96777
0208: dt=92.480000, rms=0.670 (0.028%), neg=0, invalid=96777
0209: dt=92.480000, rms=0.670 (0.035%), neg=0, invalid=96777
0210: dt=92.480000, rms=0.670 (0.038%), neg=0, invalid=96777
0211: dt=92.480000, rms=0.669 (0.039%), neg=0, invalid=96777
0212: dt=92.480000, rms=0.669 (0.037%), neg=0, invalid=96777
0213: dt=92.480000, rms=0.669 (0.028%), neg=0, invalid=96777
0214: dt=92.480000, rms=0.669 (0.021%), neg=0, invalid=96777
0215: dt=92.480000, rms=0.669 (0.023%), neg=0, invalid=96777
0216: dt=92.480000, rms=0.668 (0.023%), neg=0, invalid=96777
0217: dt=221.952000, rms=0.668 (0.011%), neg=0, invalid=96777
0218: dt=221.952000, rms=0.668 (-0.017%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.670, neg=0, invalid=96777
0219: dt=124.416000, rms=0.665 (0.803%), neg=0, invalid=96777
0220: dt=36.288000, rms=0.663 (0.199%), neg=0, invalid=96777
0221: dt=103.680000, rms=0.659 (0.685%), neg=0, invalid=96777
0222: dt=15.552000, rms=0.657 (0.221%), neg=0, invalid=96777
0223: dt=82.944000, rms=0.656 (0.265%), neg=0, invalid=96777
0224: dt=36.288000, rms=0.653 (0.434%), neg=0, invalid=96777
0225: dt=36.288000, rms=0.652 (0.098%), neg=0, invalid=96777
0226: dt=145.152000, rms=0.647 (0.697%), neg=0, invalid=96777
0227: dt=15.552000, rms=0.647 (0.136%), neg=0, invalid=96777
0228: dt=36.288000, rms=0.646 (0.108%), neg=0, invalid=96777
0229: dt=331.776000, rms=0.641 (0.822%), neg=0, invalid=96777
0230: dt=25.920000, rms=0.637 (0.561%), neg=0, invalid=96777
0231: dt=248.832000, rms=0.634 (0.468%), neg=0, invalid=96777
0232: dt=36.288000, rms=0.632 (0.367%), neg=0, invalid=96777
0233: dt=25.920000, rms=0.631 (0.101%), neg=0, invalid=96777
0234: dt=580.608000, rms=0.626 (0.761%), neg=0, invalid=96777
0235: dt=20.736000, rms=0.624 (0.438%), neg=0, invalid=96777
0236: dt=25.920000, rms=0.623 (0.093%), neg=0, invalid=96777
0237: dt=124.416000, rms=0.621 (0.265%), neg=0, invalid=96777
0238: dt=15.552000, rms=0.621 (0.069%), neg=0, invalid=96777
0239: dt=62.208000, rms=0.620 (0.061%), neg=0, invalid=96777
0240: dt=103.680000, rms=0.619 (0.188%), neg=0, invalid=96777
0241: dt=9.072000, rms=0.619 (0.037%), neg=0, invalid=96777
0242: dt=9.072000, rms=0.619 (0.020%), neg=0, invalid=96777
0243: dt=9.072000, rms=0.619 (0.001%), neg=0, invalid=96777
0244: dt=9.072000, rms=0.619 (0.010%), neg=0, invalid=96777
0245: dt=9.072000, rms=0.619 (0.025%), neg=0, invalid=96777
0246: dt=9.072000, rms=0.618 (0.063%), neg=0, invalid=96777
0247: dt=9.072000, rms=0.618 (0.089%), neg=0, invalid=96777
0248: dt=9.072000, rms=0.617 (0.088%), neg=0, invalid=96777
0249: dt=9.072000, rms=0.617 (0.075%), neg=0, invalid=96777
0250: dt=9.072000, rms=0.616 (0.071%), neg=0, invalid=96777
0251: dt=9.072000, rms=0.616 (0.076%), neg=0, invalid=96777
0252: dt=9.072000, rms=0.615 (0.067%), neg=0, invalid=96777
0253: dt=9.072000, rms=0.615 (0.068%), neg=0, invalid=96777
0254: dt=9.072000, rms=0.615 (0.078%), neg=0, invalid=96777
0255: dt=9.072000, rms=0.614 (0.086%), neg=0, invalid=96777
0256: dt=9.072000, rms=0.613 (0.097%), neg=0, invalid=96777
0257: dt=9.072000, rms=0.613 (0.012%), neg=0, invalid=96777
0258: dt=9.072000, rms=0.613 (0.027%), neg=0, invalid=96777
0259: dt=9.072000, rms=0.613 (0.034%), neg=0, invalid=96777
0260: dt=9.072000, rms=0.613 (0.033%), neg=0, invalid=96777
0261: dt=9.072000, rms=0.613 (0.042%), neg=0, invalid=96777
0262: dt=9.072000, rms=0.612 (0.043%), neg=0, invalid=96777
0263: dt=9.072000, rms=0.612 (0.049%), neg=0, invalid=96777
0264: dt=9.072000, rms=0.612 (0.053%), neg=0, invalid=96777
0265: dt=9.072000, rms=0.611 (0.057%), neg=0, invalid=96777
0266: dt=9.072000, rms=0.611 (0.060%), neg=0, invalid=96777
0267: dt=9.072000, rms=0.611 (0.065%), neg=0, invalid=96777
0268: dt=9.072000, rms=0.610 (0.068%), neg=0, invalid=96777
0269: dt=9.072000, rms=0.610 (0.010%), neg=0, invalid=96777
0270: dt=9.072000, rms=0.610 (0.017%), neg=0, invalid=96777
0271: dt=9.072000, rms=0.610 (0.021%), neg=0, invalid=96777
0272: dt=1.134000, rms=0.610 (0.000%), neg=0, invalid=96777
0273: dt=0.567000, rms=0.610 (0.001%), neg=0, invalid=96777
0274: dt=0.567000, rms=0.610 (0.001%), neg=0, invalid=96777
0275: dt=0.035437, rms=0.610 (0.000%), neg=0, invalid=96777
0276: dt=0.001107, rms=0.610 (0.000%), neg=0, invalid=96777
0277: dt=0.000277, rms=0.610 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.610, neg=0, invalid=96777
0278: dt=124.416000, rms=0.608 (0.325%), neg=0, invalid=96777
0279: dt=103.680000, rms=0.606 (0.324%), neg=0, invalid=96777
0280: dt=15.552000, rms=0.606 (0.051%), neg=0, invalid=96777
0281: dt=25.920000, rms=0.605 (0.029%), neg=0, invalid=96777
0282: dt=25.920000, rms=0.605 (0.028%), neg=0, invalid=96777
0283: dt=25.920000, rms=0.605 (0.052%), neg=0, invalid=96777
0284: dt=25.920000, rms=0.604 (0.087%), neg=0, invalid=96777
0285: dt=25.920000, rms=0.604 (0.116%), neg=0, invalid=96777
0286: dt=25.920000, rms=0.603 (0.139%), neg=0, invalid=96777
0287: dt=25.920000, rms=0.602 (0.137%), neg=0, invalid=96777
0288: dt=25.920000, rms=0.601 (0.132%), neg=0, invalid=96777
0289: dt=25.920000, rms=0.600 (0.127%), neg=0, invalid=96777
0290: dt=25.920000, rms=0.600 (0.124%), neg=0, invalid=96777
0291: dt=25.920000, rms=0.599 (0.118%), neg=0, invalid=96777
0292: dt=25.920000, rms=0.598 (0.126%), neg=0, invalid=96777
0293: dt=25.920000, rms=0.597 (0.130%), neg=0, invalid=96777
0294: dt=25.920000, rms=0.597 (0.131%), neg=0, invalid=96777
0295: dt=25.920000, rms=0.596 (0.121%), neg=0, invalid=96777
0296: dt=25.920000, rms=0.595 (0.121%), neg=0, invalid=96777
0297: dt=25.920000, rms=0.595 (0.121%), neg=0, invalid=96777
0298: dt=25.920000, rms=0.594 (0.123%), neg=0, invalid=96777
0299: dt=25.920000, rms=0.593 (0.130%), neg=0, invalid=96777
0300: dt=25.920000, rms=0.592 (0.115%), neg=0, invalid=96777
0301: dt=25.920000, rms=0.592 (0.109%), neg=0, invalid=96777
0302: dt=25.920000, rms=0.591 (0.109%), neg=0, invalid=96777
0303: dt=25.920000, rms=0.590 (0.113%), neg=0, invalid=96777
0304: dt=25.920000, rms=0.590 (0.114%), neg=0, invalid=96777
0305: dt=25.920000, rms=0.589 (0.107%), neg=0, invalid=96777
0306: dt=25.920000, rms=0.588 (0.110%), neg=0, invalid=96777
0307: dt=25.920000, rms=0.588 (0.095%), neg=0, invalid=96777
0308: dt=25.920000, rms=0.587 (0.091%), neg=0, invalid=96777
0309: dt=25.920000, rms=0.587 (0.091%), neg=0, invalid=96777
0310: dt=25.920000, rms=0.586 (0.092%), neg=0, invalid=96777
0311: dt=25.920000, rms=0.586 (0.095%), neg=0, invalid=96777
0312: dt=25.920000, rms=0.585 (0.084%), neg=0, invalid=96777
0313: dt=25.920000, rms=0.585 (0.088%), neg=0, invalid=96777
0314: dt=25.920000, rms=0.584 (0.069%), neg=0, invalid=96777
0315: dt=25.920000, rms=0.584 (0.068%), neg=0, invalid=96777
0316: dt=25.920000, rms=0.583 (0.078%), neg=0, invalid=96777
0317: dt=25.920000, rms=0.583 (0.080%), neg=0, invalid=96777
0318: dt=25.920000, rms=0.583 (0.068%), neg=0, invalid=96777
0319: dt=25.920000, rms=0.582 (0.063%), neg=0, invalid=96777
0320: dt=25.920000, rms=0.582 (0.066%), neg=0, invalid=96777
0321: dt=25.920000, rms=0.582 (0.052%), neg=0, invalid=96777
0322: dt=25.920000, rms=0.581 (0.061%), neg=0, invalid=96777
0323: dt=25.920000, rms=0.581 (0.059%), neg=0, invalid=96777
0324: dt=25.920000, rms=0.580 (0.057%), neg=0, invalid=96777
0325: dt=25.920000, rms=0.580 (0.059%), neg=0, invalid=96777
0326: dt=25.920000, rms=0.580 (0.058%), neg=0, invalid=96777
0327: dt=25.920000, rms=0.580 (0.053%), neg=0, invalid=96777
0328: dt=25.920000, rms=0.579 (0.050%), neg=0, invalid=96777
0329: dt=25.920000, rms=0.579 (0.046%), neg=0, invalid=96777
0330: dt=25.920000, rms=0.579 (0.045%), neg=0, invalid=96777
0331: dt=25.920000, rms=0.578 (0.045%), neg=0, invalid=96777
0332: dt=25.920000, rms=0.578 (0.044%), neg=0, invalid=96777
0333: dt=25.920000, rms=0.578 (0.048%), neg=0, invalid=96777
0334: dt=25.920000, rms=0.578 (0.042%), neg=0, invalid=96777
0335: dt=25.920000, rms=0.577 (0.037%), neg=0, invalid=96777
0336: dt=25.920000, rms=0.577 (0.036%), neg=0, invalid=96777
0337: dt=25.920000, rms=0.577 (0.041%), neg=0, invalid=96777
0338: dt=25.920000, rms=0.577 (0.042%), neg=0, invalid=96777
0339: dt=25.920000, rms=0.576 (0.045%), neg=0, invalid=96777
0340: dt=25.920000, rms=0.576 (0.038%), neg=0, invalid=96777
0341: dt=25.920000, rms=0.576 (0.037%), neg=0, invalid=96777
0342: dt=25.920000, rms=0.576 (0.032%), neg=0, invalid=96777
0343: dt=25.920000, rms=0.576 (0.035%), neg=0, invalid=96777
0344: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777
0345: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777
0346: dt=25.920000, rms=0.575 (0.034%), neg=0, invalid=96777
0347: dt=25.920000, rms=0.575 (0.032%), neg=0, invalid=96777
0348: dt=25.920000, rms=0.575 (0.035%), neg=0, invalid=96777
0349: dt=25.920000, rms=0.575 (0.033%), neg=0, invalid=96777
0350: dt=25.920000, rms=0.574 (0.029%), neg=0, invalid=96777
0351: dt=25.920000, rms=0.574 (0.026%), neg=0, invalid=96777
0352: dt=25.920000, rms=0.574 (0.028%), neg=0, invalid=96777
0353: dt=25.920000, rms=0.574 (0.033%), neg=0, invalid=96777
0354: dt=25.920000, rms=0.574 (0.029%), neg=0, invalid=96777
0355: dt=25.920000, rms=0.574 (0.027%), neg=0, invalid=96777
0356: dt=25.920000, rms=0.573 (0.029%), neg=0, invalid=96777
0357: dt=25.920000, rms=0.573 (0.024%), neg=0, invalid=96777
0358: dt=25.920000, rms=0.573 (0.027%), neg=0, invalid=96777
0359: dt=25.920000, rms=0.573 (0.031%), neg=0, invalid=96777
0360: dt=25.920000, rms=0.573 (0.029%), neg=0, invalid=96777
0361: dt=25.920000, rms=0.573 (0.036%), neg=0, invalid=96777
0362: dt=25.920000, rms=0.572 (0.024%), neg=0, invalid=96777
0363: dt=25.920000, rms=0.572 (0.030%), neg=0, invalid=96777
0364: dt=25.920000, rms=0.572 (0.018%), neg=0, invalid=96777
0365: dt=25.920000, rms=0.572 (0.029%), neg=0, invalid=96777
0366: dt=25.920000, rms=0.572 (0.027%), neg=0, invalid=96777
0367: dt=25.920000, rms=0.572 (0.026%), neg=0, invalid=96777
0368: dt=25.920000, rms=0.571 (0.027%), neg=0, invalid=96777
0369: dt=25.920000, rms=0.571 (0.025%), neg=0, invalid=96777
0370: dt=25.920000, rms=0.571 (0.023%), neg=0, invalid=96777
0371: dt=25.920000, rms=0.571 (0.022%), neg=0, invalid=96777
0372: dt=31.104000, rms=0.571 (0.003%), neg=0, invalid=96777
0373: dt=31.104000, rms=0.571 (0.006%), neg=0, invalid=96777
0374: dt=31.104000, rms=0.571 (0.005%), neg=0, invalid=96777
0375: dt=31.104000, rms=0.571 (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=0.580, neg=0, invalid=96777
0376: dt=32.000000, rms=0.577 (0.526%), neg=0, invalid=96777
0377: dt=11.200000, rms=0.576 (0.180%), neg=0, invalid=96777
0378: dt=102.400000, rms=0.572 (0.734%), neg=0, invalid=96777
0379: dt=7.463259, rms=0.570 (0.303%), neg=0, invalid=96777
0380: dt=44.800000, rms=0.566 (0.646%), neg=0, invalid=96777
0381: dt=8.000000, rms=0.565 (0.206%), neg=0, invalid=96777
0382: dt=76.800000, rms=0.562 (0.546%), neg=0, invalid=96777
0383: dt=2.800000, rms=0.561 (0.150%), neg=0, invalid=96777
0384: dt=2.800000, rms=0.561 (0.107%), neg=0, invalid=96777
0385: dt=2.800000, rms=0.560 (0.056%), neg=0, invalid=96777
0386: dt=19.200000, rms=0.559 (0.134%), neg=0, invalid=96777
0387: dt=11.200000, rms=0.559 (0.147%), neg=0, invalid=96777
0388: dt=11.200000, rms=0.558 (0.049%), neg=0, invalid=96777
0389: dt=11.200000, rms=0.558 (0.114%), neg=0, invalid=96777
0390: dt=11.200000, rms=0.557 (0.147%), neg=0, invalid=96777
0391: dt=11.200000, rms=0.556 (0.203%), neg=0, invalid=96777
0392: dt=11.200000, rms=0.554 (0.249%), neg=0, invalid=96777
0393: dt=11.200000, rms=0.553 (0.304%), neg=0, invalid=96777
0394: dt=11.200000, rms=0.551 (0.307%), neg=0, invalid=96777
0395: dt=11.200000, rms=0.549 (0.301%), neg=0, invalid=96777
0396: dt=11.200000, rms=0.548 (0.296%), neg=0, invalid=96777
0397: dt=11.200000, rms=0.546 (0.309%), neg=0, invalid=96777
0398: dt=11.200000, rms=0.544 (0.283%), neg=0, invalid=96777
0399: dt=11.200000, rms=0.543 (0.262%), neg=0, invalid=96777
0400: dt=11.200000, rms=0.542 (0.236%), neg=0, invalid=96777
0401: dt=11.200000, rms=0.541 (0.231%), neg=0, invalid=96777
0402: dt=11.200000, rms=0.539 (0.213%), neg=0, invalid=96777
0403: dt=11.200000, rms=0.538 (0.186%), neg=0, invalid=96777
0404: dt=11.200000, rms=0.537 (0.170%), neg=0, invalid=96777
0405: dt=11.200000, rms=0.537 (0.151%), neg=0, invalid=96777
0406: dt=11.200000, rms=0.536 (0.163%), neg=0, invalid=96777
0407: dt=11.200000, rms=0.535 (0.132%), neg=0, invalid=96777
0408: dt=11.200000, rms=0.534 (0.122%), neg=0, invalid=96777
0409: dt=11.200000, rms=0.534 (0.115%), neg=0, invalid=96777
0410: dt=11.200000, rms=0.533 (0.126%), neg=0, invalid=96777
0411: dt=11.200000, rms=0.533 (0.106%), neg=0, invalid=96777
0412: dt=11.200000, rms=0.532 (0.102%), neg=0, invalid=96777
0413: dt=11.200000, rms=0.532 (0.093%), neg=0, invalid=96777
0414: dt=11.200000, rms=0.531 (0.098%), neg=0, invalid=96777
0415: dt=11.200000, rms=0.531 (0.093%), neg=0, invalid=96777
0416: dt=11.200000, rms=0.530 (0.081%), neg=0, invalid=96777
0417: dt=11.200000, rms=0.530 (0.067%), neg=0, invalid=96777
0418: dt=11.200000, rms=0.529 (0.064%), neg=0, invalid=96777
0419: dt=11.200000, rms=0.529 (0.079%), neg=0, invalid=96777
0420: dt=11.200000, rms=0.529 (0.065%), neg=0, invalid=96777
0421: dt=11.200000, rms=0.528 (0.050%), neg=0, invalid=96777
0422: dt=11.200000, rms=0.528 (0.058%), neg=0, invalid=96777
0423: dt=11.200000, rms=0.528 (0.066%), neg=0, invalid=96777
0424: dt=11.200000, rms=0.527 (0.058%), neg=0, invalid=96777
0425: dt=11.200000, rms=0.527 (0.050%), neg=0, invalid=96777
0426: dt=11.200000, rms=0.527 (0.042%), neg=0, invalid=96777
0427: dt=11.200000, rms=0.527 (0.068%), neg=0, invalid=96777
0428: dt=11.200000, rms=0.526 (0.058%), neg=0, invalid=96777
0429: dt=11.200000, rms=0.526 (0.047%), neg=0, invalid=96777
0430: dt=11.200000, rms=0.526 (0.045%), neg=0, invalid=96777
0431: dt=11.200000, rms=0.526 (0.053%), neg=0, invalid=96777
0432: dt=11.200000, rms=0.525 (0.046%), neg=0, invalid=96777
0433: dt=11.200000, rms=0.525 (0.037%), neg=0, invalid=96777
0434: dt=11.200000, rms=0.525 (0.034%), neg=0, invalid=96777
0435: dt=11.200000, rms=0.525 (0.036%), neg=0, invalid=96777
0436: dt=11.200000, rms=0.524 (0.040%), neg=0, invalid=96777
0437: dt=11.200000, rms=0.524 (0.042%), neg=0, invalid=96777
0438: dt=11.200000, rms=0.524 (0.042%), neg=0, invalid=96777
0439: dt=11.200000, rms=0.524 (0.038%), neg=0, invalid=96777
0440: dt=11.200000, rms=0.524 (0.038%), neg=0, invalid=96777
0441: dt=11.200000, rms=0.523 (0.045%), neg=0, invalid=96777
0442: dt=11.200000, rms=0.523 (0.036%), neg=0, invalid=96777
0443: dt=11.200000, rms=0.523 (0.017%), neg=0, invalid=96777
0444: dt=11.200000, rms=0.523 (0.031%), neg=0, invalid=96777
0445: dt=11.200000, rms=0.523 (0.034%), neg=0, invalid=96777
0446: dt=11.200000, rms=0.523 (0.028%), neg=0, invalid=96777
0447: dt=11.200000, rms=0.523 (0.023%), neg=0, invalid=96777
0448: dt=11.200000, rms=0.522 (0.020%), neg=0, invalid=96777
0449: dt=11.200000, rms=0.522 (0.014%), neg=0, invalid=96777
0450: dt=11.200000, rms=0.522 (-0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.522, neg=0, invalid=96777
0451: dt=32.000000, rms=0.521 (0.240%), neg=0, invalid=96777
0452: dt=19.200000, rms=0.520 (0.140%), neg=0, invalid=96777
0453: dt=2.800000, rms=0.520 (0.002%), neg=0, invalid=96777
0454: dt=2.800000, rms=0.520 (0.012%), neg=0, invalid=96777
0455: dt=2.800000, rms=0.520 (0.005%), neg=0, invalid=96777
0456: dt=2.800000, rms=0.520 (0.006%), neg=0, invalid=96777
0457: dt=2.800000, rms=0.520 (0.012%), neg=0, invalid=96777
0458: dt=2.800000, rms=0.520 (0.016%), neg=0, invalid=96777
0459: dt=2.800000, rms=0.520 (0.026%), neg=0, invalid=96777
0460: dt=2.800000, rms=0.520 (0.019%), neg=0, invalid=96777
0461: dt=2.800000, rms=0.520 (0.004%), neg=0, invalid=96777
0462: dt=2.800000, rms=0.520 (0.005%), neg=0, invalid=96777
0463: dt=6.400000, rms=0.520 (-0.003%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.548, neg=0, invalid=96777
0464: dt=0.000000, rms=0.548 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.548, neg=0, invalid=96777
0465: dt=0.000000, rms=0.548 (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=0.604, neg=0, invalid=96777
0466: dt=1.454774, rms=0.597 (1.103%), neg=0, invalid=96777
0467: dt=0.384000, rms=0.597 (0.030%), neg=0, invalid=96777
0468: dt=0.384000, rms=0.597 (-0.013%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.597, neg=0, invalid=96777
0469: dt=0.527778, rms=0.596 (0.090%), neg=0, invalid=96777
0470: dt=0.384000, rms=0.596 (0.020%), neg=0, invalid=96777
0471: dt=0.384000, rms=0.596 (-0.015%), 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=0.540, neg=0, invalid=96777
0472: dt=0.171000, rms=0.532 (1.388%), neg=0, invalid=96777
0473: dt=0.142562, rms=0.528 (0.791%), neg=0, invalid=96777
0474: dt=0.127083, rms=0.525 (0.529%), neg=0, invalid=96777
0475: dt=0.116667, rms=0.523 (0.384%), neg=0, invalid=96777
0476: dt=0.112069, rms=0.522 (0.307%), neg=0, invalid=96777
0477: dt=0.448000, rms=0.516 (1.006%), neg=0, invalid=96777
0478: dt=0.028000, rms=0.516 (0.025%), neg=0, invalid=96777
0479: dt=0.028000, rms=0.516 (0.026%), neg=0, invalid=96777
0480: dt=0.028000, rms=0.516 (0.046%), neg=0, invalid=96777
0481: dt=0.028000, rms=0.516 (0.066%), neg=0, invalid=96777
0482: dt=0.028000, rms=0.515 (0.077%), neg=0, invalid=96777
0483: dt=0.028000, rms=0.515 (0.088%), neg=0, invalid=96777
0484: dt=0.028000, rms=0.514 (0.100%), neg=0, invalid=96777
0485: dt=0.028000, rms=0.514 (0.105%), neg=0, invalid=96777
0486: dt=0.028000, rms=0.513 (0.109%), neg=0, invalid=96777
0487: dt=0.028000, rms=0.513 (0.109%), neg=0, invalid=96777
0488: dt=0.028000, rms=0.512 (0.112%), neg=0, invalid=96777
0489: dt=0.028000, rms=0.511 (0.107%), neg=0, invalid=96777
0490: dt=0.028000, rms=0.511 (0.099%), neg=0, invalid=96777
0491: dt=0.028000, rms=0.510 (0.098%), neg=0, invalid=96777
0492: dt=0.028000, rms=0.510 (0.004%), neg=0, invalid=96777
0493: dt=0.028000, rms=0.510 (0.009%), neg=0, invalid=96777
0494: dt=0.028000, rms=0.510 (0.009%), neg=0, invalid=96777
0495: dt=0.448000, rms=0.510 (0.065%), neg=0, invalid=96777
0496: dt=0.007000, rms=0.510 (-0.003%), neg=0, invalid=96777
0497: dt=0.007000, rms=0.510 (0.001%), neg=0, invalid=96777
0498: dt=0.007000, rms=0.510 (0.002%), neg=0, invalid=96777
0499: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777
0500: dt=0.007000, rms=0.510 (0.003%), neg=0, invalid=96777
0501: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777
0502: dt=0.007000, rms=0.510 (0.007%), neg=0, invalid=96777
0503: dt=0.007000, rms=0.510 (0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.510, neg=0, invalid=96777
0504: dt=0.112000, rms=0.508 (0.289%), neg=0, invalid=96777
0505: dt=0.112000, rms=0.507 (0.217%), neg=0, invalid=96777
0506: dt=0.112000, rms=0.506 (0.166%), neg=0, invalid=96777
0507: dt=0.112000, rms=0.506 (0.129%), neg=0, invalid=96777
0508: dt=0.384000, rms=0.504 (0.333%), neg=0, invalid=96777
0509: dt=0.112000, rms=0.504 (0.017%), neg=0, invalid=96777
0510: dt=0.112000, rms=0.504 (0.028%), neg=0, invalid=96777
0511: dt=0.112000, rms=0.504 (0.034%), neg=0, invalid=96777
0512: dt=0.007000, rms=0.504 (0.003%), neg=0, invalid=96777
0513: dt=0.007000, rms=0.504 (0.002%), neg=0, invalid=96777
0514: dt=0.020000, rms=0.504 (0.002%), neg=0, invalid=96777
0515: dt=0.020000, rms=0.504 (0.004%), neg=0, invalid=96777
0516: dt=0.020000, rms=0.504 (0.004%), neg=0, invalid=96777
0517: dt=0.020000, rms=0.504 (0.001%), neg=0, invalid=96777
0518: dt=0.020000, rms=0.504 (0.006%), neg=0, invalid=96777
0519: dt=0.020000, rms=0.504 (0.007%), neg=0, invalid=96777
0520: dt=0.020000, rms=0.504 (0.010%), neg=0, invalid=96777
0521: dt=0.020000, rms=0.503 (0.009%), 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=0.501, neg=0, invalid=96777
0522: dt=73.984000, rms=0.501 (0.013%), neg=0, invalid=96777
0523: dt=73.984000, rms=0.501 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.501, neg=0, invalid=96777
0524: dt=129.472000, rms=0.501 (0.116%), neg=0, invalid=96777
0525: dt=32.368000, rms=0.501 (0.019%), neg=0, invalid=96777
0526: dt=32.368000, rms=0.501 (0.002%), neg=0, invalid=96777
0527: dt=32.368000, rms=0.501 (0.015%), neg=0, invalid=96777
0528: dt=32.368000, rms=0.500 (0.022%), neg=0, invalid=96777
0529: dt=32.368000, rms=0.500 (0.029%), neg=0, invalid=96777
0530: dt=32.368000, rms=0.500 (0.029%), neg=0, invalid=96777
0531: dt=32.368000, rms=0.500 (0.026%), neg=0, invalid=96777
0532: dt=32.368000, rms=0.500 (0.027%), neg=0, invalid=96777
0533: dt=32.368000, rms=0.500 (0.027%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.500, neg=0, invalid=96777
0534: dt=36.288000, rms=0.499 (0.186%), neg=0, invalid=96777
0535: dt=36.288000, rms=0.498 (0.083%), neg=0, invalid=96777
0536: dt=36.288000, rms=0.498 (0.070%), neg=0, invalid=96777
0537: dt=36.288000, rms=0.498 (0.052%), neg=0, invalid=96777
0538: dt=36.288000, rms=0.498 (-0.027%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.498, neg=0, invalid=96777
0539: dt=82.944000, rms=0.496 (0.368%), neg=0, invalid=96777
0540: dt=36.288000, rms=0.495 (0.153%), neg=0, invalid=96777
0541: dt=36.288000, rms=0.495 (0.085%), neg=0, invalid=96777
0542: dt=36.288000, rms=0.494 (0.127%), neg=0, invalid=96777
0543: dt=36.288000, rms=0.493 (0.170%), neg=0, invalid=96777
0544: dt=36.288000, rms=0.493 (0.161%), neg=0, invalid=96777
0545: dt=36.288000, rms=0.492 (0.146%), neg=0, invalid=96777
0546: dt=36.288000, rms=0.491 (0.141%), neg=0, invalid=96777
0547: dt=36.288000, rms=0.491 (0.113%), neg=0, invalid=96777
0548: dt=36.288000, rms=0.490 (0.103%), neg=0, invalid=96777
0549: dt=25.920000, rms=0.490 (0.025%), neg=0, invalid=96777
0550: dt=25.920000, rms=0.490 (0.014%), neg=0, invalid=96777
0551: dt=25.920000, rms=0.490 (0.014%), neg=0, invalid=96777
0552: dt=25.920000, rms=0.490 (0.029%), neg=0, invalid=96777
0553: dt=25.920000, rms=0.490 (0.034%), neg=0, invalid=96777
0554: dt=25.920000, rms=0.489 (0.043%), neg=0, invalid=96777
0555: dt=25.920000, rms=0.489 (0.041%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.489, neg=0, invalid=96777
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0556: dt=44.800000, rms=0.485 (0.830%), neg=0, invalid=96777
iter 0, gcam->neg = 8
after 8 iterations, nbhd size=1, neg = 0
0557: dt=25.600000, rms=0.484 (0.306%), neg=0, invalid=96777
0558: dt=8.000000, rms=0.483 (0.249%), neg=0, invalid=96777
0559: dt=8.000000, rms=0.482 (0.124%), neg=0, invalid=96777
0560: dt=8.000000, rms=0.481 (0.162%), neg=0, invalid=96777
0561: dt=8.000000, rms=0.480 (0.234%), neg=0, invalid=96777
0562: dt=8.000000, rms=0.479 (0.240%), neg=0, invalid=96777
0563: dt=8.000000, rms=0.478 (0.236%), neg=0, invalid=96777
0564: dt=8.000000, rms=0.477 (0.239%), neg=0, invalid=96777
0565: dt=8.000000, rms=0.476 (0.200%), neg=0, invalid=96777
0566: dt=8.000000, rms=0.475 (0.193%), neg=0, invalid=96777
0567: dt=8.000000, rms=0.474 (0.174%), neg=0, invalid=96777
0568: dt=8.000000, rms=0.473 (0.164%), neg=0, invalid=96777
0569: dt=8.000000, rms=0.473 (0.157%), neg=0, invalid=96777
0570: dt=8.000000, rms=0.472 (0.128%), neg=0, invalid=96777
0571: dt=8.000000, rms=0.471 (0.144%), neg=0, invalid=96777
0572: dt=8.000000, rms=0.471 (0.156%), neg=0, invalid=96777
0573: dt=8.000000, rms=0.470 (0.132%), neg=0, invalid=96777
0574: dt=8.000000, rms=0.469 (0.125%), neg=0, invalid=96777
0575: dt=8.000000, rms=0.469 (0.109%), neg=0, invalid=96777
0576: dt=11.200000, rms=0.469 (0.030%), neg=0, invalid=96777
0577: dt=11.200000, rms=0.469 (0.012%), neg=0, invalid=96777
0578: dt=11.200000, rms=0.468 (0.033%), neg=0, invalid=96777
0579: dt=11.200000, rms=0.468 (0.040%), neg=0, invalid=96777
0580: dt=11.200000, rms=0.468 (0.041%), neg=0, invalid=96777
0581: dt=11.200000, rms=0.468 (0.035%), neg=0, invalid=96777
0582: dt=11.200000, rms=0.468 (0.051%), neg=0, invalid=96777
0583: dt=11.200000, rms=0.467 (0.052%), neg=0, invalid=96777
0584: dt=11.200000, rms=0.467 (0.050%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.467, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0585: dt=44.800000, rms=0.464 (0.584%), neg=0, invalid=96777
0586: dt=11.200000, rms=0.464 (0.195%), neg=0, invalid=96777
0587: dt=11.200000, rms=0.463 (0.078%), neg=0, invalid=96777
0588: dt=11.200000, rms=0.463 (0.108%), neg=0, invalid=96777
0589: dt=11.200000, rms=0.462 (0.163%), neg=0, invalid=96777
0590: dt=11.200000, rms=0.461 (0.118%), neg=0, invalid=96777
0591: dt=11.200000, rms=0.461 (0.089%), neg=0, invalid=96777
0592: dt=32.000000, rms=0.461 (0.046%), neg=0, invalid=96777
0593: dt=32.000000, rms=0.461 (-0.269%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.467, neg=0, invalid=96777
0594: dt=2.304000, rms=0.466 (0.032%), neg=0, invalid=96777
0595: dt=1.008000, rms=0.466 (0.008%), neg=0, invalid=96777
0596: dt=1.008000, rms=0.466 (0.006%), neg=0, invalid=96777
0597: dt=1.008000, rms=0.466 (-0.011%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.466, neg=0, invalid=96777
0598: dt=4.032000, rms=0.466 (0.045%), neg=0, invalid=96777
0599: dt=4.032000, rms=0.466 (0.024%), neg=0, invalid=96777
0600: dt=4.032000, rms=0.466 (0.009%), neg=0, invalid=96777
0601: dt=4.032000, rms=0.466 (-0.022%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.473, neg=0, invalid=96777
0602: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.473, neg=0, invalid=96777
0603: dt=0.064000, rms=0.473 (0.000%), neg=0, invalid=96777
0604: dt=0.064000, rms=0.473 (0.001%), neg=0, invalid=96777
0605: dt=0.020000, rms=0.473 (0.002%), neg=0, invalid=96777
0606: dt=0.016000, rms=0.473 (-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=0.461, neg=0, invalid=96777
iter 0, gcam->neg = 751
after 19 iterations, nbhd size=2, neg = 0
0607: dt=1.925076, rms=0.419 (9.275%), neg=0, invalid=96777
0608: dt=0.000109, rms=0.419 (0.003%), neg=0, invalid=96777
0609: dt=0.000109, rms=0.419 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.419, neg=0, invalid=96777
0610: dt=0.000375, rms=0.419 (0.000%), neg=0, invalid=96777
0611: dt=0.000000, rms=0.419 (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=0.401, neg=0, invalid=96777
0612: dt=0.000000, rms=0.402 (-0.257%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.402, neg=0, invalid=96777
0613: dt=18.496000, rms=0.402 (0.001%), neg=0, invalid=96777
0614: dt=0.022578, rms=0.402 (0.000%), neg=0, invalid=96777
0615: dt=0.022578, rms=0.402 (-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=0.403, neg=0, invalid=96777
0616: dt=0.000000, rms=0.403 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.403, neg=0, invalid=96777
0617: dt=25.920000, rms=0.403 (0.015%), neg=0, invalid=96777
0618: dt=20.736000, rms=0.403 (0.003%), neg=0, invalid=96777
0619: dt=20.736000, rms=0.403 (0.001%), neg=0, invalid=96777
0620: dt=20.736000, rms=0.403 (-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=0.403, neg=0, invalid=96777
0621: dt=11.200000, rms=0.403 (0.085%), neg=0, invalid=96777
0622: dt=6.400000, rms=0.403 (0.013%), neg=0, invalid=96777
0623: dt=6.400000, rms=0.403 (0.012%), neg=0, invalid=96777
0624: dt=6.400000, rms=0.403 (-0.007%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.403, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0625: dt=38.400000, rms=0.402 (0.326%), neg=0, invalid=96777
0626: dt=11.200000, rms=0.401 (0.048%), neg=0, invalid=96777
0627: dt=11.200000, rms=0.401 (0.086%), neg=0, invalid=96777
0628: dt=11.200000, rms=0.400 (0.128%), neg=0, invalid=96777
0629: dt=11.200000, rms=0.400 (0.134%), neg=0, invalid=96777
iter 0, gcam->neg = 11
after 15 iterations, nbhd size=2, neg = 0
0630: dt=11.200000, rms=0.399 (0.124%), neg=0, invalid=96777
0631: dt=11.200000, rms=0.399 (0.073%), neg=0, invalid=96777
iter 0, gcam->neg = 14
after 17 iterations, nbhd size=2, neg = 0
0632: dt=76.800000, rms=0.399 (0.140%), neg=0, invalid=96777
0633: dt=2.800000, rms=0.399 (0.004%), neg=0, invalid=96777
0634: dt=2.800000, rms=0.399 (0.010%), neg=0, invalid=96777
0635: dt=2.800000, rms=0.398 (0.017%), neg=0, invalid=96777
0636: dt=2.800000, rms=0.398 (0.022%), neg=0, invalid=96777
0637: dt=2.800000, rms=0.398 (0.023%), neg=0, invalid=96777
0638: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777
0639: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777
0640: dt=2.800000, rms=0.398 (0.024%), neg=0, invalid=96777
0641: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777
0642: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777
0643: dt=2.800000, rms=0.398 (0.025%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.401, neg=0, invalid=96777
iter 0, gcam->neg = 11
after 9 iterations, nbhd size=1, neg = 0
0644: dt=4.032000, rms=0.401 (0.061%), neg=0, invalid=96777
0645: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0646: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0647: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0648: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0649: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0650: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0651: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0652: dt=0.006750, rms=0.401 (0.000%), neg=0, invalid=96777
0653: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0654: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0655: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0656: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0657: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0658: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0659: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0660: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0661: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0662: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0663: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0664: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0665: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0666: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0667: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0668: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0669: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0670: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0671: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0672: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
0673: dt=0.006750, rms=0.401 (0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.401, neg=0, invalid=96777
iter 0, gcam->neg = 83
after 38 iterations, nbhd size=3, neg = 0
0674: dt=16.128000, rms=0.399 (0.351%), neg=0, invalid=96777
0675: dt=0.003938, rms=0.399 (0.000%), neg=0, invalid=96777
0676: dt=0.003938, rms=0.399 (0.000%), neg=0, invalid=96777
0677: dt=0.003938, rms=0.399 (-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=0.405, neg=0, invalid=96777
0678: dt=0.000000, rms=0.405 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.405, neg=0, invalid=96777
0679: dt=0.000000, rms=0.405 (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=0.395, neg=0, invalid=96777
iter 0, gcam->neg = 565
after 34 iterations, nbhd size=3, neg = 0
0680: dt=0.910140, rms=0.380 (3.668%), neg=0, invalid=96777
0681: dt=0.000000, rms=0.380 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 693
after 11 iterations, nbhd size=1, neg = 0
0682: dt=0.050000, rms=0.380 (-0.343%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.380, neg=0, invalid=96777
0683: dt=0.000000, rms=0.380 (-0.000%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 4 hours, 5 minutes and 53 seconds.
#--------------------------------------
#@# CA Reg Inv Thu Aug  8 16:27:21 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 16:28:41 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...
10717596 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 23 seconds.
#--------------------------------------
#@# SkullLTA Thu Aug  8 16:30:04 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=11.0
skull bounding box = (41, 13, 12) --> (213, 203, 219)
using (98, 76, 116) as brain centroid...
mean wm in atlas = 126, using box (77,53,90) --> (119, 99,141) to find MRI wm
before smoothing, mri peak at 108
after smoothing, mri peak at 108, scaling input intensities by 1.167
scaling channel 0 by 1.16667
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 0.983  -0.021   0.024   0.151;
 0.024   1.200   0.267  -32.056;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 0.983  -0.021   0.024   0.151;
 0.022   1.110   0.247  -20.569;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 0.983  -0.021   0.024   0.151;
 0.022   1.110   0.247  -20.569;
-0.030  -0.176   0.960   17.535;
 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 =-4.0 (thresh=-4.0)
 0.983  -0.021   0.024   0.151;
 0.022   1.124   0.282  -24.015;
-0.031  -0.213   0.951   24.267;
 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)
 0.983  -0.021   0.024   0.151;
 0.022   1.124   0.282  -24.015;
-0.031  -0.213   0.951   24.267;
 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)
 0.981  -0.023   0.032  -0.221;
 0.022   1.125   0.283  -24.185;
-0.039  -0.213   0.952   25.667;
 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)
 0.981  -0.023   0.032  -0.221;
 0.022   1.122   0.282  -23.844;
-0.039  -0.213   0.950   25.855;
 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
 0.98052  -0.02259   0.03199  -0.22081;
 0.02160   1.12247   0.28205  -23.84424;
-0.03859  -0.21289   0.95010   25.85537;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 0.98052  -0.02259   0.03199  -0.22081;
 0.02160   1.12247   0.28205  -23.84424;
-0.03859  -0.21289   0.95010   25.85537;
 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: 008: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 0.981  -0.023   0.032  -0.221;
 0.022   1.122   0.282  -23.844;
-0.039  -0.213   0.950   25.855;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-4.1)
transform before final EM align:
 0.981  -0.023   0.032  -0.221;
 0.022   1.122   0.282  -23.844;
-0.039  -0.213   0.950   25.855;
 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
 0.98052  -0.02259   0.03199  -0.22081;
 0.02160   1.12247   0.28205  -23.84424;
-0.03859  -0.21289   0.95010   25.85537;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 0.98052  -0.02259   0.03199  -0.22081;
 0.02160   1.12247   0.28205  -23.84424;
-0.03859  -0.21289   0.95010   25.85537;
 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: 010: -log(p) =    4.4  tol 0.000000
final transform:
 0.981  -0.023   0.032  -0.221;
 0.022   1.122   0.282  -23.844;
-0.039  -0.213   0.950   25.855;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 36 minutes and 21 seconds.
#--------------------------------------
#@# SubCort Seg Thu Aug  8 17:06:25 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 snake6
machine  x86_64

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 0.09683 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.25 x + 0.0 (650 voxels, overlap=0.008)
Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (650 voxels, peak =  7), gca=10.8
gca peak = 0.14982 (20)
mri peak = 0.10375 (10)
Right_Lateral_Ventricle (43): linear fit = 0.31 x + 0.0 (1059 voxels, overlap=0.010)
Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1059 voxels, peak =  6), gca=8.0
gca peak = 0.28003 (97)
mri peak = 0.10452 (80)
Right_Pallidum (52): linear fit = 0.81 x + 0.0 (366 voxels, overlap=0.052)
Right_Pallidum (52): linear fit = 0.81 x + 0.0 (366 voxels, peak = 79), gca=79.1
gca peak = 0.18160 (96)
mri peak = 0.08193 (80)
Left_Pallidum (13): linear fit = 0.83 x + 0.0 (446 voxels, overlap=0.054)
Left_Pallidum (13): linear fit = 0.83 x + 0.0 (446 voxels, peak = 80), gca=80.2
gca peak = 0.27536 (62)
mri peak = 0.07808 (56)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (626 voxels, overlap=0.354)
Right_Hippocampus (53): linear fit = 0.88 x + 0.0 (626 voxels, peak = 54), gca=54.2
gca peak = 0.32745 (63)
mri peak = 0.07985 (60)
Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (798 voxels, overlap=0.998)
Left_Hippocampus (17): linear fit = 0.89 x + 0.0 (798 voxels, peak = 56), gca=56.4
gca peak = 0.08597 (105)
mri peak = 0.06779 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (42590 voxels, overlap=0.786)
Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (42590 voxels, peak = 107), gca=106.6
gca peak = 0.09209 (106)
mri peak = 0.07226 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41902 voxels, overlap=0.750)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (41902 voxels, peak = 109), gca=108.6
gca peak = 0.07826 (63)
mri peak = 0.05031 (56)
Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (19158 voxels, overlap=0.523)
Left_Cerebral_Cortex (3): linear fit = 0.86 x + 0.0 (19158 voxels, peak = 54), gca=53.9
gca peak = 0.08598 (64)
mri peak = 0.05205 (51)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (19561 voxels, overlap=0.343)
Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (19561 voxels, peak = 53), gca=52.8
gca peak = 0.24164 (71)
mri peak = 0.09348 (63)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (921 voxels, overlap=0.027)
Right_Caudate (50): linear fit = 0.88 x + 0.0 (921 voxels, peak = 62), gca=62.1
gca peak = 0.18227 (75)
mri peak = 0.09183 (63)
Left_Caudate (11): linear fit = 0.81 x + 0.0 (1188 voxels, overlap=0.028)
Left_Caudate (11): linear fit = 0.81 x + 0.0 (1188 voxels, peak = 61), gca=61.1
gca peak = 0.10629 (62)
mri peak = 0.05931 (62)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9466 voxels, overlap=0.988)
Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (9466 voxels, peak = 64), gca=63.5
gca peak = 0.11668 (59)
mri peak = 0.06138 (61)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (10220 voxels, overlap=0.998)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (10220 voxels, peak = 58), gca=58.1
gca peak = 0.17849 (88)
mri peak = 0.06123 (94)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4512 voxels, overlap=0.922)
Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (4512 voxels, peak = 95), gca=94.6
gca peak = 0.16819 (86)
mri peak = 0.06784 (93)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4332 voxels, overlap=0.945)
Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4332 voxels, peak = 92), gca=91.6
gca peak = 0.41688 (64)
mri peak = 0.08973 (59)
Left_Amygdala (18): linear fit = 0.90 x + 0.0 (434 voxels, overlap=1.037)
Left_Amygdala (18): linear fit = 0.90 x + 0.0 (434 voxels, peak = 58), gca=57.9
gca peak = 0.42394 (62)
mri peak = 0.09194 (61)
Right_Amygdala (54): linear fit = 0.88 x + 0.0 (450 voxels, overlap=1.041)
Right_Amygdala (54): linear fit = 0.88 x + 0.0 (450 voxels, peak = 55), gca=54.9
gca peak = 0.10041 (96)
mri peak = 0.07166 (85)
Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (3745 voxels, overlap=0.469)
Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (3745 voxels, peak = 87), gca=86.9
gca peak = 0.13978 (88)
mri peak = 0.07968 (81)
Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3812 voxels, overlap=0.625)
Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (3812 voxels, peak = 81), gca=81.4
gca peak = 0.08514 (81)
mri peak = 0.07115 (70)
Left_Putamen (12): linear fit = 0.81 x + 0.0 (1920 voxels, overlap=0.234)
Left_Putamen (12): linear fit = 0.81 x + 0.0 (1920 voxels, peak = 66), gca=66.0
gca peak = 0.09624 (82)
mri peak = 0.07615 (71)
Right_Putamen (51): linear fit = 0.82 x + 0.0 (1787 voxels, overlap=0.023)
Right_Putamen (51): linear fit = 0.82 x + 0.0 (1787 voxels, peak = 68), gca=67.7
gca peak = 0.07543 (88)
mri peak = 0.07619 (88)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11427 voxels, overlap=0.765)
Brain_Stem (16): linear fit = 1.01 x + 0.0 (11427 voxels, peak = 89), gca=89.3
gca peak = 0.12757 (95)
mri peak = 0.07479 (89)
Right_VentralDC (60): linear fit = 0.94 x + 0.0 (936 voxels, overlap=0.827)
Right_VentralDC (60): linear fit = 0.94 x + 0.0 (936 voxels, peak = 90), gca=89.8
gca peak = 0.17004 (92)
mri peak = 0.07026 (87)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (918 voxels, overlap=0.804)
Left_VentralDC (28): linear fit = 0.95 x + 0.0 (918 voxels, peak = 88), gca=87.9
gca peak = 0.21361 (36)
mri peak = 0.08496 (15)
gca peak = 0.26069 (23)
mri peak = 0.13778 (11)
Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (98 voxels, overlap=0.031)
Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (98 voxels, peak = 10), gca=10.0
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 0.87 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 = 0.09683 ( 8)
Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (650 voxels, overlap=0.989)
Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (650 voxels, peak =  8), gca=7.8
gca peak = 0.29325 ( 9)
mri peak = 0.10375 (10)
Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1059 voxels, overlap=1.001)
Right_Lateral_Ventricle (43): linear fit = 0.79 x + 0.0 (1059 voxels, peak =  7), gca=7.1
gca peak = 0.26534 (80)
mri peak = 0.10452 (80)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (366 voxels, overlap=1.012)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (366 voxels, peak = 80), gca=80.0
gca peak = 0.20119 (80)
mri peak = 0.08193 (80)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (446 voxels, overlap=1.013)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (446 voxels, peak = 80), gca=80.0
gca peak = 0.31053 (54)
mri peak = 0.07808 (56)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (626 voxels, overlap=1.005)
Right_Hippocampus (53): linear fit = 0.99 x + 0.0 (626 voxels, peak = 53), gca=53.2
gca peak = 0.26447 (56)
mri peak = 0.07985 (60)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (798 voxels, overlap=1.010)
Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (798 voxels, peak = 57), gca=57.4
gca peak = 0.08540 (107)
mri peak = 0.06779 (107)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42590 voxels, overlap=0.834)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42590 voxels, peak = 107), gca=107.0
gca peak = 0.08534 (108)
mri peak = 0.07226 (107)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41902 voxels, overlap=0.796)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41902 voxels, peak = 107), gca=107.5
gca peak = 0.09232 (54)
mri peak = 0.05031 (56)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (19158 voxels, overlap=0.991)
Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (19158 voxels, peak = 54), gca=54.0
gca peak = 0.10550 (53)
mri peak = 0.05205 (51)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19561 voxels, overlap=0.984)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (19561 voxels, peak = 53), gca=53.0
gca peak = 0.23948 (64)
mri peak = 0.09348 (63)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (921 voxels, overlap=1.004)
Right_Caudate (50): linear fit = 1.00 x + 0.0 (921 voxels, peak = 64), gca=64.0
gca peak = 0.18470 (61)
mri peak = 0.09183 (63)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1188 voxels, overlap=0.998)
Left_Caudate (11): linear fit = 0.99 x + 0.0 (1188 voxels, peak = 60), gca=60.1
gca peak = 0.10027 (62)
mri peak = 0.05931 (62)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9466 voxels, overlap=0.997)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (9466 voxels, peak = 61), gca=61.1
gca peak = 0.12025 (59)
mri peak = 0.06138 (61)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10220 voxels, overlap=0.997)
Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (10220 voxels, peak = 60), gca=60.5
gca peak = 0.17137 (94)
mri peak = 0.06123 (94)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4512 voxels, overlap=1.000)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4512 voxels, peak = 94), gca=93.5
gca peak = 0.16068 (92)
mri peak = 0.06784 (93)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4332 voxels, overlap=1.000)
Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4332 voxels, peak = 91), gca=90.6
gca peak = 0.40361 (58)
mri peak = 0.08973 (59)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (434 voxels, overlap=1.027)
Left_Amygdala (18): linear fit = 1.04 x + 0.0 (434 voxels, peak = 61), gca=60.6
gca peak = 0.57399 (55)
mri peak = 0.09194 (61)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (450 voxels, overlap=1.027)
Right_Amygdala (54): linear fit = 1.04 x + 0.0 (450 voxels, peak = 57), gca=57.5
gca peak = 0.11982 (87)
mri peak = 0.07166 (85)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3745 voxels, overlap=0.999)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3745 voxels, peak = 87), gca=86.6
gca peak = 0.11701 (81)
mri peak = 0.07968 (81)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3812 voxels, overlap=0.980)
Right_Thalamus_Proper (49): linear fit = 0.99 x + 0.0 (3812 voxels, peak = 80), gca=79.8
gca peak = 0.09700 (71)
mri peak = 0.07115 (70)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (1920 voxels, overlap=1.000)
Left_Putamen (12): linear fit = 1.03 x + 0.0 (1920 voxels, peak = 73), gca=73.5
gca peak = 0.10658 (68)
mri peak = 0.07615 (71)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1787 voxels, overlap=0.991)
Right_Putamen (51): linear fit = 0.99 x + 0.0 (1787 voxels, peak = 67), gca=67.0
gca peak = 0.07507 (87)
mri peak = 0.07619 (88)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11427 voxels, overlap=0.798)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (11427 voxels, peak = 87), gca=86.6
gca peak = 0.12974 (86)
mri peak = 0.07479 (89)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (936 voxels, overlap=0.817)
Right_VentralDC (60): linear fit = 1.02 x + 0.0 (936 voxels, peak = 88), gca=88.2
gca peak = 0.15097 (88)
mri peak = 0.07026 (87)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (918 voxels, overlap=0.943)
Left_VentralDC (28): linear fit = 1.00 x + 0.0 (918 voxels, peak = 88), gca=87.6
gca peak = 0.35640 (14)
mri peak = 0.08496 (15)
gca peak = 0.33827 ( 9)
mri peak = 0.13778 (11)
Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (98 voxels, overlap=0.976)
Fourth_Ventricle (15): linear fit = 1.14 x + 0.0 (98 voxels, peak = 10), gca=10.3
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.23697 (32)
gca peak Third_Ventricle = 0.35640 (14)
gca peak CSF = 0.30128 (18)
gca peak Left_Accumbens_area = 0.68092 (57)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.42552 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.33086 (28)
gca peak Right_Accumbens_area = 0.31091 (63)
gca peak Right_vessel = 0.57322 (60)
gca peak Right_choroid_plexus = 0.10278 (48)
gca peak Fifth_Ventricle = 0.45329 (19)
gca peak WM_hypointensities = 0.17567 (83)
gca peak non_WM_hypointensities = 0.12171 (54)
gca peak Optic_Chiasm = 0.34843 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 1.02 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.88 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
13374 gm and wm labels changed (%13 to gray, %87 to white out of all changed labels)
310 hippocampal voxels changed.
13 amygdala voxels changed.
pass 1: 98944 changed. image ll: -2.251, PF=1.000
pass 2: 18094 changed. image ll: -2.249, PF=1.000
pass 3: 6959 changed.
pass 4: 3144 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 18 minutes and 5 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/cc_up.lta sub016 

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/sub016/mri/transforms/cc_up.lta
reading aseg from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.auto_noCCseg.mgz
reading norm from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/norm.mgz
24264 voxels in left wm, 26205 in right wm, xrange [124, 131]
searching rotation angles z=[-6  8], y=[-6  8]

searching scale 1 Z rot -5.5  
searching scale 1 Z rot -5.3  
searching scale 1 Z rot -5.0  
searching scale 1 Z rot -4.8  
searching scale 1 Z rot -4.5  
searching scale 1 Z rot -4.3  
searching scale 1 Z rot -4.0  
searching scale 1 Z rot -3.8  
searching scale 1 Z rot -3.5  
searching scale 1 Z rot -3.3  
searching scale 1 Z rot -3.0  
searching scale 1 Z rot -2.8  
searching scale 1 Z rot -2.5  
searching scale 1 Z rot -2.3  
searching scale 1 Z rot -2.0  
searching scale 1 Z rot -1.8  
searching scale 1 Z rot -1.5  
searching scale 1 Z rot -1.3  
searching scale 1 Z rot -1.0  
searching scale 1 Z rot -0.8  
searching scale 1 Z rot -0.5  
searching scale 1 Z rot -0.3  
searching scale 1 Z rot -0.0  
searching scale 1 Z rot 0.2  
searching scale 1 Z rot 0.5  
searching scale 1 Z rot 0.7  
searching scale 1 Z rot 1.0  
searching scale 1 Z rot 1.2  
searching scale 1 Z rot 1.5  
searching scale 1 Z rot 1.7  
searching scale 1 Z rot 2.0  
searching scale 1 Z rot 2.2  
searching scale 1 Z rot 2.5  
searching scale 1 Z rot 2.7  
searching scale 1 Z rot 3.0  
searching scale 1 Z rot 3.2  
searching scale 1 Z rot 3.5  
searching scale 1 Z rot 3.7  
searching scale 1 Z rot 4.0  
searching scale 1 Z rot 4.2  
searching scale 1 Z rot 4.5  
searching scale 1 Z rot 4.7  
searching scale 1 Z rot 5.0  
searching scale 1 Z rot 5.2  
searching scale 1 Z rot 5.5  
searching scale 1 Z rot 5.7  
searching scale 1 Z rot 6.0  
searching scale 1 Z rot 6.2  
searching scale 1 Z rot 6.5  
searching scale 1 Z rot 6.7  
searching scale 1 Z rot 7.0  
searching scale 1 Z rot 7.2  
searching scale 1 Z rot 7.5  
searching scale 1 Z rot 7.7  
searching scale 1 Z rot 8.0  
searching scale 1 Z rot 8.2  global minimum found at slice 127.2, rotations (0.87, 1.46)
final transformation (x=127.2, yr=0.866, zr=1.458):
 1.000  -0.025   0.015   1.292;
 0.025   1.000   0.000   44.748;
-0.015  -0.000   1.000   26.935;
 0.000   0.000   0.000   1.000;
updating x range to be [125, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 147 116
eigenvectors:
-0.000   0.001   1.000;
-0.073  -0.997   0.001;
 0.997  -0.073   0.001;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 0.7 minutes
#--------------------------------------
#@# Merge ASeg Thu Aug  8 17:25:11 CEST 2013

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Thu Aug  8 17:25:11 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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...
3712 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 57 (57), valley at 30 (30)
csf peak at 28, setting threshold to 47
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 58 (58), valley at 30 (30)
csf peak at 29, setting threshold to 48
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 4 minutes and 10 seconds.
#--------------------------------------------
#@# Mask BFS Thu Aug  8 17:29:23 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1767582 voxels in mask (pct= 10.54)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Thu Aug  8 17:29:25 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 (107.0): 107.1 +- 5.1 [80.0 --> 125.0]
GM (68.0) : 67.4 +- 9.2 [30.0 --> 96.0]
setting bottom of white matter range to 76.6
setting top of gray matter range to 85.7
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...
10649 sparsely connected voxels removed...
thickening thin strands....
20 segments, 5279 filled
312 bright non-wm voxels segmented.
5168 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 0.65 minutes
reading wm segmentation from wm.seg.mgz...
70 voxels added to wm to prevent paths from MTL structures to cortex
1160 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 51272 voxels turned on, 46916 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 86   new 86
115,126,128 old 86   new 86
writing edited volume to wm.asegedit.mgz....

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


Iteration Number : 1
pass   1 (xy+):  28 found -  28 modified     |    TOTAL:  28
pass   2 (xy+):   0 found -  28 modified     |    TOTAL:  28
pass   1 (xy-):  25 found -  25 modified     |    TOTAL:  53
pass   2 (xy-):   0 found -  25 modified     |    TOTAL:  53
pass   1 (yz+):  32 found -  32 modified     |    TOTAL:  85
pass   2 (yz+):   0 found -  32 modified     |    TOTAL:  85
pass   1 (yz-):  23 found -  23 modified     |    TOTAL: 108
pass   2 (yz-):   0 found -  23 modified     |    TOTAL: 108
pass   1 (xz+):  18 found -  18 modified     |    TOTAL: 126
pass   2 (xz+):   0 found -  18 modified     |    TOTAL: 126
pass   1 (xz-):  23 found -  23 modified     |    TOTAL: 149
pass   2 (xz-):   0 found -  23 modified     |    TOTAL: 149
Iteration Number : 1
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):  27 found -  27 modified     |    TOTAL:  33
pass   2 (+++):   0 found -  27 modified     |    TOTAL:  33
pass   1 (+++):   9 found -   9 modified     |    TOTAL:  42
pass   2 (+++):   0 found -   9 modified     |    TOTAL:  42
pass   1 (+++):  16 found -  16 modified     |    TOTAL:  58
pass   2 (+++):   0 found -  16 modified     |    TOTAL:  58
Iteration Number : 1
pass   1 (++): 204 found - 204 modified     |    TOTAL: 204
pass   2 (++):   0 found - 204 modified     |    TOTAL: 204
pass   1 (+-): 188 found - 188 modified     |    TOTAL: 392
pass   2 (+-):   0 found - 188 modified     |    TOTAL: 392
pass   1 (--): 178 found - 178 modified     |    TOTAL: 570
pass   2 (--):   0 found - 178 modified     |    TOTAL: 570
pass   1 (-+): 166 found - 166 modified     |    TOTAL: 736
pass   2 (-+):   0 found - 166 modified     |    TOTAL: 736
Iteration Number : 2
pass   1 (xy+):   9 found -   9 modified     |    TOTAL:   9
pass   2 (xy+):   0 found -   9 modified     |    TOTAL:   9
pass   1 (xy-):   7 found -   7 modified     |    TOTAL:  16
pass   2 (xy-):   0 found -   7 modified     |    TOTAL:  16
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:  18
pass   2 (yz+):   0 found -   2 modified     |    TOTAL:  18
pass   1 (yz-):   8 found -   8 modified     |    TOTAL:  26
pass   2 (yz-):   0 found -   8 modified     |    TOTAL:  26
pass   1 (xz+):   3 found -   3 modified     |    TOTAL:  29
pass   2 (xz+):   0 found -   3 modified     |    TOTAL:  29
pass   1 (xz-):   2 found -   2 modified     |    TOTAL:  31
pass   2 (xz-):   0 found -   2 modified     |    TOTAL:  31
Iteration Number : 2
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   2
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 2
pass   1 (++):   3 found -   3 modified     |    TOTAL:   3
pass   2 (++):   0 found -   3 modified     |    TOTAL:   3
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (--):   2 found -   2 modified     |    TOTAL:   6
pass   2 (--):   0 found -   2 modified     |    TOTAL:   6
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   6
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (yz+):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   2
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   2
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   1
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (+-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (--):   0 found -   0 modified     |    TOTAL:   1
pass   1 (-+):   1 found -   1 modified     |    TOTAL:   2
pass   2 (-+):   0 found -   1 modified     |    TOTAL:   2
Iteration Number : 4
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 4
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 987 (out of 622745: 0.158492)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Thu Aug  8 17:32:05 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri

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

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 0.983  -0.021   0.024   0.151;
 0.022   1.116   0.249  -21.370;
-0.030  -0.176   0.960   17.535;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1119 (min = 350, max = 1400), aspect = 0.38 (min = 0.10, max = 0.75)
no need to search
using seed (126, 121, 149), TAL = (2.0, 21.0, 7.0)
talairach voxel to voxel transform
 1.016   0.014  -0.029   0.669;
-0.026   0.860  -0.222   22.285;
 0.027   0.158   1.000  -14.161;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (126,  121,  149) --> (2.0, 21.0, 7.0)
done.
writing output to filled.mgz...
filling took 0.9 minutes
talairach cc position changed to (2.00, 21.00, 7.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(20.00, 21.00, 7.00) SRC: (107.76, 90.46, 156.80)
search lh wm seed point around talairach space (-16.00, 21.00, 7.00), SRC: (144.33, 89.52, 157.76)
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 17:33:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

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


Iteration Number : 1
pass   1 (xy+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (xy+):   0 found -   3 modified     |    TOTAL:   3
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   4
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   4
pass   1 (yz+):   2 found -   2 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   2 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-):   0 found -   0 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   2 found -   2 modified     |    TOTAL:   3
pass   2 (+-):   0 found -   2 modified     |    TOTAL:   3
pass   1 (--):   1 found -   1 modified     |    TOTAL:   4
pass   2 (--):   0 found -   1 modified     |    TOTAL:   4
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   4
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 = 12 (out of 296303: 0.004050)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 40: 2247 vertices, 2412 faces
slice 50: 10036 vertices, 10353 faces
slice 60: 21453 vertices, 21827 faces
slice 70: 33202 vertices, 33629 faces
slice 80: 45185 vertices, 45605 faces
slice 90: 57325 vertices, 57748 faces
slice 100: 70349 vertices, 70817 faces
slice 110: 83004 vertices, 83431 faces
slice 120: 95002 vertices, 95456 faces
slice 130: 107089 vertices, 107487 faces
slice 140: 118705 vertices, 119157 faces
slice 150: 129205 vertices, 129627 faces
slice 160: 138040 vertices, 138350 faces
slice 170: 146229 vertices, 146519 faces
slice 180: 153318 vertices, 153599 faces
slice 190: 158619 vertices, 158840 faces
slice 200: 161732 vertices, 161843 faces
slice 210: 161964 vertices, 162010 faces
slice 220: 161964 vertices, 162010 faces
slice 230: 161964 vertices, 162010 faces
slice 240: 161964 vertices, 162010 faces
slice 250: 161964 vertices, 162010 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...
   161964 voxel in cpt #1: X=-46 [v=161964,e=486030,f=324020] located at (-28.711313, -18.458485, 37.919922)
For the whole surface: X=-46 [v=161964,e=486030,f=324020]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Thu Aug  8 17:33:08 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 17:33:13 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
avg radius = 49.2 mm, total surface area = 86006 mm^2
writing inflated surface to ../surf/lh.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=0.053 (target=0.015)   
step 015: RMS=0.044 (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=0.024 (target=0.015)   
step 045: RMS=0.022 (target=0.015)   
step 050: RMS=0.021 (target=0.015)   
step 055: RMS=0.021 (target=0.015)   
step 060: RMS=0.021 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Thu Aug  8 17:34:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.91 +- 0.54 (0.00-->6.75) (max @ vno 121685 --> 121686)
face area 0.02 +- 0.03 (-0.18-->0.72)
scaling brain by 0.291...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.656, avgs=0
005/300: dt: 0.9000, rms radial error=176.398, avgs=0
010/300: dt: 0.9000, rms radial error=175.843, avgs=0
015/300: dt: 0.9000, rms radial error=175.115, avgs=0
020/300: dt: 0.9000, rms radial error=174.285, avgs=0
025/300: dt: 0.9000, rms radial error=173.398, avgs=0
030/300: dt: 0.9000, rms radial error=172.480, avgs=0
035/300: dt: 0.9000, rms radial error=171.544, avgs=0
040/300: dt: 0.9000, rms radial error=170.601, avgs=0
045/300: dt: 0.9000, rms radial error=169.655, avgs=0
050/300: dt: 0.9000, rms radial error=168.709, avgs=0
055/300: dt: 0.9000, rms radial error=167.766, avgs=0
060/300: dt: 0.9000, rms radial error=166.826, avgs=0
065/300: dt: 0.9000, rms radial error=165.890, avgs=0
070/300: dt: 0.9000, rms radial error=164.959, avgs=0
075/300: dt: 0.9000, rms radial error=164.032, avgs=0
080/300: dt: 0.9000, rms radial error=163.111, avgs=0
085/300: dt: 0.9000, rms radial error=162.193, avgs=0
090/300: dt: 0.9000, rms radial error=161.281, avgs=0
095/300: dt: 0.9000, rms radial error=160.373, avgs=0
100/300: dt: 0.9000, rms radial error=159.471, avgs=0
105/300: dt: 0.9000, rms radial error=158.573, avgs=0
110/300: dt: 0.9000, rms radial error=157.680, avgs=0
115/300: dt: 0.9000, rms radial error=156.792, avgs=0
120/300: dt: 0.9000, rms radial error=155.909, avgs=0
125/300: dt: 0.9000, rms radial error=155.031, avgs=0
130/300: dt: 0.9000, rms radial error=154.157, avgs=0
135/300: dt: 0.9000, rms radial error=153.289, avgs=0
140/300: dt: 0.9000, rms radial error=152.425, avgs=0
145/300: dt: 0.9000, rms radial error=151.566, avgs=0
150/300: dt: 0.9000, rms radial error=150.711, avgs=0
155/300: dt: 0.9000, rms radial error=149.861, avgs=0
160/300: dt: 0.9000, rms radial error=149.016, avgs=0
165/300: dt: 0.9000, rms radial error=148.175, avgs=0
170/300: dt: 0.9000, rms radial error=147.339, avgs=0
175/300: dt: 0.9000, rms radial error=146.508, avgs=0
180/300: dt: 0.9000, rms radial error=145.681, avgs=0
185/300: dt: 0.9000, rms radial error=144.859, avgs=0
190/300: dt: 0.9000, rms radial error=144.042, avgs=0
195/300: dt: 0.9000, rms radial error=143.231, avgs=0
200/300: dt: 0.9000, rms radial error=142.425, avgs=0
205/300: dt: 0.9000, rms radial error=141.623, avgs=0
210/300: dt: 0.9000, rms radial error=140.825, avgs=0
215/300: dt: 0.9000, rms radial error=140.032, avgs=0
220/300: dt: 0.9000, rms radial error=139.244, avgs=0
225/300: dt: 0.9000, rms radial error=138.459, avgs=0
230/300: dt: 0.9000, rms radial error=137.679, avgs=0
235/300: dt: 0.9000, rms radial error=136.904, avgs=0
240/300: dt: 0.9000, rms radial error=136.132, avgs=0
245/300: dt: 0.9000, rms radial error=135.365, avgs=0
250/300: dt: 0.9000, rms radial error=134.602, avgs=0
255/300: dt: 0.9000, rms radial error=133.844, avgs=0
260/300: dt: 0.9000, rms radial error=133.090, avgs=0
265/300: dt: 0.9000, rms radial error=132.340, avgs=0
270/300: dt: 0.9000, rms radial error=131.595, avgs=0
275/300: dt: 0.9000, rms radial error=130.853, avgs=0
280/300: dt: 0.9000, rms radial error=130.116, avgs=0
285/300: dt: 0.9000, rms radial error=129.382, avgs=0
290/300: dt: 0.9000, rms radial error=128.653, avgs=0
295/300: dt: 0.9000, rms radial error=127.928, avgs=0
300/300: dt: 0.9000, rms radial error=127.207, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19332.81
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00015
epoch 2 (K=40.0), pass 1, starting sse = 3371.47
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00004
epoch 3 (K=160.0), pass 1, starting sse = 367.24
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/11 = 0.00481
epoch 4 (K=640.0), pass 1, starting sse = 23.51
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.09/12 = 0.00726
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.09 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Thu Aug  8 17:39:17 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/sub016/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub016 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=-46 (nv=161964, nf=324020, ne=486030, g=24)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
3711 ambiguous faces found in tessellation
segmenting defects...
26 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
26 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8304  (-4.9152)
      -vertex     loglikelihood: -6.5729  (-3.2864)
      -normal dot loglikelihood: -3.6792  (-3.6792)
      -quad curv  loglikelihood: -6.4542  (-3.2271)
      Total Loglikelihood : -26.5366

CORRECTING DEFECT 0 (vertices=25, convex hull=62)
After retessellation of defect 0, euler #=-23 (159748,478470,318699) : difference with theory (-23) = 0 

CORRECTING DEFECT 1 (vertices=694, convex hull=338)
After retessellation of defect 1, euler #=-22 (160043,479516,319451) : difference with theory (-22) = 0 

CORRECTING DEFECT 2 (vertices=33, convex hull=71)
After retessellation of defect 2, euler #=-21 (160062,479601,319518) : difference with theory (-21) = 0 

CORRECTING DEFECT 3 (vertices=5, convex hull=21)
After retessellation of defect 3, euler #=-20 (160063,479608,319525) : difference with theory (-20) = 0 

CORRECTING DEFECT 4 (vertices=40, convex hull=86)
After retessellation of defect 4, euler #=-19 (160083,479704,319602) : difference with theory (-19) = 0 

CORRECTING DEFECT 5 (vertices=6, convex hull=25)
After retessellation of defect 5, euler #=-18 (160085,479718,319615) : difference with theory (-18) = 0 

CORRECTING DEFECT 6 (vertices=152, convex hull=137)
After retessellation of defect 6, euler #=-17 (160158,480004,319829) : difference with theory (-17) = 0 

CORRECTING DEFECT 7 (vertices=238, convex hull=105)
After retessellation of defect 7, euler #=-16 (160221,480241,320004) : difference with theory (-16) = 0 

CORRECTING DEFECT 8 (vertices=31, convex hull=33)
After retessellation of defect 8, euler #=-15 (160226,480266,320025) : difference with theory (-15) = 0 

CORRECTING DEFECT 9 (vertices=30, convex hull=61)
After retessellation of defect 9, euler #=-14 (160242,480344,320088) : difference with theory (-14) = 0 

CORRECTING DEFECT 10 (vertices=179, convex hull=55)
After retessellation of defect 10, euler #=-13 (160255,480404,320136) : difference with theory (-13) = 0 

CORRECTING DEFECT 11 (vertices=75, convex hull=78)
After retessellation of defect 11, euler #=-12 (160266,480472,320194) : difference with theory (-12) = 0 

CORRECTING DEFECT 12 (vertices=12, convex hull=21)
After retessellation of defect 12, euler #=-11 (160270,480488,320207) : difference with theory (-11) = 0 

CORRECTING DEFECT 13 (vertices=34, convex hull=76)
After retessellation of defect 13, euler #=-10 (160279,480545,320256) : difference with theory (-10) = 0 

CORRECTING DEFECT 14 (vertices=5, convex hull=15)
After retessellation of defect 14, euler #=-9 (160279,480548,320260) : difference with theory (-9) = 0 

CORRECTING DEFECT 15 (vertices=46, convex hull=75)
After retessellation of defect 15, euler #=-8 (160295,480626,320323) : difference with theory (-8) = 0 

CORRECTING DEFECT 16 (vertices=175, convex hull=114)
After retessellation of defect 16, euler #=-7 (160337,480802,320458) : difference with theory (-7) = 0 

CORRECTING DEFECT 17 (vertices=125, convex hull=60)
After retessellation of defect 17, euler #=-6 (160345,480860,320509) : difference with theory (-6) = 0 

CORRECTING DEFECT 18 (vertices=123, convex hull=128)
After retessellation of defect 18, euler #=-5 (160411,481113,320697) : difference with theory (-5) = 0 

CORRECTING DEFECT 19 (vertices=40, convex hull=38)
After retessellation of defect 19, euler #=-4 (160420,481152,320728) : difference with theory (-4) = 0 

CORRECTING DEFECT 20 (vertices=34, convex hull=59)
After retessellation of defect 20, euler #=-3 (160438,481227,320786) : difference with theory (-3) = 0 

CORRECTING DEFECT 21 (vertices=10, convex hull=27)
After retessellation of defect 21, euler #=-2 (160440,481240,320798) : difference with theory (-2) = 0 

CORRECTING DEFECT 22 (vertices=22, convex hull=52)
After retessellation of defect 22, euler #=-1 (160453,481299,320845) : difference with theory (-1) = 0 

CORRECTING DEFECT 23 (vertices=16, convex hull=32)
After retessellation of defect 23, euler #=0 (160460,481331,320871) : difference with theory (0) = 0 

CORRECTING DEFECT 24 (vertices=42, convex hull=62)
After retessellation of defect 24, euler #=1 (160469,481382,320914) : difference with theory (1) = 0 

CORRECTING DEFECT 25 (vertices=25, convex hull=55)
After retessellation of defect 25, euler #=2 (160479,481431,320954) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.05-->6.34) (max @ vno 116804 --> 122752)
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 (0.05-->6.34) (max @ vno 116804 --> 122752)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
78 mutations (33.6%), 154 crossovers (66.4%), 79 vertices were eliminated
building final representation...
1485 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=160479, nf=320954, ne=481431, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 18.4 minutes
0 defective edges
removing intersecting faces
000: 224 intersecting
001: 27 intersecting
002: 11 intersecting
003: 7 intersecting
004: 2 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 160479 - 481431 + 320954 = 2 --> 0 holes
      F =2V-4:          320954 = 320958-4 (0)
      2E=3F:            962862 = 962862 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 48 intersecting
001: 35 intersecting
002: 11 intersecting
003: 8 intersecting
004: 7 intersecting
005: 2 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Thu Aug  8 17:57:56 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
22234 bright wm thresholded.
384 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
computing class statistics...
border white:    298969 voxels (1.78%)
border gray      333863 voxels (1.99%)
WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0]
GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70)
setting MAX_BORDER_WHITE to 115.8 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 36.9 (was 40)
setting MAX_GRAY to 96.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.05-->3.95) (max @ vno 159822 --> 160009)
face area 0.28 +- 0.12 (0.00-->5.04)
mean absolute distance = 0.65 +- 0.78
4287 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=62
mean inside = 93.8, mean outside = 70.2
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=74.3, 64 (64) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
%68 local maxima, %27 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 0.91 +- 0.26 (0.07-->5.11) (max @ vno 160099 --> 160100)
face area 0.28 +- 0.13 (0.00-->4.98)
mean absolute distance = 0.35 +- 0.49
4695 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7818525.5, rms=12.80
001: dt: 0.5000, sse=7902479.5, rms=9.064 (0.000%)
002: dt: 0.5000, sse=8193120.5, rms=6.997 (0.000%)
003: dt: 0.5000, sse=8398064.0, rms=5.733 (0.000%)
004: dt: 0.5000, sse=8678498.0, rms=4.997 (0.000%)
005: dt: 0.5000, sse=8757485.0, rms=4.599 (0.000%)
006: dt: 0.5000, sse=8878632.0, rms=4.381 (0.000%)
007: dt: 0.5000, sse=8860942.0, rms=4.270 (0.000%)
008: dt: 0.5000, sse=8900009.0, rms=4.192 (0.000%)
rms = 4.15, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8836779.0, rms=4.152 (0.000%)
010: dt: 0.2500, sse=5476378.0, rms=2.827 (0.000%)
011: dt: 0.2500, sse=5013794.5, rms=2.398 (0.000%)
012: dt: 0.2500, sse=4718828.5, rms=2.294 (0.000%)
013: dt: 0.2500, sse=4647839.5, rms=2.209 (0.000%)
rms = 2.18, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4549292.0, rms=2.177 (0.000%)
015: dt: 0.1250, sse=4309767.5, rms=1.938 (0.000%)
rms = 1.90, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=4266609.5, rms=1.905 (0.000%)
positioning took 2.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=79.4, 72 (44) missing vertices, mean dist -0.3 [0.4 (%81.0)->0.2 (%19.0))]
%83 local maxima, %12 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 (0.11-->4.72) (max @ vno 160104 --> 70416)
face area 0.35 +- 0.16 (0.00-->6.21)
mean absolute distance = 0.22 +- 0.31
4347 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5623246.0, rms=6.60
017: dt: 0.5000, sse=5578929.0, rms=4.370 (0.000%)
rms = 4.49, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=5083324.0, rms=3.327 (0.000%)
019: dt: 0.2500, sse=4849302.0, rms=2.589 (0.000%)
020: dt: 0.2500, sse=4754413.0, rms=2.103 (0.000%)
021: dt: 0.2500, sse=4719963.5, rms=1.946 (0.000%)
022: dt: 0.2500, sse=4634218.5, rms=1.791 (0.000%)
rms = 1.75, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=4638862.0, rms=1.752 (0.000%)
024: dt: 0.1250, sse=4476490.5, rms=1.555 (0.000%)
rms = 1.53, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=4435944.5, rms=1.528 (0.000%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=82.6, 61 (33) missing vertices, mean dist -0.1 [0.2 (%76.4)->0.2 (%23.6))]
%90 local maxima, % 5 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 0.89 +- 0.25 (0.10-->4.81) (max @ vno 160104 --> 70416)
face area 0.33 +- 0.16 (0.00-->5.67)
mean absolute distance = 0.16 +- 0.26
2934 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4852385.5, rms=4.12
026: dt: 0.5000, sse=5274197.5, rms=3.988 (0.000%)
rms = 4.18, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=4756714.5, rms=2.523 (0.000%)
028: dt: 0.2500, sse=4627541.0, rms=1.989 (0.000%)
029: dt: 0.2500, sse=4676251.0, rms=1.663 (0.000%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
030: dt: 0.1250, sse=4608184.5, rms=1.537 (0.000%)
031: dt: 0.1250, sse=4516804.0, rms=1.356 (0.000%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=4478627.0, rms=1.335 (0.000%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 3 vertex label from ripped group
removing 2 vertex label from ripped group
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=83.5, 64 (27) missing vertices, mean dist -0.0 [0.2 (%57.9)->0.2 (%42.1))]
%92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=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/sub016/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=4507100.0, rms=1.72
rms = 2.50, time step reduction 1 of 3 to 0.250...
033: dt: 0.2500, sse=4605772.0, rms=1.156 (0.000%)
034: dt: 0.2500, sse=4770604.0, rms=1.004 (0.000%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
rms = 0.99, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=4772717.5, rms=0.995 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
generating cortex label...
22 non-cortical segments detected
only using segment with 2520 vertices
erasing segment 1 (vno[0] = 73170)
erasing segment 2 (vno[0] = 94623)
erasing segment 3 (vno[0] = 99325)
erasing segment 4 (vno[0] = 107577)
erasing segment 5 (vno[0] = 110708)
erasing segment 6 (vno[0] = 110734)
erasing segment 7 (vno[0] = 112785)
erasing segment 8 (vno[0] = 112886)
erasing segment 9 (vno[0] = 114058)
erasing segment 10 (vno[0] = 114341)
erasing segment 11 (vno[0] = 115359)
erasing segment 12 (vno[0] = 115383)
erasing segment 13 (vno[0] = 116597)
erasing segment 14 (vno[0] = 117688)
erasing segment 15 (vno[0] = 117768)
erasing segment 16 (vno[0] = 121659)
erasing segment 17 (vno[0] = 122561)
erasing segment 18 (vno[0] = 122612)
erasing segment 19 (vno[0] = 124558)
erasing segment 20 (vno[0] = 126720)
erasing segment 21 (vno[0] = 128787)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area
vertex spacing 0.89 +- 0.25 (0.03-->4.83) (max @ vno 160104 --> 70416)
face area 0.33 +- 0.16 (0.00-->5.70)
refinement took 8.0 minutes
#--------------------------------------------
#@# Smooth2 lh Thu Aug  8 18:05:54 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 18:05:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

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

avg radius = 49.3 mm, total surface area = 97677 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.112 (target=0.015)   
step 005: RMS=0.078 (target=0.015)   
step 010: RMS=0.056 (target=0.015)   
step 015: RMS=0.046 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.026 (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
209 vertices thresholded to be in k1 ~ [-0.24 0.56], k2 ~ [-0.12 0.09]
total integrated curvature = 0.392*4pi (4.931) --> 1 handles
ICI = 1.8, FI = 13.8, variation=228.351
163 vertices thresholded to be in [-0.02 0.02]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
155 vertices thresholded to be in [-0.13 0.23]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.015, std = 0.025
done.

#-----------------------------------------
#@# Curvature Stats lh Thu Aug  8 18:08:39 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub016 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       [ sub016/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                      [ 306 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.080822
WARN:    S explicit min:                          0.000000	vertex = 1040
#--------------------------------------------
#@# Sphere lh Thu Aug  8 18:08:44 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.273...
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 %20.27
pass 1: epoch 2 of 3 starting distance error %20.21
unfolding complete - removing small folds...
starting distance error %20.11
removing remaining folds...
final distance error %20.12
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 1.24 hours
#--------------------------------------------
#@# Surf Reg lh Thu Aug  8 19:23:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 0.019, std = 0.933
curvature mean = 0.026, std = 0.836
Starting MRISrigidBodyAlignGlobal()
  d=32.00 min @ (0.00, -8.00, 0.00) sse = 346322.2, tmin=2.6324
  d=16.00 min @ (4.00, 0.00, 0.00) sse = 340851.3, tmin=4.0946
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 336519.5, tmin=5.5732
  d=4.00 min @ (0.00, 0.00, -1.00) sse = 335921.1, tmin=7.0874
  d=1.00 min @ (0.25, 0.00, 0.00) sse = 335842.9, tmin=10.1403
  d=0.50 min @ (0.00, 0.12, 0.00) sse = 335828.7, tmin=11.6717
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  11.67 min
curvature mean = 0.009, std = 0.939
curvature mean = 0.012, std = 0.923
curvature mean = 0.007, std = 0.950
curvature mean = 0.006, std = 0.963
curvature mean = 0.005, std = 0.950
curvature mean = 0.002, std = 0.983
2 Reading smoothwm
curvature mean = -0.024, std = 0.291
curvature mean = 0.003, std = 0.066
curvature mean = 0.072, std = 0.316
curvature mean = 0.004, std = 0.078
curvature mean = 0.035, std = 0.506
curvature mean = 0.005, std = 0.084
curvature mean = 0.019, std = 0.650
curvature mean = 0.005, std = 0.086
curvature mean = 0.007, std = 0.765
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Thu Aug  8 20:00:55 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 20:00:58 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:01:00 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
1573 labels changed using aseg
relabeling using gibbs priors...
000:   3403 changed, 160479 examined...
001:    803 changed, 14657 examined...
002:    213 changed, 4459 examined...
003:     72 changed, 1275 examined...
004:     23 changed, 437 examined...
005:     10 changed, 132 examined...
006:      3 changed, 65 examined...
007:      2 changed, 23 examined...
008:      2 changed, 11 examined...
009:      2 changed, 11 examined...
010:      1 changed, 10 examined...
011:      0 changed, 7 examined...
262 labels changed using aseg
000: 164 total segments, 119 labels (468 vertices) changed
001: 45 total segments, 4 labels (12 vertices) changed
002: 41 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 69 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1861 vertices marked for relabeling...
1861 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 1 minutes and 10 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Thu Aug  8 20:02:11 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
22234 bright wm thresholded.
384 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
computing class statistics...
border white:    298969 voxels (1.78%)
border gray      333863 voxels (1.99%)
WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0]
GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70)
setting MAX_BORDER_WHITE to 115.8 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 36.9 (was 40)
setting MAX_GRAY to 96.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=62
mean inside = 93.8, mean outside = 70.2
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/sub016/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.05-->3.95) (max @ vno 159822 --> 160009)
face area 0.28 +- 0.12 (0.00-->5.04)
mean absolute distance = 0.65 +- 0.79
4390 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 247 points - only 4.05% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 5 with 6 points - only 0.00% unknown
deleting segment 6 with 840 points - only 0.00% unknown
deleting segment 7 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 11 with 37 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
deleting segment 13 with 8 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
mean border=74.3, 66 (65) missing vertices, mean dist 0.4 [0.5 (%30.4)->0.7 (%69.6))]
%69 local maxima, %27 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 0.91 +- 0.26 (0.07-->5.11) (max @ vno 160099 --> 160100)
face area 0.28 +- 0.13 (0.00-->4.98)
mean absolute distance = 0.35 +- 0.49
4775 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=7844055.5, rms=12.77
001: dt: 0.5000, sse=7941564.5, rms=9.040 (0.000%)
002: dt: 0.5000, sse=8239249.0, rms=6.981 (0.000%)
003: dt: 0.5000, sse=8449724.0, rms=5.724 (0.000%)
004: dt: 0.5000, sse=8730856.0, rms=4.991 (0.000%)
005: dt: 0.5000, sse=8813873.0, rms=4.595 (0.000%)
006: dt: 0.5000, sse=8934122.0, rms=4.376 (0.000%)
007: dt: 0.5000, sse=8914619.0, rms=4.266 (0.000%)
008: dt: 0.5000, sse=8955723.0, rms=4.187 (0.000%)
rms = 4.15, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=8894941.0, rms=4.146 (0.000%)
010: dt: 0.2500, sse=5502699.5, rms=2.823 (0.000%)
011: dt: 0.2500, sse=5038612.0, rms=2.394 (0.000%)
012: dt: 0.2500, sse=4741387.5, rms=2.291 (0.000%)
013: dt: 0.2500, sse=4670505.5, rms=2.207 (0.000%)
rms = 2.17, time step reduction 2 of 3 to 0.125...
014: dt: 0.2500, sse=4573283.5, rms=2.175 (0.000%)
015: dt: 0.1250, sse=4333563.5, rms=1.938 (0.000%)
rms = 1.91, time step reduction 3 of 3 to 0.062...
016: dt: 0.1250, sse=4290018.5, rms=1.905 (0.000%)
positioning took 2.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 276 points - only 3.62% unknown
deleting segment 1 with 5 points - only 0.00% unknown
deleting segment 2 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 7 with 766 points - only 0.00% unknown
deleting segment 11 with 14 points - only 7.14% unknown
deleting segment 14 with 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 17 with 4 points - only 0.00% unknown
mean border=79.4, 70 (43) missing vertices, mean dist -0.3 [0.4 (%80.9)->0.2 (%19.1))]
%84 local maxima, %12 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 (0.11-->4.72) (max @ vno 160104 --> 70416)
face area 0.35 +- 0.16 (0.00-->6.21)
mean absolute distance = 0.22 +- 0.31
4410 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5655265.0, rms=6.59
017: dt: 0.5000, sse=5613595.5, rms=4.364 (0.000%)
rms = 4.49, time step reduction 1 of 3 to 0.250...
018: dt: 0.2500, sse=5116181.5, rms=3.326 (0.000%)
019: dt: 0.2500, sse=4883240.5, rms=2.592 (0.000%)
020: dt: 0.2500, sse=4788981.5, rms=2.110 (0.000%)
021: dt: 0.2500, sse=4754010.0, rms=1.954 (0.000%)
022: dt: 0.2500, sse=4670228.5, rms=1.801 (0.000%)
rms = 1.76, time step reduction 2 of 3 to 0.125...
023: dt: 0.2500, sse=4675198.5, rms=1.763 (0.000%)
024: dt: 0.1250, sse=4512359.5, rms=1.569 (0.000%)
rms = 1.54, time step reduction 3 of 3 to 0.062...
025: dt: 0.1250, sse=4471475.0, rms=1.543 (0.000%)
positioning took 1.4 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 264 points - only 3.79% unknown
deleting segment 1 with 5 points - only 0.00% unknown
deleting segment 2 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
deleting segment 5 with 862 points - only 0.00% unknown
deleting segment 6 with 11 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
deleting segment 10 with 10 points - only 10.00% unknown
deleting segment 11 with 8 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 5 points - only 0.00% unknown
mean border=82.6, 68 (34) missing vertices, mean dist -0.1 [0.2 (%76.3)->0.2 (%23.7))]
%91 local maxima, % 5 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 0.89 +- 0.25 (0.10-->4.81) (max @ vno 160104 --> 70416)
face area 0.33 +- 0.16 (0.00-->5.67)
mean absolute distance = 0.16 +- 0.25
2994 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4889192.0, rms=4.12
026: dt: 0.5000, sse=5312165.5, rms=3.986 (0.000%)
rms = 4.18, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=4792344.5, rms=2.529 (0.000%)
028: dt: 0.2500, sse=4666050.5, rms=2.000 (0.000%)
029: dt: 0.2500, sse=4714949.5, rms=1.677 (0.000%)
rms = 1.70, time step reduction 2 of 3 to 0.125...
030: dt: 0.1250, sse=4647289.0, rms=1.554 (0.000%)
031: dt: 0.1250, sse=4557666.0, rms=1.376 (0.000%)
rms = 1.36, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=4520176.0, rms=1.356 (0.000%)
positioning took 1.1 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 281 points - only 3.56% unknown
deleting segment 1 with 5 points - only 0.00% unknown
deleting segment 2 with 9 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 3 with 2 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 870 points - only 0.00% unknown
deleting segment 7 with 10 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 8 with 2 points - only 0.00% unknown
deleting segment 9 with 10 points - only 10.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
deleting segment 12 with 5 points - only 0.00% unknown
mean border=83.5, 76 (27) missing vertices, mean dist -0.0 [0.2 (%57.8)->0.2 (%42.2))]
%92 local maxima, % 3 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=4548075.5, rms=1.73
rms = 2.49, time step reduction 1 of 3 to 0.250...
033: dt: 0.2500, sse=4649222.5, rms=1.169 (0.000%)
034: dt: 0.2500, sse=4818127.0, rms=1.016 (0.000%)
rms = 1.02, time step reduction 2 of 3 to 0.125...
rms = 1.01, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=4820042.5, rms=1.007 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 33.33% unknown
smoothing surface for 5 iterations...
mean border=51.7, 111 (111) missing vertices, mean dist 1.8 [0.2 (%0.0)->2.3 (%100.0))]
%18 local maxima, %57 large gradients and %21 min vals, 1813 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=33252602.0, rms=31.32
001: dt: 0.5000, sse=23820164.0, rms=25.953 (0.000%)
002: dt: 0.5000, sse=17428042.0, rms=21.590 (0.000%)
003: dt: 0.5000, sse=13329135.0, rms=18.138 (0.000%)
004: dt: 0.5000, sse=10853808.0, rms=15.436 (0.000%)
005: dt: 0.5000, sse=9436409.0, rms=13.377 (0.000%)
006: dt: 0.5000, sse=8574854.0, rms=11.795 (0.000%)
007: dt: 0.5000, sse=8032852.0, rms=10.429 (0.000%)
008: dt: 0.5000, sse=7625669.5, rms=9.155 (0.000%)
009: dt: 0.5000, sse=7400627.5, rms=7.980 (0.000%)
010: dt: 0.5000, sse=7328718.5, rms=6.933 (0.000%)
011: dt: 0.5000, sse=7340751.0, rms=6.028 (0.000%)
012: dt: 0.5000, sse=7462176.0, rms=5.310 (0.000%)
013: dt: 0.5000, sse=7615104.5, rms=4.789 (0.000%)
014: dt: 0.5000, sse=7788750.5, rms=4.487 (0.000%)
015: dt: 0.5000, sse=7951089.5, rms=4.297 (0.000%)
016: dt: 0.5000, sse=8027350.0, rms=4.190 (0.000%)
017: dt: 0.5000, sse=8091952.0, rms=4.094 (0.000%)
rms = 4.05, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=8099899.0, rms=4.053 (0.000%)
019: dt: 0.2500, sse=5641960.0, rms=3.259 (0.000%)
020: dt: 0.2500, sse=5457684.5, rms=3.050 (0.000%)
rms = 3.02, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=5298820.0, rms=3.016 (0.000%)
022: dt: 0.1250, sse=5029088.0, rms=2.837 (0.000%)
rms = 2.81, time step reduction 3 of 3 to 0.062...
023: dt: 0.1250, sse=5006962.5, rms=2.811 (0.000%)
positioning took 3.3 minutes
mean border=48.8, 993 (28) missing vertices, mean dist 0.2 [0.2 (%43.3)->0.5 (%56.7))]
%37 local maxima, %41 large gradients and %18 min vals, 574 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=5916018.5, rms=5.31
024: dt: 0.5000, sse=6209243.5, rms=4.414 (0.000%)
025: dt: 0.5000, sse=7797205.5, rms=4.261 (0.000%)
rms = 4.30, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=6394776.5, rms=3.436 (0.000%)
027: dt: 0.2500, sse=5863477.5, rms=3.090 (0.000%)
028: dt: 0.2500, sse=5800961.0, rms=2.998 (0.000%)
029: dt: 0.2500, sse=5753294.5, rms=2.948 (0.000%)
rms = 2.93, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=5763284.0, rms=2.930 (0.000%)
031: dt: 0.1250, sse=5501244.5, rms=2.698 (0.000%)
rms = 2.66, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=5479329.0, rms=2.658 (0.000%)
positioning took 1.4 minutes
mean border=46.1, 1229 (21) missing vertices, mean dist 0.1 [0.2 (%34.9)->0.4 (%65.1))]
%56 local maxima, %22 large gradients and %17 min vals, 621 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=5883961.0, rms=4.40
033: dt: 0.5000, sse=6194537.5, rms=4.201 (0.000%)
rms = 4.17, time step reduction 1 of 3 to 0.250...
034: dt: 0.5000, sse=8006900.0, rms=4.171 (0.000%)
035: dt: 0.2500, sse=6001242.5, rms=3.119 (0.000%)
036: dt: 0.2500, sse=6192814.5, rms=2.792 (0.000%)
rms = 2.81, time step reduction 2 of 3 to 0.125...
037: dt: 0.1250, sse=6027948.5, rms=2.661 (0.000%)
038: dt: 0.1250, sse=5747886.5, rms=2.474 (0.000%)
rms = 2.44, time step reduction 3 of 3 to 0.062...
039: dt: 0.1250, sse=5683501.0, rms=2.439 (0.000%)
positioning took 1.2 minutes
mean border=44.9, 2472 (16) missing vertices, mean dist 0.0 [0.2 (%43.8)->0.2 (%56.2))]
%58 local maxima, %20 large gradients and %17 min vals, 447 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/sub016/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=5745762.5, rms=2.86
rms = 3.79, time step reduction 1 of 3 to 0.250...
040: dt: 0.2500, sse=5579690.0, rms=2.540 (0.000%)
041: dt: 0.2500, sse=5757399.5, rms=2.466 (0.000%)
rms = 2.48, time step reduction 2 of 3 to 0.125...
rms = 2.42, time step reduction 3 of 3 to 0.062...
042: dt: 0.1250, sse=5697529.5, rms=2.425 (0.000%)
positioning took 0.7 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area.pial
vertex spacing 1.01 +- 0.43 (0.05-->7.37) (max @ vno 109705 --> 108677)
face area 0.41 +- 0.31 (0.00-->7.60)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 160479 vertices processed
25000 of 160479 vertices processed
50000 of 160479 vertices processed
75000 of 160479 vertices processed
100000 of 160479 vertices processed
125000 of 160479 vertices processed
150000 of 160479 vertices processed
0 of 160479 vertices processed
25000 of 160479 vertices processed
50000 of 160479 vertices processed
75000 of 160479 vertices processed
100000 of 160479 vertices processed
125000 of 160479 vertices processed
150000 of 160479 vertices processed
thickness calculation complete, 283:849 truncations.
38541 vertices at 0 distance
110303 vertices at 1 distance
101984 vertices at 2 distance
41552 vertices at 3 distance
11775 vertices at 4 distance
3027 vertices at 5 distance
822 vertices at 6 distance
267 vertices at 7 distance
118 vertices at 8 distance
49 vertices at 9 distance
29 vertices at 10 distance
21 vertices at 11 distance
18 vertices at 12 distance
14 vertices at 13 distance
14 vertices at 14 distance
13 vertices at 15 distance
17 vertices at 16 distance
10 vertices at 17 distance
8 vertices at 18 distance
7 vertices at 19 distance
15 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.thickness
positioning took 16.2 minutes
#--------------------------------------------
#@# Surf Volume lh Thu Aug  8 20:18:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:18:21 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 pctsurfcon --s sub016 --lh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts/pctsurfcon.log
Thu Aug  8 20:18:21 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake6 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/sub016/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh --regheader sub016 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 124623
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh
Dim: 160479 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh --projfrac 0.3 --regheader sub016 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 142718
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh
Dim: 160479 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.9267/lh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.w-g.pct.mgh --annot sub016 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/lh.w-g.pct.mgh --annot sub016 lh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/stats/lh.w-g.pct.stats --snr 
sysname  Linux
hostname snake6
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/sub016/surf/lh.w-g.pct.mgh
Vertex Area is 0.660622 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   1000                            unknown       0       0.000
  1   1001                           bankssts    1512    1056.612
  2   1002            caudalanteriorcingulate    1250     846.357
  3   1003                caudalmiddlefrontal    3443    2308.520
  4   1004                     corpuscallosum       0       0.000
  5   1005                             cuneus    2906    1843.261
  6   1006                         entorhinal     750     510.895
  7   1007                           fusiform    5411    3674.410
  8   1008                   inferiorparietal    8099    5476.500
  9   1009                   inferiortemporal    7888    5305.233
 10   1010                   isthmuscingulate    2079    1352.020
 11   1011                   lateraloccipital    8202    5319.603
 12   1012               lateralorbitofrontal    4837    3217.664
 13   1013                            lingual    5239    3490.395
 14   1014                medialorbitofrontal    3096    2007.213
 15   1015                     middletemporal    5955    4078.508
 16   1016                    parahippocampal    1473     959.961
 17   1017                        paracentral    2087    1225.595
 18   1018                    parsopercularis    3193    2112.798
 19   1019                      parsorbitalis    1216     781.607
 20   1020                   parstriangularis    2274    1526.439
 21   1021                      pericalcarine    2660    1943.400
 22   1022                        postcentral    7142    4493.574
 23   1023                 posteriorcingulate    2413    1614.474
 24   1024                         precentral    8460    5267.162
 25   1025                          precuneus    7244    4771.850
 26   1026           rostralanteriorcingulate    1630    1076.536
 27   1027               rostralmiddlefrontal    8850    6006.854
 28   1028                    superiorfrontal   12261    8237.140
 29   1029                   superiorparietal   10142    6578.766
 30   1030                   superiortemporal    6058    4059.571
 31   1031                      supramarginal    7259    4838.904
 32   1032                        frontalpole     293     200.763
 33   1033                       temporalpole     701     477.017
 34   1034                 transversetemporal    1015     612.610
 35   1035                             insula    4037    2649.110

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats lh Thu Aug  8 20:18:36 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1512   1057   2788  2.484 0.577     0.109     0.030       16     1.9  bankssts
 1250    846   2519  2.694 0.558     0.132     0.039       20     1.9  caudalanteriorcingulate
 3443   2309   6884  2.643 0.506     0.124     0.038       42     5.3  caudalmiddlefrontal
 2906   1843   4888  2.270 0.557     0.151     0.065       56     8.1  cuneus
  750    511   1990  3.183 0.555     0.141     0.049       10     1.5  entorhinal
 5411   3674  11873  2.829 0.552     0.145     0.064      104    12.7  fusiform
 8099   5476  15082  2.452 0.454     0.136     0.048      147    15.8  inferiorparietal
 7888   5305  17636  2.745 0.662     0.143     0.064      184    19.7  inferiortemporal
 2079   1352   3419  2.358 0.806     0.147     0.068       58     5.9  isthmuscingulate
 8202   5320  13729  2.285 0.508     0.154     0.062      165    20.3  lateraloccipital
 4837   3218   9518  2.570 0.607     0.154     0.072       98    12.5  lateralorbitofrontal
 5239   3490   8311  2.164 0.560     0.154     0.077      104    17.9  lingual
 3096   2007   5386  2.231 0.752     0.164     0.091      112    10.3  medialorbitofrontal
 5955   4078  14688  2.876 0.629     0.146     0.053      113    12.2  middletemporal
 1473    960   3480  3.050 0.644     0.161     0.204       54     6.4  parahippocampal
 2087   1226   3632  2.649 0.600     0.113     0.183       52     4.7  paracentral
 3193   2113   6704  2.788 0.481     0.127     0.040       46     5.5  parsopercularis
 1216    782   2883  2.875 0.687     0.148     0.053       24     2.5  parsorbitalis
 2274   1526   4452  2.475 0.542     0.138     0.046       38     4.1  parstriangularis
 2660   1943   3720  2.004 0.464     0.156     0.059       48     6.9  pericalcarine
 7142   4494  11708  2.289 0.613     0.130     0.054      188    17.9  postcentral
 2413   1614   4505  2.550 0.656     0.135     0.048       39     4.1  posteriorcingulate
 8460   5267  16227  2.749 0.553     0.113     0.040      178    13.8  precentral
 7244   4772  13273  2.573 0.506     0.139     0.050      113    14.9  precuneus
 1630   1077   3658  2.643 0.838     0.156     0.058       30     3.8  rostralanteriorcingulate
 8850   6007  16555  2.345 0.560     0.145     0.052      167    19.0  rostralmiddlefrontal
12261   8237  26422  2.723 0.604     0.130     0.040      150    20.3  superiorfrontal
10142   6579  17306  2.358 0.445     0.130     0.043      162    17.5  superiorparietal
 6058   4060  14107  3.042 0.686     0.122     0.041       78     9.4  superiortemporal
 7259   4839  14989  2.719 0.528     0.141     0.049      160    14.3  supramarginal
  293    201    790  2.634 0.541     0.237     0.128       14     1.1  frontalpole
  701    477   2545  3.779 0.688     0.160     0.063       13     1.9  temporalpole
 1015    613   2006  2.729 0.354     0.150     0.130       37     6.9  transversetemporal
 4037   2649   8630  3.118 0.753     0.118     0.076       80    11.0  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Thu Aug  8 20:18:59 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
27 labels changed using aseg
relabeling using gibbs priors...
000:  11050 changed, 160479 examined...
001:   2709 changed, 41932 examined...
002:    839 changed, 13821 examined...
003:    359 changed, 4563 examined...
004:    198 changed, 1995 examined...
005:     85 changed, 1065 examined...
006:     45 changed, 501 examined...
007:     25 changed, 248 examined...
008:     15 changed, 139 examined...
009:      9 changed, 82 examined...
010:      4 changed, 50 examined...
011:      2 changed, 24 examined...
012:      0 changed, 12 examined...
1 labels changed using aseg
000: 326 total segments, 243 labels (2925 vertices) changed
001: 104 total segments, 22 labels (106 vertices) changed
002: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 128 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1047 vertices marked for relabeling...
1047 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 22 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Thu Aug  8 20:20:20 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1398    965   2614  2.232 0.588     0.153     0.052       29     3.1  G_and_S_frontomargin
 1188    747   1903  2.183 0.403     0.122     0.054       29     2.3  G_and_S_occipital_inf
 1708    930   2996  2.566 0.594     0.121     0.058       57     4.0  G_and_S_paracentral
 2065   1309   4502  2.929 0.542     0.147     0.052       37     4.4  G_and_S_subcentral
  613    424   1429  2.417 0.542     0.185     0.096       23     2.0  G_and_S_transv_frontopol
 3293   2209   6728  2.546 0.738     0.145     0.053       53     6.4  G_and_S_cingul-Ant
 1399    982   2690  2.599 0.569     0.116     0.040       15     2.0  G_and_S_cingul-Mid-Ant
 1557   1044   2801  2.580 0.491     0.108     0.033       13     2.2  G_and_S_cingul-Mid-Post
  969    616   2176  3.017 0.624     0.162     0.068       22     2.2  G_cingul-Post-dorsal
  459    275    659  2.140 0.767     0.148     0.074        8     1.3  G_cingul-Post-ventral
 2693   1742   4781  2.164 0.562     0.165     0.073       62     8.6  G_cuneus
 1741   1119   4314  2.985 0.434     0.143     0.053       35     4.0  G_front_inf-Opercular
  318    193    833  3.056 0.457     0.161     0.065        8     0.8  G_front_inf-Orbital
 1238    845   2870  2.667 0.472     0.161     0.056       30     2.8  G_front_inf-Triangul
 4770   3234  11350  2.683 0.510     0.160     0.062      112    11.8  G_front_middle
 8303   5409  19745  2.878 0.584     0.137     0.078      152    15.8  G_front_sup
  585    383   1443  3.214 0.499     0.125     0.062        8     1.2  G_Ins_lg_and_S_cent_ins
  936    587   3021  3.869 0.650     0.145     0.167       51     5.2  G_insular_short
 2895   1870   6213  2.594 0.475     0.174     0.088       99     9.8  G_occipital_middle
 1937   1278   3192  2.268 0.428     0.150     0.054       54     4.4  G_occipital_sup
 1579   1020   4156  3.069 0.447     0.159     0.065       40     3.8  G_oc-temp_lat-fusifor
 3433   2248   5849  2.169 0.597     0.175     0.100       92    15.6  G_oc-temp_med-Lingual
 1862   1244   5210  3.285 0.548     0.165     0.180       61     7.5  G_oc-temp_med-Parahip
 3134   2051   7575  2.779 0.609     0.172     0.094       92    10.2  G_orbital
 2868   1900   6701  2.675 0.474     0.158     0.063       80     7.5  G_pariet_inf-Angular
 3884   2581   9527  2.905 0.493     0.153     0.051       80     7.8  G_pariet_inf-Supramar
 4289   2725   8589  2.487 0.475     0.137     0.048       76     7.9  G_parietal_sup
 2584   1530   4729  2.368 0.475     0.139     0.077      133    10.3  G_postcentral
 3137   1796   7414  3.066 0.425     0.117     0.050      102     6.0  G_precentral
 3240   2129   7232  2.764 0.505     0.158     0.060       69     7.8  G_precuneus
 1054    665   2367  2.432 0.724     0.185     0.106       41     4.6  G_rectus
  528    336    942  2.619 0.925     0.201     0.167       42     2.7  G_subcallosal
  806    476   1868  2.876 0.428     0.157     0.150       36     6.5  G_temp_sup-G_T_transv
 2099   1376   6291  3.287 0.569     0.144     0.047       44     4.1  G_temp_sup-Lateral
  797    546   2450  3.766 0.713     0.126     0.056        9     1.8  G_temp_sup-Plan_polar
 1421    954   3002  2.826 0.481     0.111     0.036       14     2.0  G_temp_sup-Plan_tempo
 4735   3150  12232  2.902 0.696     0.168     0.085      161    15.4  G_temporal_inf
 4179   2835  11296  2.979 0.610     0.150     0.057       89     8.9  G_temporal_middle
  601    392    970  2.301 0.556     0.122     0.037        6     0.9  Lat_Fis-ant-Horizont
  405    278    716  2.510 0.515     0.108     0.027        3     0.5  Lat_Fis-ant-Vertical
 1616   1063   2328  2.569 0.489     0.119     0.037       13     2.4  Lat_Fis-post
 2348   1502   3846  2.180 0.536     0.168     0.075       51     7.6  Pole_occipital
 2019   1388   5883  3.157 0.733     0.173     0.090       48     6.8  Pole_temporal
 3836   2660   5170  2.087 0.521     0.135     0.049       53     8.1  S_calcarine
 3491   2319   4297  2.050 0.529     0.113     0.030       25     4.6  S_central
 1249    834   1902  2.301 0.389     0.108     0.028       11     1.4  S_cingul-Marginalis
  635    424   1051  2.606 0.552     0.112     0.042        5     0.9  S_circular_insula_ant
 1843   1225   3131  2.905 0.720     0.094     0.023        8     1.9  S_circular_insula_inf
 2052   1380   3127  2.685 0.520     0.101     0.030       12     2.4  S_circular_insula_sup
 1820   1250   3121  2.680 0.526     0.106     0.028       12     2.2  S_collat_transv_ant
  372    259    470  2.203 0.330     0.125     0.030        3     0.5  S_collat_transv_post
 2485   1659   3858  2.268 0.461     0.116     0.031       23     3.3  S_front_inf
 1660   1114   2382  2.089 0.458     0.127     0.045       20     3.1  S_front_middle
 3117   2120   5236  2.484 0.505     0.110     0.031       25     4.2  S_front_sup
  270    183    415  2.394 0.436     0.148     0.056        3     0.8  S_interm_prim-Jensen
 3972   2642   5744  2.295 0.389     0.114     0.032       34     5.3  S_intrapariet_and_P_trans
 1315    888   1703  1.936 0.351     0.123     0.033       14     1.7  S_oc_middle_and_Lunatus
 1148    802   1778  2.314 0.363     0.148     0.045       15     2.1  S_oc_sup_and_transversal
 1147    777   1667  2.349 0.413     0.140     0.040       13     2.0  S_occipital_ant
 1621   1128   2813  2.551 0.379     0.103     0.024       10     1.7  S_oc-temp_lat
 2180   1493   3796  2.606 0.538     0.138     0.053       27     4.5  S_oc-temp_med_and_Lingual
  500    338    636  2.086 0.492     0.101     0.024        2     0.6  S_orbital_lateral
  783    545   1203  2.192 0.724     0.126     0.040        7     1.4  S_orbital_med-olfact
 1897   1253   3345  2.495 0.628     0.147     0.056       31     4.5  S_orbital-H_Shaped
 2790   1859   4345  2.493 0.510     0.124     0.040       28     4.6  S_parieto_occipital
 1802   1186   2164  2.040 0.678     0.140     0.057       59     4.5  S_pericallosal
 3177   2122   4456  2.276 0.407     0.119     0.037       62     4.5  S_postcentral
 1723   1173   2589  2.390 0.429     0.106     0.026       11     2.0  S_precentral-inf-part
 1504   1062   2365  2.535 0.502     0.096     0.023        6     1.5  S_precentral-sup-part
  573    397    822  1.895 0.805     0.160     0.053       11     1.4  S_suborbital
 1235    833   2058  2.471 0.397     0.133     0.044       16     2.3  S_subparietal
 1969   1385   3100  2.384 0.510     0.111     0.027       13     2.4  S_temporal_inf
 5778   3972   9464  2.394 0.469     0.113     0.034       64     7.8  S_temporal_sup
  448    298    661  2.708 0.332     0.114     0.031        3     0.6  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Thu Aug  8 20:20:46 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
1036 labels changed using aseg
relabeling using gibbs priors...
000:   3290 changed, 160479 examined...
001:    797 changed, 13782 examined...
002:    203 changed, 4294 examined...
003:     71 changed, 1206 examined...
004:     42 changed, 397 examined...
005:     17 changed, 242 examined...
006:      9 changed, 105 examined...
007:      6 changed, 52 examined...
008:      3 changed, 34 examined...
009:      4 changed, 17 examined...
010:      1 changed, 15 examined...
011:      0 changed, 7 examined...
76 labels changed using aseg
000: 76 total segments, 43 labels (249 vertices) changed
001: 35 total segments, 2 labels (3 vertices) changed
002: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 60 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
969 vertices marked for relabeling...
969 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 1 minutes and 12 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Thu Aug  8 20:21:58 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1893   1283   3926  2.752 0.604     0.132     0.040       27     2.9  caudalanteriorcingulate
 3593   2400   7209  2.654 0.505     0.125     0.039       46     5.6  caudalmiddlefrontal
 4013   2602   6428  2.246 0.530     0.146     0.058       69    10.0  cuneus
  735    502   1959  3.204 0.559     0.135     0.043        8     1.3  entorhinal
 4879   3297  10290  2.812 0.529     0.142     0.058       91    10.7  fusiform
 7514   5088  13954  2.440 0.456     0.139     0.049      141    15.0  inferiorparietal
 7834   5269  17861  2.771 0.671     0.144     0.065      181    19.7  inferiortemporal
 2094   1351   3494  2.388 0.796     0.150     0.070       61     6.3  isthmuscingulate
 8527   5521  14461  2.289 0.509     0.155     0.063      194    21.8  lateraloccipital
 5148   3450  10650  2.605 0.623     0.165     0.094      131    17.8  lateralorbitofrontal
 5174   3449   8220  2.165 0.560     0.154     0.077      102    17.8  lingual
 2650   1728   4923  2.253 0.765     0.166     0.090       89     8.4  medialorbitofrontal
 8067   5546  18703  2.774 0.632     0.144     0.052      148    16.7  middletemporal
 1449    947   3427  3.051 0.641     0.161     0.206       54     6.4  parahippocampal
 2469   1480   4347  2.661 0.575     0.111     0.159       55     5.2  paracentral
 2851   1869   6007  2.818 0.479     0.126     0.041       41     5.0  parsopercularis
 1239    795   2574  2.679 0.729     0.130     0.040       16     2.0  parsorbitalis
 2842   1915   5509  2.464 0.537     0.140     0.045       50     5.3  parstriangularis
 2666   1939   3741  2.016 0.474     0.155     0.059       47     6.9  pericalcarine
 7942   5036  12997  2.297 0.607     0.129     0.051      194    18.6  postcentral
 2570   1728   4662  2.520 0.661     0.132     0.046       39     4.2  posteriorcingulate
 8474   5275  16160  2.748 0.551     0.114     0.041      178    13.9  precentral
 6877   4527  12820  2.568 0.515     0.138     0.050      108    13.9  precuneus
 2140   1408   4323  2.557 0.819     0.158     0.071       58     5.8  rostralanteriorcingulate
 6215   4195  12007  2.418 0.597     0.142     0.049      106    12.6  rostralmiddlefrontal
13430   9036  28222  2.631 0.617     0.134     0.043      190    23.9  superiorfrontal
 8234   5309  14237  2.393 0.433     0.129     0.042      118    13.7  superiorparietal
 8005   5378  18976  3.041 0.720     0.123     0.043      104    13.3  superiortemporal
 7050   4696  14499  2.709 0.539     0.142     0.049      157    13.9  supramarginal
 1007    606   1995  2.729 0.354     0.150     0.131       37     6.9  transversetemporal
 3494   2295   7719  3.170 0.723     0.109     0.052       62     6.3  insula
#--------------------------------------------
#@# Tessellate rh Thu Aug  8 20:22:22 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

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


Iteration Number : 1
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   2
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   2
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   6
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   6
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:   9
pass   2 (xz-):   0 found -   3 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 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   3 found -   3 modified     |    TOTAL:   3
pass   2 (-+):   0 found -   3 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 = 12 (out of 303005: 0.003960)
Ambiguous edge configurations... 

mri_pretess done


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

$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 40: 1681 vertices, 1847 faces
slice 50: 9012 vertices, 9345 faces
slice 60: 19700 vertices, 20123 faces
slice 70: 32179 vertices, 32646 faces
slice 80: 44565 vertices, 45009 faces
slice 90: 57262 vertices, 57668 faces
slice 100: 70063 vertices, 70480 faces
slice 110: 82614 vertices, 83037 faces
slice 120: 94695 vertices, 95131 faces
slice 130: 106511 vertices, 106941 faces
slice 140: 118494 vertices, 118916 faces
slice 150: 129325 vertices, 129675 faces
slice 160: 138302 vertices, 138625 faces
slice 170: 146915 vertices, 147215 faces
slice 180: 154406 vertices, 154657 faces
slice 190: 159885 vertices, 160074 faces
slice 200: 163409 vertices, 163504 faces
slice 210: 163856 vertices, 163888 faces
slice 220: 163856 vertices, 163888 faces
slice 230: 163856 vertices, 163888 faces
slice 240: 163856 vertices, 163888 faces
slice 250: 163856 vertices, 163888 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...
   163856 voxel in cpt #1: X=-32 [v=163856,e=491664,f=327776] located at (30.498199, -17.300087, 36.784977)
For the whole surface: X=-32 [v=163856,e=491664,f=327776]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Thu Aug  8 20:22:30 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 20:22:36 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
avg radius = 49.6 mm, total surface area = 86888 mm^2
writing inflated surface to ../surf/rh.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=0.053 (target=0.015)   
step 015: RMS=0.044 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.030 (target=0.015)   
step 035: RMS=0.028 (target=0.015)   
step 040: RMS=0.027 (target=0.015)   
step 045: RMS=0.025 (target=0.015)   
step 050: RMS=0.024 (target=0.015)   
step 055: RMS=0.024 (target=0.015)   
step 060: RMS=0.023 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Thu Aug  8 20:23:15 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.91 +- 0.54 (0.00-->8.07) (max @ vno 116886 --> 118105)
face area 0.02 +- 0.03 (-0.28-->0.62)
scaling brain by 0.290...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.534, avgs=0
005/300: dt: 0.9000, rms radial error=176.274, avgs=0
010/300: dt: 0.9000, rms radial error=175.718, avgs=0
015/300: dt: 0.9000, rms radial error=174.987, avgs=0
020/300: dt: 0.9000, rms radial error=174.154, avgs=0
025/300: dt: 0.9000, rms radial error=173.264, avgs=0
030/300: dt: 0.9000, rms radial error=172.342, avgs=0
035/300: dt: 0.9000, rms radial error=171.405, avgs=0
040/300: dt: 0.9000, rms radial error=170.459, avgs=0
045/300: dt: 0.9000, rms radial error=169.511, avgs=0
050/300: dt: 0.9000, rms radial error=168.565, avgs=0
055/300: dt: 0.9000, rms radial error=167.620, avgs=0
060/300: dt: 0.9000, rms radial error=166.680, avgs=0
065/300: dt: 0.9000, rms radial error=165.744, avgs=0
070/300: dt: 0.9000, rms radial error=164.813, avgs=0
075/300: dt: 0.9000, rms radial error=163.887, avgs=0
080/300: dt: 0.9000, rms radial error=162.965, avgs=0
085/300: dt: 0.9000, rms radial error=162.051, avgs=0
090/300: dt: 0.9000, rms radial error=161.141, avgs=0
095/300: dt: 0.9000, rms radial error=160.237, avgs=0
100/300: dt: 0.9000, rms radial error=159.337, avgs=0
105/300: dt: 0.9000, rms radial error=158.443, avgs=0
110/300: dt: 0.9000, rms radial error=157.553, avgs=0
115/300: dt: 0.9000, rms radial error=156.668, avgs=0
120/300: dt: 0.9000, rms radial error=155.788, avgs=0
125/300: dt: 0.9000, rms radial error=154.912, avgs=0
130/300: dt: 0.9000, rms radial error=154.042, avgs=0
135/300: dt: 0.9000, rms radial error=153.176, avgs=0
140/300: dt: 0.9000, rms radial error=152.315, avgs=0
145/300: dt: 0.9000, rms radial error=151.459, avgs=0
150/300: dt: 0.9000, rms radial error=150.607, avgs=0
155/300: dt: 0.9000, rms radial error=149.760, avgs=0
160/300: dt: 0.9000, rms radial error=148.918, avgs=0
165/300: dt: 0.9000, rms radial error=148.080, avgs=0
170/300: dt: 0.9000, rms radial error=147.247, avgs=0
175/300: dt: 0.9000, rms radial error=146.419, avgs=0
180/300: dt: 0.9000, rms radial error=145.595, avgs=0
185/300: dt: 0.9000, rms radial error=144.776, avgs=0
190/300: dt: 0.9000, rms radial error=143.961, avgs=0
195/300: dt: 0.9000, rms radial error=143.151, avgs=0
200/300: dt: 0.9000, rms radial error=142.345, avgs=0
205/300: dt: 0.9000, rms radial error=141.544, avgs=0
210/300: dt: 0.9000, rms radial error=140.747, avgs=0
215/300: dt: 0.9000, rms radial error=139.955, avgs=0
220/300: dt: 0.9000, rms radial error=139.167, avgs=0
225/300: dt: 0.9000, rms radial error=138.384, avgs=0
230/300: dt: 0.9000, rms radial error=137.605, avgs=0
235/300: dt: 0.9000, rms radial error=136.830, avgs=0
240/300: dt: 0.9000, rms radial error=136.060, avgs=0
245/300: dt: 0.9000, rms radial error=135.293, avgs=0
250/300: dt: 0.9000, rms radial error=134.532, avgs=0
255/300: dt: 0.9000, rms radial error=133.774, avgs=0
260/300: dt: 0.9000, rms radial error=133.021, avgs=0
265/300: dt: 0.9000, rms radial error=132.271, avgs=0
270/300: dt: 0.9000, rms radial error=131.526, avgs=0
275/300: dt: 0.9000, rms radial error=130.785, avgs=0
280/300: dt: 0.9000, rms radial error=130.049, avgs=0
285/300: dt: 0.9000, rms radial error=129.316, avgs=0
290/300: dt: 0.9000, rms radial error=128.588, avgs=0
295/300: dt: 0.9000, rms radial error=127.863, avgs=0
300/300: dt: 0.9000, rms radial error=127.143, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 19564.79
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 2 (K=40.0), pass 1, starting sse = 3392.89
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 = 370.22
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.05/11 = 0.00471
epoch 4 (K=640.0), pass 1, starting sse = 25.03
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.06/11 = 0.00562
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 20:29:05 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/sub016/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub016 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=-32 (nv=163856, nf=327776, ne=491664, g=17)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
3558 ambiguous faces found in tessellation
segmenting defects...
34 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
34 defects to be corrected 
0 vertices coincident
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -9.8298  (-4.9149)
      -vertex     loglikelihood: -6.6052  (-3.3026)
      -normal dot loglikelihood: -3.6164  (-3.6164)
      -quad curv  loglikelihood: -6.3230  (-3.1615)
      Total Loglikelihood : -26.3744

CORRECTING DEFECT 0 (vertices=51, convex hull=77)
After retessellation of defect 0, euler #=-31 (161715,484343,322597) : difference with theory (-31) = 0 

CORRECTING DEFECT 1 (vertices=8, convex hull=27)
After retessellation of defect 1, euler #=-30 (161716,484353,322607) : difference with theory (-30) = 0 

CORRECTING DEFECT 2 (vertices=8, convex hull=21)
After retessellation of defect 2, euler #=-29 (161718,484364,322617) : difference with theory (-29) = 0 

CORRECTING DEFECT 3 (vertices=9, convex hull=23)
After retessellation of defect 3, euler #=-28 (161719,484374,322627) : difference with theory (-28) = 0 

CORRECTING DEFECT 4 (vertices=25, convex hull=44)
After retessellation of defect 4, euler #=-27 (161724,484404,322653) : difference with theory (-27) = 0 

CORRECTING DEFECT 5 (vertices=36, convex hull=89)
After retessellation of defect 5, euler #=-26 (161743,484497,322728) : difference with theory (-26) = 0 

CORRECTING DEFECT 6 (vertices=44, convex hull=34)
After retessellation of defect 6, euler #=-25 (161747,484522,322750) : difference with theory (-25) = 0 

CORRECTING DEFECT 7 (vertices=32, convex hull=57)
After retessellation of defect 7, euler #=-24 (161756,484567,322787) : difference with theory (-24) = 0 

CORRECTING DEFECT 8 (vertices=448, convex hull=240)
After retessellation of defect 8, euler #=-23 (161788,484784,322973) : difference with theory (-23) = 0 

CORRECTING DEFECT 9 (vertices=33, convex hull=32)
After retessellation of defect 9, euler #=-22 (161793,484809,322994) : difference with theory (-22) = 0 

CORRECTING DEFECT 10 (vertices=15, convex hull=35)
After retessellation of defect 10, euler #=-21 (161796,484831,323014) : difference with theory (-21) = 0 

CORRECTING DEFECT 11 (vertices=25, convex hull=59)
After retessellation of defect 11, euler #=-20 (161807,484886,323059) : difference with theory (-20) = 0 

CORRECTING DEFECT 12 (vertices=58, convex hull=50)
After retessellation of defect 12, euler #=-19 (161818,484939,323102) : difference with theory (-19) = 0 

CORRECTING DEFECT 13 (vertices=25, convex hull=45)
After retessellation of defect 13, euler #=-18 (161835,485005,323152) : difference with theory (-18) = 0 

CORRECTING DEFECT 14 (vertices=88, convex hull=89)
After retessellation of defect 14, euler #=-17 (161859,485121,323245) : difference with theory (-17) = 0 

CORRECTING DEFECT 15 (vertices=16, convex hull=43)
After retessellation of defect 15, euler #=-16 (161868,485163,323279) : difference with theory (-16) = 0 

CORRECTING DEFECT 16 (vertices=437, convex hull=123)
After retessellation of defect 16, euler #=-15 (161905,485336,323416) : difference with theory (-15) = 0 

CORRECTING DEFECT 17 (vertices=16, convex hull=26)
After retessellation of defect 17, euler #=-14 (161910,485359,323435) : difference with theory (-14) = 0 

CORRECTING DEFECT 18 (vertices=21, convex hull=28)
After retessellation of defect 18, euler #=-13 (161912,485378,323453) : difference with theory (-13) = 0 

CORRECTING DEFECT 19 (vertices=15, convex hull=17)
After retessellation of defect 19, euler #=-12 (161914,485390,323464) : difference with theory (-12) = 0 

CORRECTING DEFECT 20 (vertices=81, convex hull=88)
After retessellation of defect 20, euler #=-11 (161935,485483,323537) : difference with theory (-11) = 0 

CORRECTING DEFECT 21 (vertices=17, convex hull=10)
After retessellation of defect 21, euler #=-10 (161935,485485,323540) : difference with theory (-10) = 0 

CORRECTING DEFECT 22 (vertices=33, convex hull=18)
After retessellation of defect 22, euler #=-9 (161940,485504,323555) : difference with theory (-9) = 0 

CORRECTING DEFECT 23 (vertices=117, convex hull=135)
After retessellation of defect 23, euler #=-8 (161991,485716,323717) : difference with theory (-8) = 0 

CORRECTING DEFECT 24 (vertices=90, convex hull=65)
After retessellation of defect 24, euler #=-7 (162011,485798,323780) : difference with theory (-7) = 0 

CORRECTING DEFECT 25 (vertices=113, convex hull=61)
After retessellation of defect 25, euler #=-6 (162019,485846,323821) : difference with theory (-6) = 0 

CORRECTING DEFECT 26 (vertices=6, convex hull=28)
After retessellation of defect 26, euler #=-5 (162020,485857,323832) : difference with theory (-5) = 0 

CORRECTING DEFECT 27 (vertices=16, convex hull=31)
After retessellation of defect 27, euler #=-4 (162022,485872,323846) : difference with theory (-4) = 0 

CORRECTING DEFECT 28 (vertices=93, convex hull=92)
After retessellation of defect 28, euler #=-3 (162072,486063,323988) : difference with theory (-3) = 0 

CORRECTING DEFECT 29 (vertices=54, convex hull=87)
After retessellation of defect 29, euler #=-2 (162096,486177,324079) : difference with theory (-2) = 0 

CORRECTING DEFECT 30 (vertices=55, convex hull=82)
After retessellation of defect 30, euler #=-1 (162129,486310,324180) : difference with theory (-1) = 0 

CORRECTING DEFECT 31 (vertices=25, convex hull=82)
After retessellation of defect 31, euler #=0 (162142,486381,324239) : difference with theory (0) = 0 

CORRECTING DEFECT 32 (vertices=8, convex hull=31)
Warning - incorrect dp selected!!!!(-87.980212 >= -87.980213 ) 
After retessellation of defect 32, euler #=1 (162143,486393,324251) : difference with theory (1) = 0 

CORRECTING DEFECT 33 (vertices=33, convex hull=78)
After retessellation of defect 33, euler #=2 (162159,486471,324314) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.23 (0.10-->11.94) (max @ vno 66835 --> 69415)
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 (0.10-->11.94) (max @ vno 66835 --> 69415)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
129 mutations (35.9%), 230 crossovers (64.1%), 190 vertices were eliminated
building final representation...
1697 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=162159, nf=324314, ne=486471, g=0)
writing corrected surface to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 28.8 minutes
0 defective edges
removing intersecting faces
000: 225 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 162159 - 486471 + 324314 = 2 --> 0 holes
      F =2V-4:          324314 = 324318-4 (0)
      2E=3F:            972942 = 972942 (0)

total defect index = 0
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 39 intersecting
001: 2 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Thu Aug  8 20:58:01 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
23684 bright wm thresholded.
383 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
computing class statistics...
border white:    298969 voxels (1.78%)
border gray      333863 voxels (1.99%)
WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0]
GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
setting MAX_BORDER_WHITE to 114.8 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.5 (was 40)
setting MAX_GRAY to 95.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->5.50) (max @ vno 65573 --> 70451)
face area 0.28 +- 0.12 (0.00-->5.65)
mean absolute distance = 0.66 +- 0.79
5111 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=60
mean inside = 93.5, mean outside = 69.7
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=73.5, 62 (62) missing vertices, mean dist 0.4 [0.5 (%29.6)->0.7 (%70.4))]
%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 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.91 +- 0.26 (0.11-->8.50) (max @ vno 70451 --> 68130)
face area 0.28 +- 0.13 (0.00-->5.07)
mean absolute distance = 0.36 +- 0.50
4632 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8153363.5, rms=13.09
001: dt: 0.5000, sse=8206518.0, rms=9.369 (0.000%)
002: dt: 0.5000, sse=8371105.0, rms=7.213 (0.000%)
003: dt: 0.5000, sse=8617238.0, rms=5.862 (0.000%)
004: dt: 0.5000, sse=8847876.0, rms=5.082 (0.000%)
005: dt: 0.5000, sse=8998998.0, rms=4.631 (0.000%)
006: dt: 0.5000, sse=9049736.0, rms=4.420 (0.000%)
007: dt: 0.5000, sse=9107665.0, rms=4.280 (0.000%)
008: dt: 0.5000, sse=9068589.0, rms=4.220 (0.000%)
009: dt: 0.5000, sse=9084191.0, rms=4.148 (0.000%)
rms = 4.13, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9032769.0, rms=4.134 (0.000%)
011: dt: 0.2500, sse=5589936.0, rms=2.796 (0.000%)
012: dt: 0.2500, sse=5133850.5, rms=2.355 (0.000%)
013: dt: 0.2500, sse=4815090.0, rms=2.251 (0.000%)
014: dt: 0.2500, sse=4742968.5, rms=2.161 (0.000%)
rms = 2.13, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4631043.5, rms=2.131 (0.000%)
016: dt: 0.1250, sse=4418955.5, rms=1.928 (0.000%)
rms = 1.90, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4371228.5, rms=1.900 (0.000%)
positioning took 2.5 minutes
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
mean border=78.9, 77 (16) missing vertices, mean dist -0.3 [0.4 (%82.3)->0.2 (%17.7))]
%86 local maxima, %10 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 (0.05-->9.31) (max @ vno 70451 --> 68130)
face area 0.35 +- 0.17 (0.00-->6.95)
mean absolute distance = 0.21 +- 0.29
3579 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5901340.5, rms=6.95
018: dt: 0.5000, sse=5746078.5, rms=4.582 (0.000%)
rms = 4.63, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=5250808.0, rms=3.566 (0.000%)
020: dt: 0.2500, sse=4974762.0, rms=2.789 (0.000%)
021: dt: 0.2500, sse=4867593.5, rms=2.265 (0.000%)
022: dt: 0.2500, sse=4830676.5, rms=2.073 (0.000%)
023: dt: 0.2500, sse=4749424.0, rms=1.885 (0.000%)
024: dt: 0.2500, sse=4768091.0, rms=1.810 (0.000%)
025: dt: 0.2500, sse=4708092.0, rms=1.748 (0.000%)
rms = 1.72, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=4736196.0, rms=1.725 (0.000%)
027: dt: 0.1250, sse=4562554.5, rms=1.541 (0.000%)
rms = 1.53, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=4521904.5, rms=1.529 (0.000%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=82.1, 58 (7) missing vertices, mean dist -0.1 [0.2 (%76.9)->0.2 (%23.1))]
%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 0.89 +- 0.25 (0.04-->9.68) (max @ vno 70451 --> 68130)
face area 0.33 +- 0.16 (0.00-->6.87)
mean absolute distance = 0.16 +- 0.23
3256 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4962088.0, rms=4.20
029: dt: 0.5000, sse=5376449.5, rms=4.009 (0.000%)
rms = 4.18, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=4837316.0, rms=2.522 (0.000%)
031: dt: 0.2500, sse=4704395.5, rms=1.988 (0.000%)
032: dt: 0.2500, sse=4748966.0, rms=1.651 (0.000%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
033: dt: 0.1250, sse=4679433.5, rms=1.528 (0.000%)
034: dt: 0.1250, sse=4588254.5, rms=1.352 (0.000%)
rms = 1.33, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=4547578.5, rms=1.333 (0.000%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=83.0, 51 (4) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
%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/sub016/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=4576333.0, rms=1.72
rms = 2.52, time step reduction 1 of 3 to 0.250...
036: dt: 0.2500, sse=4675320.0, rms=1.142 (0.000%)
037: dt: 0.2500, sse=4840894.5, rms=1.004 (0.000%)
rms = 1.01, time step reduction 2 of 3 to 0.125...
rms = 1.00, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=4841039.0, rms=0.995 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
20 non-cortical segments detected
only using segment with 2323 vertices
erasing segment 1 (vno[0] = 103811)
erasing segment 2 (vno[0] = 106145)
erasing segment 3 (vno[0] = 109699)
erasing segment 4 (vno[0] = 110811)
erasing segment 5 (vno[0] = 113952)
erasing segment 6 (vno[0] = 113958)
erasing segment 7 (vno[0] = 114058)
erasing segment 8 (vno[0] = 114087)
erasing segment 9 (vno[0] = 115145)
erasing segment 10 (vno[0] = 116433)
erasing segment 11 (vno[0] = 116525)
erasing segment 12 (vno[0] = 120936)
erasing segment 13 (vno[0] = 121020)
erasing segment 14 (vno[0] = 124279)
erasing segment 15 (vno[0] = 124302)
erasing segment 16 (vno[0] = 125188)
erasing segment 17 (vno[0] = 125211)
erasing segment 18 (vno[0] = 127009)
erasing segment 19 (vno[0] = 127902)
writing cortex label to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label...
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area
vertex spacing 0.89 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130)
face area 0.33 +- 0.16 (0.00-->6.86)
refinement took 8.6 minutes
#--------------------------------------------
#@# Smooth2 rh Thu Aug  8 21:06:36 CEST 2013

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

/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 21:06:41 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

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

avg radius = 49.8 mm, total surface area = 98579 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=0.056 (target=0.015)   
step 015: RMS=0.046 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.019 (target=0.015)   
step 045: RMS=0.017 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
inflation complete.
inflation took 0.6 minutes

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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
212 vertices thresholded to be in k1 ~ [-0.61 0.39], k2 ~ [-0.21 0.11]
total integrated curvature = 0.400*4pi (5.028) --> 1 handles
ICI = 1.7, FI = 14.3, variation=232.796
169 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
134 vertices thresholded to be in [-0.18 0.19]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.026
done.

#-----------------------------------------
#@# Curvature Stats rh Thu Aug  8 21:09:21 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub016 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       [ sub016/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                      [ 318 ]
Gb_filter = 0
#--------------------------------------------
#@# Sphere rh Thu Aug  8 21:09:27 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 0.271...
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 %19.61
pass 1: epoch 2 of 3 starting distance error %19.56
unfolding complete - removing small folds...
starting distance error %19.45
removing remaining folds...
final distance error %19.46
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 1.24 hours
#--------------------------------------------
#@# Surf Reg rh Thu Aug  8 22:23:50 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 0.583
curvature mean = 0.026, std = 0.944
curvature mean = 0.026, std = 0.838
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 442935.7, tmin=1.3303
  d=32.00 min @ (-8.00, -8.00, 0.00) sse = 380528.0, tmin=2.6304
  d=16.00 min @ (0.00, 4.00, 4.00) sse = 335983.4, tmin=3.9825
  d=8.00 min @ (0.00, -2.00, 0.00) sse = 330664.6, tmin=5.3504
  d=2.00 min @ (0.00, 0.50, -0.50) sse = 330548.4, tmin=8.1105
  d=1.00 min @ (-0.25, -0.25, 0.25) sse = 330150.7, tmin=9.4755
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  10.87 min
curvature mean = 0.002, std = 0.935
curvature mean = 0.011, std = 0.927
curvature mean = -0.004, std = 0.939
curvature mean = 0.006, std = 0.965
curvature mean = -0.007, std = 0.935
curvature mean = 0.001, std = 0.983
2 Reading smoothwm
curvature mean = -0.023, std = 0.289
curvature mean = 0.004, std = 0.069
curvature mean = 0.073, std = 0.319
curvature mean = 0.005, std = 0.082
curvature mean = 0.036, std = 0.504
curvature mean = 0.005, std = 0.088
curvature mean = 0.020, std = 0.646
curvature mean = 0.006, std = 0.090
curvature mean = 0.007, std = 0.759
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Thu Aug  8 22:59:28 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 22:59:32 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 22:59:35 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
1118 labels changed using aseg
relabeling using gibbs priors...
000:   3403 changed, 162159 examined...
001:    812 changed, 14508 examined...
002:    208 changed, 4507 examined...
003:     52 changed, 1249 examined...
004:     24 changed, 343 examined...
005:     12 changed, 145 examined...
006:      3 changed, 72 examined...
007:      1 changed, 19 examined...
008:      2 changed, 6 examined...
009:      1 changed, 10 examined...
010:      0 changed, 8 examined...
184 labels changed using aseg
000: 104 total segments, 64 labels (442 vertices) changed
001: 41 total segments, 1 labels (7 vertices) changed
002: 40 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 64 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
2159 vertices marked for relabeling...
2159 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 15 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Thu Aug  8 23:00:50 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub016 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/sub016/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
23684 bright wm thresholded.
383 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
computing class statistics...
border white:    298969 voxels (1.78%)
border gray      333863 voxels (1.99%)
WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0]
GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
setting MAX_BORDER_WHITE to 114.8 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.5 (was 40)
setting MAX_GRAY to 95.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=60
mean inside = 93.5, mean outside = 69.7
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/sub016/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.22 (0.03-->5.50) (max @ vno 65573 --> 70451)
face area 0.28 +- 0.12 (0.00-->5.65)
mean absolute distance = 0.66 +- 0.79
5220 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 23 points - only 0.00% unknown
deleting segment 2 with 14 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 19 points - only 0.00% unknown
deleting segment 7 with 20 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 8 with 3 points - only 0.00% unknown
deleting segment 9 with 40 points - only 0.00% unknown
deleting segment 10 with 504 points - only 0.00% unknown
deleting segment 11 with 6 points - only 0.00% unknown
deleting segment 13 with 115 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 16 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 17 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 18 with 3 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 19 with 3 points - only 0.00% unknown
mean border=73.4, 65 (64) missing vertices, mean dist 0.4 [0.5 (%29.6)->0.7 (%70.4))]
%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 0.91 +- 0.26 (0.11-->8.50) (max @ vno 70451 --> 68130)
face area 0.28 +- 0.13 (0.00-->5.07)
mean absolute distance = 0.36 +- 0.50
4697 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=8176584.0, rms=13.08
001: dt: 0.5000, sse=8234243.5, rms=9.358 (0.000%)
002: dt: 0.5000, sse=8408520.0, rms=7.207 (0.000%)
003: dt: 0.5000, sse=8659359.0, rms=5.858 (0.000%)
004: dt: 0.5000, sse=8894008.0, rms=5.080 (0.000%)
005: dt: 0.5000, sse=9050424.0, rms=4.630 (0.000%)
006: dt: 0.5000, sse=9104576.0, rms=4.419 (0.000%)
007: dt: 0.5000, sse=9161903.0, rms=4.280 (0.000%)
008: dt: 0.5000, sse=9124109.0, rms=4.218 (0.000%)
009: dt: 0.5000, sse=9137261.0, rms=4.148 (0.000%)
rms = 4.13, time step reduction 1 of 3 to 0.250...
010: dt: 0.5000, sse=9089501.0, rms=4.133 (0.000%)
011: dt: 0.2500, sse=5633577.5, rms=2.799 (0.000%)
012: dt: 0.2500, sse=5175912.0, rms=2.359 (0.000%)
013: dt: 0.2500, sse=4855685.0, rms=2.257 (0.000%)
014: dt: 0.2500, sse=4781068.5, rms=2.168 (0.000%)
rms = 2.14, time step reduction 2 of 3 to 0.125...
015: dt: 0.2500, sse=4670974.0, rms=2.137 (0.000%)
016: dt: 0.1250, sse=4458593.5, rms=1.936 (0.000%)
rms = 1.91, time step reduction 3 of 3 to 0.062...
017: dt: 0.1250, sse=4409677.5, rms=1.908 (0.000%)
positioning took 2.6 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
deleting segment 1 with 28 points - only 0.00% unknown
deleting segment 2 with 18 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 8 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 6 with 23 points - only 0.00% unknown
deleting segment 7 with 16 points - only 0.00% unknown
deleting segment 10 with 33 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 11 with 3 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 1 points - only 0.00% unknown
deleting segment 14 with 329 points - only 0.00% unknown
deleting segment 15 with 5 points - only 0.00% unknown
deleting segment 19 with 24 points - only 0.00% unknown
deleting segment 20 with 24 points - only 0.00% unknown
deleting segment 21 with 9 points - only 33.33% unknown
deleting segment 22 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 23 with 3 points - only 0.00% unknown
mean border=78.9, 88 (18) missing vertices, mean dist -0.3 [0.4 (%82.2)->0.2 (%17.8))]
%86 local maxima, %10 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 (0.05-->9.31) (max @ vno 70451 --> 68130)
face area 0.35 +- 0.17 (0.00-->6.95)
mean absolute distance = 0.21 +- 0.30
3652 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5945504.5, rms=6.94
018: dt: 0.5000, sse=5791920.5, rms=4.578 (0.000%)
rms = 4.62, time step reduction 1 of 3 to 0.250...
019: dt: 0.2500, sse=5293300.5, rms=3.565 (0.000%)
020: dt: 0.2500, sse=5015019.0, rms=2.790 (0.000%)
021: dt: 0.2500, sse=4908255.0, rms=2.268 (0.000%)
022: dt: 0.2500, sse=4870418.0, rms=2.077 (0.000%)
023: dt: 0.2500, sse=4789291.0, rms=1.889 (0.000%)
024: dt: 0.2500, sse=4807856.0, rms=1.815 (0.000%)
025: dt: 0.2500, sse=4749047.0, rms=1.753 (0.000%)
rms = 1.73, time step reduction 2 of 3 to 0.125...
026: dt: 0.2500, sse=4776147.5, rms=1.731 (0.000%)
027: dt: 0.1250, sse=4603768.0, rms=1.548 (0.000%)
rms = 1.54, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=4562413.5, rms=1.536 (0.000%)
positioning took 1.7 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 19 points - only 0.00% unknown
deleting segment 1 with 28 points - only 0.00% unknown
deleting segment 2 with 20 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 8 points - only 0.00% unknown
deleting segment 5 with 21 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 4 points - only 0.00% unknown
deleting segment 7 with 18 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 9 with 32 points - only 0.00% unknown
deleting segment 10 with 352 points - only 0.00% unknown
deleting segment 11 with 5 points - only 0.00% unknown
deleting segment 12 with 29 points - only 0.00% unknown
deleting segment 14 with 24 points - only 0.00% unknown
deleting segment 15 with 37 points - only 0.00% unknown
deleting segment 16 with 8 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 17 with 4 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 18 with 3 points - only 0.00% unknown
mean border=82.1, 68 (9) missing vertices, mean dist -0.1 [0.2 (%76.8)->0.2 (%23.2))]
%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 0.89 +- 0.25 (0.04-->9.68) (max @ vno 70451 --> 68130)
face area 0.33 +- 0.16 (0.00-->6.87)
mean absolute distance = 0.16 +- 0.23
3372 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=5002988.5, rms=4.19
029: dt: 0.5000, sse=5418778.5, rms=4.003 (0.000%)
rms = 4.17, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=4876998.0, rms=2.521 (0.000%)
031: dt: 0.2500, sse=4744753.5, rms=1.990 (0.000%)
032: dt: 0.2500, sse=4789559.5, rms=1.655 (0.000%)
rms = 1.68, time step reduction 2 of 3 to 0.125...
033: dt: 0.1250, sse=4719764.5, rms=1.533 (0.000%)
034: dt: 0.1250, sse=4626804.5, rms=1.358 (0.000%)
rms = 1.34, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=4588271.5, rms=1.340 (0.000%)
positioning took 1.2 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 18 points - only 0.00% unknown
deleting segment 1 with 23 points - only 0.00% unknown
deleting segment 2 with 19 points - only 0.00% unknown
deleting segment 3 with 6 points - only 0.00% unknown
deleting segment 4 with 21 points - only 0.00% unknown
deleting segment 5 with 17 points - only 0.00% unknown
deleting segment 6 with 38 points - only 0.00% unknown
deleting segment 7 with 346 points - only 0.00% unknown
deleting segment 8 with 5 points - only 0.00% unknown
deleting segment 9 with 36 points - only 0.00% unknown
deleting segment 10 with 24 points - only 0.00% unknown
deleting segment 11 with 51 points - only 0.00% unknown
deleting segment 12 with 8 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 13 with 2 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
mean border=83.0, 64 (6) missing vertices, mean dist -0.0 [0.2 (%58.0)->0.2 (%42.0))]
%94 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=4617414.0, rms=1.73
rms = 2.51, time step reduction 1 of 3 to 0.250...
036: dt: 0.2500, sse=4718826.5, rms=1.153 (0.000%)
037: dt: 0.2500, sse=4896739.0, rms=1.012 (0.000%)
rms = 1.02, time step reduction 2 of 3 to 0.125...
rms = 1.00, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=4889615.5, rms=1.003 (0.000%)
positioning took 0.6 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=49.8, 100 (100) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.4 (%100.0))]
%15 local maxima, %57 large gradients and %24 min vals, 1971 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=36520256.0, rms=32.77
001: dt: 0.5000, sse=26287360.0, rms=27.276 (0.000%)
002: dt: 0.5000, sse=19262446.0, rms=22.771 (0.000%)
003: dt: 0.5000, sse=14590273.0, rms=19.190 (0.000%)
004: dt: 0.5000, sse=11692645.0, rms=16.407 (0.000%)
005: dt: 0.5000, sse=10083440.0, rms=14.299 (0.000%)
006: dt: 0.5000, sse=9162082.0, rms=12.662 (0.000%)
007: dt: 0.5000, sse=8570043.0, rms=11.251 (0.000%)
008: dt: 0.5000, sse=8137810.5, rms=9.926 (0.000%)
009: dt: 0.5000, sse=7807090.0, rms=8.653 (0.000%)
010: dt: 0.5000, sse=7590589.5, rms=7.412 (0.000%)
011: dt: 0.5000, sse=7568264.0, rms=6.315 (0.000%)
012: dt: 0.5000, sse=7606946.5, rms=5.423 (0.000%)
013: dt: 0.5000, sse=7820857.5, rms=4.870 (0.000%)
014: dt: 0.5000, sse=7968421.5, rms=4.535 (0.000%)
015: dt: 0.5000, sse=8149022.5, rms=4.367 (0.000%)
016: dt: 0.5000, sse=8199023.0, rms=4.246 (0.000%)
rms = 4.21, time step reduction 1 of 3 to 0.250...
017: dt: 0.5000, sse=8339397.5, rms=4.210 (0.000%)
018: dt: 0.2500, sse=5771961.0, rms=3.380 (0.000%)
019: dt: 0.2500, sse=5591880.0, rms=3.164 (0.000%)
rms = 3.15, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=5431412.5, rms=3.154 (0.000%)
021: dt: 0.1250, sse=5119481.0, rms=2.926 (0.000%)
rms = 2.90, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=5087547.5, rms=2.895 (0.000%)
positioning took 3.2 minutes
mean border=47.4, 982 (23) missing vertices, mean dist 0.1 [0.2 (%47.6)->0.5 (%52.4))]
%34 local maxima, %41 large gradients and %20 min vals, 595 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=5842710.5, rms=4.86
023: dt: 0.5000, sse=6254044.5, rms=4.286 (0.000%)
rms = 4.24, time step reduction 1 of 3 to 0.250...
024: dt: 0.5000, sse=8056153.0, rms=4.242 (0.000%)
025: dt: 0.2500, sse=5984153.0, rms=3.279 (0.000%)
026: dt: 0.2500, sse=6065187.5, rms=3.020 (0.000%)
rms = 3.00, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=5908627.0, rms=2.998 (0.000%)
028: dt: 0.1250, sse=5647260.5, rms=2.720 (0.000%)
rms = 2.68, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=5628531.0, rms=2.676 (0.000%)
positioning took 1.0 minutes
mean border=44.9, 1247 (6) missing vertices, mean dist 0.1 [0.2 (%36.8)->0.3 (%63.2))]
%54 local maxima, %21 large gradients and %20 min vals, 785 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=5971874.0, rms=4.17
rms = 4.25, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=5692742.0, rms=3.447 (0.000%)
031: dt: 0.2500, sse=5601804.0, rms=2.962 (0.000%)
032: dt: 0.2500, sse=5887626.0, rms=2.847 (0.000%)
rms = 2.86, time step reduction 2 of 3 to 0.125...
033: dt: 0.1250, sse=5791303.0, rms=2.764 (0.000%)
034: dt: 0.1250, sse=5689471.0, rms=2.644 (0.000%)
rms = 2.62, time step reduction 3 of 3 to 0.062...
035: dt: 0.1250, sse=5678918.0, rms=2.618 (0.000%)
positioning took 1.1 minutes
mean border=43.8, 2605 (4) missing vertices, mean dist 0.0 [0.2 (%45.3)->0.3 (%54.7))]
%56 local maxima, %18 large gradients and %20 min vals, 612 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/sub016/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=5742438.0, rms=3.01
rms = 3.94, time step reduction 1 of 3 to 0.250...
036: dt: 0.2500, sse=5610674.5, rms=2.712 (0.000%)
037: dt: 0.2500, sse=5872142.0, rms=2.638 (0.000%)
rms = 2.63, time step reduction 2 of 3 to 0.125...
038: dt: 0.2500, sse=5959964.5, rms=2.632 (0.000%)
039: dt: 0.1250, sse=5855301.0, rms=2.482 (0.000%)
rms = 2.46, time step reduction 3 of 3 to 0.062...
040: dt: 0.1250, sse=5874691.5, rms=2.456 (0.000%)
positioning took 0.9 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area.pial
vertex spacing 1.01 +- 0.42 (0.07-->10.54) (max @ vno 70451 --> 68130)
face area 0.41 +- 0.30 (0.00-->8.44)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 162159 vertices processed
25000 of 162159 vertices processed
50000 of 162159 vertices processed
75000 of 162159 vertices processed
100000 of 162159 vertices processed
125000 of 162159 vertices processed
150000 of 162159 vertices processed
0 of 162159 vertices processed
25000 of 162159 vertices processed
50000 of 162159 vertices processed
75000 of 162159 vertices processed
100000 of 162159 vertices processed
125000 of 162159 vertices processed
150000 of 162159 vertices processed
thickness calculation complete, 368:737 truncations.
38776 vertices at 0 distance
112698 vertices at 1 distance
103614 vertices at 2 distance
41260 vertices at 3 distance
11150 vertices at 4 distance
2941 vertices at 5 distance
936 vertices at 6 distance
295 vertices at 7 distance
133 vertices at 8 distance
81 vertices at 9 distance
42 vertices at 10 distance
24 vertices at 11 distance
18 vertices at 12 distance
13 vertices at 13 distance
13 vertices at 14 distance
14 vertices at 15 distance
14 vertices at 16 distance
7 vertices at 17 distance
7 vertices at 18 distance
17 vertices at 19 distance
15 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.thickness
positioning took 16.8 minutes
#--------------------------------------------
#@# Surf Volume rh Thu Aug  8 23:17:38 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 23:17:40 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 pctsurfcon --s sub016 --rh-only 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts/pctsurfcon.log
Thu Aug  8 23:17:40 CEST 2013
setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
/opt/freesurfer/5.3.0/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux snake6 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/sub016/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh --regheader sub016 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 125587
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh
Dim: 162159 1 1
mri_vol2surf --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh --projfrac 0.3 --regheader sub016 --cortex
srcvol = /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig.mgz as target reference.
Loading label /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
Reading surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white
Done reading source surface
Reading thickness /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 144176
Masking with /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.cortex.label
Writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh
Dim: 162159 1 1
mri_concat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.wm.mgh /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/tmp.pctsurfcon.24216/rh.gm.mgh --paired-diff-norm --mul 100 --o /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh
mri_segstats --in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.w-g.pct.mgh --annot sub016 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.w-g.pct.mgh --annot sub016 rh aparc --sum /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/stats/rh.w-g.pct.stats --snr 
sysname  Linux
hostname snake6
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/sub016/surf/rh.w-g.pct.mgh
Vertex Area is 0.659965 mm^3
Generating list of segmentation ids
Found  36 segmentations
Computing statistics for each segmentation
  0   2000                            unknown       0       0.000
  1   2001                           bankssts    1538    1060.178
  2   2002            caudalanteriorcingulate     744     498.773
  3   2003                caudalmiddlefrontal    3373    2197.764
  4   2004                     corpuscallosum       0       0.000
  5   2005                             cuneus    2869    1883.642
  6   2006                         entorhinal     690     475.663
  7   2007                           fusiform    5435    3635.177
  8   2008                   inferiorparietal   10204    6793.776
  9   2009                   inferiortemporal    6788    4625.739
 10   2010                   isthmuscingulate    2352    1535.103
 11   2011                   lateraloccipital    8661    5648.796
 12   2012               lateralorbitofrontal    4716    3174.235
 13   2013                            lingual    5406    3594.387
 14   2014                medialorbitofrontal    3155    2060.892
 15   2015                     middletemporal    6473    4426.597
 16   2016                    parahippocampal    1241     845.652
 17   2017                        paracentral    3127    1926.372
 18   2018                    parsopercularis    3195    2085.679
 19   2019                      parsorbitalis    1295     920.021
 20   2020                   parstriangularis    2843    1916.146
 21   2021                      pericalcarine    2969    1987.918
 22   2022                        postcentral    7380    4679.101
 23   2023                 posteriorcingulate    2178    1427.377
 24   2024                         precentral    8535    5212.754
 25   2025                          precuneus    6617    4442.093
 26   2026           rostralanteriorcingulate     957     615.840
 27   2027               rostralmiddlefrontal    9516    6459.534
 28   2028                    superiorfrontal   13925    9212.408
 29   2029                   superiorparietal    9031    5771.498
 30   2030                   superiortemporal    5912    4041.441
 31   2031                      supramarginal    6201    4178.135
 32   2032                        frontalpole     435     286.539
 33   2033                       temporalpole     695     510.966
 34   2034                 transversetemporal     724     436.670
 35   2035                             insula    4226    2783.282

Reporting on  34 segmentations
mri_segstats done
Cleaning up
#-----------------------------------------
#@# Parcellation Stats rh Thu Aug  8 23:17:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1538   1060   2781  2.609 0.461     0.113     0.025       12     1.5  bankssts
  744    499   1460  2.758 0.537     0.137     0.031       10     0.9  caudalanteriorcingulate
 3373   2198   7148  2.880 0.490     0.131     0.085       61     6.6  caudalmiddlefrontal
 2869   1884   4653  2.212 0.457     0.156     0.063       53     7.6  cuneus
  690    476   1929  3.237 0.729     0.138     0.053        8     1.6  entorhinal
 5435   3635  11899  2.707 0.545     0.146     0.066      107    15.3  fusiform
10204   6794  19774  2.558 0.499     0.143     0.053      188    20.3  inferiorparietal
 6788   4626  15324  2.720 0.628     0.148     0.058      183    15.4  inferiortemporal
 2352   1535   3946  2.362 0.936     0.160     0.084       70     8.9  isthmuscingulate
 8661   5649  15111  2.353 0.485     0.153     0.059      174    20.3  lateraloccipital
 4716   3174  10076  2.788 0.666     0.154     0.069      132    14.5  lateralorbitofrontal
 5406   3594   8505  2.179 0.597     0.164     0.114      129    16.7  lingual
 3155   2061   6074  2.505 0.732     0.155     0.089       95    12.8  medialorbitofrontal
 6473   4427  15580  2.785 0.728     0.137     0.047      118    12.9  middletemporal
 1241    846   2556  2.650 0.566     0.140     0.050       20     2.6  parahippocampal
 3127   1926   5458  2.595 0.490     0.118     0.037       34     5.3  paracentral
 3195   2086   6449  2.742 0.484     0.113     0.041       33     4.2  parsopercularis
 1295    920   3171  2.710 0.557     0.179     0.075       34     3.5  parsorbitalis
 2843   1916   5723  2.549 0.555     0.131     0.070       90     4.4  parstriangularis
 2969   1988   3908  2.060 0.409     0.147     0.059       45     7.0  pericalcarine
 7380   4679  12299  2.251 0.549     0.115     0.101      112    11.4  postcentral
 2178   1427   4317  2.694 0.719     0.148     0.055       40     5.5  posteriorcingulate
 8535   5213  15798  2.770 0.601     0.111     0.143      327    60.1  precentral
 6617   4442  12727  2.601 0.539     0.143     0.051      117    13.4  precuneus
  957    616   1784  2.977 0.788     0.122     0.150      131     5.9  rostralanteriorcingulate
 9516   6460  18680  2.468 0.516     0.151     0.052      180    19.9  rostralmiddlefrontal
13925   9212  30286  2.842 0.528     0.130     0.046      234    26.0  superiorfrontal
 9031   5771  14961  2.320 0.425     0.128     0.057      174    21.9  superiorparietal
 5912   4041  14092  3.032 0.644     0.132     0.039       73     9.8  superiortemporal
 6201   4178  12336  2.627 0.535     0.137     0.089      169    10.6  supramarginal
  435    287   1023  2.472 0.637     0.208     0.100       20     2.1  frontalpole
  695    511   2594  3.604 0.666     0.145     0.054       11     1.7  temporalpole
  724    437   1532  2.915 0.317     0.122     0.046        8     1.2  transversetemporal
 4226   2783   9058  3.049 0.957     0.131     0.065       70     9.6  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Thu Aug  8 23:18:19 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
7 labels changed using aseg
relabeling using gibbs priors...
000:  11017 changed, 162159 examined...
001:   2717 changed, 42462 examined...
002:    854 changed, 13815 examined...
003:    385 changed, 4642 examined...
004:    167 changed, 2104 examined...
005:     83 changed, 924 examined...
006:     62 changed, 468 examined...
007:     36 changed, 333 examined...
008:      8 changed, 185 examined...
009:      8 changed, 51 examined...
010:      9 changed, 47 examined...
011:      5 changed, 47 examined...
012:      1 changed, 26 examined...
013:      0 changed, 6 examined...
8 labels changed using aseg
000: 314 total segments, 229 labels (3312 vertices) changed
001: 99 total segments, 14 labels (43 vertices) changed
002: 85 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 190 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
1277 vertices marked for relabeling...
1277 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 22 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Thu Aug  8 23:19:41 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1096    752   2031  2.274 0.613     0.168     0.064       29     3.2  G_and_S_frontomargin
 1490    988   2829  2.438 0.528     0.143     0.046       22     2.8  G_and_S_occipital_inf
 1927   1097   3660  2.663 0.500     0.125     0.047       29     3.8  G_and_S_paracentral
 1882   1226   3765  2.615 0.447     0.143     0.045       30     3.4  G_and_S_subcentral
 1332    919   2841  2.470 0.516     0.172     0.062       34     3.6  G_and_S_transv_frontopol
 3701   2483   7190  2.739 0.578     0.123     0.038       41     6.0  G_and_S_cingul-Ant
 1779   1209   3639  2.736 0.465     0.130     0.052       23     3.1  G_and_S_cingul-Mid-Ant
 1893   1251   3748  2.869 0.514     0.128     0.044       23     3.8  G_and_S_cingul-Mid-Post
  889    575   2307  3.096 0.550     0.180     0.065       23     2.3  G_cingul-Post-dorsal
  478    311   1199  2.950 0.740     0.164     0.082       12     1.4  G_cingul-Post-ventral
 2709   1774   4465  2.141 0.435     0.165     0.076       59     8.4  G_cuneus
 2036   1331   4855  2.855 0.442     0.133     0.052       32     3.3  G_front_inf-Opercular
  420    286   1196  2.985 0.301     0.179     0.274       63     1.1  G_front_inf-Orbital
 1567   1044   4008  2.840 0.506     0.149     0.050       30     3.1  G_front_inf-Triangul
 4421   2987  11147  2.808 0.493     0.160     0.092      116    11.2  G_front_middle
 8623   5535  20666  2.939 0.542     0.136     0.051      185    19.0  G_front_sup
  693    447   1467  3.083 1.136     0.149     0.101       20     2.3  G_Ins_lg_and_S_cent_ins
  630    409   2384  3.973 0.807     0.170     0.114       14     2.2  G_insular_short
 2805   1773   6473  2.725 0.438     0.176     0.080       91     8.7  G_occipital_middle
 2014   1254   3540  2.341 0.430     0.154     0.094       63    10.1  G_occipital_sup
 1879   1203   4450  2.753 0.523     0.157     0.079       45     6.7  G_oc-temp_lat-fusifor
 3604   2365   5923  2.141 0.611     0.176     0.144      106    12.6  G_oc-temp_med-Lingual
 1831   1249   4931  3.056 0.754     0.159     0.078       38     5.4  G_oc-temp_med-Parahip
 3321   2254   8708  2.942 0.633     0.180     0.077       90    10.7  G_orbital
 3908   2565   8611  2.601 0.538     0.158     0.069       97     9.1  G_pariet_inf-Angular
 3482   2356   8290  2.762 0.530     0.153     0.134      146     6.9  G_pariet_inf-Supramar
 2579   1667   5060  2.473 0.462     0.132     0.043       40     4.5  G_parietal_sup
 2697   1571   4949  2.408 0.503     0.115     0.221       64     5.1  G_postcentral
 3108   1654   7103  3.209 0.474     0.107     0.339      285    52.9  G_precentral
 2531   1707   6237  2.769 0.493     0.154     0.058       56     6.0  G_precuneus
  831    534   1873  2.531 0.702     0.207     0.198       59     7.7  G_rectus
  720    485   1550  2.850 0.877     0.175     0.233      146     6.8  G_subcallosal
  668    408   1559  2.984 0.349     0.139     0.053       10     1.3  G_temp_sup-G_T_transv
 2006   1348   6337  3.307 0.557     0.160     0.053       40     4.5  G_temp_sup-Lateral
  848    615   2421  3.453 0.688     0.123     0.039        7     1.4  G_temp_sup-Plan_polar
 1067    715   2144  2.849 0.491     0.117     0.034       11     1.6  G_temp_sup-Plan_tempo
 3975   2690  10435  2.865 0.619     0.168     0.072      149    11.1  G_temporal_inf
 3685   2521  10596  3.003 0.710     0.147     0.051       83     7.7  G_temporal_middle
  630    411    847  2.232 0.444     0.093     0.019        3     0.5  Lat_Fis-ant-Horizont
  395    263    547  2.533 0.383     0.096     0.023        2     0.4  Lat_Fis-ant-Vertical
 1732   1151   2400  2.383 0.561     0.119     0.034       13     2.5  Lat_Fis-post
 3856   2540   6340  2.205 0.478     0.157     0.067       75    10.0  Pole_occipital
 2199   1555   6553  2.987 0.896     0.159     0.074       50     6.9  Pole_temporal
 3545   2377   4758  2.182 0.586     0.137     0.049       46     7.1  S_calcarine
 3502   2325   4313  2.047 0.580     0.104     0.029       19     4.5  S_central
 1702   1132   2575  2.381 0.384     0.111     0.031       13     2.2  S_cingul-Marginalis
  715    454   1395  3.296 0.629     0.124     0.062        8     1.3  S_circular_insula_ant
 1422    946   2353  2.876 0.648     0.100     0.025        7     1.5  S_circular_insula_inf
 1874   1269   3079  2.632 0.547     0.105     0.030       12     2.5  S_circular_insula_sup
 1613   1099   2899  2.641 0.492     0.107     0.030       14     2.0  S_collat_transv_ant
  487    325    780  2.491 0.456     0.159     0.055        8     1.2  S_collat_transv_post
 2003   1348   3072  2.351 0.469     0.112     0.029       14     2.6  S_front_inf
 2655   1772   4046  2.340 0.430     0.135     0.048       35     4.6  S_front_middle
 3026   2041   5273  2.633 0.460     0.120     0.033       30     4.2  S_front_sup
  363    245    556  2.499 0.510     0.132     0.032        3     0.5  S_interm_prim-Jensen
 3607   2342   5253  2.233 0.381     0.110     0.032       38     4.7  S_intrapariet_and_P_trans
 1529   1035   2207  2.262 0.419     0.124     0.036       15     2.1  S_oc_middle_and_Lunatus
 1889   1247   2824  2.294 0.370     0.136     0.038       22     3.1  S_oc_sup_and_transversal
 1026    689   1491  2.324 0.402     0.131     0.049       14     2.2  S_occipital_ant
 1031    721   1710  2.572 0.471     0.108     0.029        5     1.3  S_oc-temp_lat
 1926   1310   3304  2.645 0.453     0.131     0.042       23     3.6  S_oc-temp_med_and_Lingual
  607    397    748  2.132 0.415     0.136     0.040        8     0.9  S_orbital_lateral
  908    629   1432  2.399 0.729     0.117     0.080       51     4.1  S_orbital_med-olfact
 1809   1235   3281  2.498 0.577     0.147     0.049       28     3.6  S_orbital-H_Shaped
 3013   2007   4711  2.508 0.468     0.136     0.043       45     5.1  S_parieto_occipital
 1788   1129   1989  1.998 0.976     0.154     0.077       53     6.8  S_pericallosal
 2867   1919   3863  2.227 0.347     0.102     0.051       44     4.8  S_postcentral
 1452    960   2390  2.687 0.386     0.109     0.030       12     1.6  S_precentral-inf-part
 1761   1207   2737  2.457 0.492     0.111     0.026       12     2.0  S_precentral-sup-part
  426    276    571  2.092 0.733     0.116     0.036        5     0.7  S_suborbital
 1218    831   2140  2.524 0.485     0.133     0.047       16     2.4  S_subparietal
 2137   1470   3119  2.265 0.558     0.130     0.045       31     3.7  S_temporal_inf
 7180   4873  12323  2.568 0.482     0.117     0.031       68     9.1  S_temporal_sup
  388    264    552  2.681 0.398     0.115     0.024        2     0.4  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Thu Aug  8 23:20:05 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub016 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...
1104 labels changed using aseg
relabeling using gibbs priors...
000:   3246 changed, 162159 examined...
001:    744 changed, 13762 examined...
002:    171 changed, 4059 examined...
003:     78 changed, 1021 examined...
004:     39 changed, 437 examined...
005:     18 changed, 219 examined...
006:      8 changed, 102 examined...
007:      9 changed, 52 examined...
008:      5 changed, 57 examined...
009:      5 changed, 33 examined...
010:      3 changed, 26 examined...
011:      3 changed, 21 examined...
012:      5 changed, 21 examined...
013:      6 changed, 29 examined...
014:      7 changed, 33 examined...
015:      6 changed, 39 examined...
016:      6 changed, 33 examined...
017:      4 changed, 30 examined...
018:      2 changed, 17 examined...
019:      3 changed, 10 examined...
020:      5 changed, 14 examined...
021:      2 changed, 19 examined...
022:      4 changed, 14 examined...
023:      5 changed, 19 examined...
024:      1 changed, 27 examined...
025:      1 changed, 8 examined...
026:      1 changed, 6 examined...
027:      1 changed, 7 examined...
028:      1 changed, 7 examined...
029:      1 changed, 7 examined...
030:      1 changed, 7 examined...
031:      0 changed, 7 examined...
223 labels changed using aseg
000: 72 total segments, 38 labels (218 vertices) changed
001: 34 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 59 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1230 vertices marked for relabeling...
1230 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 10 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Thu Aug  8 23:21:16 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 sub016 rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

  825    539   1678  2.803 0.558     0.143     0.058       13     1.1  caudalanteriorcingulate
 3459   2269   7161  2.846 0.509     0.130     0.082       59     6.4  caudalmiddlefrontal
 3488   2305   5757  2.268 0.457     0.149     0.057       58     8.4  cuneus
  719    499   1968  3.209 0.724     0.138     0.051        8     1.6  entorhinal
 4652   3113  10238  2.740 0.517     0.144     0.063       88    12.7  fusiform
 9665   6411  18366  2.536 0.502     0.144     0.054      176    19.6  inferiorparietal
 7469   5086  16763  2.696 0.637     0.149     0.061      201    17.9  inferiortemporal
 2357   1539   3956  2.365 0.939     0.161     0.084       70     8.9  isthmuscingulate
 9192   5987  16108  2.350 0.476     0.154     0.067      204    26.9  lateraloccipital
 5244   3537  11285  2.718 0.679     0.160     0.072      159    16.9  lateralorbitofrontal
 5477   3641   8694  2.183 0.605     0.163     0.113      130    16.8  lingual
 2886   1874   5726  2.500 0.771     0.157     0.116      106    13.0  medialorbitofrontal
 7553   5192  17626  2.749 0.691     0.133     0.044      130    14.0  middletemporal
 1246    851   2573  2.668 0.562     0.140     0.051       20     2.6  parahippocampal
 3214   1977   5663  2.609 0.492     0.118     0.037       34     5.4  paracentral
 3328   2163   6592  2.723 0.477     0.114     0.041       36     4.4  parsopercularis
 1436   1011   3342  2.708 0.569     0.159     0.063       29     3.2  parsorbitalis
 2973   2006   5940  2.518 0.579     0.132     0.068       92     4.8  parstriangularis
 2921   1957   3836  2.062 0.403     0.147     0.059       45     6.8  pericalcarine
 8046   5091  13212  2.250 0.539     0.117     0.127      195    12.4  postcentral
 2270   1487   4441  2.686 0.708     0.146     0.055       41     5.7  posteriorcingulate
 8099   4949  15152  2.780 0.605     0.110     0.149      323    59.6  precentral
 6594   4411  12746  2.591 0.537     0.142     0.051      118    13.4  precuneus
 1018    656   1863  3.000 0.735     0.120     0.082      126     5.4  rostralanteriorcingulate
 5927   3980  11386  2.484 0.480     0.146     0.049      104    12.1  rostralmiddlefrontal
17813  11902  38228  2.763 0.558     0.136     0.047      313    34.8  superiorfrontal
 7643   4886  12640  2.319 0.436     0.125     0.040      108    12.1  superiorparietal
 7917   5409  19364  3.068 0.662     0.135     0.042      102    13.8  superiortemporal
 5709   3860  11375  2.638 0.534     0.136     0.063      113    11.4  supramarginal
  719    434   1520  2.912 0.320     0.122     0.046        8     1.2  transversetemporal
 3547   2326   7814  3.148 0.923     0.130     0.063       53     8.1  insula
#--------------------------------------------
#@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 23:21:39 CEST 2013

 bbregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta --init-fsl --T2 

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.log
Thu Aug  8 23:21:40 CEST 2013

setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
/opt/freesurfer/5.3.0/bin/bbregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta --init-fsl --T2

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux snake6 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/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999248, 0.0307568, 0.0236215)
j_ras = (0.0317878, 0.9985, 0.0445881)
k_ras = (0.0222147, -0.0453054, 0.998726)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii...
fslregister --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fslregister.log

Thu Aug  8 23:21:45 CEST 2013
--s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
snake6
Linux snake6 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/sub016/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/brainmask.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (1.86265e-09, 0, -1)
k_ras = (-1.97906e-09, 1, -3.72529e-09)
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii --frame 0
mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999248, 0.0307568, 0.0236215)
j_ras = (0.0317878, 0.9985, 0.0445881)
k_ras = (0.0222147, -0.0453054, 0.998726)
keeping frame 0
writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii...
Mov determinant is -0.311066
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/reg0.24460.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat0 --s sub016 --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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/reg0.24460.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/sub016/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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/movvol.fslregister.nii
Tmov: --------------------
-0.700   0.000   0.000   95.886;
 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  -0.031  -0.024  -0.000;
 0.022  -0.045   0.999  -0.000;
-0.032  -0.998  -0.045  -0.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.031  -0.024  -0.000;
 0.022  -0.045   0.999  -0.000;
-0.032  -0.998  -0.045  -0.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub016
RegMat ---------------------------
 0.999  -0.031  -0.024  -0.000;
 0.022  -0.045   0.999  -0.000;
-0.032  -0.998  -0.045  -0.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -0.311066, ref det = -1
Thu Aug  8 23:21:54 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat0
Thu Aug  8 23:26:14 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts
flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s sub016 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat.fsl.mat --noedit
tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.999  -0.033  -0.022   39.132;
-0.023  -0.039  -0.999   265.314;
 0.032   0.999  -0.040   0.697;
 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/sub016/mri/transforms/tmp.bbregister.24421/template.nii
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/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/sub016/mri/transforms/tmp.bbregister.24421/template.nii
Tmov: --------------------
-0.700   0.000   0.000   95.886;
 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 = -0.311066, ref det = -1
---- Input registration matrix (computed) --------
 0.999  -0.032  -0.023  -0.073;
 0.022  -0.040   0.999   2.189;
-0.033  -0.999  -0.039  -1.621;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.999  -0.032  -0.023  -0.073;
 0.022  -0.040   0.999   2.189;
-0.033  -0.999  -0.039  -1.621;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub016
RegMat ---------------------------
 0.999  -0.032  -0.023  -0.073;
 0.022  -0.040   0.999   2.189;
-0.033  -0.999  -0.039  -1.621;
 0.000   0.000   0.000   1.000;
 
Started at Thu Aug 8 23:21:45 CEST 2013 
Ended   at Thu Aug  8 23:31:55 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --surf orig
 
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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 snake6
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.init.dat
subject sub016
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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 1376727398
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.032  -0.023  -0.073;
 0.022  -0.040   0.999   2.189;
-0.033  -0.999  -0.039  -1.621;
 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   0.991698
 1  -25.0 -25.0  25.0   1.017919
 2  -25.0  25.0 -25.0   1.014961
 3  -25.0  25.0  25.0   1.012154
 4   25.0 -25.0 -25.0   1.053511
 5   25.0 -25.0  25.0   1.038265
 6   25.0  25.0 -25.0   1.025332
 7   25.0  25.0  25.0   1.040335
REL:  8  0.497330    8.194174  1.024272 rel = 0.485545 
Initial costs ----------------
Number of surface hits 3047
WM  Intensity    58.1412 +/-   8.4125
Ctx Intensity    68.1580 +/-  13.9941
Pct Contrast     14.7458 +/-  22.3937
Cost   0.4973
RelCost   0.4855

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9706   0.9706  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9683   0.9683  0.0
     3  -4.0000  -4.0000  -4.0000  -4.0000   0.0000  -4.0000      0.9651   0.9651  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8698   0.8698  0.0
    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.8503   0.8503  0.0
    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8111   0.8111  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.7265   0.7265  0.0
   346   0.0000   0.0000  -4.0000   4.0000   0.0000   0.0000      0.7237   0.7237  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.4973   0.4973  0.0
Brute Force --------------------------
Min cost was 0.497330
Number of iterations   729
Search time 2.336000 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  0.058  0.000  0.000  0.000  0.000  0.000   0.4962479741
   8  0.173  0.000  0.000  0.000  0.000  0.000   0.4956493570
   9  0.150  0.000  0.000  0.000  0.000  0.000   0.4954339777
  11  0.148  0.000  0.000  0.000  0.000  0.000   0.4954213621
  12  0.144  0.000  0.000  0.000  0.000  0.000   0.4954030878
  18  0.144 -1.618  0.000  0.000  0.000  0.000   0.3123496406
  23  0.144 -1.481  0.000  0.000  0.000  0.000   0.3072172974
  24  0.144 -1.427  0.000  0.000  0.000  0.000   0.3064682236
  26  0.144 -1.443  0.000  0.000  0.000  0.000   0.3063398337
  27  0.144 -1.442  0.000  0.000  0.000  0.000   0.3063332070
  28  0.144 -1.439  0.000  0.000  0.000  0.000   0.3063242057
  33  0.144 -1.439  1.000  0.000  0.000  0.000   0.1447468946
  38  0.144 -1.439  1.258  0.000  0.000  0.000   0.1406853989
  39  0.144 -1.439  1.242  0.000  0.000  0.000   0.1403118087
  40  0.144 -1.439  1.178  0.000  0.000  0.000   0.1399896185
  42  0.144 -1.439  1.199  0.000  0.000  0.000   0.1397496399
  44  0.144 -1.439  1.200  0.000  0.000  0.000   0.1397479461
  57  0.144 -1.439  1.200  0.009  0.000  0.000   0.1395871869
  58  0.144 -1.439  1.200  0.011  0.000  0.000   0.1395814210
  67  0.144 -1.439  1.200  0.011 -0.164  0.000   0.1379313531
  68  0.144 -1.439  1.200  0.011 -0.132  0.000   0.1376534846
  69  0.144 -1.439  1.200  0.011 -0.118  0.000   0.1373763056
  71  0.144 -1.439  1.200  0.011 -0.103  0.000   0.1372832564
  80  0.144 -1.439  1.200  0.011 -0.103  0.119   0.1361960394
  81  0.144 -1.439  1.200  0.011 -0.103  0.101   0.1360196246
  82  0.144 -1.439  1.200  0.011 -0.103  0.083   0.1359179116
  84  0.144 -1.439  1.200  0.011 -0.103  0.079   0.1359153918
  85  0.144 -1.439  1.200  0.011 -0.103  0.080   0.1359150338
  97  0.151 -1.439  1.200  0.011 -0.103  0.080   0.1359105495
  98  0.149 -1.439  1.200  0.011 -0.103  0.080   0.1359064688
  99  0.148 -1.439  1.200  0.011 -0.103  0.080   0.1359061504
 107  0.148 -1.462  1.200  0.011 -0.103  0.080   0.1354371527
 109  0.148 -1.526  1.200  0.011 -0.103  0.080   0.1348476725
 110  0.148 -1.545  1.200  0.011 -0.103  0.080   0.1346955371
 111  0.148 -1.577  1.200  0.011 -0.103  0.080   0.1345269131
 113  0.148 -1.565  1.200  0.011 -0.103  0.080   0.1345157736
 114  0.148 -1.570  1.200  0.011 -0.103  0.080   0.1345017495
 115  0.148 -1.571  1.200  0.011 -0.103  0.080   0.1345011534
 124  0.148 -1.571  1.153  0.011 -0.103  0.080   0.1344975072
 125  0.148 -1.571  1.176  0.011 -0.103  0.080   0.1343772027
 127  0.148 -1.571  1.171  0.011 -0.103  0.080   0.1343579904
 129  0.148 -1.571  1.169  0.011 -0.103  0.080   0.1343552516
 141  0.148 -1.571  1.169  0.010 -0.103  0.080   0.1343542902
 150  0.148 -1.571  1.169  0.010 -0.131  0.080   0.1339936964
 152  0.148 -1.571  1.169  0.010 -0.132  0.080   0.1339928523
 162  0.148 -1.571  1.169  0.010 -0.132  0.045   0.1339816050
 163  0.148 -1.571  1.169  0.010 -0.132  0.062   0.1338638798
 166  0.148 -1.571  1.169  0.010 -0.132  0.064   0.1338620199
 175  0.141 -1.571  1.169  0.010 -0.132  0.064   0.1337887306
 179  0.138 -1.571  1.169  0.010 -0.132  0.064   0.1337767557
 191  0.138 -1.582  1.169  0.010 -0.132  0.064   0.1337187231
 193  0.138 -1.581  1.169  0.010 -0.132  0.064   0.1337185913
 206  0.138 -1.581  1.164  0.010 -0.132  0.064   0.1336990090
 208  0.138 -1.581  1.163  0.010 -0.132  0.064   0.1336987668
 218  0.138 -1.581  1.163  0.012 -0.132  0.064   0.1336981293
 241  0.138 -1.581  1.163  0.012 -0.132  0.048   0.1336249538
 244  0.128 -1.592  1.156  0.014 -0.132  0.033   0.1335438535
 251  0.129 -1.591  1.157  0.014 -0.132  0.034   0.1335415787
 252  0.129 -1.590  1.157  0.014 -0.132  0.035   0.1335407690
 257  0.129 -1.590  1.157  0.014 -0.132  0.035   0.1335407147
 261  0.129 -1.590  1.157  0.014 -0.132  0.035   0.1335406048
 270  0.129 -1.590  1.157  0.014 -0.132  0.038   0.1335310703
 272  0.129 -1.590  1.157  0.014 -0.132  0.040   0.1335282673
 273  0.129 -1.590  1.157  0.014 -0.132  0.041   0.1335277339
 282  0.129 -1.581  1.157  0.014 -0.132  0.041   0.1334871275
 283  0.129 -1.579  1.157  0.014 -0.132  0.041   0.1334814295
 287  0.129 -1.577  1.157  0.014 -0.132  0.041   0.1334805825
 301  0.129 -1.577  1.152  0.014 -0.132  0.041   0.1334726852
 312  0.129 -1.577  1.152  0.015 -0.132  0.041   0.1334665716
 313  0.129 -1.577  1.152  0.017 -0.132  0.041   0.1334652903
 324  0.129 -1.577  1.152  0.017 -0.135  0.041   0.1334594948
 328  0.120 -1.588  1.146  0.019 -0.135  0.026   0.1334288625
 332  0.123 -1.584  1.149  0.018 -0.135  0.031   0.1334217989
 334  0.123 -1.584  1.148  0.018 -0.135  0.031   0.1334216584
 339  0.123 -1.584  1.149  0.018 -0.135  0.031   0.1334215674
 341  0.123 -1.584  1.149  0.018 -0.135  0.031   0.1334214761
 344  0.109 -1.587  1.134  0.024 -0.137  0.014   0.1333468299
 351  0.107 -1.588  1.133  0.025 -0.138  0.012   0.1333424901
 352  0.106 -1.588  1.132  0.026 -0.138  0.011   0.1333423748
 353  0.106 -1.588  1.132  0.025 -0.138  0.011   0.1333422128
 354  0.106 -1.588  1.132  0.025 -0.138  0.011   0.1333421542
 374  0.112 -1.581  1.136  0.024 -0.138  0.021   0.1333064110
 380  0.112 -1.581  1.136  0.024 -0.138  0.021   0.1333063697
 411  0.112 -1.581  1.136  0.022 -0.138  0.021   0.1332996639
 421  0.112 -1.581  1.136  0.022 -0.137  0.021   0.1332967946
 422  0.112 -1.581  1.136  0.022 -0.135  0.021   0.1332967036
 430  0.107 -1.582  1.131  0.025 -0.136  0.014   0.1332811809
 431  0.106 -1.582  1.130  0.025 -0.136  0.013   0.1332794866
 434  0.106 -1.582  1.130  0.025 -0.136  0.013   0.1332792467
 451  0.106 -1.582  1.130  0.025 -0.136  0.011   0.1332780862
 459  0.108 -1.579  1.131  0.025 -0.136  0.015   0.1332721868
 460  0.108 -1.580  1.131  0.025 -0.136  0.015   0.1332718205
 461  0.108 -1.580  1.131  0.025 -0.136  0.014   0.1332717118
 470  0.108 -1.580  1.131  0.025 -0.136  0.014   0.1332716711
 482  0.108 -1.580  1.139  0.025 -0.136  0.014   0.1332685167
 483  0.108 -1.580  1.135  0.025 -0.136  0.014   0.1332621981
 494  0.108 -1.580  1.135  0.022 -0.136  0.014   0.1332613604
 496  0.108 -1.580  1.135  0.023 -0.136  0.014   0.1332588580
 508  0.108 -1.580  1.135  0.023 -0.137  0.014   0.1332585011
 514  0.102 -1.581  1.130  0.025 -0.138  0.008   0.1332576465
 515  0.105 -1.581  1.133  0.024 -0.138  0.011   0.1332523634
 516  0.105 -1.581  1.133  0.024 -0.138  0.011   0.1332522537
 518  0.105 -1.581  1.133  0.024 -0.138  0.011   0.1332522008
 526  0.105 -1.579  1.136  0.023 -0.139  0.009   0.1332483876
 586  0.106 -1.580  1.136  0.023 -0.135  0.013   0.1332471225
 587  0.106 -1.580  1.136  0.023 -0.136  0.013   0.1332467187
 594  0.103 -1.581  1.133  0.024 -0.137  0.010   0.1332410557
Powell done niters = 6
Computing relative cost
 0  -25.0 -25.0 -25.0   0.987108
 1  -25.0 -25.0  25.0   1.009174
 2  -25.0  25.0 -25.0   0.994077
 3  -25.0  25.0  25.0   1.024224
 4   25.0 -25.0 -25.0   1.032857
 5   25.0 -25.0  25.0   1.005481
 6   25.0  25.0 -25.0   0.980632
 7   25.0  25.0  25.0   1.024402
REL:  8  0.133241    8.057954  1.007244 rel = 0.132283 
Number of iterations     6
Min cost was 0.133241
Number of FunctionCalls   602
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 1.771000 sec
Parameters at optimum (transmm)  0.10308 -1.58084  1.13322
Parameters at optimum (rotdeg)  0.02365 -0.13659  0.00979 
Final costs ----------------
Number of surface hits 3047
WM  Intensity    56.4536 +/-   7.1833
Ctx Intensity    67.5397 +/-   7.6173
Pct Contrast     17.8999 +/-  12.3774
Cost   0.1332
RelCost   0.4855
Reg at min cost was 
 0.999  -0.029  -0.023   0.034;
 0.022  -0.039   0.999   0.608;
-0.030  -0.999  -0.039  -0.487;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat, type = 14 
Original Reg 
 0.999  -0.032  -0.023  -0.073;
 0.022  -0.040   0.999   2.189;
-0.033  -0.999  -0.039  -1.621;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000  -0.002   0.000  -0.107;
-0.000  -0.000  -0.000   1.580;
-0.002   0.000  -0.000  -1.134;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 1.928128
Computing change in rh position
Surface RMS Diff (mm) 1.965314 2.053568
mri_segreg done
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/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/sub016/scripts
mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/template.nii
regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/tmp.bbregister.24421/bbr.pass1.dat
subject sub016
dof 6
outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1376990004
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.029  -0.023   0.034;
 0.022  -0.039   0.999   0.608;
-0.030  -0.999  -0.039  -0.487;
 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   1.013674
 1  -25.0 -25.0  25.0   0.994273
 2  -25.0  25.0 -25.0   0.995462
 3  -25.0  25.0  25.0   1.013802
 4   25.0 -25.0 -25.0   1.027246
 5   25.0 -25.0  25.0   1.007479
 6   25.0  25.0 -25.0   0.998557
 7   25.0  25.0  25.0   1.024932
REL:  8  0.141688    8.075426  1.009428 rel = 0.140364 
Initial costs ----------------
Number of surface hits 304481
WM  Intensity    56.5409 +/-   7.1624
Ctx Intensity    67.6348 +/-   7.7629
Pct Contrast     17.8592 +/-  12.5660
Cost   0.1417
RelCost   0.1404

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1471   0.1471  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1459   0.1459  0.0
     9  -0.1000  -0.1000  -0.1000   0.0000  -0.1000  -0.1000      0.1439   0.1439  0.0
    12  -0.1000  -0.1000  -0.1000   0.0000   0.0000  -0.1000      0.1434   0.1434  0.0
    13  -0.1000  -0.1000  -0.1000   0.0000   0.0000   0.0000      0.1426   0.1426  0.0
    22  -0.1000  -0.1000  -0.1000   0.1000   0.0000   0.0000      0.1399   0.1399  0.0
    39  -0.1000  -0.1000   0.0000   0.0000   0.0000  -0.1000      0.1396   0.1396  0.0
    40  -0.1000  -0.1000   0.0000   0.0000   0.0000   0.0000      0.1377   0.1377  0.0
    49  -0.1000  -0.1000   0.0000   0.1000   0.0000   0.0000      0.1362   0.1362  0.0
    67  -0.1000  -0.1000   0.1000   0.0000   0.0000   0.0000      0.1344   0.1344  0.0
   130  -0.1000   0.0000   0.0000   0.1000   0.0000   0.0000      0.1344   0.1344  0.0
   148  -0.1000   0.0000   0.1000   0.0000   0.0000   0.0000      0.1342   0.1342  0.0
   157  -0.1000   0.0000   0.1000   0.1000   0.0000   0.0000      0.1342   0.1342  0.0
   211  -0.1000   0.1000   0.0000   0.1000   0.0000   0.0000      0.1332   0.1332  0.0
Brute Force --------------------------
Min cost was 0.133165
Number of iterations   729
Search time 2.128000 sec
Parameters at best (transmm, rotdeg)
 -0.100   0.100   0.000  0.100  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 -0.1
1 0.1
2 0
3 0.1
4 0
5 0
   7 -0.040  0.100  0.000  0.100  0.000  0.000   0.1383786066
   8 -0.060  0.100  0.000  0.100  0.000  0.000   0.1383350291
  10 -0.059  0.100  0.000  0.100  0.000  0.000   0.1383349480
  19 -0.059  0.196  0.000  0.100  0.000  0.000   0.1372708911
  28 -0.059  0.196  0.126  0.100  0.000  0.000   0.1360247476
  29 -0.059  0.196  0.120  0.100  0.000  0.000   0.1360163550
  30 -0.059  0.196  0.116  0.100  0.000  0.000   0.1360147204
  39 -0.059  0.196  0.116  0.051  0.000  0.000   0.1354389563
  40 -0.059  0.196  0.116  0.044  0.000  0.000   0.1354184637
  41 -0.059  0.196  0.116  0.038  0.000  0.000   0.1354155472
  42 -0.059  0.196  0.116  0.040  0.000  0.000   0.1354152911
  50 -0.059  0.196  0.116  0.040 -0.061  0.000   0.1348322987
  52 -0.059  0.196  0.116  0.040 -0.065  0.000   0.1348295650
  53 -0.059  0.196  0.116  0.040 -0.064  0.000   0.1348295083
  61 -0.059  0.196  0.116  0.040 -0.064  0.015   0.1348115263
  62 -0.059  0.196  0.116  0.040 -0.064  0.013   0.1348100653
  63 -0.059  0.196  0.116  0.040 -0.064  0.012   0.1348097944
  72 -0.023  0.196  0.116  0.040 -0.064  0.012   0.1347987256
  73 -0.039  0.196  0.116  0.040 -0.064  0.012   0.1347666581
  83 -0.039  0.189  0.116  0.040 -0.064  0.012   0.1347613712
  92 -0.039  0.189  0.182  0.040 -0.064  0.012   0.1345687690
  93 -0.039  0.189  0.167  0.040 -0.064  0.012   0.1345484474
  95 -0.039  0.189  0.162  0.040 -0.064  0.012   0.1345484171
  97 -0.039  0.189  0.164  0.040 -0.064  0.012   0.1345479816
 106 -0.039  0.189  0.164  0.026 -0.064  0.012   0.1344668773
 107 -0.039  0.189  0.164  0.016 -0.064  0.012   0.1344402774
 108 -0.039  0.189  0.164  0.012 -0.064  0.012   0.1344367260
 117 -0.039  0.189  0.164  0.012 -0.067  0.012   0.1344335818
 118 -0.039  0.189  0.164  0.012 -0.071  0.012   0.1344296615
 120 -0.039  0.189  0.164  0.012 -0.076  0.012   0.1344282299
 122 -0.039  0.189  0.164  0.012 -0.075  0.012   0.1344281565
 130 -0.039  0.189  0.164  0.012 -0.075  0.026   0.1344084441
 131 -0.039  0.189  0.164  0.012 -0.075  0.025   0.1344074875
 132 -0.039  0.189  0.164  0.012 -0.075  0.023   0.1344071491
 134 -0.019  0.182  0.212 -0.015 -0.085  0.035   0.1343182007
 140 -0.027  0.185  0.194 -0.005 -0.081  0.030   0.1343139430
 141 -0.024  0.184  0.201 -0.009 -0.083  0.032   0.1343115115
 142 -0.024  0.184  0.201 -0.009 -0.082  0.032   0.1343114196
 144 -0.024  0.184  0.200 -0.009 -0.082  0.032   0.1343114161
 145 -0.024  0.184  0.201 -0.009 -0.082  0.032   0.1343113993
 146 -0.024  0.184  0.201 -0.009 -0.082  0.032   0.1343113763
 156 -0.023  0.184  0.201 -0.009 -0.082  0.032   0.1343113219
 165 -0.023  0.168  0.201 -0.009 -0.082  0.032   0.1342921102
 168 -0.023  0.169  0.201 -0.009 -0.082  0.032   0.1342919357
 186 -0.023  0.169  0.201 -0.010 -0.082  0.032   0.1342918736
 194 -0.023  0.169  0.201 -0.010 -0.077  0.032   0.1342895233
 196 -0.023  0.169  0.201 -0.010 -0.076  0.032   0.1342893447
 204 -0.016  0.167  0.219 -0.020 -0.080  0.036   0.1342801141
 205 -0.017  0.167  0.215 -0.018 -0.079  0.035   0.1342795104
 206 -0.017  0.167  0.215 -0.018 -0.079  0.035   0.1342794935
 207 -0.017  0.167  0.215 -0.018 -0.079  0.035   0.1342794915
 208 -0.017  0.167  0.215 -0.018 -0.079  0.035   0.1342794695
 220 -0.018  0.167  0.215 -0.018 -0.079  0.035   0.1342793241
 228 -0.018  0.166  0.215 -0.018 -0.079  0.035   0.1342780381
 229 -0.018  0.163  0.215 -0.018 -0.079  0.035   0.1342773814
 231 -0.018  0.164  0.215 -0.018 -0.079  0.035   0.1342773395
 240 -0.018  0.164  0.215 -0.018 -0.079  0.034   0.1342769522
 251 -0.018  0.164  0.215 -0.014 -0.079  0.034   0.1342747860
 269 -0.017  0.163  0.219 -0.016 -0.080  0.035   0.1342731830
 270 -0.016  0.163  0.220 -0.017 -0.080  0.035   0.1342730505
 271 -0.016  0.163  0.220 -0.017 -0.080  0.035   0.1342730021
 274 -0.016  0.163  0.221 -0.017 -0.080  0.036   0.1342729395
 288 -0.018  0.163  0.221 -0.017 -0.080  0.036   0.1342724065
 306 -0.018  0.163  0.221 -0.017 -0.080  0.034   0.1342722990
 307 -0.018  0.163  0.221 -0.017 -0.080  0.033   0.1342721992
 321 -0.018  0.163  0.221 -0.016 -0.080  0.033   0.1342720073
 330 -0.018  0.163  0.221 -0.016 -0.078  0.033   0.1342712016
 341 -0.018  0.163  0.222 -0.017 -0.078  0.033   0.1342711738
 344 -0.018  0.163  0.222 -0.017 -0.078  0.033   0.1342711728
 357 -0.020  0.163  0.222 -0.017 -0.078  0.033   0.1342708052
 366 -0.020  0.164  0.222 -0.017 -0.078  0.033   0.1342707798
 375 -0.020  0.164  0.222 -0.017 -0.078  0.032   0.1342707229
 384 -0.020  0.164  0.222 -0.016 -0.078  0.032   0.1342706602
 393 -0.020  0.164  0.222 -0.016 -0.077  0.032   0.1342704408
 417 -0.021  0.164  0.222 -0.016 -0.077  0.032   0.1342703886
 454 -0.021  0.164  0.222 -0.016 -0.076  0.032   0.1342703700
 466 -0.021  0.164  0.222 -0.016 -0.076  0.032   0.1342703523
Powell done niters = 7
Computing relative cost
 0  -25.0 -25.0 -25.0   1.014724
 1  -25.0 -25.0  25.0   0.993885
 2  -25.0  25.0 -25.0   0.993645
 3  -25.0  25.0  25.0   1.012720
 4   25.0 -25.0 -25.0   1.028029
 5   25.0 -25.0  25.0   1.005782
 6   25.0  25.0 -25.0   0.999341
 7   25.0  25.0  25.0   1.024793
REL:  8  0.134270    8.072920  1.009115 rel = 0.133058 
Number of iterations     7
Min cost was 0.134270
Number of FunctionCalls   527
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 69.051000 sec
Parameters at optimum (transmm) -0.02074  0.16374  0.22181
Parameters at optimum (rotdeg) -0.01581 -0.07641  0.03234 
Final costs ----------------
Number of surface hits 304481
WM  Intensity    56.5318 +/-   7.1402
Ctx Intensity    67.5968 +/-   7.7119
Pct Contrast     17.8233 +/-  12.4061
Cost   0.1343
RelCost   0.1404
Reg at min cost was 
 0.999  -0.028  -0.023   0.013;
 0.022  -0.040   0.999   0.772;
-0.029  -0.999  -0.039  -0.265;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat, type = 14 
Original Reg 
 0.999  -0.029  -0.023   0.034;
 0.022  -0.039   0.999   0.608;
-0.030  -0.999  -0.039  -0.487;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.000  -0.001   0.001   0.020;
-0.001   0.000   0.000  -0.164;
-0.001   0.000   0.000  -0.222;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.244708
Computing change in rh position
Surface RMS Diff (mm) 0.284066 0.379271
mri_segreg done
tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz
reg file       /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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  -0.028  -0.023   0.013;
 0.022  -0.040   0.999   0.772;
-0.029  -0.999  -0.039  -0.265;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz
Tmov: --------------------
-0.700   0.000   0.000   95.886;
 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  -0.028  -0.023   0.013;
 0.022  -0.040   0.999   0.772;
-0.029  -0.999  -0.039  -0.265;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = sub016
RegMat ---------------------------
 0.999  -0.028  -0.023   0.013;
 0.022  -0.040   0.999   0.772;
-0.029  -0.999  -0.039  -0.265;
 0.000   0.000   0.000   1.000;
transformed matrix:
 1.000  -0.003  -0.000   0.059;
 0.003   1.000   0.006  -0.142;
 0.000  -0.006   1.000  -0.599;
 0.000   0.000   0.000   1.000;
transformed matrix:
 0.699  -0.019  -0.015   38.752;
-0.016  -0.026  -0.666   263.892;
 0.020   0.666  -0.026   2.326;
 0.000   0.000   0.000   1.000;
Cleaning up
 
Started at Thu Aug 8 23:21:39 CEST 2013 
Ended   at Thu Aug  8 23:33:58 CEST 2013
BBR-Run-Time-Sec 739
 
bbregister Done
To check results, run:
tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.dat --surf
 

 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/T2.mgz 

mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/orig/T2raw.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999248, 0.0307568, 0.0236215)
j_ras = (0.0317878, 0.9985, 0.0445881)
k_ras = (0.0222147, -0.0453054, 0.998726)
INFO: Reading transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta...
Reading transform with LTAreadEx()
reading extra input line subject sub016
reading extra input line fscale 0.150000
reading template info from volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/orig.mgz...
INFO: Applying transformation from file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/transforms/T2raw.lta...
---------------------------------
INFO: Transform Matrix (linear_ras_to_ras)
 1.000  -0.003  -0.000   0.059;
 0.003   1.000   0.006  -0.142;
 0.000  -0.006   1.000  -0.599;
 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/sub016/mri/T2.mgz...

 mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/T2.mgz...
computing distance transform
computing distance transform
computing nonmaximum suppression
15456 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/sub016/mri/T2.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub016 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/sub016/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
22234 bright wm thresholded.
384 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.orig...
computing class statistics...
border white:    298969 voxels (1.78%)
border gray      333863 voxels (1.99%)
WM (93.0): 93.9 +- 9.8 [70.0 --> 110.0]
GM (77.0) : 75.0 +- 12.6 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 49.4 (was 70)
setting MAX_BORDER_WHITE to 115.8 (was 105)
setting MIN_BORDER_WHITE to 62.0 (was 85)
setting MAX_CSF to 36.9 (was 40)
setting MAX_GRAY to 96.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 55.7 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 24.3 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=62
mean inside = 93.8, mean outside = 70.2
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/sub016/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.26 (0.03-->5.11) (max @ vno 160099 --> 160100)
face area 0.33 +- 0.16 (0.00-->5.68)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 247 points - only 4.05% unknown
deleting segment 1 with 5 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 5 points - only 0.00% unknown
deleting segment 6 with 6 points - only 0.00% unknown
deleting segment 7 with 881 points - only 0.00% unknown
deleting segment 8 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 9 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 12 with 37 points - only 0.00% unknown
deleting segment 13 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 15 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 16 with 3 points - only 0.00% unknown
deleting segment 17 with 5 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 (0.03-->4.83) (max @ vno 160104 --> 70416)
face area 0.33 +- 0.16 (0.00-->5.68)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4771560.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, 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=4771560.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 247 points - only 4.05% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 881 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 37 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
deleting segment 14 with 5 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 (0.03-->4.83) (max @ vno 160104 --> 70416)
face area 0.33 +- 0.16 (0.00-->5.68)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4771560.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, 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=4771560.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 247 points - only 4.05% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 881 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 37 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
deleting segment 14 with 5 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 (0.03-->4.83) (max @ vno 160104 --> 70416)
face area 0.33 +- 0.16 (0.00-->5.68)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4771560.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, 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=4771560.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 247 points - only 4.05% unknown
deleting segment 1 with 5 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 2 with 2 points - only 0.00% unknown
deleting segment 3 with 5 points - only 0.00% unknown
deleting segment 4 with 6 points - only 0.00% unknown
deleting segment 5 with 881 points - only 0.00% unknown
deleting segment 6 with 7 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 7 with 2 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 9 with 37 points - only 0.00% unknown
deleting segment 10 with 8 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 11 with 1 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 12 with 2 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 13 with 3 points - only 0.00% unknown
deleting segment 14 with 5 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=4771560.0, rms=0.00
rms = 1.14, time step reduction 1 of 3 to 0.250...
rms = 0.29, 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=4771560.0, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 7 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 [90.50 201.50], gm=146.00+-18.50, and vertices in regions > 136.7
54026 surface locations found to contain inconsistent values (5139 in, 48887 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=562411.2, rms=0.25
001: dt: 0.5000, sse=527796.3, rms=0.244 (0.000%)
002: dt: 0.5000, sse=506658.5, rms=0.230 (0.000%)
003: dt: 0.5000, sse=493634.9, rms=0.220 (0.000%)
004: dt: 0.5000, sse=483524.0, rms=0.210 (0.000%)
005: dt: 0.5000, sse=476287.5, rms=0.202 (0.000%)
006: dt: 0.5000, sse=470805.8, rms=0.195 (0.000%)
007: dt: 0.5000, sse=466676.5, rms=0.188 (0.000%)
008: dt: 0.5000, sse=463023.4, rms=0.183 (0.000%)
009: dt: 0.5000, sse=460242.7, rms=0.178 (0.000%)
010: dt: 0.5000, sse=457962.3, rms=0.174 (0.000%)
011: dt: 0.5000, sse=456483.0, rms=0.170 (0.000%)
012: dt: 0.5000, sse=454198.5, rms=0.166 (0.000%)
013: dt: 0.5000, sse=452938.7, rms=0.163 (0.000%)
014: dt: 0.5000, sse=451551.8, rms=0.161 (0.000%)
015: dt: 0.5000, sse=450075.8, rms=0.158 (0.000%)
016: dt: 0.5000, sse=448673.4, rms=0.156 (0.000%)
017: dt: 0.5000, sse=447105.9, rms=0.154 (0.000%)
018: dt: 0.5000, sse=445862.4, rms=0.152 (0.000%)
019: dt: 0.5000, sse=444415.1, rms=0.151 (0.000%)
020: dt: 0.5000, sse=442952.5, rms=0.149 (0.000%)
021: dt: 0.5000, sse=442219.8, rms=0.148 (0.000%)
022: dt: 0.5000, sse=440692.2, rms=0.147 (0.000%)
023: dt: 0.5000, sse=439257.3, rms=0.146 (0.000%)
024: dt: 0.5000, sse=438124.2, rms=0.145 (0.000%)
025: dt: 0.5000, sse=436748.1, rms=0.144 (0.000%)
026: dt: 0.5000, sse=435682.4, rms=0.144 (0.000%)
027: dt: 0.5000, sse=434302.8, rms=0.143 (0.000%)
028: dt: 0.5000, sse=433407.2, rms=0.143 (0.000%)
029: dt: 0.5000, sse=432330.4, rms=0.142 (0.000%)
030: dt: 0.5000, sse=431423.0, rms=0.142 (0.000%)
positioning took 4.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [89.00 203.00], gm=146.00+-19.00, and vertices in regions > 136.5
45632 surface locations found to contain inconsistent values (2102 in, 43530 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=45237.0, rms=0.13
031: dt: 0.5000, sse=44966.7, rms=0.127 (0.000%)
032: dt: 0.5000, sse=46114.0, rms=0.117 (0.000%)
033: dt: 0.5000, sse=47380.2, rms=0.110 (0.000%)
034: dt: 0.5000, sse=48373.9, rms=0.105 (0.000%)
035: dt: 0.5000, sse=49166.3, rms=0.100 (0.000%)
036: dt: 0.5000, sse=49909.8, rms=0.095 (0.000%)
037: dt: 0.5000, sse=50589.5, rms=0.091 (0.000%)
038: dt: 0.5000, sse=51284.1, rms=0.087 (0.000%)
039: dt: 0.5000, sse=51925.8, rms=0.084 (0.000%)
040: dt: 0.5000, sse=52511.0, rms=0.080 (0.000%)
041: dt: 0.5000, sse=53114.1, rms=0.077 (0.000%)
042: dt: 0.5000, sse=53633.8, rms=0.074 (0.000%)
043: dt: 0.5000, sse=54133.5, rms=0.071 (0.000%)
044: dt: 0.5000, sse=54613.6, rms=0.069 (0.000%)
045: dt: 0.5000, sse=55071.5, rms=0.066 (0.000%)
046: dt: 0.5000, sse=55508.4, rms=0.064 (0.000%)
047: dt: 0.5000, sse=55901.6, rms=0.062 (0.000%)
048: dt: 0.5000, sse=56286.2, rms=0.060 (0.000%)
049: dt: 0.5000, sse=56608.5, rms=0.058 (0.000%)
050: dt: 0.5000, sse=56914.4, rms=0.056 (0.000%)
051: dt: 0.5000, sse=57187.7, rms=0.054 (0.000%)
052: dt: 0.5000, sse=57457.3, rms=0.053 (0.000%)
053: dt: 0.5000, sse=57711.3, rms=0.051 (0.000%)
054: dt: 0.5000, sse=57931.1, rms=0.050 (0.000%)
055: dt: 0.5000, sse=58145.2, rms=0.049 (0.000%)
056: dt: 0.5000, sse=58316.2, rms=0.048 (0.000%)
057: dt: 0.5000, sse=58474.2, rms=0.047 (0.000%)
058: dt: 0.5000, sse=58636.4, rms=0.045 (0.000%)
059: dt: 0.5000, sse=58802.0, rms=0.045 (0.000%)
060: dt: 0.5000, sse=58943.7, rms=0.044 (0.000%)
positioning took 4.2 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [87.50 204.50], gm=146.00+-19.50, and vertices in regions > 136.2
44528 surface locations found to contain inconsistent values (409 in, 44119 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=6391.9, rms=0.06
061: dt: 0.5000, sse=6374.1, rms=0.056 (0.000%)
062: dt: 0.5000, sse=6430.7, rms=0.050 (0.000%)
063: dt: 0.5000, sse=6488.5, rms=0.047 (0.000%)
064: dt: 0.5000, sse=6531.4, rms=0.045 (0.000%)
065: dt: 0.5000, sse=6554.4, rms=0.043 (0.000%)
066: dt: 0.5000, sse=6563.4, rms=0.041 (0.000%)
067: dt: 0.5000, sse=6572.1, rms=0.040 (0.000%)
068: dt: 0.5000, sse=6573.9, rms=0.039 (0.000%)
069: dt: 0.5000, sse=6574.2, rms=0.038 (0.000%)
070: dt: 0.5000, sse=6576.4, rms=0.036 (0.000%)
071: dt: 0.5000, sse=6576.7, rms=0.035 (0.000%)
072: dt: 0.5000, sse=6579.1, rms=0.035 (0.000%)
073: dt: 0.5000, sse=6580.4, rms=0.034 (0.000%)
074: dt: 0.5000, sse=6582.4, rms=0.033 (0.000%)
075: dt: 0.5000, sse=6582.9, rms=0.032 (0.000%)
076: dt: 0.5000, sse=6584.1, rms=0.031 (0.000%)
077: dt: 0.5000, sse=6586.4, rms=0.031 (0.000%)
078: dt: 0.5000, sse=6588.9, rms=0.030 (0.000%)
079: dt: 0.5000, sse=6589.1, rms=0.030 (0.000%)
080: dt: 0.5000, sse=6590.0, rms=0.029 (0.000%)
081: dt: 0.5000, sse=6594.9, rms=0.029 (0.000%)
082: dt: 0.5000, sse=6596.0, rms=0.028 (0.000%)
083: dt: 0.5000, sse=6596.7, rms=0.028 (0.000%)
084: dt: 0.5000, sse=6599.7, rms=0.028 (0.000%)
085: dt: 0.5000, sse=6600.9, rms=0.027 (0.000%)
086: dt: 0.5000, sse=6604.3, rms=0.027 (0.000%)
087: dt: 0.5000, sse=6604.2, rms=0.027 (0.000%)
088: dt: 0.5000, sse=6605.7, rms=0.027 (0.000%)
089: dt: 0.5000, sse=6606.5, rms=0.026 (0.000%)
090: dt: 0.5000, sse=6611.2, rms=0.026 (0.000%)
positioning took 4.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [87.50 204.50], gm=146.00+-19.50, and vertices in regions > 136.2
44069 surface locations found to contain inconsistent values (113 in, 43956 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/sub016/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=814.6, rms=0.03
091: dt: 0.5000, sse=813.8, rms=0.032 (0.000%)
092: dt: 0.5000, sse=803.1, rms=0.031 (0.000%)
093: dt: 0.5000, sse=793.9, rms=0.030 (0.000%)
094: dt: 0.5000, sse=786.1, rms=0.029 (0.000%)
095: dt: 0.5000, sse=779.1, rms=0.028 (0.000%)
096: dt: 0.5000, sse=773.7, rms=0.028 (0.000%)
097: dt: 0.5000, sse=769.7, rms=0.027 (0.000%)
098: dt: 0.5000, sse=767.7, rms=0.027 (0.000%)
099: dt: 0.5000, sse=764.6, rms=0.027 (0.000%)
100: dt: 0.5000, sse=761.1, rms=0.026 (0.000%)
101: dt: 0.5000, sse=759.5, rms=0.026 (0.000%)
102: dt: 0.5000, sse=758.9, rms=0.026 (0.000%)
103: dt: 0.5000, sse=755.6, rms=0.025 (0.000%)
104: dt: 0.5000, sse=752.5, rms=0.025 (0.000%)
105: dt: 0.5000, sse=750.5, rms=0.025 (0.000%)
106: dt: 0.5000, sse=748.2, rms=0.024 (0.000%)
107: dt: 0.5000, sse=746.3, rms=0.024 (0.000%)
108: dt: 0.5000, sse=744.5, rms=0.024 (0.000%)
109: dt: 0.5000, sse=745.6, rms=0.024 (0.000%)
110: dt: 0.5000, sse=743.9, rms=0.024 (0.000%)
111: dt: 0.5000, sse=742.1, rms=0.024 (0.000%)
112: dt: 0.5000, sse=742.7, rms=0.024 (0.000%)
113: dt: 0.5000, sse=743.1, rms=0.024 (0.000%)
114: dt: 0.5000, sse=742.2, rms=0.024 (0.000%)
115: dt: 0.5000, sse=740.9, rms=0.023 (0.000%)
116: dt: 0.5000, sse=739.1, rms=0.023 (0.000%)
117: dt: 0.5000, sse=738.5, rms=0.023 (0.000%)
118: dt: 0.5000, sse=739.1, rms=0.023 (0.000%)
119: dt: 0.5000, sse=738.0, rms=0.023 (0.000%)
120: dt: 0.5000, sse=740.1, rms=0.023 (0.000%)
positioning took 4.2 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.area.pial
vertex spacing 1.02 +- 0.44 (0.05-->7.32) (max @ vno 103206 --> 104423)
face area 0.41 +- 0.32 (0.00-->7.45)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 160479 vertices processed
25000 of 160479 vertices processed
50000 of 160479 vertices processed
75000 of 160479 vertices processed
100000 of 160479 vertices processed
125000 of 160479 vertices processed
150000 of 160479 vertices processed
0 of 160479 vertices processed
25000 of 160479 vertices processed
50000 of 160479 vertices processed
75000 of 160479 vertices processed
100000 of 160479 vertices processed
125000 of 160479 vertices processed
150000 of 160479 vertices processed
thickness calculation complete, 355:897 truncations.
37984 vertices at 0 distance
109456 vertices at 1 distance
102099 vertices at 2 distance
42033 vertices at 3 distance
12152 vertices at 4 distance
3266 vertices at 5 distance
931 vertices at 6 distance
266 vertices at 7 distance
118 vertices at 8 distance
58 vertices at 9 distance
39 vertices at 10 distance
24 vertices at 11 distance
13 vertices at 12 distance
14 vertices at 13 distance
9 vertices at 14 distance
18 vertices at 15 distance
14 vertices at 16 distance
11 vertices at 17 distance
5 vertices at 18 distance
4 vertices at 19 distance
16 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.thickness
positioning took 20.8 minutes
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/scripts

 cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.woT2.pial 

`/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial' -> `/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.woT2.pial'

 mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub016 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/sub016/mri/filled.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/brain.finalsurfs.mgz...
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
23684 bright wm thresholded.
383 bright non-wm voxels segmented.
reading original surface position from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.orig...
computing class statistics...
border white:    298969 voxels (1.78%)
border gray      333863 voxels (1.99%)
WM (93.0): 94.0 +- 9.8 [70.0 --> 110.0]
GM (76.0) : 74.9 +- 12.7 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 47.3 (was 70)
setting MAX_BORDER_WHITE to 114.8 (was 105)
setting MIN_BORDER_WHITE to 60.0 (was 85)
setting MAX_CSF to 34.5 (was 40)
setting MAX_GRAY to 95.2 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 53.6 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 21.8 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=105,    GM=60
mean inside = 93.5, mean outside = 69.7
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/sub016/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.89 +- 0.26 (0.03-->9.83) (max @ vno 68130 --> 70451)
face area 0.33 +- 0.16 (0.00-->6.84)
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 14 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 5 points - only 0.00% unknown
deleting segment 6 with 19 points - only 0.00% unknown
deleting segment 8 with 20 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 10 with 3 points - only 0.00% unknown
deleting segment 11 with 40 points - only 0.00% unknown
deleting segment 12 with 487 points - only 0.00% unknown
deleting segment 13 with 6 points - only 0.00% unknown
deleting segment 15 with 105 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 18 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 19 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 20 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 21 with 2 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 +- 0.25 (0.05-->9.83) (max @ vno 70451 --> 68130)
face area 0.33 +- 0.16 (0.00-->6.84)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4833013.5, rms=0.00
rms = 1.31, time step reduction 1 of 3 to 0.250...
rms = 0.32, 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=4833013.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 14 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 5 points - only 0.00% unknown
deleting segment 5 with 19 points - only 0.00% unknown
deleting segment 6 with 20 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 40 points - only 0.00% unknown
deleting segment 9 with 487 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 105 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 16 with 2 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 (0.05-->9.83) (max @ vno 70451 --> 68130)
face area 0.33 +- 0.16 (0.00-->6.84)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4833013.5, rms=0.00
rms = 1.33, time step reduction 1 of 3 to 0.250...
rms = 0.33, 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=4833013.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 14 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 5 points - only 0.00% unknown
deleting segment 5 with 19 points - only 0.00% unknown
deleting segment 6 with 20 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 40 points - only 0.00% unknown
deleting segment 9 with 487 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 105 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 16 with 2 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 (0.05-->9.83) (max @ vno 70451 --> 68130)
face area 0.33 +- 0.16 (0.00-->6.84)
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4833013.5, rms=0.00
rms = 1.31, time step reduction 1 of 3 to 0.250...
rms = 0.32, 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=4833013.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
deleting segment 0 with 12 points - only 0.00% unknown
deleting segment 1 with 21 points - only 0.00% unknown
deleting segment 2 with 14 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 5 points - only 0.00% unknown
deleting segment 5 with 19 points - only 0.00% unknown
deleting segment 6 with 20 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 40 points - only 0.00% unknown
deleting segment 9 with 487 points - only 0.00% unknown
deleting segment 10 with 6 points - only 0.00% unknown
deleting segment 11 with 105 points - only 0.00% unknown
removing 2 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 13 with 4 points - only 0.00% unknown
removing 1 vertex label from ripped group
deleting segment 14 with 1 points - only 0.00% unknown
removing 3 vertex label from ripped group
deleting segment 15 with 3 points - only 0.00% unknown
removing 2 vertex label from ripped group
deleting segment 16 with 2 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=4833013.5, rms=0.00
rms = 1.33, time step reduction 1 of 3 to 0.250...
rms = 0.33, 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=4833013.5, rms=0.000 (1.000%)
positioning took 0.3 minutes
inhibiting deformation at non-cortical midline structures...
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 [92.30 205.70], gm=149.00+-18.90, and vertices in regions > 139.5
53781 surface locations found to contain inconsistent values (6053 in, 47728 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=577312.1, rms=0.22
001: dt: 0.5000, sse=540316.5, rms=0.215 (0.000%)
002: dt: 0.5000, sse=518240.6, rms=0.201 (0.000%)
003: dt: 0.5000, sse=504950.8, rms=0.190 (0.000%)
004: dt: 0.5000, sse=494329.2, rms=0.180 (0.000%)
005: dt: 0.5000, sse=487119.2, rms=0.172 (0.000%)
006: dt: 0.5000, sse=481500.6, rms=0.166 (0.000%)
007: dt: 0.5000, sse=476917.7, rms=0.160 (0.000%)
008: dt: 0.5000, sse=473099.1, rms=0.155 (0.000%)
009: dt: 0.5000, sse=470895.4, rms=0.151 (0.000%)
010: dt: 0.5000, sse=468088.1, rms=0.147 (0.000%)
011: dt: 0.5000, sse=466238.7, rms=0.144 (0.000%)
012: dt: 0.5000, sse=464480.7, rms=0.142 (0.000%)
013: dt: 0.5000, sse=463018.3, rms=0.140 (0.000%)
014: dt: 0.5000, sse=461407.7, rms=0.138 (0.000%)
015: dt: 0.5000, sse=460017.0, rms=0.137 (0.000%)
016: dt: 0.5000, sse=458620.0, rms=0.136 (0.000%)
017: dt: 0.5000, sse=457024.2, rms=0.135 (0.000%)
018: dt: 0.5000, sse=455395.4, rms=0.135 (0.000%)
019: dt: 0.5000, sse=453960.3, rms=0.135 (0.000%)
020: dt: 0.5000, sse=453225.4, rms=0.135 (0.000%)
021: dt: 0.5000, sse=452069.9, rms=0.135 (0.000%)
022: dt: 0.5000, sse=450405.6, rms=0.135 (0.000%)
023: dt: 0.5000, sse=449234.2, rms=0.135 (0.000%)
024: dt: 0.5000, sse=448341.0, rms=0.135 (0.000%)
025: dt: 0.5000, sse=446750.0, rms=0.135 (0.000%)
026: dt: 0.5000, sse=446009.4, rms=0.136 (0.000%)
027: dt: 0.5000, sse=444634.4, rms=0.136 (0.000%)
028: dt: 0.5000, sse=443450.3, rms=0.136 (0.000%)
029: dt: 0.5000, sse=442174.8, rms=0.137 (0.000%)
030: dt: 0.5000, sse=441035.6, rms=0.137 (0.000%)
positioning took 4.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [89.80 206.20], gm=148.00+-19.40, and vertices in regions > 138.3
43282 surface locations found to contain inconsistent values (2125 in, 41157 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=45524.7, rms=0.11
031: dt: 0.5000, sse=45359.8, rms=0.109 (0.000%)
032: dt: 0.5000, sse=46338.8, rms=0.099 (0.000%)
033: dt: 0.5000, sse=47439.3, rms=0.093 (0.000%)
034: dt: 0.5000, sse=48338.7, rms=0.088 (0.000%)
035: dt: 0.5000, sse=49099.1, rms=0.084 (0.000%)
036: dt: 0.5000, sse=49763.9, rms=0.080 (0.000%)
037: dt: 0.5000, sse=50400.2, rms=0.076 (0.000%)
038: dt: 0.5000, sse=51024.8, rms=0.073 (0.000%)
039: dt: 0.5000, sse=51626.3, rms=0.069 (0.000%)
040: dt: 0.5000, sse=52250.5, rms=0.067 (0.000%)
041: dt: 0.5000, sse=52839.6, rms=0.064 (0.000%)
042: dt: 0.5000, sse=53378.6, rms=0.062 (0.000%)
043: dt: 0.5000, sse=53894.7, rms=0.059 (0.000%)
044: dt: 0.5000, sse=54327.8, rms=0.057 (0.000%)
045: dt: 0.5000, sse=54761.2, rms=0.056 (0.000%)
046: dt: 0.5000, sse=55220.6, rms=0.054 (0.000%)
047: dt: 0.5000, sse=55600.4, rms=0.052 (0.000%)
048: dt: 0.5000, sse=55980.4, rms=0.051 (0.000%)
049: dt: 0.5000, sse=56346.9, rms=0.050 (0.000%)
050: dt: 0.5000, sse=56656.5, rms=0.049 (0.000%)
051: dt: 0.5000, sse=56945.3, rms=0.047 (0.000%)
052: dt: 0.5000, sse=57205.8, rms=0.046 (0.000%)
053: dt: 0.5000, sse=57428.1, rms=0.045 (0.000%)
054: dt: 0.5000, sse=57662.9, rms=0.044 (0.000%)
055: dt: 0.5000, sse=57878.0, rms=0.044 (0.000%)
056: dt: 0.5000, sse=58036.0, rms=0.043 (0.000%)
057: dt: 0.5000, sse=58191.1, rms=0.042 (0.000%)
058: dt: 0.5000, sse=58353.2, rms=0.041 (0.000%)
059: dt: 0.5000, sse=58484.9, rms=0.041 (0.000%)
060: dt: 0.5000, sse=58627.5, rms=0.040 (0.000%)
positioning took 4.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [89.50 206.50], gm=148.00+-19.50, and vertices in regions > 138.2
41413 surface locations found to contain inconsistent values (523 in, 40890 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=6252.5, rms=0.05
061: dt: 0.5000, sse=6250.9, rms=0.050 (0.000%)
062: dt: 0.5000, sse=6288.3, rms=0.046 (0.000%)
063: dt: 0.5000, sse=6318.4, rms=0.044 (0.000%)
064: dt: 0.5000, sse=6338.7, rms=0.042 (0.000%)
065: dt: 0.5000, sse=6347.6, rms=0.040 (0.000%)
066: dt: 0.5000, sse=6352.7, rms=0.038 (0.000%)
067: dt: 0.5000, sse=6353.5, rms=0.037 (0.000%)
068: dt: 0.5000, sse=6354.3, rms=0.036 (0.000%)
069: dt: 0.5000, sse=6355.8, rms=0.035 (0.000%)
070: dt: 0.5000, sse=6358.2, rms=0.034 (0.000%)
071: dt: 0.5000, sse=6364.1, rms=0.033 (0.000%)
072: dt: 0.5000, sse=6367.2, rms=0.033 (0.000%)
073: dt: 0.5000, sse=6371.2, rms=0.032 (0.000%)
074: dt: 0.5000, sse=6373.3, rms=0.031 (0.000%)
075: dt: 0.5000, sse=6375.0, rms=0.030 (0.000%)
076: dt: 0.5000, sse=6377.8, rms=0.030 (0.000%)
077: dt: 0.5000, sse=6379.8, rms=0.029 (0.000%)
078: dt: 0.5000, sse=6383.7, rms=0.028 (0.000%)
079: dt: 0.5000, sse=6387.8, rms=0.028 (0.000%)
080: dt: 0.5000, sse=6391.2, rms=0.028 (0.000%)
081: dt: 0.5000, sse=6395.9, rms=0.027 (0.000%)
082: dt: 0.5000, sse=6399.5, rms=0.027 (0.000%)
083: dt: 0.5000, sse=6405.0, rms=0.027 (0.000%)
084: dt: 0.5000, sse=6407.4, rms=0.027 (0.000%)
085: dt: 0.5000, sse=6411.0, rms=0.026 (0.000%)
086: dt: 0.5000, sse=6413.6, rms=0.026 (0.000%)
087: dt: 0.5000, sse=6416.7, rms=0.026 (0.000%)
088: dt: 0.5000, sse=6419.7, rms=0.026 (0.000%)
089: dt: 0.5000, sse=6420.7, rms=0.026 (0.000%)
090: dt: 0.5000, sse=6420.5, rms=0.026 (0.000%)
positioning took 4.3 minutes
repositioning pial surface locations using  ../mri/T2.mgz
locating cortical regions not in the range [88.50 205.50], gm=147.00+-19.50, and vertices in regions > 137.2
34465 surface locations found to contain inconsistent values (509 in, 33956 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/sub016/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=924.1, rms=0.04
091: dt: 0.5000, sse=921.2, rms=0.043 (0.000%)
092: dt: 0.5000, sse=891.2, rms=0.041 (0.000%)
093: dt: 0.5000, sse=867.7, rms=0.039 (0.000%)
094: dt: 0.5000, sse=846.4, rms=0.037 (0.000%)
095: dt: 0.5000, sse=828.1, rms=0.035 (0.000%)
096: dt: 0.5000, sse=815.2, rms=0.034 (0.000%)
097: dt: 0.5000, sse=805.5, rms=0.033 (0.000%)
098: dt: 0.5000, sse=798.8, rms=0.032 (0.000%)
099: dt: 0.5000, sse=792.5, rms=0.032 (0.000%)
100: dt: 0.5000, sse=786.2, rms=0.031 (0.000%)
101: dt: 0.5000, sse=779.7, rms=0.030 (0.000%)
102: dt: 0.5000, sse=774.9, rms=0.030 (0.000%)
103: dt: 0.5000, sse=770.3, rms=0.029 (0.000%)
104: dt: 0.5000, sse=766.4, rms=0.029 (0.000%)
105: dt: 0.5000, sse=762.4, rms=0.028 (0.000%)
106: dt: 0.5000, sse=759.3, rms=0.028 (0.000%)
107: dt: 0.5000, sse=756.1, rms=0.027 (0.000%)
108: dt: 0.5000, sse=753.5, rms=0.027 (0.000%)
109: dt: 0.5000, sse=750.8, rms=0.026 (0.000%)
110: dt: 0.5000, sse=749.4, rms=0.026 (0.000%)
111: dt: 0.5000, sse=747.7, rms=0.026 (0.000%)
112: dt: 0.5000, sse=748.8, rms=0.026 (0.000%)
113: dt: 0.5000, sse=747.9, rms=0.026 (0.000%)
114: dt: 0.5000, sse=746.2, rms=0.026 (0.000%)
115: dt: 0.5000, sse=744.9, rms=0.025 (0.000%)
116: dt: 0.5000, sse=744.1, rms=0.025 (0.000%)
117: dt: 0.5000, sse=742.9, rms=0.025 (0.000%)
118: dt: 0.5000, sse=742.5, rms=0.025 (0.000%)
119: dt: 0.5000, sse=741.8, rms=0.025 (0.000%)
120: dt: 0.5000, sse=742.3, rms=0.025 (0.000%)
positioning took 4.2 minutes
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.area.pial
vertex spacing 1.02 +- 0.43 (0.05-->10.65) (max @ vno 70451 --> 68130)
face area 0.41 +- 0.31 (0.00-->8.47)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 162159 vertices processed
25000 of 162159 vertices processed
50000 of 162159 vertices processed
75000 of 162159 vertices processed
100000 of 162159 vertices processed
125000 of 162159 vertices processed
150000 of 162159 vertices processed
0 of 162159 vertices processed
25000 of 162159 vertices processed
50000 of 162159 vertices processed
75000 of 162159 vertices processed
100000 of 162159 vertices processed
125000 of 162159 vertices processed
150000 of 162159 vertices processed
thickness calculation complete, 487:848 truncations.
38169 vertices at 0 distance
112062 vertices at 1 distance
103989 vertices at 2 distance
41599 vertices at 3 distance
11472 vertices at 4 distance
3120 vertices at 5 distance
962 vertices at 6 distance
336 vertices at 7 distance
162 vertices at 8 distance
95 vertices at 9 distance
65 vertices at 10 distance
30 vertices at 11 distance
19 vertices at 12 distance
22 vertices at 13 distance
14 vertices at 14 distance
19 vertices at 15 distance
22 vertices at 16 distance
15 vertices at 17 distance
9 vertices at 18 distance
11 vertices at 19 distance
14 vertices at 20 distance
writing curvature file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.thickness
positioning took 20.9 minutes
#--------------------------------------------
#@# Surf Volume lh Fri Aug  9 00:17:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 00:17:18 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 00:17:19 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub016 

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 = 37
writing volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Fri Aug  9 00:39:03 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 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 sub016 


$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 sub016 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1402840 mm^3    (det: 1.388687 )
Computing euler number
orig.nofix lheno =  -46, rheno = -32
orig.nofix lhholes =   24, rhholes = 17
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 306260.490 305489.000  diff=  771.5  pctdiff= 0.252
rhCtxGM: 309907.285 309138.000  diff=  769.3  pctdiff= 0.248
lhCtxWM: 253268.933 253103.500  diff=  165.4  pctdiff= 0.065
rhCtxWM: 258556.463 258667.500  diff= -111.0  pctdiff=-0.043
SubCortGMVol  75858.000
SupraTentVol  1220313.171 (1217624.000) diff=2689.171 pctdiff=0.220
SupraTentVolNotVent  1205373.171 (1202684.000) diff=2689.171 pctdiff=0.223
BrainSegVol  1369384.000 (1366874.000) diff=2510.000 pctdiff=0.183
BrainSegVolNotVent  1350669.000 (1351917.171) diff=-1248.171 pctdiff=-0.092
BrainSegVolNotVent  1350669.000
CerebellumVol 147638.000
VentChorVol   14940.000
3rd4th5thCSF   3775.000
CSFVol  1308.000, OptChiasmVol   304.000
MaskVol 1848686.000
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    5205    5204.545
  4     5                  Left-Inf-Lat-Vent     587     587.482
  5     7       Left-Cerebellum-White-Matter   15848   15847.543
  6     8             Left-Cerebellum-Cortex   57326   57326.152
  7    10               Left-Thalamus-Proper    9388    9388.153
  8    11                       Left-Caudate    5055    5055.190
  9    12                       Left-Putamen    7345    7345.435
 10    13                      Left-Pallidum    2485    2484.961
 11    14                      3rd-Ventricle     878     878.457
 12    15                      4th-Ventricle    1789    1788.563
 13    16                         Brain-Stem   25619   25619.164
 14    17                   Left-Hippocampus    5163    5163.188
 15    18                      Left-Amygdala    1837    1837.226
 16    24                                CSF    1269    1268.591
 17    26                Left-Accumbens-area     926     926.388
 18    28                     Left-VentralDC    4287    4287.005
 19    30                        Left-vessel     252     252.209
 20    31                Left-choroid-plexus    1120    1119.660
 23    43            Right-Lateral-Ventricle    6175    6175.496
 24    44                 Right-Inf-Lat-Vent     417     417.325
 25    46      Right-Cerebellum-White-Matter   16511   16510.811
 26    47            Right-Cerebellum-Cortex   60517   60517.289
 27    49              Right-Thalamus-Proper    8712    8711.553
 28    50                      Right-Caudate    6116    6115.571
 29    51                      Right-Putamen    6870    6870.305
 30    52                     Right-Pallidum    2510    2509.738
 31    53                  Right-Hippocampus    4969    4968.664
 32    54                     Right-Amygdala    2274    2273.631
 33    58               Right-Accumbens-area    1003    1003.480
 34    60                    Right-VentralDC    4570    4569.587
 35    62                       Right-vessel     123     123.374
 36    63               Right-choroid-plexus    1462    1462.179
 37    72                      5th-Ventricle       0       0.000
 38    77                 WM-hypointensities    3867    3866.558
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities      39      39.195
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     301     300.605
 45   251                       CC_Posterior     857     856.593
 46   252                   CC_Mid_Posterior     412     411.740
 47   253                         CC_Central     428     427.937
 48   254                    CC_Mid_Anterior     500     499.593
 49   255                        CC_Anterior     905     904.610

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Fri Aug  9 00:41:45 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 mri_aparc2aseg --s sub016 --volmask 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub016
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/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/sub016/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 = 611610
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc+aseg.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 mri_aparc2aseg --s sub016 --volmask --a2009s 

SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer
subject sub016
outvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/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/sub016/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 = 611610
Used brute-force search on 0 voxels
Writing output aseg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Fri Aug  9 00:47:13 CEST 2013
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 mri_aparc2aseg --s sub016 --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 sub016
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/sub016/mri/aparc+aseg.mgz

Reading lh white surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white

Reading lh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial

Loading lh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/surf/rh.white

Reading rh pial surface 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial

Loading rh annotations from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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/sub016/mri/ribbon.mgz
Loading filled from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 9404 vertices from left hemi
Ripped 8753 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/sub016/mri/aseg.mgz
Loading Ctx Seg File /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 = 1123151
Used brute-force search on 127 voxels
Fixing Parahip LH WM
  Found 8 clusters
     0 k 2078.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1.000000
     5 k 12.000000
     6 k 1.000000
     7 k 12.000000
Fixing Parahip RH WM
  Found 9 clusters
     0 k 1.000000
     1 k 1929.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1.000000
     6 k 1.000000
     7 k 2.000000
     8 k 1.000000
Writing output aseg to mri/wmparc.mgz
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016

 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 sub016 --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 sub016 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname snake6
machine  x86_64
user     fkaule
UseRobust  0
atlas_icv (eTIV) = 1402840 mm^3    (det: 1.388687 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 306260.490 305489.000  diff=  771.5  pctdiff= 0.252
rhCtxGM: 309907.285 309138.000  diff=  769.3  pctdiff= 0.248
lhCtxWM: 253268.933 253103.500  diff=  165.4  pctdiff= 0.065
rhCtxWM: 258556.463 258667.500  diff= -111.0  pctdiff=-0.043
SubCortGMVol  75858.000
SupraTentVol  1220313.171 (1217624.000) diff=2689.171 pctdiff=0.220
SupraTentVolNotVent  1205373.171 (1202684.000) diff=2689.171 pctdiff=0.223
BrainSegVol  1369384.000 (1366874.000) diff=2510.000 pctdiff=0.183
BrainSegVolNotVent  1350669.000 (1351917.171) diff=-1248.171 pctdiff=-0.092
BrainSegVolNotVent  1350669.000
CerebellumVol 147638.000
VentChorVol   14940.000
3rd4th5thCSF   3775.000
CSFVol  1308.000, OptChiasmVol   304.000
MaskVol 1848686.000
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    2452    2451.532
  2   3002      wm-lh-caudalanteriorcingulate    3946    3945.573
  3   3003          wm-lh-caudalmiddlefrontal    6079    6078.784
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    2961    2961.475
  6   3006                   wm-lh-entorhinal    1284    1284.438
  7   3007                     wm-lh-fusiform    7966    7965.979
  8   3008             wm-lh-inferiorparietal   11257   11256.769
  9   3009             wm-lh-inferiortemporal    9263    9262.991
 10   3010             wm-lh-isthmuscingulate    4640    4639.525
 11   3011             wm-lh-lateraloccipital    9338    9337.695
 12   3012         wm-lh-lateralorbitofrontal    7724    7724.123
 13   3013                      wm-lh-lingual    6364    6364.017
 14   3014          wm-lh-medialorbitofrontal    3724    3724.163
 15   3015               wm-lh-middletemporal    7293    7293.097
 16   3016              wm-lh-parahippocampal    2142    2141.513
 17   3017                  wm-lh-paracentral    3707    3707.155
 18   3018              wm-lh-parsopercularis    4535    4534.863
 19   3019                wm-lh-parsorbitalis    1171    1171.051
 20   3020             wm-lh-parstriangularis    3172    3171.806
 21   3021                wm-lh-pericalcarine    4592    4591.900
 22   3022                  wm-lh-postcentral    7609    7608.956
 23   3023           wm-lh-posteriorcingulate    5355    5355.249
 24   3024                   wm-lh-precentral   14215   14214.800
 25   3025                    wm-lh-precuneus   11123   11122.730
 26   3026     wm-lh-rostralanteriorcingulate    2619    2619.199
 27   3027         wm-lh-rostralmiddlefrontal   12685   12685.373
 28   3028              wm-lh-superiorfrontal   20937   20937.270
 29   3029             wm-lh-superiorparietal   14351   14350.940
 30   3030             wm-lh-superiortemporal    9641    9641.078
 31   3031                wm-lh-supramarginal   10236   10236.092
 32   3032                  wm-lh-frontalpole     151     151.290
 33   3033                 wm-lh-temporalpole     731     730.634
 34   3034           wm-lh-transversetemporal     929     928.537
 35   3035                       wm-lh-insula   10118   10118.451
 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    2831    2831.255
120   4002      wm-rh-caudalanteriorcingulate    2638    2637.598
121   4003          wm-rh-caudalmiddlefrontal    5731    5730.535
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    3045    3045.040
124   4006                   wm-rh-entorhinal    1034    1033.776
125   4007                     wm-rh-fusiform    7612    7611.993
126   4008             wm-rh-inferiorparietal   13814   13813.651
127   4009             wm-rh-inferiortemporal    8415    8414.678
128   4010             wm-rh-isthmuscingulate    5231    5230.636
129   4011             wm-rh-lateraloccipital    9901    9900.562
130   4012         wm-rh-lateralorbitofrontal    7480    7480.153
131   4013                      wm-rh-lingual    6713    6712.950
132   4014          wm-rh-medialorbitofrontal    3751    3750.894
133   4015               wm-rh-middletemporal    7945    7944.837
134   4016              wm-rh-parahippocampal    1995    1995.037
135   4017                  wm-rh-paracentral    6093    6093.256
136   4018              wm-rh-parsopercularis    5347    5346.578
137   4019                wm-rh-parsorbitalis    1301    1301.438
138   4020             wm-rh-parstriangularis    4404    4404.237
139   4021                wm-rh-pericalcarine    4362    4361.587
140   4022                  wm-rh-postcentral    8380    8379.893
141   4023           wm-rh-posteriorcingulate    4716    4716.122
142   4024                   wm-rh-precentral   14818   14817.553
143   4025                    wm-rh-precuneus   10880   10879.696
144   4026     wm-rh-rostralanteriorcingulate    2748    2747.739
145   4027         wm-rh-rostralmiddlefrontal   12665   12665.396
146   4028              wm-rh-superiorfrontal   22764   22763.979
147   4029             wm-rh-superiorparietal   11638   11637.731
148   4030             wm-rh-superiortemporal    7994    7994.231
149   4031                wm-rh-supramarginal    9586    9586.322
150   4032                  wm-rh-frontalpole     256     256.280
151   4033                 wm-rh-temporalpole     654     653.627
152   4034           wm-rh-transversetemporal     747     747.147
153   4035                       wm-rh-insula   10469   10468.917
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   30700   30700.072
237   5002       Right-UnsegmentedWhiteMatter   32089   32089.314
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/sub016/label
#--------------------------------------------
#@# BA Labels lh Fri Aug  9 00:59:53 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 398
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4527
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 926
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8835
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 241
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4318
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 611
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6594
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 681
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6465
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 406
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4476
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 1787
Checking for and removing duplicates
Writing label file ./lh.BA6.label 15376
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 889
Checking for and removing duplicates
Writing label file ./lh.BA44.label 5070
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 1201
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4623
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 2377
Checking for and removing duplicates
Writing label file ./lh.V1.label 7018
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 3898
Checking for and removing duplicates
Writing label file ./lh.V2.label 12012
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 833
Checking for and removing duplicates
Writing label file ./lh.MT.label 2851
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 351
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1550
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 86
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1100
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 166
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2258
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 23
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1527
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 248
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2244
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 433
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2752
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 157
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1706
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 635
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 7670
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 512
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2424
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 510
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1661
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 1745
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 5150
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 1781
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 5115
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/lh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 160479
Number of reverse mapping hits = 271
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 784
mri_label2label: Done


 mris_label2annot --s sub016 --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/sub016/label
cmdline mris_label2annot --s sub016 --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 snake6
machine  x86_64
user     fkaule

subject sub016
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/sub016/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 112515 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.BA.annot

 mris_label2annot --s sub016 --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/sub016/label
cmdline mris_label2annot --s sub016 --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 snake6
machine  x86_64
user     fkaule

subject sub016
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/sub016/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 132861 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub016 lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1149    613   2316  2.623 0.404     0.163     0.131      114     8.4  BA1
 4525   2973   8268  2.566 0.464     0.121     0.034       50     6.3  BA2
  983    673    962  1.921 0.366     0.143     0.049       10     2.0  BA3a
 2836   1812   4720  2.242 0.614     0.120     0.037       35     4.4  BA3b
 1949   1016   4013  3.077 0.491     0.110     0.210       60     5.3  BA4a
 1569    944   2751  2.818 0.448     0.105     0.030       12     2.0  BA4p
10174   6679  25171  3.070 0.614     0.119     0.035      191    15.6  BA6
 3033   1986   6744  2.844 0.490     0.120     0.038       40     5.0  BA44
 3724   2528   7712  2.570 0.571     0.142     0.046       66     7.1  BA45
 4613   3269   6851  2.042 0.462     0.156     0.067       92    13.4  V1
 9425   6060  14706  2.214 0.545     0.158     0.071      208    29.0  V2
 2623   1768   4380  2.381 0.448     0.140     0.049       43     4.9  MT
 1361    949   3783  3.229 0.681     0.163     0.072       26     4.0  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub016 lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

  701    335   1409  2.627 0.332     0.181     0.181      105     7.5  BA1
 1576   1045   2963  2.516 0.433     0.116     0.030       15     1.9  BA2
  781    533    718  1.886 0.361     0.155     0.051        8     1.7  BA3a
 1753   1164   2431  1.925 0.344     0.102     0.028       15     1.8  BA3b
 2046   1043   4172  3.119 0.492     0.111     0.208      149     6.3  BA4a
 1224    760   1963  2.666 0.406     0.102     0.027        8     1.3  BA4p
 5405   3525  13798  3.144 0.580     0.117     0.035       56     8.0  BA6
 2112   1377   4634  2.831 0.460     0.126     0.041       32     3.8  BA44
 1587   1072   3832  2.814 0.450     0.163     0.058       38     3.7  BA45
 4860   3446   7264  2.031 0.465     0.157     0.073      100    16.5  V1
 4822   3104   7146  2.140 0.516     0.169     0.081      108    16.2  V2
  751    475   1281  2.497 0.423     0.144     0.052       12     1.5  MT
#--------------------------------------------
#@# BA Labels rh Fri Aug  9 01:04:52 CEST 2013

 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 604
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4566
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 676
Checking for and removing duplicates
Writing label file ./rh.BA2.label 7363
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 228
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4208
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 555
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 5077
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 895
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6642
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 447
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4920
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 2322
Checking for and removing duplicates
Writing label file ./rh.BA6.label 14578
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 1756
Checking for and removing duplicates
Writing label file ./rh.BA44.label 8668
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 1802
Checking for and removing duplicates
Writing label file ./rh.BA45.label 7157
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 2730
Checking for and removing duplicates
Writing label file ./rh.V1.label 7457
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 4422
Checking for and removing duplicates
Writing label file ./rh.V2.label 12438
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 925
Checking for and removing duplicates
Writing label file ./rh.MT.label 2857
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 192
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 944
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 272
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 1148
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 194
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 2882
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 59
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1757
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 347
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2530
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 238
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1626
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 152
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1641
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 1149
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 8108
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 471
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1483
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 568
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1746
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 1953
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 5185
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 2003
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 5440
mri_label2label: Done


 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub016 --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 = sub016
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/sub016/surf/rh.white
Reading target registration 
 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 162159
Number of reverse mapping hits = 127
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 395
mri_label2label: Done


 mris_label2annot --s sub016 --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/sub016/label
cmdline mris_label2annot --s sub016 --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 snake6
machine  x86_64
user     fkaule

subject sub016
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/sub016/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 111800 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.BA.annot

 mris_label2annot --s sub016 --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/sub016/label
cmdline mris_label2annot --s sub016 --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 snake6
machine  x86_64
user     fkaule

subject sub016
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/sub016/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 133862 unhit vertices
Writing annot to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub016 rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

 1234    622   2657  2.836 0.465     0.128     0.447       48     3.2  BA1
 3411   2318   5760  2.412 0.397     0.101     0.026       26     3.6  BA2
 1110    754   1172  1.983 0.380     0.131     0.038        9     1.8  BA3a
 2380   1505   3726  2.079 0.543     0.106     0.031       23     3.0  BA3b
 2154   1136   4370  3.141 0.553     0.104     0.294      211    47.9  BA4a
 1389    887   2423  2.795 0.441     0.098     0.031       12     1.8  BA4p
10186   6414  23606  3.041 0.597     0.120     0.078      212    22.4  BA6
 4529   2987   8799  2.749 0.447     0.113     0.036       42     5.6  BA44
 5076   3432  11633  2.717 0.589     0.142     0.064      133     9.4  BA45
 5217   3502   7631  2.067 0.413     0.155     0.071       97    15.4  V1
10109   6603  16061  2.250 0.529     0.161     0.092      238    31.4  V2
 2738   1871   4700  2.415 0.459     0.142     0.055       51     5.9  MT
  826    562   1993  3.049 0.765     0.149     0.064       11     2.1  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub016 rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

  939    455   1971  2.804 0.481     0.129     0.576       46     2.7  BA1
 1971   1324   3546  2.430 0.392     0.092     0.023       13     1.9  BA2
  951    644    912  1.977 0.367     0.132     0.036        7     1.5  BA3a
 1988   1285   2678  1.914 0.438     0.096     0.026       14     2.3  BA3b
 1224    601   2317  3.155 0.551     0.099     0.044       16     2.6  BA4a
 1173    746   2044  2.887 0.495     0.098     0.032       10     1.6  BA4p
 6353   3964  14626  3.011 0.600     0.116     0.101      169    16.1  BA6
 1412    937   3367  2.868 0.383     0.112     0.043       15     1.7  BA44
 1662   1115   4315  2.933 0.476     0.138     0.043       28     3.0  BA45
 5008   3350   7193  2.063 0.420     0.153     0.070       90    14.5  V1
 5235   3453   7829  2.089 0.483     0.174     0.075      111    15.5  V2
  381    250    753  2.535 0.449     0.144     0.051        8     0.8  MT
/home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Fri Aug  9 01:09:53 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub016 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject sub016.
processing subject lh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1259 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub016 lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/lh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

  470    298   1375  3.150 0.616     0.126     0.042        4     0.9  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Fri Aug  9 01:10:09 CEST 2013

 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub016 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject sub016.
processing subject rh.EC_average...
reading output surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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 1079 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub016 rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/mri/wm.mgz...
reading input surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.white...
reading input pial surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/surf/rh.pial...
reading input white surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub016/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

  447    289   1300  3.259 0.643     0.131     0.064        5     1.1  ./rh.entorhinal_exvivo.label

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

Started at Thu Aug 8 10:54:16 CEST 2013 
Ended   at Fri Aug 9 01:10:26 CEST 2013
#@#%# recon-all-run-time-hours 14.269
recon-all -s sub016 finished without error at Fri Aug  9 01:10:26 CEST 2013