Tue Jan 30 14:41:25 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base
/opt/freesurfer/5.3.0/bin/recon-all
-base BPD0072_base -tp BPD0072A -tp BPD0072B -tp BPD0072C -tp BPD0072D -all
subjid BPD0072_base
setenv SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
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 e21.hpcc.dartmouth.edu 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Jan 11 20:56:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    unlimited
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  32768 
memorylocked unlimited
maxproc      257225 

             total       used       free     shared    buffers     cached
Mem:      65941040   47177196   18763844          8     292640   40653244
-/+ buffers/cache:    6231312   59709728
Swap:     67108860      39496   67069364

########################################
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: 2018/01/30-19:41:26-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  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: 2018/01/30-19:41:26-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  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: 2018/01/30-19:41:26-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:26-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:26-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:26-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

 ======= NUMBER OF OPENMP THREADS = 1 ======= 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:27-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:28-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  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: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  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: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:29-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:30-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:30-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2018/01/30-19:41:30-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: zbasgoze  Machine: e21.hpcc.dartmouth.edu  Platform: Linux  PlatformVersion: 2.6.32-642.13.1.el6.x86_64  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
#######################################
#--------------------------------------------
#@# Longitudinal Base Subject Creation Tue Jan 30 14:41:30 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base

 mri_diff --notallow-pix /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/rawavg.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/rawavg.mgz 

Volumes differ in resolution
v1res 0.999985 1.000000 1.000000
v2res 0.999957 1.000000 1.000000
diff 0.000027 0.000000 0.000000

 mri_diff --notallow-pix /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/rawavg.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/rawavg.mgz 

Volumes differ in resolution
v1res 0.999948 1.000000 1.000000
v2res 0.999957 1.000000 1.000000
diff -0.000010 0.000000 0.000000

 mri_diff --notallow-pix /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/rawavg.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/rawavg.mgz 

Volumes differ in resolution
v1res 0.999996 1.000000 1.000000
v2res 0.999957 1.000000 1.000000
diff 0.000038 0.000000 0.000000

*******************************************************************************
WARNING: Image geometries differ across time, maybe due to aquisition changes?
         This can potentially bias a longitudinal study! Will continue in 10s.
*******************************************************************************

 mri_robust_template --mov /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz --lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072A_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072B_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072C_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072D_to_BPD0072_base.lta --template /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/norm_template.mgz --average 1 --sat 4.685 

$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz as movable/source volume.
    Total: 4 input volumes
--lta: Will output LTA transforms
--template: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/norm_template.mgz as template output volume.
--average: Using method 1 for template computation.
--sat: Using saturation 4.685 in M-estimator!
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz' to bspline ...
MRItoBSpline degree 3
Will use TP 3 as random initial target (seed 41324 ).

MultiRegistration::initializing Xforms (init 3 , maxres 0 , iterate 5 , epsit 0.01 ) : 

[init] ========================= TP 2 to TP 3 ==============================
         Register TP 2 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz )
          to      TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz )

[init] ========================= TP 1 to TP 3 ==============================
         Register TP 1 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz )
          to      TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz )

[init] ========================= TP 4 to TP 3 ==============================
         Register TP 4 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz )
          to      TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz )

  computing coord of TP 2 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz )
   wrt to TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz )
  computing coord of TP 1 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz )
   wrt to TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz )
  computing coord of TP 4 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz )
   wrt to TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz )
  computing mean coord of TP 3 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/norm.mgz ) 
   mapping back to rot, err = 4.35773e-08
  computing mean coord of TP 2 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/norm.mgz ) 
   mapping back to rot, err = 2.52568e-08
  computing mean coord of TP 1 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/norm.mgz ) 
   mapping back to rot, err = 4.87651e-08
  computing mean coord of TP 4 ( /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/norm.mgz ) 
   mapping back to rot, err = 8.49832e-08
Computing first template
mapping movs and creating initial template...
 using median 

=======================================================

Working on global iteration : 1

=======================================================
  noxformits = 3

Working on TP 1

 - running multi-resolutional registration on TP 1...
   tp 1 distance: 0.00961251
 - mapping tp 1 to template (cubic bspline) ...

Finished TP : 1

=====================================================

Working on TP 2

 - running multi-resolutional registration on TP 2...
   tp 2 distance: 0.0183742
 - mapping tp 2 to template (cubic bspline) ...

Finished TP : 2

=====================================================

Working on TP 3

 - running multi-resolutional registration on TP 3...
   tp 3 distance: 0.00541377
 - mapping tp 3 to template (cubic bspline) ...

Finished TP : 3

=====================================================

Working on TP 4

 - running multi-resolutional registration on TP 4...
   tp 4 distance: 0.0229984
 - mapping tp 4 to template (cubic bspline) ...

Finished TP : 4

=====================================================

Global Iteration 1 Distances: 
0.00961251 0.0183742 0.00541377 0.0229984 
Maxchange: 0.0229984

Computing new template 1
 using median 
 DONE : computeTemplate 
Writing final template: /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/norm_template.mgz
Writing final transforms (warps etc.)...
 Determinant( lta[ 0 ]) : 1

 Determinant( lta[ 1 ]) : 1

 Determinant( lta[ 2 ]) : 1

 Determinant( lta[ 3 ]) : 1

registration took 6 minutes and 48 seconds.

 Thank you for using RobustTemplate! 
 If you find it useful and use it for a publication, please cite: 

 Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis
 M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012.
 http://dx.doi.org/10.1016/j.neuroimage.2012.02.084
 http://reuter.mit.edu/papers/reuter-long12.pdf

 mri_robust_template --mov /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/orig.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/orig.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/orig.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/orig.mgz --average 1 --ixforms /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072A_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072B_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072C_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072D_to_BPD0072_base.lta --noit --template /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/orig.mgz 

$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/orig.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/orig.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/orig.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/orig.mgz as movable/source volume.
    Total: 4 input volumes
--average: Using method 1 for template computation.
--ixforms: Will use init XFORMS.
--noit: Will output only first template (no iterations)!
--template: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/orig.mgz as template output volume.
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/orig.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/orig.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/orig.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/orig.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/orig.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/orig.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/orig.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/orig.mgz' to bspline ...
MRItoBSpline degree 3
mapping movs and creating initial template...
 using median 
Writing final template: /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/orig.mgz
Writing final transforms (warps etc.)...
registration took 1 minutes and 16 seconds.

 Thank you for using RobustTemplate! 
 If you find it useful and use it for a publication, please cite: 

 Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis
 M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012.
 http://dx.doi.org/10.1016/j.neuroimage.2012.02.084
 http://reuter.mit.edu/papers/reuter-long12.pdf

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms

 mri_concatenate_lta -invert1 BPD0072A_to_BPD0072_base.lta identity.nofile BPD0072_base_to_BPD0072A.lta 

invert the first LTA before applying it 
Read individual LTAs
Writing  LTA to file BPD0072_base_to_BPD0072A.lta...
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 BPD0072B_to_BPD0072_base.lta identity.nofile BPD0072_base_to_BPD0072B.lta 

invert the first LTA before applying it 
Read individual LTAs
Writing  LTA to file BPD0072_base_to_BPD0072B.lta...
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 BPD0072C_to_BPD0072_base.lta identity.nofile BPD0072_base_to_BPD0072C.lta 

invert the first LTA before applying it 
Read individual LTAs
Writing  LTA to file BPD0072_base_to_BPD0072C.lta...
mri_concatenate_lta successful.

 mri_concatenate_lta -invert1 BPD0072D_to_BPD0072_base.lta identity.nofile BPD0072_base_to_BPD0072D.lta 

invert the first LTA before applying it 
Read individual LTAs
Writing  LTA to file BPD0072_base_to_BPD0072D.lta...
mri_concatenate_lta successful.
#--------------------------------------------
#@# MotionCor Tue Jan 30 14:49:54 EST 2018

 mri_add_xform_to_header -c /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/talairach.xfm /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/orig.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/orig.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Talairach Tue Jan 30 14:49:59 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Tue Jan 30 14:53:53 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7886, pval=0.8469 >= threshold=0.0050)

 awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/talairach_avi.log 

 tal_QC_AZS /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/talairach_avi.log 

TalAviQA: 0.97362
z-score: -1
#--------------------------------------------
#@# Nu Intensity Correction Tue Jan 30 14:53:54 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 e21.hpcc.dartmouth.edu 2.6.32-642.13.1.el6.x86_64 #1 SMP Wed Jan 11 20:56:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Tue Jan 30 14:53:54 EST 2018
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.49284
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.49284/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.49284/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=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 3.25963e-09, 0)
j_ras = (-9.31323e-10, 1.49012e-08, -1)
k_ras = (5.58794e-09, 1, 1.49012e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.49284/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Tue Jan 30 14:54:01 EST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.49284/nu0.mnc ./tmp.mri_nu_correct.mni.49284/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.49284/0/
[zbasgoze@e21.hpcc.dartmouth.edu:/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/] [2018-01-30 14:54:01] running:
  /opt/freesurfer/5.3.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.49284/0/ ./tmp.mri_nu_correct.mni.49284/nu0.mnc ./tmp.mri_nu_correct.mni.49284/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 37 
CV of field change: 0.000960818
[zbasgoze@e21.hpcc.dartmouth.edu:/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/] [2018-01-30 14:54:54] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.49284/nu0.mnc ./tmp.mri_nu_correct.mni.49284/0//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done

--------------------------------------------------------
Iteration 2 Tue Jan 30 14:55:04 EST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.49284/nu1.mnc ./tmp.mri_nu_correct.mni.49284/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.49284/1/
[zbasgoze@e21.hpcc.dartmouth.edu:/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/] [2018-01-30 14:55:04] 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.49284/1/ ./tmp.mri_nu_correct.mni.49284/nu1.mnc ./tmp.mri_nu_correct.mni.49284/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 20 
CV of field change: 0.000956367
[zbasgoze@e21.hpcc.dartmouth.edu:/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/] [2018-01-30 14:55:36] running:
  /opt/freesurfer/5.3.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.49284/nu1.mnc ./tmp.mri_nu_correct.mni.49284/1//template.mnc

Transforming slices:......................................................................................Done
Transforming slices:................................................................................................................................................................................................................................................................Done

 
mri_binarize --i ./tmp.mri_nu_correct.mni.49284/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.49284/ones.mgz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri
cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.49284/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.49284/ones.mgz 
sysname  Linux
hostname e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze

input      ./tmp.mri_nu_correct.mni.49284/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.49284/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.49284/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.49284/sum.junk --avgwf ./tmp.mri_nu_correct.mni.49284/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.49284/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.49284/sum.junk --avgwf ./tmp.mri_nu_correct.mni.49284/input.mean.dat 
sysname  Linux
hostname e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.49284/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.49284/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.49284/ones.mgz --i ./tmp.mri_nu_correct.mni.49284/nu2.mnc --sum ./tmp.mri_nu_correct.mni.49284/sum.junk --avgwf ./tmp.mri_nu_correct.mni.49284/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.49284/ones.mgz --i ./tmp.mri_nu_correct.mni.49284/nu2.mnc --sum ./tmp.mri_nu_correct.mni.49284/sum.junk --avgwf ./tmp.mri_nu_correct.mni.49284/output.mean.dat 
sysname  Linux
hostname e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.49284/ones.mgz
Loading ./tmp.mri_nu_correct.mni.49284/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.49284/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.49284/nu2.mnc ./tmp.mri_nu_correct.mni.49284/nu2.mnc mul .99091241497510144627
Saving result to './tmp.mri_nu_correct.mni.49284/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.49284/nu2.mnc nu.mgz --like orig.mgz
mri_convert ./tmp.mri_nu_correct.mni.49284/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.49284/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 3.25963e-09, 0)
j_ras = (-9.31323e-10, 1.49012e-08, -1)
k_ras = (5.58794e-09, 1, 1.49012e-08)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 12 seconds.
mapping (12, 157) to ( 3, 110)

Tue Jan 30 14:56:51 EST 2018
mri_nu_correct.mni done

 mri_add_xform_to_header -c /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Tue Jan 30 14:56:53 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

 mri_normalize -g 1 -W ctrl_vol.mgz bias_vol.mgz nu.mgz T1.mgz 

using max gradient = 1.000
writing ctrl pts to   ctrl_vol.mgz
writing bias field to bias_vol.mgz
reading from nu.mgz...
normalizing image...
talairach transform
 1.036   0.019  -0.027  -1.071;
-0.037   1.050   0.292  -25.277;
-0.005  -0.187   1.128  -7.787;
 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 = 15
Starting OpenSpline(): npoints = 15
writing control point volume to ctrl_vol.mgz...
writing control point volume to ctrl_vol.mgz...
writing control point volume to ctrl_vol.mgz...
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 79 (79), valley at 43 (43)
csf peak at 39, setting threshold to 65
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 78 (78), valley at 41 (41)
csf peak at 39, setting threshold to 65
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing bias field to bias_vol.mgz....
writing output to T1.mgz
3D bias adjustment took 3 minutes and 32 seconds.
#--------------------------------------------
#@# Skull Stripping Tue Jan 30 15:00:27 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

 mri_robust_template --mov /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/brainmask.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/brainmask.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/brainmask.mgz /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/brainmask.mgz --average 0 --ixforms /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072A_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072B_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072C_to_BPD0072_base.lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/BPD0072D_to_BPD0072_base.lta --noit --finalnearest --template brainmask_template.mgz 

$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $

--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/brainmask.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/brainmask.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/brainmask.mgz as movable/source volume.
--mov: Using /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/brainmask.mgz as movable/source volume.
    Total: 4 input volumes
--average: Using method 0 for template computation.
--ixforms: Will use init XFORMS.
--noit: Will output only first template (no iterations)!
--finalnearest: Use nearest neighbor interpolation for final average!
--template: Using brainmask_template.mgz as template output volume.
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/brainmask.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072A/mri/brainmask.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/brainmask.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072B/mri/brainmask.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/brainmask.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072C/mri/brainmask.mgz' to bspline ...
MRItoBSpline degree 3
reading source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/brainmask.mgz'...
converting source '/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072D/mri/brainmask.mgz' to bspline ...
MRItoBSpline degree 3
mapping movs and creating initial template...
    using mean
Writing final template: brainmask_template.mgz
Writing final transforms (warps etc.)...
registration took 0 minutes and 29 seconds.

 Thank you for using RobustTemplate! 
 If you find it useful and use it for a publication, please cite: 

 Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis
 M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012.
 http://dx.doi.org/10.1016/j.neuroimage.2012.02.084
 http://reuter.mit.edu/papers/reuter-long12.pdf

 mri_mask -keep_mask_deletion_edits T1.mgz brainmask_template.mgz brainmask.auto.mgz 

Transferring mask edits ('1' voxels) to dst vol
DoAbs = 0
Writing masked volume to brainmask.auto.mgz...done.

 mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_template.mgz brainmask.auto.mgz 

transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
DoAbs = 0
Writing masked volume to brainmask.auto.mgz...done.

 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Tue Jan 30 15:01:05 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

 mri_em_register -mask brainmask.mgz norm_template.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta 

 ======= NUMBER OF OPENMP THREADS = 1 ======= 
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 'norm_template.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 14.9 or > 790.2 
total sample mean = 84.0 (478 zeros)
************************************************
spacing=8, using 2185 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2185, 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=29.3
skull bounding box = (58, 74, 55) --> (196, 194, 215)
using (104, 114, 135) as brain centroid...
mean wm in atlas = 107, using box (87,99,115) --> (120, 128,154) 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 = -4.8
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.204831 @ (-9.091, -9.091, -27.273)
max log p =    -4.101418 @ (4.545, -4.545, 4.545)
max log p =    -4.044152 @ (2.273, 2.273, -2.273)
max log p =    -4.014019 @ (-1.136, 3.409, -1.136)
max log p =    -4.014019 @ (0.000, 0.000, 0.000)
max log p =    -4.014019 @ (0.000, 0.000, 0.000)
Found translation: (-3.4, -8.0, -26.1): log p = -4.014
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-4.0 (thresh=-4.0)
 1.075   0.000   0.000  -13.175;
 0.000   1.194   0.320  -74.637;
 0.000  -0.298   1.111   4.542;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 1.075   0.000   0.000  -13.175;
 0.000   1.194   0.320  -74.637;
 0.000  -0.275   1.028   12.101;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.4, old_max_log_p =-3.4 (thresh=-3.4)
 1.075   0.000   0.000  -13.175;
 0.000   1.194   0.320  -74.637;
 0.000  -0.275   1.028   12.101;
 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=-3.2, old_max_log_p =-3.4 (thresh=-3.4)
 1.054   0.000   0.000  -8.577;
 0.000   1.237   0.223  -69.759;
 0.000  -0.155   1.054  -10.394;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 4 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2)
 1.054   0.000   0.000  -8.577;
 0.000   1.237   0.223  -69.759;
 0.000  -0.155   1.054  -10.394;
 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=-3.1, old_max_log_p =-3.2 (thresh=-3.2)
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 6 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-3.1, old_max_log_p =-3.1 (thresh=-3.1)
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 2185 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.05395   0.02015   0.00421  -12.64317;
-0.01731   1.23548   0.25814  -71.87244;
 0.00000  -0.19609   1.04759  -4.28845;
 0.00000   0.00000   0.00000   1.00000;
nsamples 2185
Quasinewton: input matrix
 1.05395   0.02015   0.00421  -12.64317;
-0.01731   1.23548   0.25814  -71.87244;
 0.00000  -0.19609   1.04759  -4.28845;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -3.1 (old=-4.8)
transform before final EM align:
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 244171 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.05395   0.02015   0.00421  -12.64317;
-0.01731   1.23548   0.25814  -71.87244;
 0.00000  -0.19609   1.04759  -4.28845;
 0.00000   0.00000   0.00000   1.00000;
nsamples 244171
Quasinewton: input matrix
 1.05395   0.02015   0.00421  -12.64317;
-0.01731   1.23548   0.25814  -71.87244;
 0.00000  -0.19609   1.04759  -4.28845;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) =    3.9  tol 0.000000
final transform:
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach.lta...
registration took 27 minutes and 16 seconds.
#--------------------------------------
#@# CA Normalize Tue Jan 30 15:28:21 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz norm_template.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 norm_template.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=29.3
skull bounding box = (58, 74, 55) --> (196, 194, 215)
using (104, 114, 135) as brain centroid...
mean wm in atlas = 107, using box (87,99,115) --> (120, 128,154) 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
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 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 (126, 76, 57) --> (191, 169, 212)
Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 147.0
0 of 3549 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 76, 56) --> (129, 166, 212)
Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 147.0
2 of 3444 (0.1%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 147, 82) --> (175, 184, 132)
Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 147.0
0 of 199 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (84, 147, 80) --> (128, 182, 133)
Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 147.0
0 of 221 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (113, 138, 115) --> (143, 195, 142)
Brain_Stem: limiting intensities to 83.0 --> 147.0
0 of 177 (0.0%) samples deleted
using 7590 total control points for intensity normalization...
bias field = 0.996 +- 0.029
21 of 7588 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 76, 57) --> (191, 169, 212)
Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 144.0
1 of 3379 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 76, 56) --> (129, 166, 212)
Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 144.0
0 of 3460 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 147, 82) --> (175, 184, 132)
Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 144.0
0 of 210 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (84, 147, 80) --> (128, 182, 133)
Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 144.0
0 of 231 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (113, 138, 115) --> (143, 195, 142)
Brain_Stem: limiting intensities to 85.0 --> 144.0
27 of 227 (11.9%) samples deleted
using 7507 total control points for intensity normalization...
bias field = 1.004 +- 0.027
28 of 7479 control points discarded
finding control points in Left_Cerebral_White_Matter....
found 41584 control points for structure...
bounding box (126, 76, 57) --> (191, 169, 212)
Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 143.0
1 of 3618 (0.0%) samples deleted
finding control points in Right_Cerebral_White_Matter....
found 40735 control points for structure...
bounding box (67, 76, 56) --> (129, 166, 212)
Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 143.0
0 of 3742 (0.0%) samples deleted
finding control points in Left_Cerebellum_White_Matter....
found 3012 control points for structure...
bounding box (130, 147, 82) --> (175, 184, 132)
Left_Cerebellum_White_Matter: limiting intensities to 83.0 --> 143.0
0 of 212 (0.0%) samples deleted
finding control points in Right_Cerebellum_White_Matter....
found 2764 control points for structure...
bounding box (84, 147, 80) --> (128, 182, 133)
Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 143.0
0 of 275 (0.0%) samples deleted
finding control points in Brain_Stem....
found 3520 control points for structure...
bounding box (113, 138, 115) --> (143, 195, 142)
Brain_Stem: limiting intensities to 84.0 --> 143.0
42 of 282 (14.9%) samples deleted
using 8129 total control points for intensity normalization...
bias field = 1.007 +- 0.028
23 of 8086 control points discarded
writing normalized volume to norm.mgz...
writing control points to ctrl_pts.mgz
freeing GCA...done.
normalization took 2 minutes and 23 seconds.
#--------------------------------------
#@# CA Reg Tue Jan 30 15:30:45 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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) = 1.42 (predicted orig area = 5.6)
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=0.771, neg=0, invalid=96777
0001: dt=129.472000, rms=0.716 (7.189%), neg=0, invalid=96777
0002: dt=129.472000, rms=0.702 (1.909%), neg=0, invalid=96777
0003: dt=129.472000, rms=0.686 (2.301%), neg=0, invalid=96777
0004: dt=92.480000, rms=0.683 (0.473%), neg=0, invalid=96777
0005: dt=369.920000, rms=0.670 (1.904%), neg=0, invalid=96777
0006: dt=32.368000, rms=0.667 (0.413%), neg=0, invalid=96777
0007: dt=32.368000, rms=0.666 (0.124%), neg=0, invalid=96777
0008: dt=32.368000, rms=0.666 (0.063%), neg=0, invalid=96777
0009: dt=32.368000, rms=0.665 (0.071%), neg=0, invalid=96777
0010: dt=32.368000, rms=0.664 (0.128%), neg=0, invalid=96777
0011: dt=32.368000, rms=0.663 (0.239%), neg=0, invalid=96777
0012: dt=32.368000, rms=0.660 (0.353%), neg=0, invalid=96777
0013: dt=32.368000, rms=0.658 (0.393%), neg=0, invalid=96777
0014: dt=32.368000, rms=0.656 (0.339%), neg=0, invalid=96777
0015: dt=32.368000, rms=0.654 (0.291%), neg=0, invalid=96777
0016: dt=32.368000, rms=0.652 (0.246%), neg=0, invalid=96777
0017: dt=32.368000, rms=0.651 (0.215%), neg=0, invalid=96777
0018: dt=32.368000, rms=0.650 (0.180%), neg=0, invalid=96777
0019: dt=32.368000, rms=0.648 (0.179%), neg=0, invalid=96777
0020: dt=32.368000, rms=0.647 (0.215%), neg=0, invalid=96777
0021: dt=32.368000, rms=0.645 (0.239%), neg=0, invalid=96777
0022: dt=32.368000, rms=0.644 (0.230%), neg=0, invalid=96777
0023: dt=32.368000, rms=0.643 (0.195%), neg=0, invalid=96777
0024: dt=32.368000, rms=0.642 (0.158%), neg=0, invalid=96777
0025: dt=32.368000, rms=0.641 (0.127%), neg=0, invalid=96777
0026: dt=32.368000, rms=0.640 (0.098%), neg=0, invalid=96777
0027: dt=32.368000, rms=0.640 (0.080%), neg=0, invalid=96777
0028: dt=443.904000, rms=0.638 (0.285%), neg=0, invalid=96777
0029: dt=32.368000, rms=0.638 (0.027%), neg=0, invalid=96777
0030: dt=32.368000, rms=0.638 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.638, neg=0, invalid=96777
0031: dt=92.480000, rms=0.637 (0.124%), neg=0, invalid=96777
0032: dt=369.920000, rms=0.635 (0.246%), neg=0, invalid=96777
0033: dt=73.984000, rms=0.635 (0.032%), neg=0, invalid=96777
0034: dt=73.984000, rms=0.635 (0.060%), neg=0, invalid=96777
0035: dt=73.984000, rms=0.634 (0.056%), neg=0, invalid=96777
0036: dt=73.984000, rms=0.634 (0.065%), neg=0, invalid=96777
0037: dt=73.984000, rms=0.634 (0.072%), neg=0, invalid=96777
0038: dt=73.984000, rms=0.633 (0.092%), neg=0, invalid=96777
0039: dt=73.984000, rms=0.632 (0.116%), neg=0, invalid=96777
0040: dt=73.984000, rms=0.632 (0.099%), neg=0, invalid=96777
setting smoothness coefficient to 0.154
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.635, neg=0, invalid=96777
0041: dt=82.944000, rms=0.629 (0.921%), neg=0, invalid=96777
0042: dt=124.416000, rms=0.618 (1.727%), neg=0, invalid=96777
0043: dt=20.736000, rms=0.615 (0.415%), neg=0, invalid=96777
0044: dt=36.288000, rms=0.614 (0.248%), neg=0, invalid=96777
0045: dt=36.288000, rms=0.612 (0.287%), neg=0, invalid=96777
0046: dt=36.288000, rms=0.609 (0.527%), neg=0, invalid=96777
0047: dt=36.288000, rms=0.605 (0.702%), neg=0, invalid=96777
0048: dt=36.288000, rms=0.600 (0.795%), neg=0, invalid=96777
0049: dt=36.288000, rms=0.595 (0.819%), neg=0, invalid=96777
0050: dt=36.288000, rms=0.590 (0.773%), neg=0, invalid=96777
0051: dt=36.288000, rms=0.587 (0.650%), neg=0, invalid=96777
0052: dt=36.288000, rms=0.583 (0.522%), neg=0, invalid=96777
0053: dt=36.288000, rms=0.581 (0.461%), neg=0, invalid=96777
0054: dt=36.288000, rms=0.578 (0.423%), neg=0, invalid=96777
0055: dt=36.288000, rms=0.576 (0.408%), neg=0, invalid=96777
0056: dt=36.288000, rms=0.574 (0.347%), neg=0, invalid=96777
0057: dt=36.288000, rms=0.572 (0.274%), neg=0, invalid=96777
0058: dt=36.288000, rms=0.571 (0.244%), neg=0, invalid=96777
0059: dt=36.288000, rms=0.570 (0.224%), neg=0, invalid=96777
0060: dt=36.288000, rms=0.569 (0.179%), neg=0, invalid=96777
0061: dt=36.288000, rms=0.568 (0.149%), neg=0, invalid=96777
0062: dt=36.288000, rms=0.567 (0.190%), neg=0, invalid=96777
0063: dt=36.288000, rms=0.566 (0.180%), neg=0, invalid=96777
0064: dt=36.288000, rms=0.565 (0.124%), neg=0, invalid=96777
0065: dt=36.288000, rms=0.564 (0.124%), neg=0, invalid=96777
0066: dt=36.288000, rms=0.564 (0.117%), neg=0, invalid=96777
0067: dt=145.152000, rms=0.563 (0.144%), neg=0, invalid=96777
0068: dt=5.184000, rms=0.563 (-0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.563, neg=0, invalid=96777
0069: dt=36.288000, rms=0.562 (0.162%), neg=0, invalid=96777
0070: dt=82.944000, rms=0.561 (0.187%), neg=0, invalid=96777
0071: dt=9.072000, rms=0.561 (0.021%), neg=0, invalid=96777
0072: dt=9.072000, rms=0.561 (0.020%), neg=0, invalid=96777
0073: dt=9.072000, rms=0.561 (0.004%), neg=0, invalid=96777
0074: dt=9.072000, rms=0.561 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 0.588
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.589, neg=0, invalid=96777
0075: dt=9.600000, rms=0.588 (0.213%), neg=0, invalid=96777
0076: dt=6.400000, rms=0.587 (0.043%), neg=0, invalid=96777
0077: dt=6.400000, rms=0.587 (0.025%), neg=0, invalid=96777
0078: dt=6.400000, rms=0.587 (-0.055%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.587, neg=0, invalid=96777
0079: dt=4.800000, rms=0.587 (0.029%), neg=0, invalid=96777
0080: dt=2.400000, rms=0.587 (0.001%), neg=0, invalid=96777
0081: dt=2.400000, rms=0.587 (0.001%), neg=0, invalid=96777
0082: dt=2.400000, rms=0.587 (-0.013%), neg=0, invalid=96777
setting smoothness coefficient to 2.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.643, neg=0, invalid=96777
0083: dt=4.777042, rms=0.633 (1.561%), neg=0, invalid=96777
0084: dt=4.032000, rms=0.631 (0.195%), neg=0, invalid=96777
0085: dt=4.032000, rms=0.631 (-0.030%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.631, neg=0, invalid=96777
0086: dt=0.000000, rms=0.631 (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=0.686, neg=0, invalid=96777
0087: dt=0.529412, rms=0.685 (0.167%), neg=0, invalid=96777
0088: dt=1.064327, rms=0.684 (0.222%), neg=0, invalid=96777
0089: dt=2.045455, rms=0.681 (0.437%), neg=0, invalid=96777
0090: dt=1.024000, rms=0.680 (0.073%), neg=0, invalid=96777
0091: dt=1.024000, rms=0.679 (0.111%), neg=0, invalid=96777
0092: dt=1.024000, rms=0.679 (0.084%), neg=0, invalid=96777
0093: dt=1.024000, rms=0.679 (-0.073%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.679, neg=0, invalid=96777
0094: dt=1.029126, rms=0.678 (0.125%), neg=0, invalid=96777
0095: dt=0.000000, rms=0.678 (-0.001%), neg=0, invalid=96777
resetting metric properties...
setting smoothness coefficient to 10.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.643, neg=0, invalid=96777
0096: dt=0.142009, rms=0.638 (0.849%), neg=0, invalid=96777
0097: dt=0.096000, rms=0.638 (0.066%), neg=0, invalid=96777
0098: dt=0.096000, rms=0.637 (0.141%), neg=0, invalid=96777
0099: dt=0.096000, rms=0.635 (0.223%), neg=0, invalid=96777
0100: dt=0.096000, rms=0.634 (0.263%), neg=0, invalid=96777
0101: dt=0.096000, rms=0.632 (0.252%), neg=0, invalid=96777
0102: dt=0.096000, rms=0.632 (0.009%), neg=0, invalid=96777
0103: dt=0.096000, rms=0.632 (0.015%), neg=0, invalid=96777
0104: dt=0.096000, rms=0.632 (0.030%), neg=0, invalid=96777
0105: dt=0.096000, rms=0.631 (0.054%), neg=0, invalid=96777
0106: dt=0.096000, rms=0.631 (0.087%), neg=0, invalid=96777
0107: dt=0.096000, rms=0.630 (0.114%), neg=0, invalid=96777
0108: dt=0.096000, rms=0.629 (0.129%), neg=0, invalid=96777
0109: dt=0.096000, rms=0.628 (0.122%), neg=0, invalid=96777
0110: dt=0.096000, rms=0.628 (0.103%), neg=0, invalid=96777
0111: dt=0.016000, rms=0.628 (0.001%), neg=0, invalid=96777
0112: dt=0.016000, rms=0.628 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.628, neg=0, invalid=96777
0113: dt=0.112000, rms=0.627 (0.179%), neg=0, invalid=96777
0114: dt=0.000000, rms=0.627 (0.001%), neg=0, invalid=96777
0115: dt=0.050000, rms=0.627 (-0.018%), neg=0, invalid=96777
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.11725 (24)
mri peak = 0.14655 (26)
Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (1524 voxels, overlap=0.533)
Left_Lateral_Ventricle (4): linear fit = 1.09 x + 0.0 (1524 voxels, peak = 26), gca=26.0
gca peak = 0.14022 (22)
mri peak = 0.19142 (28)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (837 voxels, overlap=0.460)
Right_Lateral_Ventricle (43): linear fit = 1.18 x + 0.0 (837 voxels, peak = 26), gca=26.1
gca peak = 0.24234 (100)
mri peak = 0.12157 (99)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (406 voxels, overlap=1.003)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (406 voxels, peak = 100), gca=100.5
gca peak = 0.19192 (97)
mri peak = 0.07812 (91)
Left_Pallidum (13): linear fit = 0.93 x + 0.0 (376 voxels, overlap=1.006)
Left_Pallidum (13): linear fit = 0.93 x + 0.0 (376 voxels, peak = 90), gca=89.7
gca peak = 0.24007 (63)
mri peak = 0.10715 (77)
Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (859 voxels, overlap=0.017)
Right_Hippocampus (53): linear fit = 1.18 x + 0.0 (859 voxels, peak = 75), gca=74.7
gca peak = 0.29892 (64)
mri peak = 0.10546 (76)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (793 voxels, overlap=0.018)
Left_Hippocampus (17): linear fit = 1.16 x + 0.0 (793 voxels, peak = 75), gca=74.6
gca peak = 0.12541 (104)
mri peak = 0.11757 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (65262 voxels, overlap=0.696)
Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (65262 voxels, peak = 108), gca=107.6
gca peak = 0.13686 (104)
mri peak = 0.10498 (108)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (68978 voxels, overlap=0.713)
Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (68978 voxels, peak = 108), gca=107.6
gca peak = 0.11691 (63)
mri peak = 0.04252 (72)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (28318 voxels, overlap=0.186)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (28318 voxels, peak = 75), gca=75.3
gca peak = 0.13270 (63)
mri peak = 0.04332 (72)
Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (32297 voxels, overlap=0.251)
Right_Cerebral_Cortex (42): linear fit = 1.14 x + 0.0 (32297 voxels, peak = 72), gca=72.1
gca peak = 0.15182 (70)
mri peak = 0.11250 (81)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (319 voxels, overlap=0.128)
Right_Caudate (50): linear fit = 1.13 x + 0.0 (319 voxels, peak = 79), gca=79.4
gca peak = 0.14251 (76)
mri peak = 0.10407 (87)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (672 voxels, overlap=0.490)
Left_Caudate (11): linear fit = 1.09 x + 0.0 (672 voxels, peak = 82), gca=82.5
gca peak = 0.12116 (60)
mri peak = 0.04645 (67)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (23245 voxels, overlap=0.606)
Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (23245 voxels, peak = 68), gca=67.5
gca peak = 0.12723 (61)
mri peak = 0.04834 (67)
Right_Cerebellum_Cortex (47): linear fit = 1.14 x + 0.0 (26115 voxels, overlap=0.511)
Right_Cerebellum_Cortex (47): linear fit = 1.14 x + 0.0 (26115 voxels, peak = 70), gca=69.8
gca peak = 0.22684 (88)
mri peak = 0.12344 (92)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7915 voxels, overlap=0.477)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (7915 voxels, peak = 93), gca=92.8
gca peak = 0.21067 (87)
mri peak = 0.11884 (91)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7246 voxels, overlap=0.693)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (7246 voxels, peak = 91), gca=90.9
gca peak = 0.25455 (62)
mri peak = 0.11333 (75)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (301 voxels, overlap=0.051)
Left_Amygdala (18): linear fit = 1.22 x + 0.0 (301 voxels, peak = 75), gca=75.3
gca peak = 0.39668 (62)
mri peak = 0.14801 (72)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (277 voxels, overlap=0.024)
Right_Amygdala (54): linear fit = 1.18 x + 0.0 (277 voxels, peak = 73), gca=73.5
gca peak = 0.10129 (93)
mri peak = 0.08493 (105)
Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4706 voxels, overlap=0.086)
Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4706 voxels, peak = 105), gca=104.6
gca peak = 0.12071 (89)
mri peak = 0.07995 (101)
Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3412 voxels, overlap=0.556)
Right_Thalamus_Proper (49): linear fit = 1.11 x + 0.0 (3412 voxels, peak = 98), gca=98.3
gca peak = 0.13716 (82)
mri peak = 0.07101 (94)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2288 voxels, overlap=0.459)
Left_Putamen (12): linear fit = 1.10 x + 0.0 (2288 voxels, peak = 90), gca=89.8
gca peak = 0.15214 (84)
mri peak = 0.07085 (91)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2328 voxels, overlap=0.852)
Right_Putamen (51): linear fit = 1.08 x + 0.0 (2328 voxels, peak = 90), gca=90.3
gca peak = 0.08983 (85)
mri peak = 0.07122 (97)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (10587 voxels, overlap=0.386)
Brain_Stem (16): linear fit = 1.12 x + 0.0 (10587 voxels, peak = 96), gca=95.6
gca peak = 0.11809 (92)
mri peak = 0.09727 (99)
Right_VentralDC (60): linear fit = 1.08 x + 0.0 (781 voxels, overlap=0.334)
Right_VentralDC (60): linear fit = 1.08 x + 0.0 (781 voxels, peak = 99), gca=98.9
gca peak = 0.12914 (94)
mri peak = 0.11465 (101)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (996 voxels, overlap=0.227)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (996 voxels, peak = 102), gca=102.0
gca peak = 0.21100 (36)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.13542 (27)
mri peak = 0.22234 (28)
Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (274 voxels, overlap=0.532)
Fourth_Ventricle (15): linear fit = 0.92 x + 0.0 (274 voxels, peak = 25), gca=24.7
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.21802 (40)
gca peak Third_Ventricle = 0.21100 (36)
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 1.18 x + 0.0
estimating mean wm scale to be 1.03 x + 0.0
estimating mean csf scale to be 1.06 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=0.623, neg=0, invalid=96777
0116: dt=110.976000, rms=0.613 (1.502%), neg=0, invalid=96777
0117: dt=129.472000, rms=0.611 (0.378%), neg=0, invalid=96777
0118: dt=295.936000, rms=0.606 (0.855%), neg=0, invalid=96777
0119: dt=55.488000, rms=0.604 (0.216%), neg=0, invalid=96777
0120: dt=517.888000, rms=0.601 (0.640%), neg=0, invalid=96777
0121: dt=92.480000, rms=0.598 (0.470%), neg=0, invalid=96777
0122: dt=55.488000, rms=0.598 (0.036%), neg=0, invalid=96777
0123: dt=55.488000, rms=0.597 (0.051%), neg=0, invalid=96777
0124: dt=55.488000, rms=0.597 (0.093%), neg=0, invalid=96777
0125: dt=55.488000, rms=0.596 (0.141%), neg=0, invalid=96777
0126: dt=55.488000, rms=0.595 (0.185%), neg=0, invalid=96777
0127: dt=55.488000, rms=0.594 (0.205%), neg=0, invalid=96777
0128: dt=55.488000, rms=0.592 (0.210%), neg=0, invalid=96777
0129: dt=55.488000, rms=0.591 (0.195%), neg=0, invalid=96777
0130: dt=55.488000, rms=0.590 (0.175%), neg=0, invalid=96777
0131: dt=55.488000, rms=0.589 (0.166%), neg=0, invalid=96777
0132: dt=55.488000, rms=0.588 (0.159%), neg=0, invalid=96777
0133: dt=55.488000, rms=0.587 (0.141%), neg=0, invalid=96777
0134: dt=55.488000, rms=0.587 (0.122%), neg=0, invalid=96777
0135: dt=55.488000, rms=0.586 (0.099%), neg=0, invalid=96777
0136: dt=55.488000, rms=0.586 (0.074%), neg=0, invalid=96777
0137: dt=55.488000, rms=0.585 (0.075%), neg=0, invalid=96777
0138: dt=55.488000, rms=0.585 (0.088%), neg=0, invalid=96777
0139: dt=55.488000, rms=0.584 (0.089%), neg=0, invalid=96777
0140: dt=55.488000, rms=0.584 (0.075%), neg=0, invalid=96777
0141: dt=55.488000, rms=0.583 (0.055%), neg=0, invalid=96777
0142: dt=55.488000, rms=0.583 (0.060%), neg=0, invalid=96777
0143: dt=55.488000, rms=0.583 (0.063%), neg=0, invalid=96777
0144: dt=55.488000, rms=0.582 (0.064%), neg=0, invalid=96777
0145: dt=55.488000, rms=0.582 (0.063%), neg=0, invalid=96777
0146: dt=55.488000, rms=0.581 (0.079%), neg=0, invalid=96777
0147: dt=55.488000, rms=0.581 (0.068%), neg=0, invalid=96777
0148: dt=55.488000, rms=0.581 (0.063%), neg=0, invalid=96777
0149: dt=55.488000, rms=0.580 (0.062%), neg=0, invalid=96777
0150: dt=55.488000, rms=0.580 (0.068%), neg=0, invalid=96777
0151: dt=55.488000, rms=0.580 (0.068%), neg=0, invalid=96777
0152: dt=55.488000, rms=0.579 (0.067%), neg=0, invalid=96777
0153: dt=55.488000, rms=0.579 (0.071%), neg=0, invalid=96777
0154: dt=55.488000, rms=0.578 (0.068%), neg=0, invalid=96777
0155: dt=55.488000, rms=0.578 (0.063%), neg=0, invalid=96777
0156: dt=55.488000, rms=0.578 (0.065%), neg=0, invalid=96777
0157: dt=55.488000, rms=0.577 (0.067%), neg=0, invalid=96777
0158: dt=55.488000, rms=0.577 (0.065%), neg=0, invalid=96777
0159: dt=55.488000, rms=0.577 (0.058%), neg=0, invalid=96777
0160: dt=55.488000, rms=0.576 (0.058%), neg=0, invalid=96777
0161: dt=55.488000, rms=0.576 (0.061%), neg=0, invalid=96777
0162: dt=55.488000, rms=0.575 (0.063%), neg=0, invalid=96777
0163: dt=55.488000, rms=0.575 (0.060%), neg=0, invalid=96777
0164: dt=55.488000, rms=0.575 (0.054%), neg=0, invalid=96777
0165: dt=55.488000, rms=0.575 (0.047%), neg=0, invalid=96777
0166: dt=55.488000, rms=0.574 (0.055%), neg=0, invalid=96777
0167: dt=55.488000, rms=0.574 (0.046%), neg=0, invalid=96777
0168: dt=55.488000, rms=0.574 (0.048%), neg=0, invalid=96777
0169: dt=55.488000, rms=0.573 (0.049%), neg=0, invalid=96777
0170: dt=55.488000, rms=0.573 (0.049%), neg=0, invalid=96777
0171: dt=55.488000, rms=0.573 (0.046%), neg=0, invalid=96777
0172: dt=55.488000, rms=0.573 (0.041%), neg=0, invalid=96777
0173: dt=55.488000, rms=0.572 (0.043%), neg=0, invalid=96777
0174: dt=55.488000, rms=0.572 (0.041%), neg=0, invalid=96777
0175: dt=55.488000, rms=0.572 (0.041%), neg=0, invalid=96777
0176: dt=55.488000, rms=0.572 (0.036%), neg=0, invalid=96777
0177: dt=55.488000, rms=0.572 (0.026%), neg=0, invalid=96777
0178: dt=55.488000, rms=0.571 (0.032%), neg=0, invalid=96777
0179: dt=55.488000, rms=0.571 (0.033%), neg=0, invalid=96777
0180: dt=55.488000, rms=0.571 (0.029%), neg=0, invalid=96777
0181: dt=55.488000, rms=0.571 (0.030%), neg=0, invalid=96777
0182: dt=55.488000, rms=0.571 (0.040%), neg=0, invalid=96777
0183: dt=55.488000, rms=0.570 (0.044%), neg=0, invalid=96777
0184: dt=55.488000, rms=0.570 (0.036%), neg=0, invalid=96777
0185: dt=55.488000, rms=0.570 (0.025%), neg=0, invalid=96777
0186: dt=55.488000, rms=0.570 (0.024%), neg=0, invalid=96777
0187: dt=55.488000, rms=0.570 (0.022%), neg=0, invalid=96777
0188: dt=295.936000, rms=0.570 (0.038%), neg=0, invalid=96777
0189: dt=18.496000, rms=0.570 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.570, neg=0, invalid=96777
0190: dt=73.984000, rms=0.569 (0.058%), neg=0, invalid=96777
0191: dt=129.472000, rms=0.569 (0.076%), neg=0, invalid=96777
0192: dt=73.984000, rms=0.569 (0.003%), neg=0, invalid=96777
0193: dt=73.984000, rms=0.569 (0.024%), neg=0, invalid=96777
0194: dt=73.984000, rms=0.568 (0.033%), neg=0, invalid=96777
0195: dt=73.984000, rms=0.568 (0.037%), neg=0, invalid=96777
0196: dt=73.984000, rms=0.568 (0.040%), neg=0, invalid=96777
0197: dt=73.984000, rms=0.568 (0.039%), neg=0, invalid=96777
0198: dt=73.984000, rms=0.568 (0.030%), neg=0, invalid=96777
0199: dt=73.984000, rms=0.567 (0.041%), neg=0, invalid=96777
0200: dt=73.984000, rms=0.567 (0.024%), neg=0, invalid=96777
0201: dt=73.984000, rms=0.567 (0.023%), neg=0, invalid=96777
0202: dt=1775.616000, rms=0.567 (0.103%), neg=0, invalid=96777
0203: dt=18.496000, rms=0.567 (0.001%), neg=0, invalid=96777
0204: dt=18.496000, rms=0.567 (0.001%), neg=0, invalid=96777
0205: dt=18.496000, rms=0.567 (-0.006%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.568, neg=0, invalid=96777
0206: dt=36.288000, rms=0.566 (0.333%), neg=0, invalid=96777
0207: dt=145.152000, rms=0.560 (0.971%), neg=0, invalid=96777
0208: dt=25.920000, rms=0.559 (0.312%), neg=0, invalid=96777
0209: dt=124.416000, rms=0.554 (0.797%), neg=0, invalid=96777
0210: dt=15.552000, rms=0.552 (0.356%), neg=0, invalid=96777
0211: dt=36.288000, rms=0.551 (0.163%), neg=0, invalid=96777
0212: dt=103.680000, rms=0.549 (0.430%), neg=0, invalid=96777
0213: dt=15.552000, rms=0.548 (0.207%), neg=0, invalid=96777
0214: dt=82.944000, rms=0.547 (0.218%), neg=0, invalid=96777
0215: dt=31.104000, rms=0.545 (0.353%), neg=0, invalid=96777
0216: dt=25.920000, rms=0.544 (0.072%), neg=0, invalid=96777
0217: dt=331.776000, rms=0.540 (0.721%), neg=0, invalid=96777
0218: dt=20.736000, rms=0.538 (0.486%), neg=0, invalid=96777
0219: dt=124.416000, rms=0.536 (0.333%), neg=0, invalid=96777
0220: dt=36.288000, rms=0.535 (0.173%), neg=0, invalid=96777
0221: dt=103.680000, rms=0.534 (0.211%), neg=0, invalid=96777
0222: dt=25.920000, rms=0.533 (0.108%), neg=0, invalid=96777
0223: dt=124.416000, rms=0.532 (0.216%), neg=0, invalid=96777
0224: dt=20.736000, rms=0.531 (0.110%), neg=0, invalid=96777
0225: dt=414.720000, rms=0.529 (0.452%), neg=0, invalid=96777
0226: dt=20.736000, rms=0.528 (0.260%), neg=0, invalid=96777
0227: dt=124.416000, rms=0.527 (0.224%), neg=0, invalid=96777
0228: dt=36.288000, rms=0.526 (0.057%), neg=0, invalid=96777
0229: dt=103.680000, rms=0.526 (0.136%), neg=0, invalid=96777
0230: dt=20.736000, rms=0.525 (0.045%), neg=0, invalid=96777
0231: dt=20.736000, rms=0.525 (0.039%), neg=0, invalid=96777
0232: dt=20.736000, rms=0.525 (0.044%), neg=0, invalid=96777
0233: dt=20.736000, rms=0.524 (0.072%), neg=0, invalid=96777
0234: dt=20.736000, rms=0.524 (0.098%), neg=0, invalid=96777
0235: dt=20.736000, rms=0.523 (0.105%), neg=0, invalid=96777
0236: dt=20.736000, rms=0.523 (0.105%), neg=0, invalid=96777
0237: dt=20.736000, rms=0.522 (0.117%), neg=0, invalid=96777
0238: dt=20.736000, rms=0.522 (0.131%), neg=0, invalid=96777
0239: dt=20.736000, rms=0.521 (0.137%), neg=0, invalid=96777
0240: dt=20.736000, rms=0.520 (0.136%), neg=0, invalid=96777
0241: dt=20.736000, rms=0.519 (0.138%), neg=0, invalid=96777
0242: dt=20.736000, rms=0.519 (0.129%), neg=0, invalid=96777
0243: dt=20.736000, rms=0.518 (0.124%), neg=0, invalid=96777
0244: dt=20.736000, rms=0.517 (0.120%), neg=0, invalid=96777
0245: dt=20.736000, rms=0.517 (0.127%), neg=0, invalid=96777
0246: dt=20.736000, rms=0.516 (0.115%), neg=0, invalid=96777
0247: dt=20.736000, rms=0.516 (0.106%), neg=0, invalid=96777
0248: dt=20.736000, rms=0.515 (0.111%), neg=0, invalid=96777
0249: dt=20.736000, rms=0.514 (0.120%), neg=0, invalid=96777
0250: dt=20.736000, rms=0.514 (0.117%), neg=0, invalid=96777
0251: dt=20.736000, rms=0.513 (0.111%), neg=0, invalid=96777
0252: dt=20.736000, rms=0.513 (0.111%), neg=0, invalid=96777
0253: dt=20.736000, rms=0.512 (0.112%), neg=0, invalid=96777
0254: dt=20.736000, rms=0.512 (0.108%), neg=0, invalid=96777
0255: dt=20.736000, rms=0.511 (0.094%), neg=0, invalid=96777
0256: dt=20.736000, rms=0.511 (0.073%), neg=0, invalid=96777
0257: dt=20.736000, rms=0.510 (0.076%), neg=0, invalid=96777
0258: dt=20.736000, rms=0.510 (0.083%), neg=0, invalid=96777
0259: dt=20.736000, rms=0.509 (0.091%), neg=0, invalid=96777
0260: dt=20.736000, rms=0.509 (0.076%), neg=0, invalid=96777
0261: dt=20.736000, rms=0.509 (0.067%), neg=0, invalid=96777
0262: dt=20.736000, rms=0.508 (0.066%), neg=0, invalid=96777
0263: dt=20.736000, rms=0.508 (0.074%), neg=0, invalid=96777
0264: dt=20.736000, rms=0.508 (0.067%), neg=0, invalid=96777
0265: dt=20.736000, rms=0.507 (0.059%), neg=0, invalid=96777
0266: dt=20.736000, rms=0.507 (0.059%), neg=0, invalid=96777
0267: dt=20.736000, rms=0.507 (0.063%), neg=0, invalid=96777
0268: dt=20.736000, rms=0.507 (0.048%), neg=0, invalid=96777
0269: dt=20.736000, rms=0.506 (0.060%), neg=0, invalid=96777
0270: dt=20.736000, rms=0.506 (0.060%), neg=0, invalid=96777
0271: dt=20.736000, rms=0.506 (0.053%), neg=0, invalid=96777
0272: dt=20.736000, rms=0.505 (0.054%), neg=0, invalid=96777
0273: dt=20.736000, rms=0.505 (0.050%), neg=0, invalid=96777
0274: dt=20.736000, rms=0.505 (0.049%), neg=0, invalid=96777
0275: dt=20.736000, rms=0.505 (0.053%), neg=0, invalid=96777
0276: dt=20.736000, rms=0.504 (0.043%), neg=0, invalid=96777
0277: dt=20.736000, rms=0.504 (0.043%), neg=0, invalid=96777
0278: dt=20.736000, rms=0.504 (0.050%), neg=0, invalid=96777
0279: dt=20.736000, rms=0.504 (0.038%), neg=0, invalid=96777
0280: dt=20.736000, rms=0.504 (0.033%), neg=0, invalid=96777
0281: dt=20.736000, rms=0.503 (0.035%), neg=0, invalid=96777
0282: dt=20.736000, rms=0.503 (0.050%), neg=0, invalid=96777
0283: dt=20.736000, rms=0.503 (0.044%), neg=0, invalid=96777
0284: dt=20.736000, rms=0.503 (0.036%), neg=0, invalid=96777
0285: dt=20.736000, rms=0.503 (0.025%), neg=0, invalid=96777
0286: dt=20.736000, rms=0.503 (0.024%), neg=0, invalid=96777
0287: dt=20.736000, rms=0.502 (0.027%), neg=0, invalid=96777
0288: dt=20.736000, rms=0.502 (0.031%), neg=0, invalid=96777
0289: dt=20.736000, rms=0.502 (0.039%), neg=0, invalid=96777
0290: dt=20.736000, rms=0.502 (0.040%), neg=0, invalid=96777
0291: dt=20.736000, rms=0.502 (0.016%), neg=0, invalid=96777
0292: dt=20.736000, rms=0.502 (0.034%), neg=0, invalid=96777
0293: dt=20.736000, rms=0.501 (0.040%), neg=0, invalid=96777
0294: dt=20.736000, rms=0.501 (0.033%), neg=0, invalid=96777
0295: dt=20.736000, rms=0.501 (0.042%), neg=0, invalid=96777
0296: dt=20.736000, rms=0.501 (0.032%), neg=0, invalid=96777
0297: dt=20.736000, rms=0.501 (0.026%), neg=0, invalid=96777
0298: dt=20.736000, rms=0.501 (0.016%), neg=0, invalid=96777
0299: dt=20.736000, rms=0.500 (0.028%), neg=0, invalid=96777
0300: dt=20.736000, rms=0.500 (0.035%), neg=0, invalid=96777
0301: dt=20.736000, rms=0.500 (0.039%), neg=0, invalid=96777
0302: dt=20.736000, rms=0.500 (0.030%), neg=0, invalid=96777
0303: dt=20.736000, rms=0.500 (0.018%), neg=0, invalid=96777
0304: dt=20.736000, rms=0.500 (0.005%), neg=0, invalid=96777
0305: dt=36.288000, rms=0.500 (0.039%), neg=0, invalid=96777
0306: dt=0.000000, rms=0.500 (0.000%), neg=0, invalid=96777
0307: dt=0.450000, rms=0.500 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.500, neg=0, invalid=96777
0308: dt=82.944000, rms=0.499 (0.224%), neg=0, invalid=96777
0309: dt=36.288000, rms=0.498 (0.143%), neg=0, invalid=96777
0310: dt=20.736000, rms=0.498 (0.024%), neg=0, invalid=96777
0311: dt=20.736000, rms=0.498 (0.032%), neg=0, invalid=96777
0312: dt=20.736000, rms=0.497 (0.040%), neg=0, invalid=96777
0313: dt=20.736000, rms=0.497 (0.055%), neg=0, invalid=96777
0314: dt=20.736000, rms=0.497 (0.069%), neg=0, invalid=96777
0315: dt=20.736000, rms=0.496 (0.064%), neg=0, invalid=96777
0316: dt=20.736000, rms=0.496 (0.069%), neg=0, invalid=96777
0317: dt=20.736000, rms=0.496 (0.068%), neg=0, invalid=96777
0318: dt=20.736000, rms=0.495 (0.051%), neg=0, invalid=96777
0319: dt=20.736000, rms=0.495 (0.050%), neg=0, invalid=96777
0320: dt=20.736000, rms=0.495 (0.050%), neg=0, invalid=96777
0321: dt=20.736000, rms=0.495 (0.052%), neg=0, invalid=96777
0322: dt=20.736000, rms=0.494 (0.051%), neg=0, invalid=96777
0323: dt=20.736000, rms=0.494 (0.038%), neg=0, invalid=96777
0324: dt=20.736000, rms=0.494 (0.041%), neg=0, invalid=96777
0325: dt=20.736000, rms=0.494 (0.042%), neg=0, invalid=96777
0326: dt=20.736000, rms=0.494 (0.050%), neg=0, invalid=96777
0327: dt=20.736000, rms=0.493 (0.039%), neg=0, invalid=96777
0328: dt=20.736000, rms=0.493 (0.043%), neg=0, invalid=96777
0329: dt=20.736000, rms=0.493 (0.037%), neg=0, invalid=96777
0330: dt=20.736000, rms=0.493 (0.035%), neg=0, invalid=96777
0331: dt=20.736000, rms=0.493 (0.036%), neg=0, invalid=96777
0332: dt=20.736000, rms=0.493 (0.035%), neg=0, invalid=96777
0333: dt=20.736000, rms=0.492 (0.035%), neg=0, invalid=96777
0334: dt=20.736000, rms=0.492 (0.038%), neg=0, invalid=96777
0335: dt=20.736000, rms=0.492 (0.038%), neg=0, invalid=96777
0336: dt=20.736000, rms=0.492 (0.033%), neg=0, invalid=96777
0337: dt=20.736000, rms=0.492 (0.023%), neg=0, invalid=96777
0338: dt=20.736000, rms=0.492 (0.019%), neg=0, invalid=96777
0339: dt=62.208000, rms=0.491 (0.039%), neg=0, invalid=96777
0340: dt=6.480000, rms=0.491 (-0.000%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.500, neg=0, invalid=96777
0341: dt=19.200000, rms=0.499 (0.244%), neg=0, invalid=96777
0342: dt=38.400000, rms=0.497 (0.483%), neg=0, invalid=96777
0343: dt=6.432990, rms=0.496 (0.169%), neg=0, invalid=96777
0344: dt=102.400000, rms=0.492 (0.805%), neg=0, invalid=96777
0345: dt=9.327014, rms=0.490 (0.354%), neg=0, invalid=96777
0346: dt=25.600000, rms=0.488 (0.386%), neg=0, invalid=96777
0347: dt=5.931034, rms=0.488 (0.098%), neg=0, invalid=96777
0348: dt=44.800000, rms=0.486 (0.309%), neg=0, invalid=96777
0349: dt=11.200000, rms=0.485 (0.218%), neg=0, invalid=96777
0350: dt=8.000000, rms=0.485 (0.051%), neg=0, invalid=96777
0351: dt=128.000000, rms=0.483 (0.458%), neg=0, invalid=96777
0352: dt=6.022814, rms=0.481 (0.309%), neg=0, invalid=96777
0353: dt=25.600000, rms=0.480 (0.253%), neg=0, invalid=96777
0354: dt=11.200000, rms=0.480 (0.111%), neg=0, invalid=96777
0355: dt=11.200000, rms=0.479 (0.027%), neg=0, invalid=96777
0356: dt=11.200000, rms=0.479 (0.071%), neg=0, invalid=96777
0357: dt=11.200000, rms=0.479 (0.081%), neg=0, invalid=96777
0358: dt=11.200000, rms=0.478 (0.105%), neg=0, invalid=96777
0359: dt=11.200000, rms=0.477 (0.150%), neg=0, invalid=96777
0360: dt=11.200000, rms=0.477 (0.194%), neg=0, invalid=96777
0361: dt=11.200000, rms=0.476 (0.190%), neg=0, invalid=96777
0362: dt=11.200000, rms=0.475 (0.184%), neg=0, invalid=96777
0363: dt=11.200000, rms=0.474 (0.205%), neg=0, invalid=96777
0364: dt=11.200000, rms=0.473 (0.218%), neg=0, invalid=96777
0365: dt=11.200000, rms=0.472 (0.185%), neg=0, invalid=96777
0366: dt=11.200000, rms=0.471 (0.161%), neg=0, invalid=96777
0367: dt=11.200000, rms=0.470 (0.166%), neg=0, invalid=96777
0368: dt=11.200000, rms=0.470 (0.158%), neg=0, invalid=96777
0369: dt=11.200000, rms=0.469 (0.148%), neg=0, invalid=96777
0370: dt=11.200000, rms=0.468 (0.124%), neg=0, invalid=96777
0371: dt=11.200000, rms=0.468 (0.148%), neg=0, invalid=96777
0372: dt=11.200000, rms=0.467 (0.141%), neg=0, invalid=96777
0373: dt=11.200000, rms=0.466 (0.112%), neg=0, invalid=96777
0374: dt=11.200000, rms=0.466 (0.094%), neg=0, invalid=96777
0375: dt=11.200000, rms=0.466 (0.076%), neg=0, invalid=96777
0376: dt=11.200000, rms=0.465 (0.078%), neg=0, invalid=96777
0377: dt=11.200000, rms=0.465 (0.089%), neg=0, invalid=96777
0378: dt=11.200000, rms=0.465 (0.071%), neg=0, invalid=96777
0379: dt=11.200000, rms=0.464 (0.072%), neg=0, invalid=96777
0380: dt=11.200000, rms=0.464 (0.069%), neg=0, invalid=96777
0381: dt=11.200000, rms=0.464 (0.055%), neg=0, invalid=96777
0382: dt=11.200000, rms=0.463 (0.040%), neg=0, invalid=96777
0383: dt=11.200000, rms=0.463 (0.033%), neg=0, invalid=96777
0384: dt=11.200000, rms=0.463 (0.042%), neg=0, invalid=96777
0385: dt=11.200000, rms=0.463 (0.045%), neg=0, invalid=96777
0386: dt=11.200000, rms=0.463 (0.047%), neg=0, invalid=96777
0387: dt=11.200000, rms=0.462 (0.047%), neg=0, invalid=96777
0388: dt=11.200000, rms=0.462 (0.040%), neg=0, invalid=96777
0389: dt=11.200000, rms=0.462 (0.057%), neg=0, invalid=96777
0390: dt=11.200000, rms=0.462 (0.040%), neg=0, invalid=96777
0391: dt=11.200000, rms=0.462 (0.020%), neg=0, invalid=96777
0392: dt=11.200000, rms=0.462 (0.039%), neg=0, invalid=96777
0393: dt=11.200000, rms=0.461 (0.037%), neg=0, invalid=96777
0394: dt=11.200000, rms=0.461 (0.024%), neg=0, invalid=96777
0395: dt=11.200000, rms=0.461 (0.010%), neg=0, invalid=96777
0396: dt=11.200000, rms=0.461 (0.033%), neg=0, invalid=96777
0397: dt=8.000000, rms=0.461 (0.002%), neg=0, invalid=96777
0398: dt=8.000000, rms=0.461 (0.012%), neg=0, invalid=96777
0399: dt=8.000000, rms=0.461 (0.008%), neg=0, invalid=96777
0400: dt=8.000000, rms=0.461 (0.013%), neg=0, invalid=96777
0401: dt=8.000000, rms=0.461 (-0.002%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.461, neg=0, invalid=96777
0402: dt=38.400000, rms=0.459 (0.390%), neg=0, invalid=96777
0403: dt=11.200000, rms=0.459 (0.113%), neg=0, invalid=96777
0404: dt=11.200000, rms=0.459 (0.023%), neg=0, invalid=96777
0405: dt=11.200000, rms=0.458 (0.050%), neg=0, invalid=96777
0406: dt=11.200000, rms=0.458 (0.055%), neg=0, invalid=96777
0407: dt=11.200000, rms=0.458 (0.034%), neg=0, invalid=96777
0408: dt=11.200000, rms=0.458 (0.054%), neg=0, invalid=96777
0409: dt=11.200000, rms=0.457 (0.041%), neg=0, invalid=96777
0410: dt=11.200000, rms=0.457 (0.017%), neg=0, invalid=96777
0411: dt=11.200000, rms=0.457 (0.008%), neg=0, invalid=96777
0412: dt=25.600000, rms=0.457 (0.046%), neg=0, invalid=96777
0413: dt=2.800000, rms=0.457 (0.001%), neg=0, invalid=96777
0414: dt=2.800000, rms=0.457 (0.008%), neg=0, invalid=96777
0415: dt=2.800000, rms=0.457 (-0.001%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.480, neg=0, invalid=96777
0416: dt=0.000000, rms=0.480 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.480, neg=0, invalid=96777
0417: dt=0.000000, rms=0.480 (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=0.525, neg=0, invalid=96777
0418: dt=1.800000, rms=0.518 (1.339%), neg=0, invalid=96777
0419: dt=0.500000, rms=0.518 (0.064%), neg=0, invalid=96777
0420: dt=0.325000, rms=0.518 (0.012%), neg=0, invalid=96777
0421: dt=0.325000, rms=0.518 (-0.003%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.518, neg=0, invalid=96777
0422: dt=1.309859, rms=0.517 (0.179%), neg=0, invalid=96777
0423: dt=0.384000, rms=0.517 (0.008%), neg=0, invalid=96777
0424: dt=0.384000, rms=0.517 (-0.003%), 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=0.477, neg=0, invalid=96777
0425: dt=0.448000, rms=0.464 (2.618%), neg=0, invalid=96777
0426: dt=0.448000, rms=0.462 (0.577%), neg=0, invalid=96777
0427: dt=0.090047, rms=0.461 (0.077%), neg=0, invalid=96777
0428: dt=0.007000, rms=0.461 (0.004%), neg=0, invalid=96777
0429: dt=0.007000, rms=0.461 (0.007%), neg=0, invalid=96777
0430: dt=0.007000, rms=0.461 (0.010%), neg=0, invalid=96777
0431: dt=0.007000, rms=0.461 (0.016%), neg=0, invalid=96777
0432: dt=0.007000, rms=0.461 (0.021%), neg=0, invalid=96777
0433: dt=0.007000, rms=0.461 (0.022%), neg=0, invalid=96777
0434: dt=0.007000, rms=0.461 (0.006%), neg=0, invalid=96777
0435: dt=0.007000, rms=0.461 (0.010%), neg=0, invalid=96777
0436: dt=0.007000, rms=0.461 (0.015%), neg=0, invalid=96777
0437: dt=0.007000, rms=0.461 (0.019%), neg=0, invalid=96777
0438: dt=0.007000, rms=0.460 (0.022%), neg=0, invalid=96777
0439: dt=0.007000, rms=0.460 (0.025%), neg=0, invalid=96777
0440: dt=0.007000, rms=0.460 (0.027%), neg=0, invalid=96777
0441: dt=0.007000, rms=0.460 (0.028%), neg=0, invalid=96777
0442: dt=0.007000, rms=0.460 (0.030%), neg=0, invalid=96777
0443: dt=0.007000, rms=0.460 (0.034%), neg=0, invalid=96777
0444: dt=0.007000, rms=0.460 (0.032%), neg=0, invalid=96777
0445: dt=0.007000, rms=0.460 (0.033%), neg=0, invalid=96777
0446: dt=0.007000, rms=0.459 (0.034%), neg=0, invalid=96777
0447: dt=0.007000, rms=0.459 (0.036%), neg=0, invalid=96777
0448: dt=0.007000, rms=0.459 (0.033%), neg=0, invalid=96777
0449: dt=0.007000, rms=0.459 (0.034%), neg=0, invalid=96777
0450: dt=0.001750, rms=0.459 (-0.000%), neg=0, invalid=96777
0451: dt=0.001750, rms=0.459 (0.001%), neg=0, invalid=96777
0452: dt=0.028000, rms=0.459 (0.014%), neg=0, invalid=96777
0453: dt=0.320000, rms=0.458 (0.150%), neg=0, invalid=96777
0454: dt=0.006000, rms=0.458 (0.003%), neg=0, invalid=96777
0455: dt=0.006000, rms=0.458 (0.003%), neg=0, invalid=96777
0456: dt=0.006000, rms=0.458 (0.005%), neg=0, invalid=96777
0457: dt=0.006000, rms=0.458 (0.006%), neg=0, invalid=96777
0458: dt=0.006000, rms=0.458 (0.008%), neg=0, invalid=96777
0459: dt=0.006000, rms=0.458 (0.000%), neg=0, invalid=96777
0460: dt=0.006000, rms=0.458 (0.004%), neg=0, invalid=96777
0461: dt=0.006000, rms=0.458 (0.002%), neg=0, invalid=96777
0462: dt=0.112000, rms=0.458 (0.042%), neg=0, invalid=96777
0463: dt=0.320000, rms=0.457 (0.108%), neg=0, invalid=96777
0464: dt=0.028000, rms=0.457 (0.009%), neg=0, invalid=96777
0465: dt=0.028000, rms=0.457 (0.010%), neg=0, invalid=96777
0466: dt=0.028000, rms=0.457 (0.014%), neg=0, invalid=96777
0467: dt=0.028000, rms=0.457 (0.024%), neg=0, invalid=96777
0468: dt=0.028000, rms=0.457 (0.027%), neg=0, invalid=96777
0469: dt=0.028000, rms=0.457 (0.033%), neg=0, invalid=96777
0470: dt=0.014000, rms=0.457 (0.002%), neg=0, invalid=96777
0471: dt=0.014000, rms=0.457 (0.007%), neg=0, invalid=96777
0472: dt=0.014000, rms=0.457 (0.011%), neg=0, invalid=96777
0473: dt=0.014000, rms=0.457 (0.009%), neg=0, invalid=96777
0474: dt=0.112000, rms=0.457 (0.027%), neg=0, invalid=96777
0475: dt=0.112000, rms=0.456 (0.026%), neg=0, invalid=96777
0476: dt=0.112000, rms=0.456 (0.025%), neg=0, invalid=96777
0477: dt=0.112000, rms=0.456 (0.044%), neg=0, invalid=96777
0478: dt=0.056000, rms=0.456 (0.009%), neg=0, invalid=96777
0479: dt=0.014000, rms=0.456 (0.002%), neg=0, invalid=96777
0480: dt=0.028000, rms=0.456 (0.006%), neg=0, invalid=96777
0481: dt=0.112000, rms=0.456 (0.021%), neg=0, invalid=96777
0482: dt=0.112000, rms=0.456 (0.022%), neg=0, invalid=96777
0483: dt=0.112000, rms=0.456 (0.018%), neg=0, invalid=96777
0484: dt=0.014000, rms=0.456 (0.003%), neg=0, invalid=96777
0485: dt=0.014000, rms=0.456 (0.003%), neg=0, invalid=96777
0486: dt=0.014000, rms=0.456 (0.004%), neg=0, invalid=96777
0487: dt=0.014000, rms=0.456 (0.007%), neg=0, invalid=96777
0488: dt=0.014000, rms=0.456 (0.006%), neg=0, invalid=96777
0489: dt=0.014000, rms=0.456 (0.010%), neg=0, invalid=96777
0490: dt=0.014000, rms=0.456 (0.009%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.456, neg=0, invalid=96777
0491: dt=0.028000, rms=0.455 (0.053%), neg=0, invalid=96777
0492: dt=0.001750, rms=0.455 (0.005%), neg=0, invalid=96777
0493: dt=0.001750, rms=0.455 (0.003%), neg=0, invalid=96777
0494: dt=0.001750, rms=0.455 (0.006%), neg=0, invalid=96777
0495: dt=0.001750, rms=0.455 (0.009%), neg=0, invalid=96777
0496: dt=0.001750, rms=0.455 (0.011%), neg=0, invalid=96777
0497: dt=0.001750, rms=0.455 (0.010%), neg=0, invalid=96777
0498: dt=0.001750, rms=0.455 (0.014%), neg=0, invalid=96777
0499: dt=0.001750, rms=0.455 (0.017%), neg=0, invalid=96777
0500: dt=0.001750, rms=0.455 (0.018%), neg=0, invalid=96777
0501: dt=0.001750, rms=0.455 (0.018%), neg=0, invalid=96777
0502: dt=0.001750, rms=0.455 (0.018%), neg=0, invalid=96777
0503: dt=0.112000, rms=0.454 (0.168%), neg=0, invalid=96777
0504: dt=0.112000, rms=0.453 (0.134%), neg=0, invalid=96777
0505: dt=0.028000, rms=0.453 (0.023%), neg=0, invalid=96777
0506: dt=0.028000, rms=0.453 (0.023%), neg=0, invalid=96777
0507: dt=0.028000, rms=0.453 (0.046%), neg=0, invalid=96777
0508: dt=0.028000, rms=0.453 (0.060%), neg=0, invalid=96777
0509: dt=0.028000, rms=0.452 (0.069%), neg=0, invalid=96777
0510: dt=0.028000, rms=0.452 (0.078%), neg=0, invalid=96777
0511: dt=0.028000, rms=0.452 (0.075%), neg=0, invalid=96777
0512: dt=0.028000, rms=0.451 (0.076%), neg=0, invalid=96777
0513: dt=0.028000, rms=0.451 (0.067%), neg=0, invalid=96777
0514: dt=0.028000, rms=0.451 (0.057%), neg=0, invalid=96777
0515: dt=0.028000, rms=0.451 (0.049%), neg=0, invalid=96777
0516: dt=0.028000, rms=0.450 (0.039%), neg=0, invalid=96777
0517: dt=0.028000, rms=0.450 (0.031%), neg=0, invalid=96777
0518: dt=0.028000, rms=0.450 (0.019%), neg=0, invalid=96777
0519: dt=0.028000, rms=0.450 (0.008%), neg=0, invalid=96777
0520: dt=0.000000, rms=0.450 (-0.000%), 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=0.448, neg=0, invalid=96777
0521: dt=4.624000, rms=0.448 (0.000%), neg=0, invalid=96777
0522: dt=4.624000, rms=0.448 (0.000%), neg=0, invalid=96777
0523: dt=2.023000, rms=0.448 (0.001%), neg=0, invalid=96777
0524: dt=0.018063, rms=0.448 (-0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.448, neg=0, invalid=96777
0525: dt=369.920000, rms=0.447 (0.162%), neg=0, invalid=96777
0526: dt=92.480000, rms=0.447 (0.057%), neg=0, invalid=96777
0527: dt=92.480000, rms=0.447 (0.011%), neg=0, invalid=96777
0528: dt=92.480000, rms=0.447 (0.017%), neg=0, invalid=96777
0529: dt=92.480000, rms=0.447 (0.027%), neg=0, invalid=96777
0530: dt=92.480000, rms=0.447 (0.041%), neg=0, invalid=96777
0531: dt=92.480000, rms=0.446 (0.055%), neg=0, invalid=96777
0532: dt=92.480000, rms=0.446 (0.038%), neg=0, invalid=96777
0533: dt=92.480000, rms=0.446 (0.028%), neg=0, invalid=96777
setting smoothness coefficient to 0.031
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.446, neg=0, invalid=96777
0534: dt=25.920000, rms=0.446 (0.067%), neg=0, invalid=96777
0535: dt=36.288000, rms=0.446 (0.067%), neg=0, invalid=96777
0536: dt=36.288000, rms=0.445 (0.059%), neg=0, invalid=96777
0537: dt=36.288000, rms=0.445 (0.063%), neg=0, invalid=96777
0538: dt=36.288000, rms=0.445 (0.058%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0539: dt=36.288000, rms=0.445 (0.042%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.445, neg=0, invalid=96777
0540: dt=82.944000, rms=0.442 (0.600%), neg=0, invalid=96777
0541: dt=36.288000, rms=0.441 (0.206%), neg=0, invalid=96777
0542: dt=36.288000, rms=0.441 (0.053%), neg=0, invalid=96777
0543: dt=36.288000, rms=0.440 (0.142%), neg=0, invalid=96777
0544: dt=36.288000, rms=0.439 (0.170%), neg=0, invalid=96777
0545: dt=36.288000, rms=0.439 (0.158%), neg=0, invalid=96777
0546: dt=36.288000, rms=0.438 (0.130%), neg=0, invalid=96777
0547: dt=36.288000, rms=0.438 (0.139%), neg=0, invalid=96777
0548: dt=36.288000, rms=0.437 (0.093%), neg=0, invalid=96777
0549: dt=36.288000, rms=0.437 (0.139%), neg=0, invalid=96777
0550: dt=36.288000, rms=0.436 (0.051%), neg=0, invalid=96777
0551: dt=36.288000, rms=0.436 (0.130%), neg=0, invalid=96777
0552: dt=36.288000, rms=0.435 (0.071%), neg=0, invalid=96777
0553: dt=36.288000, rms=0.435 (0.097%), neg=0, invalid=96777
0554: dt=36.288000, rms=0.435 (0.071%), neg=0, invalid=96777
0555: dt=25.920000, rms=0.435 (0.019%), neg=0, invalid=96777
0556: dt=25.920000, rms=0.435 (0.020%), neg=0, invalid=96777
0557: dt=25.920000, rms=0.434 (0.019%), neg=0, invalid=96777
0558: dt=25.920000, rms=0.434 (0.022%), neg=0, invalid=96777
0559: dt=25.920000, rms=0.434 (0.027%), neg=0, invalid=96777
0560: dt=25.920000, rms=0.434 (0.031%), neg=0, invalid=96777
0561: dt=25.920000, rms=0.434 (0.029%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.435, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0562: dt=25.600000, rms=0.434 (0.228%), neg=0, invalid=96777
iter 0, gcam->neg = 17
after 8 iterations, nbhd size=1, neg = 0
0563: dt=38.400000, rms=0.432 (0.413%), neg=0, invalid=96777
0564: dt=8.000000, rms=0.432 (0.101%), neg=0, invalid=96777
0565: dt=8.000000, rms=0.431 (0.092%), neg=0, invalid=96777
0566: dt=8.000000, rms=0.431 (0.119%), neg=0, invalid=96777
0567: dt=8.000000, rms=0.430 (0.155%), neg=0, invalid=96777
0568: dt=8.000000, rms=0.429 (0.164%), neg=0, invalid=96777
0569: dt=8.000000, rms=0.429 (0.169%), neg=0, invalid=96777
0570: dt=8.000000, rms=0.428 (0.188%), neg=0, invalid=96777
0571: dt=8.000000, rms=0.427 (0.186%), neg=0, invalid=96777
0572: dt=8.000000, rms=0.426 (0.169%), neg=0, invalid=96777
0573: dt=8.000000, rms=0.426 (0.156%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0574: dt=8.000000, rms=0.425 (0.145%), neg=0, invalid=96777
0575: dt=8.000000, rms=0.424 (0.150%), neg=0, invalid=96777
0576: dt=8.000000, rms=0.424 (0.136%), neg=0, invalid=96777
0577: dt=8.000000, rms=0.423 (0.145%), neg=0, invalid=96777
iter 0, gcam->neg = 2
after 35 iterations, nbhd size=4, neg = 0
0578: dt=8.000000, rms=0.423 (0.088%), neg=0, invalid=96777
0579: dt=8.000000, rms=0.422 (0.142%), neg=0, invalid=96777
0580: dt=8.000000, rms=0.422 (0.115%), neg=0, invalid=96777
0581: dt=8.000000, rms=0.421 (0.106%), neg=0, invalid=96777
0582: dt=8.000000, rms=0.421 (0.009%), neg=0, invalid=96777
0583: dt=8.000000, rms=0.421 (0.028%), neg=0, invalid=96777
0584: dt=8.000000, rms=0.421 (0.014%), neg=0, invalid=96777
0585: dt=8.000000, rms=0.421 (0.025%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 12 iterations, nbhd size=2, neg = 0
0586: dt=8.000000, rms=0.421 (0.017%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.421, neg=0, invalid=96777
0587: dt=44.800000, rms=0.418 (0.680%), neg=0, invalid=96777
0588: dt=11.200000, rms=0.417 (0.145%), neg=0, invalid=96777
0589: dt=11.200000, rms=0.417 (0.114%), neg=0, invalid=96777
0590: dt=11.200000, rms=0.416 (0.123%), neg=0, invalid=96777
0591: dt=11.200000, rms=0.416 (0.125%), neg=0, invalid=96777
0592: dt=11.200000, rms=0.415 (0.128%), neg=0, invalid=96777
iter 0, gcam->neg = 5
after 32 iterations, nbhd size=3, neg = 0
0593: dt=11.200000, rms=0.415 (0.121%), neg=0, invalid=96777
0594: dt=11.200000, rms=0.415 (0.072%), neg=0, invalid=96777
0595: dt=9.600000, rms=0.414 (0.026%), neg=0, invalid=96777
0596: dt=9.600000, rms=0.414 (0.039%), neg=0, invalid=96777
0597: dt=9.600000, rms=0.414 (0.025%), neg=0, invalid=96777
0598: dt=9.600000, rms=0.414 (0.024%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.420, neg=0, invalid=96777
0599: dt=1.728000, rms=0.420 (0.016%), neg=0, invalid=96777
0600: dt=0.720000, rms=0.420 (0.002%), neg=0, invalid=96777
0601: dt=0.720000, rms=0.420 (-0.004%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.420, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0602: dt=4.032000, rms=0.420 (0.081%), neg=0, invalid=96777
0603: dt=2.880000, rms=0.420 (0.019%), neg=0, invalid=96777
0604: dt=2.880000, rms=0.419 (0.024%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0605: dt=2.880000, rms=0.419 (0.001%), neg=0, invalid=96777
iter 0, gcam->neg = 4
after 8 iterations, nbhd size=1, neg = 0
0606: dt=2.880000, rms=0.419 (-0.070%), neg=0, invalid=96777
setting smoothness coefficient to 1.000
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.427, neg=0, invalid=96777
0607: dt=0.000000, rms=0.427 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.427, neg=0, invalid=96777
0608: dt=0.024000, rms=0.427 (0.000%), neg=0, invalid=96777
0609: dt=0.096000, rms=0.427 (0.000%), neg=0, invalid=96777
0610: dt=0.028000, rms=0.427 (0.002%), neg=0, invalid=96777
0611: dt=0.016000, rms=0.427 (0.001%), neg=0, invalid=96777
0612: dt=0.016000, rms=0.427 (0.001%), neg=0, invalid=96777
0613: dt=0.016000, rms=0.427 (-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=0.415, neg=0, invalid=96777
iter 0, gcam->neg = 440
after 11 iterations, nbhd size=1, neg = 0
0614: dt=1.611801, rms=0.391 (5.642%), neg=0, invalid=96777
0615: dt=0.000109, rms=0.391 (0.004%), neg=0, invalid=96777
0616: dt=0.000109, rms=0.391 (-0.001%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.391, neg=0, invalid=96777
0617: dt=0.000375, rms=0.391 (0.000%), neg=0, invalid=96777
0618: dt=0.000000, rms=0.391 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 45
after 7 iterations, nbhd size=1, neg = 0
0619: dt=0.050000, rms=0.391 (-0.122%), 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=0.382, neg=0, invalid=96777
0620: dt=0.000000, rms=0.383 (-0.147%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.383, neg=0, invalid=96777
0621: dt=18.496000, rms=0.383 (0.001%), neg=0, invalid=96777
0622: dt=4.624000, rms=0.383 (0.000%), neg=0, invalid=96777
0623: dt=4.624000, rms=0.383 (-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=0.383, neg=0, invalid=96777
0624: dt=0.000000, rms=0.383 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.383, neg=0, invalid=96777
0625: dt=36.288000, rms=0.383 (0.019%), neg=0, invalid=96777
0626: dt=103.680000, rms=0.383 (0.037%), neg=0, invalid=96777
0627: dt=36.288000, rms=0.383 (0.015%), neg=0, invalid=96777
0628: dt=36.288000, rms=0.383 (0.020%), neg=0, invalid=96777
0629: dt=36.288000, rms=0.382 (0.025%), neg=0, invalid=96777
0630: dt=36.288000, rms=0.382 (0.024%), neg=0, invalid=96777
0631: dt=36.288000, rms=0.382 (0.020%), neg=0, invalid=96777
setting smoothness coefficient to 0.118
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.383, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0632: dt=11.200000, rms=0.382 (0.052%), neg=0, invalid=96777
0633: dt=2.800000, rms=0.382 (0.003%), neg=0, invalid=96777
0634: dt=2.800000, rms=0.382 (0.007%), neg=0, invalid=96777
0635: dt=2.800000, rms=0.382 (0.006%), neg=0, invalid=96777
0636: dt=2.800000, rms=0.382 (-0.007%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.382, neg=0, invalid=96777
iter 0, gcam->neg = 9
after 17 iterations, nbhd size=2, neg = 0
0637: dt=44.800000, rms=0.381 (0.422%), neg=0, invalid=96777
iter 0, gcam->neg = 3
after 0 iterations, nbhd size=0, neg = 0
0638: dt=25.600000, rms=0.380 (0.182%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0639: dt=25.600000, rms=0.380 (-0.165%), neg=0, invalid=96777
setting smoothness coefficient to 0.400
blurring input image with Gaussian with sigma=2.000...
0000: dt=0.000, rms=0.382, neg=0, invalid=96777
iter 0, gcam->neg = 2
after 1 iterations, nbhd size=0, neg = 0
0640: dt=0.720000, rms=0.382 (0.016%), neg=0, invalid=96777
iter 0, gcam->neg = 107
after 23 iterations, nbhd size=2, neg = 0
0641: dt=9.058824, rms=0.380 (0.347%), neg=0, invalid=96777
0642: dt=0.015750, rms=0.380 (0.001%), neg=0, invalid=96777
0643: dt=0.015750, rms=0.380 (0.000%), neg=0, invalid=96777
0644: dt=0.015750, rms=0.380 (0.001%), neg=0, invalid=96777
0645: dt=0.015750, rms=0.380 (0.001%), neg=0, invalid=96777
0646: dt=0.015750, rms=0.380 (0.001%), neg=0, invalid=96777
0647: dt=0.015750, rms=0.380 (0.001%), neg=0, invalid=96777
0648: dt=0.015750, rms=0.380 (0.001%), neg=0, invalid=96777
0649: dt=0.015750, rms=0.380 (0.002%), neg=0, invalid=96777
0650: dt=0.015750, rms=0.380 (0.002%), neg=0, invalid=96777
0651: dt=0.015750, rms=0.380 (0.002%), neg=0, invalid=96777
0652: dt=0.015750, rms=0.380 (0.002%), neg=0, invalid=96777
0653: dt=0.015750, rms=0.380 (0.002%), neg=0, invalid=96777
0654: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0655: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0656: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0657: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0658: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0659: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0660: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0661: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0662: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0663: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0664: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0665: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0666: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0667: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0668: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0669: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
0670: dt=0.015750, rms=0.380 (0.003%), neg=0, invalid=96777
iter 0, gcam->neg = 33
after 19 iterations, nbhd size=2, neg = 0
0671: dt=9.216000, rms=0.380 (0.140%), neg=0, invalid=96777
0672: dt=0.009000, rms=0.380 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.380, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0673: dt=1.008000, rms=0.379 (0.037%), neg=0, invalid=96777
iter 0, gcam->neg = 76
after 35 iterations, nbhd size=3, neg = 0
0674: dt=10.120735, rms=0.377 (0.565%), neg=0, invalid=96777
0675: dt=0.015750, rms=0.377 (0.000%), neg=0, invalid=96777
0676: dt=0.015750, rms=0.377 (0.000%), neg=0, invalid=96777
0677: dt=0.015750, rms=0.377 (0.001%), neg=0, invalid=96777
0678: dt=0.015750, rms=0.377 (0.001%), neg=0, invalid=96777
0679: dt=0.015750, rms=0.377 (0.001%), neg=0, invalid=96777
0680: dt=0.015750, rms=0.377 (0.001%), neg=0, invalid=96777
0681: dt=0.015750, rms=0.377 (0.002%), neg=0, invalid=96777
0682: dt=0.015750, rms=0.377 (0.002%), neg=0, invalid=96777
0683: dt=0.015750, rms=0.377 (0.002%), neg=0, invalid=96777
0684: dt=0.015750, rms=0.377 (0.002%), neg=0, invalid=96777
0685: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0686: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0687: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0688: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0689: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0690: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0691: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0692: dt=0.015750, rms=0.377 (0.003%), neg=0, invalid=96777
0693: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0694: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0695: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0696: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0697: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0698: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0699: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0700: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
0701: dt=0.015750, rms=0.377 (0.004%), neg=0, invalid=96777
iter 0, gcam->neg = 44
after 27 iterations, nbhd size=3, neg = 0
0702: dt=16.128000, rms=0.376 (0.260%), neg=0, invalid=96777
0703: dt=0.013500, rms=0.376 (0.000%), neg=0, invalid=96777
0704: dt=0.013500, rms=0.376 (0.000%), neg=0, invalid=96777
0705: dt=0.013500, rms=0.376 (-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=0.380, neg=0, invalid=96777
0706: dt=0.000000, rms=0.380 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.380, neg=0, invalid=96777
0707: dt=0.000000, rms=0.380 (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=0.373, neg=0, invalid=96777
iter 0, gcam->neg = 164
after 20 iterations, nbhd size=2, neg = 0
0708: dt=0.448000, rms=0.368 (1.452%), neg=0, invalid=96777
0709: dt=0.000047, rms=0.368 (0.001%), neg=0, invalid=96777
0710: dt=0.000047, rms=0.368 (0.000%), neg=0, invalid=96777
0711: dt=0.000047, rms=0.368 (0.000%), neg=0, invalid=96777
0712: dt=0.000047, rms=0.368 (0.000%), neg=0, invalid=96777
0713: dt=0.000047, rms=0.368 (0.000%), neg=0, invalid=96777
iter 0, gcam->neg = 1
after 0 iterations, nbhd size=0, neg = 0
0714: dt=0.020000, rms=0.368 (0.003%), neg=0, invalid=96777
0715: dt=0.000002, rms=0.368 (0.000%), neg=0, invalid=96777
blurring input image with Gaussian with sigma=0.500...
0000: dt=0.000, rms=0.368, neg=0, invalid=96777
iter 0, gcam->neg = 1
after 5 iterations, nbhd size=1, neg = 0
0716: dt=0.005002, rms=0.368 (0.009%), neg=0, invalid=96777
0717: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0718: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0719: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0720: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0721: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0722: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0723: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0724: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0725: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0726: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0727: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0728: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0729: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0730: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0731: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0732: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0733: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0734: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0735: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0736: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0737: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0738: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0739: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0740: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0741: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
0742: dt=0.000004, rms=0.368 (0.000%), neg=0, invalid=96777
writing output transformation to transforms/talairach.m3z...
GCAMwrite
registration took 4 hours, 41 minutes and 52 seconds.
#--------------------------------------
#@# CA Reg Inv Tue Jan 30 20:12:37 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

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

Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z 
Inverting GCAM
Saving inverse 
#--------------------------------------
#@# Remove Neck Tue Jan 30 20:13:59 EST 2018

 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...
11445492 nonbrain voxels erased
writing output to nu_noneck.mgz...
nonbrain removal took 1 minutes and 31 seconds.
#--------------------------------------
#@# SkullLTA Tue Jan 30 20:15:29 EST 2018

 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=10.0
skull bounding box = (45, 55, 38) --> (210, 227, 236)
using (100, 112, 137) as brain centroid...
mean wm in atlas = 126, using box (80,91,113) --> (120, 133,161) to find MRI wm
before smoothing, mri peak at 105
after smoothing, mri peak at 104, scaling input intensities by 1.212
scaling channel 0 by 1.21154
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-3.9 (thresh=-3.9)
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
 0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 1 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1)
 1.034  -0.022  -0.001  -3.945;
 0.017   1.320   0.160  -72.876;
-0.002  -0.076   1.047  -23.545;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 2 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.054  -0.022  -0.001  -6.377;
 0.017   1.345   0.163  -76.513;
-0.002  -0.076   1.047  -21.670;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.054  -0.022  -0.001  -6.377;
 0.017   1.345   0.163  -76.513;
-0.002  -0.076   1.047  -21.670;
 0.000   0.000   0.000   1.000;
reducing scale to 0.0625
****************************************
Nine parameter search.  iteration 4 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.055  -0.022  -0.001  -6.063;
 0.017   1.346   0.164  -76.744;
-0.002  -0.076   1.044  -22.308;
 0.000   0.000   0.000   1.000;
****************************************
Nine parameter search.  iteration 5 nscales = 2 ...
****************************************
Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0)
 1.056  -0.034   0.006  -5.617;
 0.026   1.344   0.172  -78.634;
-0.010  -0.086   1.043  -19.603;
 0.000   0.000   0.000   1.000;
min search scale 0.025000 reached
***********************************************
Computing MAP estimate using 3481 samples...
***********************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-05
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.05584  -0.03403   0.00619  -5.61713;
 0.02586   1.34376   0.17197  -78.63378;
-0.01039  -0.08638   1.04293  -19.60255;
 0.00000   0.00000   0.00000   1.00000;
nsamples 3481
Quasinewton: input matrix
 1.05584  -0.03403   0.00619  -5.61713;
 0.02586   1.34376   0.17197  -78.63378;
-0.01039  -0.08638   1.04293  -19.60255;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) =   -0.0  tol 0.000010
Resulting transform:
 1.056  -0.034   0.006  -5.617;
 0.026   1.344   0.172  -78.634;
-0.010  -0.086   1.043  -19.603;
 0.000   0.000   0.000   1.000;

pass 1, spacing 8: log(p) = -4.0 (old=-3.9)
transform before final EM align:
 1.056  -0.034   0.006  -5.617;
 0.026   1.344   0.172  -78.634;
-0.010  -0.086   1.043  -19.603;
 0.000   0.000   0.000   1.000;

**************************************************
 EM alignment process ...
 Computing final MAP estimate using 382743 samples. 
**************************************************
dt = 5.00e-06, momentum=0.80, tol=1.00e-07
l_intensity = 1.0000
Aligning input volume to GCA...
Transform matrix
 1.05584  -0.03403   0.00619  -5.61713;
 0.02586   1.34376   0.17197  -78.63378;
-0.01039  -0.08638   1.04293  -19.60255;
 0.00000   0.00000   0.00000   1.00000;
nsamples 382743
Quasinewton: input matrix
 1.05584  -0.03403   0.00619  -5.61713;
 0.02586   1.34376   0.17197  -78.63378;
-0.01039  -0.08638   1.04293  -19.60255;
 0.00000   0.00000   0.00000   1.00000;
 IFLAG= -1  LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) =    4.4  tol 0.000000
final transform:
 1.056  -0.034   0.006  -5.617;
 0.026   1.344   0.172  -78.634;
-0.010  -0.086   1.043  -19.603;
 0.000   0.000   0.000   1.000;

writing output transformation to transforms/talairach_with_skull_2.lta...
registration took 31 minutes and 25 seconds.
#--------------------------------------
#@# SubCort Seg Tue Jan 30 20:46:55 EST 2018

 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 e21.hpcc.dartmouth.edu
machine  x86_64

setenv SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
cd /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 = 0.19698 (28)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (204 voxels, overlap=0.637)
Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (204 voxels, peak = 27), gca=27.4
gca peak = 0.14982 (20)
mri peak = 0.16066 (27)
Right_Lateral_Ventricle (43): linear fit = 1.23 x + 0.0 (203 voxels, overlap=0.326)
Right_Lateral_Ventricle (43): linear fit = 1.23 x + 0.0 (203 voxels, peak = 24), gca=24.5
gca peak = 0.28003 (97)
mri peak = 0.13828 (103)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (278 voxels, overlap=1.012)
Right_Pallidum (52): linear fit = 1.02 x + 0.0 (278 voxels, peak = 99), gca=99.4
gca peak = 0.18160 (96)
mri peak = 0.10390 (103)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (253 voxels, overlap=1.027)
Left_Pallidum (13): linear fit = 1.01 x + 0.0 (253 voxels, peak = 97), gca=97.4
gca peak = 0.27536 (62)
mri peak = 0.15606 (76)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (831 voxels, overlap=0.016)
Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (831 voxels, peak = 75), gca=74.7
gca peak = 0.32745 (63)
mri peak = 0.13721 (78)
Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (779 voxels, overlap=0.016)
Left_Hippocampus (17): linear fit = 1.22 x + 0.0 (779 voxels, peak = 77), gca=76.5
gca peak = 0.08597 (105)
mri peak = 0.13034 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (36218 voxels, overlap=0.608)
Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (36218 voxels, peak = 108), gca=107.6
gca peak = 0.09209 (106)
mri peak = 0.12127 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (34762 voxels, overlap=0.484)
Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (34762 voxels, peak = 109), gca=108.6
gca peak = 0.07826 (63)
mri peak = 0.04852 (72)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (29325 voxels, overlap=0.406)
Left_Cerebral_Cortex (3): linear fit = 1.20 x + 0.0 (29325 voxels, peak = 75), gca=75.3
gca peak = 0.08598 (64)
mri peak = 0.04914 (72)
Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (26485 voxels, overlap=0.491)
Right_Cerebral_Cortex (42): linear fit = 1.13 x + 0.0 (26485 voxels, peak = 73), gca=72.6
gca peak = 0.24164 (71)
mri peak = 0.12990 (85)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (485 voxels, overlap=0.017)
Right_Caudate (50): linear fit = 1.15 x + 0.0 (485 voxels, peak = 82), gca=82.0
gca peak = 0.18227 (75)
mri peak = 0.14514 (85)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (751 voxels, overlap=0.421)
Left_Caudate (11): linear fit = 1.12 x + 0.0 (751 voxels, peak = 84), gca=83.6
gca peak = 0.10629 (62)
mri peak = 0.05581 (70)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (22367 voxels, overlap=0.549)
Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (22367 voxels, peak = 70), gca=70.4
gca peak = 0.11668 (59)
mri peak = 0.05974 (69)
Right_Cerebellum_Cortex (47): linear fit = 1.14 x + 0.0 (22676 voxels, overlap=0.541)
Right_Cerebellum_Cortex (47): linear fit = 1.14 x + 0.0 (22676 voxels, peak = 68), gca=67.6
gca peak = 0.17849 (88)
mri peak = 0.17268 (93)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4931 voxels, overlap=0.430)
Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4931 voxels, peak = 93), gca=92.8
gca peak = 0.16819 (86)
mri peak = 0.17344 (92)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4849 voxels, overlap=0.423)
Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (4849 voxels, peak = 90), gca=89.9
gca peak = 0.41688 (64)
mri peak = 0.12821 (81)
Left_Amygdala (18): linear fit = 1.26 x + 0.0 (234 voxels, overlap=0.055)
Left_Amygdala (18): linear fit = 1.26 x + 0.0 (234 voxels, peak = 81), gca=81.0
gca peak = 0.42394 (62)
mri peak = 0.19283 (79)
Right_Amygdala (54): linear fit = 1.26 x + 0.0 (221 voxels, overlap=0.050)
Right_Amygdala (54): linear fit = 1.26 x + 0.0 (221 voxels, peak = 78), gca=78.4
gca peak = 0.10041 (96)
mri peak = 0.08590 (105)
Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (3991 voxels, overlap=0.453)
Left_Thalamus_Proper (10): linear fit = 1.10 x + 0.0 (3991 voxels, peak = 105), gca=105.1
gca peak = 0.13978 (88)
mri peak = 0.08649 (100)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3590 voxels, overlap=0.380)
Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3590 voxels, peak = 99), gca=99.0
gca peak = 0.08514 (81)
mri peak = 0.08397 (90)
Left_Putamen (12): linear fit = 1.09 x + 0.0 (1439 voxels, overlap=0.470)
Left_Putamen (12): linear fit = 1.09 x + 0.0 (1439 voxels, peak = 88), gca=87.9
gca peak = 0.09624 (82)
mri peak = 0.08145 (90)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1768 voxels, overlap=0.688)
Right_Putamen (51): linear fit = 1.05 x + 0.0 (1768 voxels, peak = 87), gca=86.5
gca peak = 0.07543 (88)
mri peak = 0.07269 (97)
Brain_Stem (16): linear fit = 1.09 x + 0.0 (9244 voxels, overlap=0.596)
Brain_Stem (16): linear fit = 1.09 x + 0.0 (9244 voxels, peak = 95), gca=95.5
gca peak = 0.12757 (95)
mri peak = 0.13816 (106)
Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1039 voxels, overlap=0.370)
Right_VentralDC (60): linear fit = 1.11 x + 0.0 (1039 voxels, peak = 105), gca=105.0
gca peak = 0.17004 (92)
mri peak = 0.11090 (106)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1073 voxels, overlap=0.335)
Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1073 voxels, peak = 100), gca=99.8
gca peak = 0.21361 (36)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.26069 (23)
mri peak = 0.24885 (28)
Fourth_Ventricle (15): linear fit = 1.15 x + 0.0 (217 voxels, overlap=0.495)
Fourth_Ventricle (15): linear fit = 1.15 x + 0.0 (217 voxels, peak = 27), gca=26.6
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.31795 (35)
gca peak Third_Ventricle = 0.21361 (36)
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 1.21 x + 0.0
estimating mean wm scale to be 1.02 x + 0.0
estimating mean csf scale to be 1.13 x + 0.0
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
renormalizing by structure alignment....
renormalizing input #0
gca peak = 0.15238 (28)
mri peak = 0.19698 (28)
Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (204 voxels, overlap=0.635)
Left_Lateral_Ventricle (4): linear fit = 0.96 x + 0.0 (204 voxels, peak = 27), gca=27.0
gca peak = 0.17187 (25)
mri peak = 0.16066 (27)
Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (203 voxels, overlap=0.570)
Right_Lateral_Ventricle (43): linear fit = 1.01 x + 0.0 (203 voxels, peak = 25), gca=25.4
gca peak = 0.30211 (100)
mri peak = 0.13828 (103)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (278 voxels, overlap=1.004)
Right_Pallidum (52): linear fit = 1.00 x + 0.0 (278 voxels, peak = 100), gca=100.5
gca peak = 0.16526 (97)
mri peak = 0.10390 (103)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (253 voxels, overlap=1.016)
Left_Pallidum (13): linear fit = 1.00 x + 0.0 (253 voxels, peak = 97), gca=97.5
gca peak = 0.26366 (75)
mri peak = 0.15606 (76)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (831 voxels, overlap=0.822)
Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (831 voxels, peak = 75), gca=75.0
gca peak = 0.23220 (81)
mri peak = 0.13721 (78)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (779 voxels, overlap=0.925)
Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (779 voxels, peak = 79), gca=79.0
gca peak = 0.08345 (108)
mri peak = 0.13034 (108)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36218 voxels, overlap=0.696)
Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (36218 voxels, peak = 109), gca=108.5
gca peak = 0.08541 (108)
mri peak = 0.12127 (109)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34762 voxels, overlap=0.630)
Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (34762 voxels, peak = 108), gca=108.0
gca peak = 0.06658 (75)
mri peak = 0.04852 (72)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29325 voxels, overlap=0.859)
Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (29325 voxels, peak = 74), gca=73.9
gca peak = 0.07728 (72)
mri peak = 0.04914 (72)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (26485 voxels, overlap=0.934)
Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (26485 voxels, peak = 72), gca=72.0
gca peak = 0.27200 (85)
mri peak = 0.12990 (85)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (485 voxels, overlap=1.001)
Right_Caudate (50): linear fit = 0.99 x + 0.0 (485 voxels, peak = 84), gca=83.7
gca peak = 0.16044 (83)
mri peak = 0.14514 (85)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (751 voxels, overlap=0.627)
Left_Caudate (11): linear fit = 1.00 x + 0.0 (751 voxels, peak = 83), gca=83.0
gca peak = 0.09337 (69)
mri peak = 0.05581 (70)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (22367 voxels, overlap=0.976)
Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (22367 voxels, peak = 68), gca=68.0
gca peak = 0.10844 (68)
mri peak = 0.05974 (69)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22676 voxels, overlap=0.984)
Right_Cerebellum_Cortex (47): linear fit = 0.99 x + 0.0 (22676 voxels, peak = 67), gca=67.0
gca peak = 0.17166 (92)
mri peak = 0.17268 (93)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4931 voxels, overlap=0.902)
Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4931 voxels, peak = 92), gca=91.5
gca peak = 0.15903 (90)
mri peak = 0.17344 (92)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4849 voxels, overlap=0.878)
Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (4849 voxels, peak = 90), gca=89.6
gca peak = 0.28672 (80)
mri peak = 0.12821 (81)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (234 voxels, overlap=1.009)
Left_Amygdala (18): linear fit = 1.00 x + 0.0 (234 voxels, peak = 80), gca=80.0
gca peak = 0.30395 (78)
mri peak = 0.19283 (79)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (221 voxels, overlap=1.000)
Right_Amygdala (54): linear fit = 1.00 x + 0.0 (221 voxels, peak = 78), gca=78.0
gca peak = 0.09437 (105)
mri peak = 0.08590 (105)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3991 voxels, overlap=0.905)
Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3991 voxels, peak = 104), gca=104.5
gca peak = 0.12621 (99)
mri peak = 0.08649 (100)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3590 voxels, overlap=0.892)
Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3590 voxels, peak = 99), gca=98.5
gca peak = 0.07892 (88)
mri peak = 0.08397 (90)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1439 voxels, overlap=0.819)
Left_Putamen (12): linear fit = 1.00 x + 0.0 (1439 voxels, peak = 88), gca=87.6
gca peak = 0.10577 (80)
mri peak = 0.08145 (90)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (1768 voxels, overlap=0.997)
Right_Putamen (51): linear fit = 1.01 x + 0.0 (1768 voxels, peak = 81), gca=81.2
gca peak = 0.07135 (93)
mri peak = 0.07269 (97)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (9244 voxels, overlap=0.839)
Brain_Stem (16): linear fit = 1.00 x + 0.0 (9244 voxels, peak = 93), gca=93.5
gca peak = 0.12505 (105)
mri peak = 0.13816 (106)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1039 voxels, overlap=0.815)
Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1039 voxels, peak = 105), gca=105.0
gca peak = 0.16039 (100)
mri peak = 0.11090 (106)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1073 voxels, overlap=0.813)
Left_VentralDC (28): linear fit = 1.01 x + 0.0 (1073 voxels, peak = 102), gca=101.5
gca peak = 0.19676 (41)
uniform distribution in MR - rejecting arbitrary fit
gca peak = 0.18638 (27)
mri peak = 0.24885 (28)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (217 voxels, overlap=0.536)
Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (217 voxels, peak = 26), gca=26.3
gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.22716 (43)
gca peak Third_Ventricle = 0.19676 (41)
gca peak CSF = 0.14103 (44)
gca peak Left_Accumbens_area = 0.57797 (78)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.63638 (62)
gca peak Left_choroid_plexus = 0.09086 (48)
gca peak Right_Inf_Lat_Vent = 0.24517 (38)
gca peak Right_Accumbens_area = 0.30179 (83)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10190 (48)
gca peak Fifth_Ventricle = 0.73407 (47)
gca peak WM_hypointensities = 0.15047 (84)
gca peak non_WM_hypointensities = 0.11940 (54)
gca peak Optic_Chiasm = 0.34484 (76)
not using caudate to estimate GM means
estimating mean gm scale to be 0.99 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 0.98 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
27112 gm and wm labels changed (%26 to gray, %74 to white out of all changed labels)
315 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 66884 changed. image ll: -2.122, PF=1.000
pass 2: 9811 changed.
pass 3: 3183 changed.
writing labeled volume to aseg.auto_noCCseg.mgz...
auto-labeling took 18 minutes and 46 seconds.

 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/cc_up.lta BPD0072_base 

will read input aseg from aseg.auto_noCCseg.mgz
writing aseg with cc labels to aseg.auto.mgz
will write lta as /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/transforms/cc_up.lta
reading aseg from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.auto_noCCseg.mgz
reading norm from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/norm.mgz
25287 voxels in left wm, 35202 in right wm, xrange [124, 131]
searching rotation angles z=[-7  7], y=[-8  6]

searching scale 1 Z rot -7.1  
searching scale 1 Z rot -6.9  
searching scale 1 Z rot -6.6  
searching scale 1 Z rot -6.4  
searching scale 1 Z rot -6.1  
searching scale 1 Z rot -5.9  
searching scale 1 Z rot -5.6  
searching scale 1 Z rot -5.4  
searching scale 1 Z rot -5.1  
searching scale 1 Z rot -4.9  
searching scale 1 Z rot -4.6  
searching scale 1 Z rot -4.4  
searching scale 1 Z rot -4.1  
searching scale 1 Z rot -3.9  
searching scale 1 Z rot -3.6  
searching scale 1 Z rot -3.4  
searching scale 1 Z rot -3.1  
searching scale 1 Z rot -2.9  
searching scale 1 Z rot -2.6  
searching scale 1 Z rot -2.4  
searching scale 1 Z rot -2.1  
searching scale 1 Z rot -1.9  
searching scale 1 Z rot -1.6  
searching scale 1 Z rot -1.4  
searching scale 1 Z rot -1.1  
searching scale 1 Z rot -0.9  
searching scale 1 Z rot -0.6  
searching scale 1 Z rot -0.4  
searching scale 1 Z rot -0.1  
searching scale 1 Z rot 0.1  
searching scale 1 Z rot 0.4  
searching scale 1 Z rot 0.6  
searching scale 1 Z rot 0.9  
searching scale 1 Z rot 1.1  
searching scale 1 Z rot 1.4  
searching scale 1 Z rot 1.6  
searching scale 1 Z rot 1.9  
searching scale 1 Z rot 2.1  
searching scale 1 Z rot 2.4  
searching scale 1 Z rot 2.6  
searching scale 1 Z rot 2.9  
searching scale 1 Z rot 3.1  
searching scale 1 Z rot 3.4  
searching scale 1 Z rot 3.6  
searching scale 1 Z rot 3.9  
searching scale 1 Z rot 4.1  
searching scale 1 Z rot 4.4  
searching scale 1 Z rot 4.6  
searching scale 1 Z rot 4.9  
searching scale 1 Z rot 5.1  
searching scale 1 Z rot 5.4  
searching scale 1 Z rot 5.6  
searching scale 1 Z rot 5.9  
searching scale 1 Z rot 6.1  
searching scale 1 Z rot 6.4  
searching scale 1 Z rot 6.6  global minimum found at slice 127.6, rotations (-1.07, -0.12)
final transformation (x=127.6, yr=-1.075, zr=-0.117):
 1.000   0.002  -0.019   2.539;
-0.002   1.000   0.000   12.256;
 0.019  -0.000   1.000   0.629;
 0.000   0.000   0.000   1.000;
updating x range to be [126, 131] in xformed coordinates
best xformed slice 128
cc center is found at 128 145 118
eigenvectors:
-0.003   0.017   1.000;
-0.025  -1.000   0.017;
 1.000  -0.025   0.003;
writing aseg with callosum to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.auto.mgz...
corpus callosum matter segmentation took 0.6 minutes
#--------------------------------------
#@# Merge ASeg Tue Jan 30 21:06:17 EST 2018

 cp aseg.auto.mgz aseg.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Tue Jan 30 21:06:17 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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...
899 control points removed
Building bias image
building Voronoi diagram...
performing soap bubble smoothing, sigma = 0...
Smoothing with sigma 8
Applying bias correction
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 111
white matter peak found at 110
gm peak at 81 (81), valley at 45 (45)
csf peak at 30, setting threshold to 64
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 82 (82), valley at 45 (45)
csf peak at 32, setting threshold to 65
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to brain.mgz
3D bias adjustment took 3 minutes and 59 seconds.
#--------------------------------------------
#@# Mask BFS Tue Jan 30 21:10:19 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

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

threshold mask volume at 5
DoAbs = 0
Found 1607034 voxels in mask (pct=  9.58)
Writing masked volume to brain.finalsurfs.mgz...done.
#--------------------------------------------
#@# WM Segmentation Tue Jan 30 21:10:21 EST 2018

 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 (104.0): 103.3 +- 5.9 [80.0 --> 125.0]
GM (80.0) : 79.4 +- 9.3 [30.0 --> 96.0]
setting bottom of white matter range to 88.6
setting top of gray matter range to 97.9
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...
2810 sparsely connected voxels removed...
thickening thin strands....
20 segments, 4698 filled
120 bright non-wm voxels segmented.
1632 diagonally connected voxels added...
white matter segmentation took 2.1 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 0.70 minutes
reading wm segmentation from wm.seg.mgz...
41 voxels added to wm to prevent paths from MTL structures to cortex
2660 additional wm voxels added
0 additional wm voxels added
SEG EDIT: 29919 voxels turned on, 33905 voxels turned off.
propagating editing to output volume from wm.seg.mgz
115,126,128 old 102   new 102
115,126,128 old 102   new 102
writing edited volume to wm.asegedit.mgz....

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

Iteration Number : 1
pass   1 (xy+):  23 found -  23 modified     |    TOTAL:  23
pass   2 (xy+):   0 found -  23 modified     |    TOTAL:  23
pass   1 (xy-):  11 found -  11 modified     |    TOTAL:  34
pass   2 (xy-):   0 found -  11 modified     |    TOTAL:  34
pass   1 (yz+):  23 found -  23 modified     |    TOTAL:  57
pass   2 (yz+):   0 found -  23 modified     |    TOTAL:  57
pass   1 (yz-):  18 found -  18 modified     |    TOTAL:  75
pass   2 (yz-):   0 found -  18 modified     |    TOTAL:  75
pass   1 (xz+):  14 found -  14 modified     |    TOTAL:  89
pass   2 (xz+):   0 found -  14 modified     |    TOTAL:  89
pass   1 (xz-):  13 found -  13 modified     |    TOTAL: 102
pass   2 (xz-):   0 found -  13 modified     |    TOTAL: 102
Iteration Number : 1
pass   1 (+++):   6 found -   6 modified     |    TOTAL:   6
pass   2 (+++):   0 found -   6 modified     |    TOTAL:   6
pass   1 (+++):  10 found -  10 modified     |    TOTAL:  16
pass   2 (+++):   0 found -  10 modified     |    TOTAL:  16
pass   1 (+++):   2 found -   2 modified     |    TOTAL:  18
pass   2 (+++):   0 found -   2 modified     |    TOTAL:  18
pass   1 (+++):   8 found -   8 modified     |    TOTAL:  26
pass   2 (+++):   0 found -   8 modified     |    TOTAL:  26
Iteration Number : 1
pass   1 (++):  55 found -  55 modified     |    TOTAL:  55
pass   2 (++):   0 found -  55 modified     |    TOTAL:  55
pass   1 (+-):  72 found -  72 modified     |    TOTAL: 127
pass   2 (+-):   0 found -  72 modified     |    TOTAL: 127
pass   1 (--):  58 found -  58 modified     |    TOTAL: 185
pass   2 (--):   0 found -  58 modified     |    TOTAL: 185
pass   1 (-+):  54 found -  54 modified     |    TOTAL: 239
pass   2 (-+):   0 found -  54 modified     |    TOTAL: 239
Iteration Number : 2
pass   1 (xy+):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy+):   0 found -   1 modified     |    TOTAL:   1
pass   1 (xy-):   4 found -   4 modified     |    TOTAL:   5
pass   2 (xy-):   0 found -   4 modified     |    TOTAL:   5
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   5
pass   1 (yz-):   1 found -   1 modified     |    TOTAL:   6
pass   2 (yz-):   0 found -   1 modified     |    TOTAL:   6
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   6
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   6
Iteration Number : 2
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 2
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 3
pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0

Total Number of Modified Voxels = 373 (out of 509947: 0.073145)
binarizing input wm segmentation...
Ambiguous edge configurations... 

mri_pretess done

#--------------------------------------------
#@# Fill Tue Jan 30 21:13:12 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

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

logging cutting plane coordinates to ../scripts/ponscc.cut.log...
INFO: Using transforms/talairach.lta and its offset for Talairach volume ...
using segmentation aseg.auto_noCCseg.mgz...
reading input volume...done.
searching for cutting planes...voxel to talairach voxel transform
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
-0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;
voxel to talairach voxel transform
 1.054   0.020   0.004  -12.643;
-0.017   1.235   0.258  -71.872;
-0.000  -0.196   1.048  -4.288;
 0.000   0.000   0.000   1.000;
reading segmented volume aseg.auto_noCCseg.mgz...
Looking for area (min, max) = (350, 1400)
area[0] = 1018 (min = 350, max = 1400), aspect = 0.44 (min = 0.10, max = 0.75)
no need to search
using seed (125, 105, 122), TAL = (3.0, -6.0, 23.0)
talairach voxel to voxel transform
 0.949  -0.015  -0.000   10.881;
 0.013   0.779  -0.192   55.308;
 0.002   0.146   0.919   14.446;
 0.000   0.000   0.000   1.000;
segmentation indicates cc at (125,  105,  122) --> (3.0, -6.0, 23.0)
done.
writing output to filled.mgz...
filling took 0.8 minutes
talairach cc position changed to (3.00, -6.00, 23.00)
Erasing brainstem...done.
seed_search_size = 9, min_neighbors = 5
search rh wm seed point around talairach space:(21.00, -6.00, 23.00) SRC: (110.75, 115.03, 142.08)
search lh wm seed point around talairach space (-15.00, -6.00, 23.00), SRC: (144.90, 115.49, 142.17)
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 Tue Jan 30 21:13:58 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

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

Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   4 found -   4 modified     |    TOTAL:   5
pass   2 (yz+):   0 found -   4 modified     |    TOTAL:   5
pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   5
pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   5
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 (-+):   0 found -   0 modified     |    TOTAL:   0
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 = 5 (out of 242844: 0.002059)
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 60: 1837 vertices, 1942 faces
slice 70: 7622 vertices, 7844 faces
slice 80: 16661 vertices, 16986 faces
slice 90: 27604 vertices, 27970 faces
slice 100: 38243 vertices, 38580 faces
slice 110: 48974 vertices, 49348 faces
slice 120: 61158 vertices, 61568 faces
slice 130: 72975 vertices, 73373 faces
slice 140: 83288 vertices, 83664 faces
slice 150: 93065 vertices, 93435 faces
slice 160: 102404 vertices, 102724 faces
slice 170: 110278 vertices, 110563 faces
slice 180: 117223 vertices, 117477 faces
slice 190: 123481 vertices, 123712 faces
slice 200: 128344 vertices, 128521 faces
slice 210: 131084 vertices, 131123 faces
slice 220: 131130 vertices, 131160 faces
slice 230: 131130 vertices, 131160 faces
slice 240: 131130 vertices, 131160 faces
slice 250: 131130 vertices, 131160 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...
   131130 voxel in cpt #1: X=-30 [v=131130,e=393480,f=262320] located at (-27.018478, -2.766834, 4.977854)
For the whole surface: X=-30 [v=131130,e=393480,f=262320]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 lh Tue Jan 30 21:14:09 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Tue Jan 30 21:14:13 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts
avg radius = 45.6 mm, total surface area = 69912 mm^2
writing inflated surface to ../surf/lh.inflated.nofix
inflation took 0.5 minutes
Not saving sulc

step 000: RMS=0.098 (target=0.015)   
step 005: RMS=0.073 (target=0.015)   
step 010: RMS=0.054 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.039 (target=0.015)   
step 025: RMS=0.034 (target=0.015)   
step 030: RMS=0.031 (target=0.015)   
step 035: RMS=0.029 (target=0.015)   
step 040: RMS=0.027 (target=0.015)   
step 045: RMS=0.027 (target=0.015)   
step 050: RMS=0.026 (target=0.015)   
step 055: RMS=0.025 (target=0.015)   
step 060: RMS=0.025 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere lh Tue Jan 30 21:14:43 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 1.01 +- 0.58 (0.00-->7.12) (max @ vno 94757 --> 94758)
face area 0.03 +- 0.03 (-0.10-->0.76)
scaling brain by 0.318...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.779, avgs=0
005/300: dt: 0.9000, rms radial error=176.522, avgs=0
010/300: dt: 0.9000, rms radial error=175.968, avgs=0
015/300: dt: 0.9000, rms radial error=175.241, avgs=0
020/300: dt: 0.9000, rms radial error=174.412, avgs=0
025/300: dt: 0.9000, rms radial error=173.525, avgs=0
030/300: dt: 0.9000, rms radial error=172.606, avgs=0
035/300: dt: 0.9000, rms radial error=171.669, avgs=0
040/300: dt: 0.9000, rms radial error=170.723, avgs=0
045/300: dt: 0.9000, rms radial error=169.775, avgs=0
050/300: dt: 0.9000, rms radial error=168.826, avgs=0
055/300: dt: 0.9000, rms radial error=167.880, avgs=0
060/300: dt: 0.9000, rms radial error=166.938, avgs=0
065/300: dt: 0.9000, rms radial error=165.999, avgs=0
070/300: dt: 0.9000, rms radial error=165.065, avgs=0
075/300: dt: 0.9000, rms radial error=164.135, avgs=0
080/300: dt: 0.9000, rms radial error=163.210, avgs=0
085/300: dt: 0.9000, rms radial error=162.289, avgs=0
090/300: dt: 0.9000, rms radial error=161.374, avgs=0
095/300: dt: 0.9000, rms radial error=160.463, avgs=0
100/300: dt: 0.9000, rms radial error=159.556, avgs=0
105/300: dt: 0.9000, rms radial error=158.654, avgs=0
110/300: dt: 0.9000, rms radial error=157.757, avgs=0
115/300: dt: 0.9000, rms radial error=156.865, avgs=0
120/300: dt: 0.9000, rms radial error=155.977, avgs=0
125/300: dt: 0.9000, rms radial error=155.095, avgs=0
130/300: dt: 0.9000, rms radial error=154.217, avgs=0
135/300: dt: 0.9000, rms radial error=153.347, avgs=0
140/300: dt: 0.9000, rms radial error=152.482, avgs=0
145/300: dt: 0.9000, rms radial error=151.622, avgs=0
150/300: dt: 0.9000, rms radial error=150.766, avgs=0
155/300: dt: 0.9000, rms radial error=149.915, avgs=0
160/300: dt: 0.9000, rms radial error=149.069, avgs=0
165/300: dt: 0.9000, rms radial error=148.228, avgs=0
170/300: dt: 0.9000, rms radial error=147.392, avgs=0
175/300: dt: 0.9000, rms radial error=146.560, avgs=0
180/300: dt: 0.9000, rms radial error=145.733, avgs=0
185/300: dt: 0.9000, rms radial error=144.910, avgs=0
190/300: dt: 0.9000, rms radial error=144.091, avgs=0
195/300: dt: 0.9000, rms radial error=143.278, avgs=0
200/300: dt: 0.9000, rms radial error=142.468, avgs=0
205/300: dt: 0.9000, rms radial error=141.664, avgs=0
210/300: dt: 0.9000, rms radial error=140.864, avgs=0
215/300: dt: 0.9000, rms radial error=140.068, avgs=0
220/300: dt: 0.9000, rms radial error=139.277, avgs=0
225/300: dt: 0.9000, rms radial error=138.490, avgs=0
230/300: dt: 0.9000, rms radial error=137.707, avgs=0
235/300: dt: 0.9000, rms radial error=136.929, avgs=0
240/300: dt: 0.9000, rms radial error=136.156, avgs=0
245/300: dt: 0.9000, rms radial error=135.386, avgs=0
250/300: dt: 0.9000, rms radial error=134.621, avgs=0
255/300: dt: 0.9000, rms radial error=133.860, avgs=0
260/300: dt: 0.9000, rms radial error=133.104, avgs=0
265/300: dt: 0.9000, rms radial error=132.351, avgs=0
270/300: dt: 0.9000, rms radial error=131.603, avgs=0
275/300: dt: 0.9000, rms radial error=130.859, avgs=0
280/300: dt: 0.9000, rms radial error=130.120, avgs=0
285/300: dt: 0.9000, rms radial error=129.384, avgs=0
290/300: dt: 0.9000, rms radial error=128.653, avgs=0
295/300: dt: 0.9000, rms radial error=127.925, avgs=0
300/300: dt: 0.9000, rms radial error=127.202, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15204.30
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00019
epoch 2 (K=40.0), pass 1, starting sse = 2497.73
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00013
epoch 3 (K=160.0), pass 1, starting sse = 254.28
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.12/13 = 0.00901
epoch 4 (K=640.0), pass 1, starting sse = 15.16
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.17/16 = 0.01072
final writing spherical brain to ../surf/lh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology lh Tue Jan 30 21:19:28 EST 2018

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

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 BPD0072_base lh 

reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234

*************************************************************
Topology Correction Parameters
retessellation mode:           genetic search
number of patches/generation : 10
number of generations :        10
surface mri loglikelihood coefficient :         1.0
volume mri loglikelihood coefficient :          10.0
normal dot loglikelihood coefficient :          1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :                             2
eliminate vertices during search :              1
initial patch selection :                       1
select all defect vertices :                    0
ordering dependant retessellation:              0
use precomputed edge table :                    0
smooth retessellated patch :                    2
match retessellated patch :                     1
verbose mode :                                  0

*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
before topology correction, eno=-30 (nv=131130, nf=262320, ne=393480, g=16)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 9 iterations
marking ambiguous vertices...
3327 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -8.9017  (-4.4509)
      -vertex     loglikelihood: -5.6566  (-2.8283)
      -normal dot loglikelihood: -3.6436  (-3.6436)
      -quad curv  loglikelihood: -6.3651  (-3.1826)
      Total Loglikelihood : -24.5671

CORRECTING DEFECT 0 (vertices=16, convex hull=48)
After retessellation of defect 0, euler #=-23 (129198,387054,257833) : difference with theory (-23) = 0 

CORRECTING DEFECT 1 (vertices=20, convex hull=33)
After retessellation of defect 1, euler #=-22 (129203,387079,257854) : difference with theory (-22) = 0 

CORRECTING DEFECT 2 (vertices=21, convex hull=22)
Warning - incorrect dp selected!!!!(-67.177353 >= -67.177358 ) 
After retessellation of defect 2, euler #=-21 (129205,387092,257866) : difference with theory (-21) = 0 

CORRECTING DEFECT 3 (vertices=23, convex hull=34)
After retessellation of defect 3, euler #=-20 (129212,387126,257894) : difference with theory (-20) = 0 

CORRECTING DEFECT 4 (vertices=8, convex hull=27)
After retessellation of defect 4, euler #=-19 (129217,387147,257911) : difference with theory (-19) = 0 

CORRECTING DEFECT 5 (vertices=43, convex hull=77)
After retessellation of defect 5, euler #=-18 (129244,387261,257999) : difference with theory (-18) = 0 

CORRECTING DEFECT 6 (vertices=252, convex hull=149)
normal vector of length zero at vertex 129538 with 3 faces
normal vector of length zero at vertex 129538 with 3 faces
normal vector of length zero at vertex 129538 with 3 faces
normal vector of length zero at vertex 129538 with 3 faces
normal vector of length zero at vertex 129538 with 3 faces
normal vector of length zero at vertex 129538 with 3 faces
After retessellation of defect 6, euler #=-17 (129268,387398,258113) : difference with theory (-17) = 0 

CORRECTING DEFECT 7 (vertices=53, convex hull=29)
After retessellation of defect 7, euler #=-16 (129272,387418,258130) : difference with theory (-16) = 0 

CORRECTING DEFECT 8 (vertices=49, convex hull=64)
After retessellation of defect 8, euler #=-15 (129305,387544,258224) : difference with theory (-15) = 0 

CORRECTING DEFECT 9 (vertices=26, convex hull=36)
After retessellation of defect 9, euler #=-14 (129307,387566,258245) : difference with theory (-14) = 0 

CORRECTING DEFECT 10 (vertices=163, convex hull=116)
After retessellation of defect 10, euler #=-13 (129373,387816,258430) : difference with theory (-13) = 0 

CORRECTING DEFECT 11 (vertices=5, convex hull=23)
After retessellation of defect 11, euler #=-12 (129375,387829,258442) : difference with theory (-12) = 0 

CORRECTING DEFECT 12 (vertices=95, convex hull=81)
After retessellation of defect 12, euler #=-11 (129388,387906,258507) : difference with theory (-11) = 0 

CORRECTING DEFECT 13 (vertices=30, convex hull=30)
After retessellation of defect 13, euler #=-10 (129393,387930,258527) : difference with theory (-10) = 0 

CORRECTING DEFECT 14 (vertices=6, convex hull=17)
After retessellation of defect 14, euler #=-9 (129394,387936,258533) : difference with theory (-9) = 0 

CORRECTING DEFECT 15 (vertices=27, convex hull=33)
After retessellation of defect 15, euler #=-8 (129401,387969,258560) : difference with theory (-8) = 0 

CORRECTING DEFECT 16 (vertices=855, convex hull=115)
After retessellation of defect 16, euler #=-7 (129439,388136,258690) : difference with theory (-7) = 0 

CORRECTING DEFECT 17 (vertices=83, convex hull=98)
After retessellation of defect 17, euler #=-6 (129476,388288,258806) : difference with theory (-6) = 0 

CORRECTING DEFECT 18 (vertices=21, convex hull=31)
After retessellation of defect 18, euler #=-5 (129481,388315,258829) : difference with theory (-5) = 0 

CORRECTING DEFECT 19 (vertices=20, convex hull=55)
After retessellation of defect 19, euler #=-4 (129489,388359,258866) : difference with theory (-4) = 0 

CORRECTING DEFECT 20 (vertices=23, convex hull=68)
After retessellation of defect 20, euler #=-3 (129498,388415,258914) : difference with theory (-3) = 0 

CORRECTING DEFECT 21 (vertices=19, convex hull=22)
After retessellation of defect 21, euler #=-2 (129504,388437,258931) : difference with theory (-2) = 0 

CORRECTING DEFECT 22 (vertices=35, convex hull=60)
After retessellation of defect 22, euler #=-1 (129519,388504,258984) : difference with theory (-1) = 0 

CORRECTING DEFECT 23 (vertices=19, convex hull=57)
After retessellation of defect 23, euler #=0 (129528,388551,259023) : difference with theory (0) = 0 

CORRECTING DEFECT 24 (vertices=18, convex hull=55)
After retessellation of defect 24, euler #=1 (129539,388604,259066) : difference with theory (1) = 0 

CORRECTING DEFECT 25 (vertices=6, convex hull=20)
After retessellation of defect 25, euler #=2 (129540,388614,259076) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.88 +- 0.22 (0.07-->17.05) (max @ vno 94895 --> 106969)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.88 +- 0.22 (0.07-->17.05) (max @ vno 94895 --> 106969)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
112 mutations (39.0%), 175 crossovers (61.0%), 160 vertices were eliminated
building final representation...
1590 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=129540, nf=259076, ne=388614, g=0)
writing corrected surface to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 16.6 minutes
0 defective edges
removing intersecting faces
000: 232 intersecting
001: 5 intersecting
002: 4 intersecting

 mris_euler_number ../surf/lh.orig 

euler # = v-e+f = 2g-2: 129540 - 388614 + 259076 = 2 --> 0 holes
      F =2V-4:          259076 = 259080-4 (0)
      2E=3F:            777228 = 777228 (0)

total defect index = 0
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 43 intersecting
001: 10 intersecting
writing corrected surface to ../surf/lh.orig

 rm ../surf/lh.inflated 

#--------------------------------------------
#@# Make White Surf lh Tue Jan 30 21:36:12 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs BPD0072_base 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/filled.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/brain.finalsurfs.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
11645 bright wm thresholded.
156 bright non-wm voxels segmented.
reading original surface position from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.orig...
computing class statistics...
border white:    242805 voxels (1.45%)
border gray      268383 voxels (1.60%)
WM (98.0): 99.4 +- 6.2 [70.0 --> 110.0]
GM (89.0) : 87.8 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 70.1 (was 70)
setting MAX_BORDER_WHITE to 112.2 (was 105)
setting MIN_BORDER_WHITE to 80.0 (was 85)
setting MAX_CSF to 60.1 (was 40)
setting MAX_GRAY to 99.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 75.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 50.2 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.03-->5.68) (max @ vno 55533 --> 56805)
face area 0.28 +- 0.12 (0.00-->2.51)
mean absolute distance = 0.82 +- 0.99
3335 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=80
mean inside = 99.1, mean outside = 85.2
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
mean border=87.0, 110 (110) missing vertices, mean dist 0.4 [0.7 (%28.9)->0.9 (%71.1))]
%57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=e21.h, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.06-->5.89) (max @ vno 55533 --> 54338)
face area 0.28 +- 0.13 (0.00-->2.25)
mean absolute distance = 0.43 +- 0.62
3200 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4061111.0, rms=8.55
001: dt: 0.5000, sse=4356098.0, rms=6.168 (0.000%)
002: dt: 0.5000, sse=4385271.5, rms=4.605 (0.000%)
003: dt: 0.5000, sse=4481376.5, rms=3.562 (0.000%)
004: dt: 0.5000, sse=4538255.5, rms=2.891 (0.000%)
005: dt: 0.5000, sse=4577436.5, rms=2.493 (0.000%)
006: dt: 0.5000, sse=4559776.0, rms=2.273 (0.000%)
007: dt: 0.5000, sse=4595649.0, rms=2.154 (0.000%)
008: dt: 0.5000, sse=4579801.0, rms=2.091 (0.000%)
rms = 2.05, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=4607031.5, rms=2.054 (0.000%)
010: dt: 0.2500, sse=2956036.5, rms=1.535 (0.000%)
011: dt: 0.2500, sse=2821776.2, rms=1.465 (0.000%)
rms = 1.45, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=2778422.2, rms=1.450 (0.000%)
rms = 1.44, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=2754917.0, rms=1.436 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
removing 4 vertex label from ripped group
mean border=90.2, 76 (24) missing vertices, mean dist -0.3 [0.5 (%76.2)->0.3 (%23.8))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=e21.h, 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 (0.07-->6.43) (max @ vno 55533 --> 54338)
face area 0.35 +- 0.16 (0.00-->3.40)
mean absolute distance = 0.28 +- 0.37
3537 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3319258.2, rms=4.49
014: dt: 0.5000, sse=3446932.0, rms=2.864 (0.000%)
015: dt: 0.5000, sse=3621727.8, rms=2.159 (0.000%)
016: dt: 0.5000, sse=3761662.2, rms=1.785 (0.000%)
017: dt: 0.5000, sse=4024116.2, rms=1.710 (0.000%)
rms = 1.68, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=4148136.8, rms=1.682 (0.000%)
019: dt: 0.2500, sse=3235236.5, rms=1.229 (0.000%)
020: dt: 0.2500, sse=3102644.5, rms=1.178 (0.000%)
rms = 1.18, time step reduction 2 of 3 to 0.125...
021: dt: 0.2500, sse=3066184.2, rms=1.178 (0.000%)
rms = 1.17, time step reduction 3 of 3 to 0.062...
022: dt: 0.1250, sse=3042370.8, rms=1.172 (0.000%)
positioning took 0.9 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=92.8, 69 (13) missing vertices, mean dist -0.2 [0.3 (%79.2)->0.2 (%20.8))]
%87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=e21.h, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.25 (0.04-->6.75) (max @ vno 129259 --> 58039)
face area 0.33 +- 0.16 (0.00-->3.55)
mean absolute distance = 0.19 +- 0.27
3268 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3245100.8, rms=3.33
023: dt: 0.5000, sse=3368625.0, rms=1.769 (0.000%)
024: dt: 0.5000, sse=3403686.5, rms=1.555 (0.000%)
025: dt: 0.5000, sse=3565704.2, rms=1.408 (0.000%)
rms = 1.56, time step reduction 1 of 3 to 0.250...
026: dt: 0.2500, sse=3270227.0, rms=1.158 (0.000%)
027: dt: 0.2500, sse=3163980.8, rms=1.076 (0.000%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
028: dt: 0.2500, sse=3131352.0, rms=1.074 (0.000%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
029: dt: 0.1250, sse=3117899.8, rms=1.071 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=93.6, 67 (8) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.2 (%40.2))]
%90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=e21.h, 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
writing smoothed curvature to lh.curv
000: dt: 0.0000, sse=3112995.5, rms=1.38
030: dt: 0.5000, sse=3676543.5, rms=1.032 (0.000%)
rms = 1.23, time step reduction 1 of 3 to 0.250...
031: dt: 0.2500, sse=3452987.5, rms=0.901 (0.000%)
rms = 0.88, time step reduction 2 of 3 to 0.125...
032: dt: 0.2500, sse=3354236.2, rms=0.882 (0.000%)
rms = 0.88, time step reduction 3 of 3 to 0.062...
033: dt: 0.1250, sse=3383202.8, rms=0.876 (0.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
13 non-cortical segments detected
only using segment with 2186 vertices
erasing segment 1 (vno[0] = 74360)
erasing segment 2 (vno[0] = 87045)
erasing segment 3 (vno[0] = 91899)
erasing segment 4 (vno[0] = 92965)
erasing segment 5 (vno[0] = 95856)
erasing segment 6 (vno[0] = 96744)
erasing segment 7 (vno[0] = 99139)
erasing segment 8 (vno[0] = 99154)
erasing segment 9 (vno[0] = 99974)
erasing segment 10 (vno[0] = 100823)
erasing segment 11 (vno[0] = 101637)
erasing segment 12 (vno[0] = 129451)
writing cortex label to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label/lh.cortex.label...
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.curv
writing smoothed area to lh.area
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.area
vertex spacing 0.88 +- 0.25 (0.04-->6.89) (max @ vno 129259 --> 58039)
face area 0.33 +- 0.16 (0.00-->3.50)
refinement took 5.3 minutes
#--------------------------------------------
#@# Smooth2 lh Tue Jan 30 21:41:31 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Tue Jan 30 21:41:35 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

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

avg radius = 45.7 mm, total surface area = 77747 mm^2
writing inflated surface to ../surf/lh.inflated
writing sulcal depths to ../surf/lh.sulc

step 000: RMS=0.109 (target=0.015)   
step 005: RMS=0.077 (target=0.015)   
step 010: RMS=0.055 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.038 (target=0.015)   
step 025: RMS=0.032 (target=0.015)   
step 030: RMS=0.027 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.017 (target=0.015)   
step 055: RMS=0.016 (target=0.015)   
step 060: RMS=0.016 (target=0.015)   
inflation complete.
inflation took 0.5 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
132 vertices thresholded to be in k1 ~ [-0.48 1.23], k2 ~ [-0.12 0.06]
total integrated curvature = 0.565*4pi (7.100) --> 0 handles
ICI = 1.6, FI = 9.3, variation=161.355
113 vertices thresholded to be in [-0.03 0.02]
writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
106 vertices thresholded to be in [-0.21 0.34]
done.
writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023
done.

#-----------------------------------------
#@# Curvature Stats lh Tue Jan 30 21:43:31 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm BPD0072_base 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 [ BPD0072_base/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                      [ 239 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.121348
WARN:    S explicit min:                          0.000000	vertex = 51
#--------------------------------------------
#@# Sphere lh Tue Jan 30 21:43:36 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 0.299...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=e21.h, 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 %20.35
pass 1: epoch 2 of 3 starting distance error %20.28
unfolding complete - removing small folds...
starting distance error %20.20
removing remaining folds...
final distance error %20.21
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.67 hours
#--------------------------------------------
#@# Surf Reg lh Tue Jan 30 22:24:01 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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=e21.h, 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=e21.h, 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 = 0.608
curvature mean = 0.022, std = 0.930
curvature mean = 0.027, std = 0.867
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (0.00, -16.00, 0.00) sse = 323954.7, tmin=0.9197
  d=32.00 min @ (8.00, 8.00, 8.00) sse = 224608.2, tmin=1.8756
  d=16.00 min @ (0.00, 0.00, -4.00) sse = 208817.9, tmin=2.8508
  d=8.00 min @ (-2.00, 0.00, 0.00) sse = 206228.0, tmin=3.8340
  d=4.00 min @ (1.00, 1.00, 1.00) sse = 203927.4, tmin=4.8152
  d=2.00 min @ (0.00, -0.50, 0.00) sse = 203803.1, tmin=5.7994
  d=1.00 min @ (0.00, 0.25, -0.25) sse = 203672.3, tmin=6.7916
  d=0.50 min @ (-0.12, -0.12, 0.00) sse = 203653.7, tmin=7.7987
tol=1.0e+00, sigma=0.5, host=e21.h, 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   7.80 min
curvature mean = 0.002, std = 0.953
curvature mean = 0.011, std = 0.944
curvature mean = 0.001, std = 0.965
curvature mean = 0.005, std = 0.975
curvature mean = -0.002, std = 0.967
curvature mean = 0.001, std = 0.989
2 Reading smoothwm
curvature mean = -0.028, std = 0.303
curvature mean = 0.003, std = 0.067
curvature mean = 0.062, std = 0.341
curvature mean = 0.002, std = 0.080
curvature mean = 0.023, std = 0.535
curvature mean = 0.003, std = 0.087
curvature mean = 0.010, std = 0.667
curvature mean = 0.003, std = 0.089
curvature mean = 0.004, std = 0.765
MRISregister() return, current seed 0
writing registered surface to ../surf/lh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white lh Tue Jan 30 22:48:17 EST 2018

 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 Tue Jan 30 22:48:19 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Tue Jan 30 22:48:21 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 BPD0072_base 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...
1200 labels changed using aseg
relabeling using gibbs priors...
000:   2772 changed, 129540 examined...
001:    641 changed, 11983 examined...
002:    140 changed, 3543 examined...
003:     64 changed, 857 examined...
004:     26 changed, 401 examined...
005:     14 changed, 165 examined...
006:      3 changed, 77 examined...
007:      0 changed, 18 examined...
171 labels changed using aseg
000: 98 total segments, 54 labels (172 vertices) changed
001: 44 total segments, 2 labels (4 vertices) changed
002: 42 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 48 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
1466 vertices marked for relabeling...
1466 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification took 0 minutes and 59 seconds.
#--------------------------------------------
#@# Make Pial Surf lh Tue Jan 30 22:49:21 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs BPD0072_base 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/filled.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/brain.finalsurfs.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
11645 bright wm thresholded.
156 bright non-wm voxels segmented.
reading original surface position from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.orig...
computing class statistics...
border white:    242805 voxels (1.45%)
border gray      268383 voxels (1.60%)
WM (98.0): 99.4 +- 6.2 [70.0 --> 110.0]
GM (89.0) : 87.8 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 70.1 (was 70)
setting MAX_BORDER_WHITE to 112.2 (was 105)
setting MIN_BORDER_WHITE to 80.0 (was 85)
setting MAX_CSF to 60.1 (was 40)
setting MAX_GRAY to 99.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 75.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 50.2 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=80
mean inside = 99.1, mean outside = 85.2
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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.82 +- 0.21 (0.03-->5.68) (max @ vno 55533 --> 56805)
face area 0.28 +- 0.12 (0.00-->2.51)
mean absolute distance = 0.82 +- 0.99
3369 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
deleting segment 2 with 383 points - only 0.00% unknown
deleting segment 3 with 24 points - only 0.00% unknown
deleting segment 4 with 14 points - only 0.00% unknown
mean border=87.0, 110 (110) missing vertices, mean dist 0.4 [0.7 (%28.9)->0.9 (%71.1))]
%57 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=e21.h, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.06-->5.89) (max @ vno 55533 --> 54338)
face area 0.28 +- 0.13 (0.00-->2.25)
mean absolute distance = 0.43 +- 0.62
3230 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4067537.8, rms=8.54
001: dt: 0.5000, sse=4367056.0, rms=6.160 (0.000%)
002: dt: 0.5000, sse=4397350.5, rms=4.599 (0.000%)
003: dt: 0.5000, sse=4491101.0, rms=3.557 (0.000%)
004: dt: 0.5000, sse=4547893.0, rms=2.888 (0.000%)
005: dt: 0.5000, sse=4586965.5, rms=2.490 (0.000%)
006: dt: 0.5000, sse=4568996.5, rms=2.270 (0.000%)
007: dt: 0.5000, sse=4606107.0, rms=2.152 (0.000%)
008: dt: 0.5000, sse=4590690.0, rms=2.089 (0.000%)
rms = 2.05, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=4619351.0, rms=2.051 (0.000%)
010: dt: 0.2500, sse=2963854.2, rms=1.533 (0.000%)
011: dt: 0.2500, sse=2829344.0, rms=1.463 (0.000%)
rms = 1.45, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=2785860.0, rms=1.448 (0.000%)
rms = 1.44, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=2762647.5, rms=1.435 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 2 with 248 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 4 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 6 with 36 points - only 0.00% unknown
deleting segment 7 with 5 points - only 20.00% unknown
deleting segment 9 with 21 points - only 0.00% unknown
mean border=90.2, 75 (24) missing vertices, mean dist -0.3 [0.5 (%76.2)->0.3 (%23.8))]
%74 local maxima, %21 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=e21.h, 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 +- 0.24 (0.06-->6.38) (max @ vno 55533 --> 54338)
face area 0.35 +- 0.16 (0.00-->3.09)
mean absolute distance = 0.28 +- 0.37
3624 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3331029.5, rms=4.49
014: dt: 0.5000, sse=3457842.5, rms=2.863 (0.000%)
015: dt: 0.5000, sse=3634902.0, rms=2.158 (0.000%)
016: dt: 0.5000, sse=3774112.8, rms=1.784 (0.000%)
017: dt: 0.5000, sse=4038907.2, rms=1.709 (0.000%)
rms = 1.68, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=4158135.2, rms=1.681 (0.000%)
019: dt: 0.2500, sse=3243498.0, rms=1.229 (0.000%)
020: dt: 0.2500, sse=3113717.2, rms=1.178 (0.000%)
rms = 1.18, time step reduction 2 of 3 to 0.125...
rms = 1.17, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=3100015.5, rms=1.174 (0.000%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 4 vertex label from ripped group
deleting segment 3 with 263 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 5 with 4 points - only 0.00% unknown
deleting segment 7 with 46 points - only 0.00% unknown
deleting segment 8 with 25 points - only 0.00% unknown
mean border=92.8, 67 (16) missing vertices, mean dist -0.2 [0.3 (%79.2)->0.2 (%20.8))]
%88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=e21.h, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.88 +- 0.24 (0.08-->6.61) (max @ vno 55533 --> 54338)
face area 0.33 +- 0.16 (0.00-->3.04)
mean absolute distance = 0.19 +- 0.27
3322 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3299215.2, rms=3.33
022: dt: 0.5000, sse=3383505.8, rms=1.772 (0.000%)
023: dt: 0.5000, sse=3424113.8, rms=1.558 (0.000%)
024: dt: 0.5000, sse=3595106.8, rms=1.420 (0.000%)
rms = 1.56, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=3286374.2, rms=1.161 (0.000%)
026: dt: 0.2500, sse=3179321.0, rms=1.074 (0.000%)
rms = 1.07, time step reduction 2 of 3 to 0.125...
027: dt: 0.2500, sse=3146090.2, rms=1.073 (0.000%)
rms = 1.07, time step reduction 3 of 3 to 0.062...
028: dt: 0.1250, sse=3136903.2, rms=1.070 (0.000%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 2 with 282 points - only 0.00% unknown
deleting segment 3 with 74 points - only 0.00% unknown
deleting segment 4 with 35 points - only 0.00% unknown
mean border=93.6, 82 (10) missing vertices, mean dist -0.0 [0.2 (%59.8)->0.2 (%40.2))]
%91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=e21.h, 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=3140240.0, rms=1.39
029: dt: 0.5000, sse=3710832.8, rms=1.040 (0.000%)
rms = 1.24, time step reduction 1 of 3 to 0.250...
030: dt: 0.2500, sse=3484895.0, rms=0.913 (0.000%)
rms = 0.89, time step reduction 2 of 3 to 0.125...
031: dt: 0.2500, sse=3378996.0, rms=0.892 (0.000%)
rms = 0.89, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=3403463.0, rms=0.888 (0.000%)
positioning took 0.5 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=70.2, 85 (85) missing vertices, mean dist 1.9 [3.9 (%0.0)->2.4 (%100.0))]
%24 local maxima, %52 large gradients and %20 min vals, 1572 gradients ignored
tol=1.0e-04, sigma=2.0, host=e21.h, 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=16774411.0, rms=24.15
001: dt: 0.5000, sse=13459613.0, rms=21.198 (0.000%)
002: dt: 0.5000, sse=10940990.0, rms=18.678 (0.000%)
003: dt: 0.5000, sse=9114751.0, rms=16.583 (0.000%)
004: dt: 0.5000, sse=7896589.0, rms=14.841 (0.000%)
005: dt: 0.5000, sse=7036883.0, rms=13.410 (0.000%)
006: dt: 0.5000, sse=6461527.0, rms=12.190 (0.000%)
007: dt: 0.5000, sse=5984953.5, rms=11.029 (0.000%)
008: dt: 0.5000, sse=5624302.0, rms=9.876 (0.000%)
009: dt: 0.5000, sse=5299072.5, rms=8.716 (0.000%)
010: dt: 0.5000, sse=5103597.5, rms=7.565 (0.000%)
011: dt: 0.5000, sse=4904579.5, rms=6.413 (0.000%)
012: dt: 0.5000, sse=4830837.5, rms=5.329 (0.000%)
013: dt: 0.5000, sse=4816240.5, rms=4.455 (0.000%)
014: dt: 0.5000, sse=4928574.0, rms=3.888 (0.000%)
015: dt: 0.5000, sse=4961581.0, rms=3.594 (0.000%)
016: dt: 0.5000, sse=5028763.0, rms=3.435 (0.000%)
017: dt: 0.5000, sse=5058098.5, rms=3.350 (0.000%)
018: dt: 0.5000, sse=5085711.0, rms=3.291 (0.000%)
rms = 3.26, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=5098424.0, rms=3.255 (0.000%)
020: dt: 0.2500, sse=3392710.0, rms=2.422 (0.000%)
021: dt: 0.2500, sse=3231341.0, rms=2.210 (0.000%)
rms = 2.17, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=3160249.0, rms=2.168 (0.000%)
023: dt: 0.1250, sse=3032372.2, rms=2.037 (0.000%)
rms = 2.02, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=3008757.0, rms=2.020 (0.000%)
positioning took 2.3 minutes
mean border=67.4, 680 (18) missing vertices, mean dist 0.2 [0.2 (%39.1)->0.5 (%60.9))]
%51 local maxima, %31 large gradients and %14 min vals, 421 gradients ignored
tol=1.0e-04, sigma=1.0, host=e21.h, 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=3663581.0, rms=4.69
025: dt: 0.5000, sse=3750767.5, rms=3.423 (0.000%)
026: dt: 0.5000, sse=4586213.5, rms=3.358 (0.000%)
rms = 3.36, time step reduction 1 of 3 to 0.250...
027: dt: 0.2500, sse=3830259.8, rms=2.591 (0.000%)
028: dt: 0.2500, sse=3578287.5, rms=2.245 (0.000%)
029: dt: 0.2500, sse=3534551.0, rms=2.174 (0.000%)
rms = 2.13, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=3505478.8, rms=2.132 (0.000%)
031: dt: 0.1250, sse=3398032.2, rms=1.993 (0.000%)
rms = 1.97, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=3390274.8, rms=1.971 (0.000%)
positioning took 0.8 minutes
mean border=65.5, 874 (17) missing vertices, mean dist 0.1 [0.2 (%33.0)->0.3 (%67.0))]
%66 local maxima, %16 large gradients and %14 min vals, 526 gradients ignored
tol=1.0e-04, sigma=0.5, host=e21.h, 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=3551835.0, rms=3.13
033: dt: 0.5000, sse=3680235.0, rms=3.004 (0.000%)
rms = 3.36, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3477210.8, rms=2.299 (0.000%)
035: dt: 0.2500, sse=3575935.5, rms=2.004 (0.000%)
rms = 1.96, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=3554254.5, rms=1.965 (0.000%)
037: dt: 0.1250, sse=3472614.8, rms=1.840 (0.000%)
rms = 1.82, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=3463864.8, rms=1.822 (0.000%)
positioning took 0.6 minutes
mean border=64.7, 1674 (16) missing vertices, mean dist 0.0 [0.2 (%42.6)->0.2 (%57.4))]
%70 local maxima, %11 large gradients and %14 min vals, 384 gradients ignored
tol=1.0e-04, sigma=0.2, host=e21.h, 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
writing smoothed curvature to lh.curv.pial
000: dt: 0.0000, sse=3482179.0, rms=2.05
rms = 2.48, time step reduction 1 of 3 to 0.250...
039: dt: 0.2500, sse=3411608.2, rms=1.842 (0.000%)
040: dt: 0.2500, sse=3488440.8, rms=1.771 (0.000%)
rms = 1.75, time step reduction 2 of 3 to 0.125...
041: dt: 0.2500, sse=3526128.5, rms=1.754 (0.000%)
042: dt: 0.1250, sse=3473717.8, rms=1.695 (0.000%)
rms = 1.69, time step reduction 3 of 3 to 0.062...
043: dt: 0.1250, sse=3478032.5, rms=1.688 (0.000%)
positioning took 0.6 minutes
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.curv.pial
writing smoothed area to lh.area.pial
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.area.pial
vertex spacing 0.99 +- 0.41 (0.06-->7.83) (max @ vno 87978 --> 87075)
face area 0.39 +- 0.29 (0.00-->8.54)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 129540 vertices processed
25000 of 129540 vertices processed
50000 of 129540 vertices processed
75000 of 129540 vertices processed
100000 of 129540 vertices processed
125000 of 129540 vertices processed
0 of 129540 vertices processed
25000 of 129540 vertices processed
50000 of 129540 vertices processed
75000 of 129540 vertices processed
100000 of 129540 vertices processed
125000 of 129540 vertices processed
thickness calculation complete, 721:1001 truncations.
34950 vertices at 0 distance
89787 vertices at 1 distance
76681 vertices at 2 distance
32084 vertices at 3 distance
10167 vertices at 4 distance
3013 vertices at 5 distance
1047 vertices at 6 distance
340 vertices at 7 distance
142 vertices at 8 distance
78 vertices at 9 distance
58 vertices at 10 distance
31 vertices at 11 distance
27 vertices at 12 distance
22 vertices at 13 distance
14 vertices at 14 distance
18 vertices at 15 distance
10 vertices at 16 distance
7 vertices at 17 distance
5 vertices at 18 distance
9 vertices at 19 distance
20 vertices at 20 distance
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.thickness
positioning took 10.7 minutes
#--------------------------------------------
#@# Surf Volume lh Tue Jan 30 23:00:00 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 ]
#-----------------------------------------
#@# Parcellation Stats lh Tue Jan 30 23:00:01 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 BPD0072_base lh white 

computing statistics for each annotation in ../label/lh.aparc.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

 1252    875   1931  2.296 0.419     0.074     0.011        4     0.6  bankssts
 1030    681   2376  2.984 0.684     0.147     0.084       23     4.3  caudalanteriorcingulate
 3144   2040   6171  2.763 0.636     0.118     0.032       32     4.1  caudalmiddlefrontal
 2225   1409   3013  1.955 0.496     0.154     0.057       39     5.0  cuneus
  459    330   1623  4.087 0.767     0.098     0.026        3     0.4  entorhinal
 4565   3050   9656  2.881 0.730     0.140     0.166      347     8.5  fusiform
 6201   4085  11764  2.579 0.655     0.134     0.043      101    10.8  inferiorparietal
 4810   3178  10237  2.721 0.736     0.125     0.042       76     8.2  inferiortemporal
 1461    962   2707  2.572 0.742     0.163     0.145      232     8.2  isthmuscingulate
 6924   4200  10585  2.190 0.597     0.136     0.053      112    16.1  lateraloccipital
 4102   2730   8465  2.872 0.654     0.135     0.040       57     6.6  lateralorbitofrontal
 4816   3088   7047  2.090 0.560     0.144     0.050       70     9.7  lingual
 2640   1764   5103  2.438 0.725     0.140     0.155      383     4.6  medialorbitofrontal
 4636   2984  10855  2.946 0.776     0.130     0.041       73     7.5  middletemporal
 1081    696   2482  3.070 0.641     0.097     0.026       11     0.9  parahippocampal
 1939   1190   3383  2.446 0.567     0.121     0.032       20     2.6  paracentral
 2330   1558   4793  2.666 0.482     0.113     0.031       24     2.9  parsopercularis
  884    593   2273  2.842 0.577     0.160     0.062       21     2.4  parsorbitalis
 1884   1245   3390  2.473 0.490     0.119     0.029       21     2.4  parstriangularis
 2329   1487   2215  1.642 0.439     0.133     0.050       85     5.4  pericalcarine
 6197   3809   9478  2.191 0.596     0.109     0.036       65     7.9  postcentral
 1664   1076   3138  2.702 0.801     0.150     0.048       31     3.1  posteriorcingulate
 6918   4091  13073  2.829 0.588     0.103     0.032       74     8.9  precentral
 5899   3931  10632  2.488 0.530     0.136     0.040       90     9.3  precuneus
 1131    720   2590  3.343 0.806     0.168     0.082       34     3.9  rostralanteriorcingulate
 7263   4887  14095  2.466 0.654     0.147     0.060      161    16.1  rostralmiddlefrontal
10108   6647  22308  2.974 0.637     0.126     0.036      114    14.9  superiorfrontal
 8097   5295  13842  2.284 0.583     0.127     0.036      102    11.4  superiorparietal
 5186   3357  10796  2.862 0.635     0.104     0.023       62     5.1  superiortemporal
 5962   3972  12356  2.697 0.544     0.129     0.038       88     9.5  supramarginal
  260    183    823  3.064 0.602     0.212     0.094        9     1.3  frontalpole
  581    412   2504  4.138 0.496     0.159     0.090       11     1.5  temporalpole
  620    372   1190  2.830 0.343     0.122     0.033        7     0.8  transversetemporal
 3099   1993   6676  3.346 0.806     0.115     0.056       52     7.6  insula
#-----------------------------------------
#@# Cortical Parc 2 lh Tue Jan 30 23:00:24 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 BPD0072_base 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...
36 labels changed using aseg
relabeling using gibbs priors...
000:   8421 changed, 129540 examined...
001:   1937 changed, 32617 examined...
002:    632 changed, 10130 examined...
003:    284 changed, 3529 examined...
004:    133 changed, 1649 examined...
005:     61 changed, 727 examined...
006:     25 changed, 308 examined...
007:     13 changed, 133 examined...
008:      5 changed, 79 examined...
009:      1 changed, 25 examined...
010:      1 changed, 7 examined...
011:      1 changed, 7 examined...
012:      0 changed, 5 examined...
4 labels changed using aseg
000: 250 total segments, 171 labels (2182 vertices) changed
001: 94 total segments, 15 labels (70 vertices) changed
002: 80 total segments, 1 labels (5 vertices) changed
003: 79 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 121 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
881 vertices marked for relabeling...
881 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classification took 1 minutes and 9 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 lh Tue Jan 30 23:01:33 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 BPD0072_base lh white 

computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  807    596   1740  2.523 0.721     0.166     0.084       23     2.7  G_and_S_frontomargin
 1636   1056   3261  2.504 0.643     0.135     0.034       20     2.3  G_and_S_occipital_inf
 1673    972   2583  2.271 0.538     0.124     0.039       19     2.6  G_and_S_paracentral
 1237    780   2583  2.765 0.551     0.117     0.032       14     1.6  G_and_S_subcentral
  626    449   1328  2.345 0.665     0.197     0.136       41     2.6  G_and_S_transv_frontopol
 2177   1409   4443  2.989 0.731     0.132     0.045       31     3.7  G_and_S_cingul-Ant
 1360    927   2892  2.931 0.485     0.129     0.070       23     4.6  G_and_S_cingul-Mid-Ant
 1340    877   2558  2.888 0.552     0.142     0.044       20     2.4  G_and_S_cingul-Mid-Post
  480    323   1254  2.980 0.591     0.164     0.071       10     1.1  G_cingul-Post-dorsal
  319    191    490  2.233 0.761     0.220     0.308      206     5.3  G_cingul-Post-ventral
 1975   1242   2801  1.924 0.553     0.158     0.064       37     5.0  G_cuneus
 1466    903   3513  2.840 0.402     0.128     0.040       23     2.4  G_front_inf-Opercular
  233    145    618  2.931 0.414     0.174     0.059        8     0.6  G_front_inf-Orbital
 1029    677   2287  2.715 0.407     0.141     0.043       17     1.9  G_front_inf-Triangul
 4170   2656   9888  2.825 0.675     0.146     0.054       80     9.2  G_front_middle
 7099   4566  18107  3.166 0.626     0.137     0.044      105    13.3  G_front_sup
  442    280   1194  3.611 0.573     0.144     0.069        9     1.2  G_Ins_lg_and_S_cent_ins
  642    386   2128  4.053 0.582     0.144     0.110       28     3.3  G_insular_short
 1899   1124   3854  2.721 0.469     0.159     0.054       42     4.1  G_occipital_middle
 1802   1127   3048  2.202 0.597     0.128     0.039       25     2.7  G_occipital_sup
 1829   1186   4353  2.816 0.512     0.146     0.040       37     3.0  G_oc-temp_lat-fusifor
 3297   2048   5025  2.042 0.531     0.158     0.061       59     7.9  G_oc-temp_med-Lingual
 1022    662   3026  3.597 0.758     0.097     0.029       11     1.0  G_oc-temp_med-Parahip
 2771   1784   6860  2.968 0.586     0.154     0.059       57     7.0  G_orbital
 2429   1556   5788  2.974 0.545     0.151     0.054       51     5.0  G_pariet_inf-Angular
 3354   2199   8057  2.828 0.506     0.136     0.045       63     6.3  G_pariet_inf-Supramar
 2531   1638   5532  2.610 0.497     0.146     0.047       46     4.6  G_parietal_sup
 2364   1313   3913  2.322 0.498     0.113     0.035       29     3.5  G_postcentral
 2781   1367   6305  3.191 0.483     0.102     0.043       44     4.8  G_precentral
 2710   1785   6035  2.626 0.511     0.157     0.072       64     5.5  G_precuneus
  862    585   2294  2.720 0.517     0.158     0.063       26     1.9  G_rectus
  417    263    792  2.564 1.067     0.194     0.765      345     1.3  G_subcallosal
  429    251    942  2.853 0.332     0.130     0.038        6     0.7  G_temp_sup-G_T_transv
 1837   1113   4744  3.026 0.597     0.123     0.032       28     2.5  G_temp_sup-Lateral
  651    414   1719  3.723 0.783     0.079     0.023        5     0.7  G_temp_sup-Plan_polar
 1004    710   2088  2.672 0.448     0.125     0.027       26     1.2  G_temp_sup-Plan_tempo
 2342   1522   6119  2.922 0.717     0.137     0.058       55     5.5  G_temporal_inf
 3267   2020   8442  3.202 0.629     0.147     0.052       69     6.6  G_temporal_middle
  275    189    367  2.185 0.379     0.112     0.018        2     0.2  Lat_Fis-ant-Horizont
  291    215    438  2.237 0.257     0.095     0.013        1     0.2  Lat_Fis-ant-Vertical
 1313    876   1975  2.666 0.558     0.112     0.025        9     1.4  Lat_Fis-post
 2401   1317   3027  2.055 0.557     0.143     0.082       54     9.6  Pole_occipital
 1469   1017   5265  3.719 0.916     0.144     0.055       21     2.7  Pole_temporal
 3091   2004   3497  1.968 0.761     0.129     0.044       93     6.3  S_calcarine
 2941   1991   3485  1.985 0.676     0.102     0.032       20     2.8  S_central
  856    597   1460  2.395 0.511     0.115     0.029        9     1.0  S_cingul-Marginalis
  460    318    853  3.062 0.526     0.090     0.017        2     0.3  S_circular_insula_ant
 1316    888   2256  3.053 0.597     0.075     0.015        5     0.8  S_circular_insula_inf
 1700   1147   2638  2.613 0.439     0.097     0.021        7     1.4  S_circular_insula_sup
  841    580   1636  3.157 0.850     0.120     0.028        8     1.0  S_collat_transv_ant
  447    292    503  2.031 0.375     0.148     0.042        5     0.7  S_collat_transv_post
 2092   1436   3262  2.266 0.444     0.112     0.030       20     2.2  S_front_inf
 1380    933   2214  2.234 0.595     0.141     0.050       23     2.5  S_front_middle
 2590   1774   4126  2.515 0.451     0.110     0.027       18     2.7  S_front_sup
  434    289    654  2.387 0.527     0.131     0.030        7     0.7  S_interm_prim-Jensen
 3194   2118   4304  2.043 0.544     0.119     0.030       30     4.0  S_intrapariet_and_P_trans
  970    660   1088  1.700 0.330     0.105     0.021        5     0.9  S_oc_middle_and_Lunatus
 1366    911   1798  1.953 0.453     0.123     0.030       12     1.6  S_oc_sup_and_transversal
  857    558   1125  2.097 0.561     0.108     0.025        5     0.9  S_occipital_ant
  844    588   1366  2.425 0.533     0.118     0.038        7     0.9  S_oc-temp_lat
 2450   1695   3952  2.620 0.644     0.125     0.270      301     4.6  S_oc-temp_med_and_Lingual
  431    293    553  1.930 0.438     0.121     0.032        4     0.5  S_orbital_lateral
  858    608   1331  2.474 0.723     0.117     0.036        8     1.2  S_orbital_med-olfact
 1415    978   2626  2.784 0.775     0.137     0.037       17     2.2  S_orbital-H_Shaped
 2020   1359   2992  2.402 0.491     0.115     0.028       17     2.3  S_parieto_occipital
 1174    717   1316  2.286 0.832     0.141     0.042       24     2.2  S_pericallosal
 2714   1816   3838  2.248 0.431     0.096     0.020       16     2.3  S_postcentral
 1287    901   2084  2.592 0.366     0.092     0.017        6     0.9  S_precentral-inf-part
 1308    888   2020  2.652 0.461     0.107     0.025        9     1.3  S_precentral-sup-part
  570    385    737  2.168 0.844     0.107     0.018        4     0.4  S_suborbital
 1348    929   1942  2.180 0.399     0.113     0.024       10     1.4  S_subparietal
 1477   1027   2237  2.376 0.522     0.103     0.019        8     1.2  S_temporal_inf
 4886   3287   7521  2.368 0.521     0.099     0.025       40     5.1  S_temporal_sup
  322    208    482  2.698 0.520     0.097     0.019        2     0.3  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 lh Tue Jan 30 23:01:55 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 BPD0072_base 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...
1225 labels changed using aseg
relabeling using gibbs priors...
000:   2648 changed, 129540 examined...
001:    602 changed, 11220 examined...
002:    163 changed, 3245 examined...
003:     57 changed, 938 examined...
004:     15 changed, 328 examined...
005:      3 changed, 83 examined...
006:      1 changed, 18 examined...
007:      0 changed, 7 examined...
103 labels changed using aseg
000: 67 total segments, 34 labels (332 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 47 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
561 vertices marked for relabeling...
561 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas40.annot...
classification took 0 minutes and 59 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 lh Tue Jan 30 23:02:55 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 BPD0072_base lh white 

computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

 1539   1013   3132  2.934 0.615     0.132     0.063       26     4.7  caudalanteriorcingulate
 3233   2084   6377  2.776 0.654     0.118     0.032       33     4.2  caudalmiddlefrontal
 2998   1938   4296  2.039 0.525     0.142     0.048       46     6.0  cuneus
  401    289   1386  3.984 0.772     0.094     0.024        2     0.3  entorhinal
 4213   2820   8459  2.775 0.646     0.139     0.177      343     7.9  fusiform
 6092   4004  11537  2.587 0.659     0.134     0.042       94    10.1  inferiorparietal
 4610   3061  10497  2.851 0.841     0.127     0.043       74     8.0  inferiortemporal
 1480    974   2729  2.572 0.750     0.162     0.143      232     8.2  isthmuscingulate
 7248   4397  10928  2.167 0.605     0.136     0.052      116    16.5  lateraloccipital
 4402   2933   9343  2.906 0.727     0.147     0.057       80    10.4  lateralorbitofrontal
 4786   3071   7009  2.087 0.548     0.144     0.050       70     9.7  lingual
 2065   1382   4031  2.389 0.734     0.140     0.182      373     3.5  medialorbitofrontal
 6026   3901  13113  2.835 0.751     0.124     0.039       88     9.6  middletemporal
 1091    708   2533  3.091 0.640     0.098     0.026       11     0.9  parahippocampal
 2107   1305   3770  2.500 0.579     0.119     0.030       21     2.7  paracentral
 2195   1455   4392  2.662 0.493     0.110     0.029       21     2.5  parsopercularis
  917    620   2123  2.810 0.546     0.125     0.035       13     1.3  parsorbitalis
 2245   1504   4201  2.469 0.501     0.126     0.036       29     3.4  parstriangularis
 2367   1506   2250  1.648 0.443     0.135     0.051       87     5.5  pericalcarine
 6854   4272  10566  2.206 0.589     0.109     0.034       69     8.5  postcentral
 1798   1161   3311  2.712 0.776     0.149     0.047       32     3.2  posteriorcingulate
 6806   4031  12818  2.825 0.576     0.103     0.032       73     8.8  precentral
 5676   3770  10550  2.516 0.530     0.140     0.043       94     9.5  precuneus
 1635   1040   3450  3.131 0.824     0.159     0.074       43     4.8  rostralanteriorcingulate
 4918   3263   9363  2.457 0.633     0.135     0.042       77     8.2  rostralmiddlefrontal
11559   7670  25887  2.899 0.677     0.137     0.048      186    21.2  superiorfrontal
 6640   4335  11459  2.310 0.575     0.127     0.035       82     9.4  superiorparietal
 6841   4485  15039  2.909 0.770     0.106     0.029       82     7.7  superiortemporal
 5698   3801  11863  2.700 0.546     0.129     0.038       85     9.0  supramarginal
  634    380   1213  2.827 0.349     0.124     0.033        7     0.9  transversetemporal
 2623   1717   5945  3.349 0.752     0.110     0.049       42     5.6  insula
#--------------------------------------------
#@# Tessellate rh Tue Jan 30 23:03:16 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

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

Iteration Number : 1
pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
pass   1 (xy-):   1 found -   1 modified     |    TOTAL:   1
pass   2 (xy-):   0 found -   1 modified     |    TOTAL:   1
pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   1
pass   1 (yz-):   3 found -   3 modified     |    TOTAL:   4
pass   2 (yz-):   0 found -   3 modified     |    TOTAL:   4
pass   1 (xz+):   1 found -   1 modified     |    TOTAL:   5
pass   2 (xz+):   0 found -   1 modified     |    TOTAL:   5
pass   1 (xz-):   3 found -   3 modified     |    TOTAL:   8
pass   2 (xz-):   0 found -   3 modified     |    TOTAL:   8
Iteration Number : 1
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
Iteration Number : 1
pass   1 (++):   1 found -   1 modified     |    TOTAL:   1
pass   2 (++):   0 found -   1 modified     |    TOTAL:   1
pass   1 (+-):   0 found -   0 modified     |    TOTAL:   1
pass   1 (--):   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 (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 = 10 (out of 250511: 0.003992)
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 60: 945 vertices, 1020 faces
slice 70: 6781 vertices, 7019 faces
slice 80: 15286 vertices, 15624 faces
slice 90: 25754 vertices, 26157 faces
slice 100: 37446 vertices, 37847 faces
slice 110: 47960 vertices, 48267 faces
slice 120: 60502 vertices, 60917 faces
slice 130: 72062 vertices, 72443 faces
slice 140: 82314 vertices, 82686 faces
slice 150: 92533 vertices, 92903 faces
slice 160: 102236 vertices, 102554 faces
slice 170: 110341 vertices, 110629 faces
slice 180: 117634 vertices, 117885 faces
slice 190: 124240 vertices, 124469 faces
slice 200: 129336 vertices, 129519 faces
slice 210: 133066 vertices, 133150 faces
slice 220: 133444 vertices, 133456 faces
slice 230: 133444 vertices, 133456 faces
slice 240: 133444 vertices, 133456 faces
slice 250: 133444 vertices, 133456 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...
   133444 voxel in cpt #1: X=-12 [v=133444,e=400368,f=266912] located at (28.897297, -0.840495, 6.500030)
For the whole surface: X=-12 [v=133444,e=400368,f=266912]
One single component has been found
nothing to do
done

#--------------------------------------------
#@# Smooth1 rh Tue Jan 30 23:03:27 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Tue Jan 30 23:03:32 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts
avg radius = 45.6 mm, total surface area = 71638 mm^2
writing inflated surface to ../surf/rh.inflated.nofix
inflation took 0.6 minutes
Not saving sulc

step 000: RMS=0.096 (target=0.015)   
step 005: RMS=0.071 (target=0.015)   
step 010: RMS=0.052 (target=0.015)   
step 015: RMS=0.043 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.033 (target=0.015)   
step 030: RMS=0.029 (target=0.015)   
step 035: RMS=0.026 (target=0.015)   
step 040: RMS=0.025 (target=0.015)   
step 045: RMS=0.024 (target=0.015)   
step 050: RMS=0.022 (target=0.015)   
step 055: RMS=0.022 (target=0.015)   
step 060: RMS=0.022 (target=0.015)   
inflation complete.
Not saving sulc
#--------------------------------------------
#@# QSphere rh Tue Jan 30 23:04:07 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 1.01 +- 0.56 (0.00-->8.31) (max @ vno 48636 --> 48637)
face area 0.03 +- 0.03 (-0.06-->1.04)
scaling brain by 0.312...
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial error=176.676, avgs=0
005/300: dt: 0.9000, rms radial error=176.416, avgs=0
010/300: dt: 0.9000, rms radial error=175.857, avgs=0
015/300: dt: 0.9000, rms radial error=175.123, avgs=0
020/300: dt: 0.9000, rms radial error=174.287, avgs=0
025/300: dt: 0.9000, rms radial error=173.393, avgs=0
030/300: dt: 0.9000, rms radial error=172.469, avgs=0
035/300: dt: 0.9000, rms radial error=171.532, avgs=0
040/300: dt: 0.9000, rms radial error=170.588, avgs=0
045/300: dt: 0.9000, rms radial error=169.641, avgs=0
050/300: dt: 0.9000, rms radial error=168.695, avgs=0
055/300: dt: 0.9000, rms radial error=167.752, avgs=0
060/300: dt: 0.9000, rms radial error=166.814, avgs=0
065/300: dt: 0.9000, rms radial error=165.879, avgs=0
070/300: dt: 0.9000, rms radial error=164.950, avgs=0
075/300: dt: 0.9000, rms radial error=164.025, avgs=0
080/300: dt: 0.9000, rms radial error=163.105, avgs=0
085/300: dt: 0.9000, rms radial error=162.189, avgs=0
090/300: dt: 0.9000, rms radial error=161.279, avgs=0
095/300: dt: 0.9000, rms radial error=160.373, avgs=0
100/300: dt: 0.9000, rms radial error=159.472, avgs=0
105/300: dt: 0.9000, rms radial error=158.575, avgs=0
110/300: dt: 0.9000, rms radial error=157.684, avgs=0
115/300: dt: 0.9000, rms radial error=156.797, avgs=0
120/300: dt: 0.9000, rms radial error=155.915, avgs=0
125/300: dt: 0.9000, rms radial error=155.038, avgs=0
130/300: dt: 0.9000, rms radial error=154.166, avgs=0
135/300: dt: 0.9000, rms radial error=153.298, avgs=0
140/300: dt: 0.9000, rms radial error=152.435, avgs=0
145/300: dt: 0.9000, rms radial error=151.577, avgs=0
150/300: dt: 0.9000, rms radial error=150.723, avgs=0
155/300: dt: 0.9000, rms radial error=149.874, avgs=0
160/300: dt: 0.9000, rms radial error=149.029, avgs=0
165/300: dt: 0.9000, rms radial error=148.190, avgs=0
170/300: dt: 0.9000, rms radial error=147.354, avgs=0
175/300: dt: 0.9000, rms radial error=146.524, avgs=0
180/300: dt: 0.9000, rms radial error=145.698, avgs=0
185/300: dt: 0.9000, rms radial error=144.876, avgs=0
190/300: dt: 0.9000, rms radial error=144.059, avgs=0
195/300: dt: 0.9000, rms radial error=143.247, avgs=0
200/300: dt: 0.9000, rms radial error=142.439, avgs=0
205/300: dt: 0.9000, rms radial error=141.636, avgs=0
210/300: dt: 0.9000, rms radial error=140.837, avgs=0
215/300: dt: 0.9000, rms radial error=140.042, avgs=0
220/300: dt: 0.9000, rms radial error=139.252, avgs=0
225/300: dt: 0.9000, rms radial error=138.466, avgs=0
230/300: dt: 0.9000, rms radial error=137.685, avgs=0
235/300: dt: 0.9000, rms radial error=136.908, avgs=0
240/300: dt: 0.9000, rms radial error=136.135, avgs=0
245/300: dt: 0.9000, rms radial error=135.366, avgs=0
250/300: dt: 0.9000, rms radial error=134.602, avgs=0
255/300: dt: 0.9000, rms radial error=133.842, avgs=0
260/300: dt: 0.9000, rms radial error=133.086, avgs=0
265/300: dt: 0.9000, rms radial error=132.335, avgs=0
270/300: dt: 0.9000, rms radial error=131.588, avgs=0
275/300: dt: 0.9000, rms radial error=130.844, avgs=0
280/300: dt: 0.9000, rms radial error=130.105, avgs=0
285/300: dt: 0.9000, rms radial error=129.371, avgs=0
290/300: dt: 0.9000, rms radial error=128.640, avgs=0
295/300: dt: 0.9000, rms radial error=127.913, avgs=0
300/300: dt: 0.9000, rms radial error=127.190, avgs=0

spherical inflation complete.
epoch 1 (K=10.0), pass 1, starting sse = 15509.95
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00016
epoch 2 (K=40.0), pass 1, starting sse = 2529.65
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.00/10 = 0.00007
epoch 3 (K=160.0), pass 1, starting sse = 252.56
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.11/12 = 0.00939
epoch 4 (K=640.0), pass 1, starting sse = 13.67
taking momentum steps...
taking momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.31/21 = 0.01469
final writing spherical brain to ../surf/rh.qsphere.nofix
spherical transformation took 0.08 hours
distance error %100000.00
#--------------------------------------------
#@# Fix Topology rh Tue Jan 30 23:09:09 EST 2018

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

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 BPD0072_base 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=-12 (nv=133444, nf=266912, ne=400368, g=7)
using quasi-homeomorphic spherical map to tessellate cortical surface...

Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 10 iterations
marking ambiguous vertices...
1416 ambiguous faces found in tessellation
segmenting defects...
19 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
19 defects to be corrected 
0 vertices coincident
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
      -face       loglikelihood: -8.8453  (-4.4226)
      -vertex     loglikelihood: -5.6795  (-2.8398)
      -normal dot loglikelihood: -3.6243  (-3.6243)
      -quad curv  loglikelihood: -6.4451  (-3.2226)
      Total Loglikelihood : -24.5942

CORRECTING DEFECT 0 (vertices=23, convex hull=62)
After retessellation of defect 0, euler #=-16 (132587,397452,264849) : difference with theory (-16) = 0 

CORRECTING DEFECT 1 (vertices=23, convex hull=74)
After retessellation of defect 1, euler #=-15 (132598,397518,264905) : difference with theory (-15) = 0 

CORRECTING DEFECT 2 (vertices=28, convex hull=55)
After retessellation of defect 2, euler #=-14 (132609,397579,264956) : difference with theory (-14) = 0 

CORRECTING DEFECT 3 (vertices=15, convex hull=41)
After retessellation of defect 3, euler #=-13 (132612,397602,264977) : difference with theory (-13) = 0 

CORRECTING DEFECT 4 (vertices=36, convex hull=51)
After retessellation of defect 4, euler #=-12 (132633,397681,265036) : difference with theory (-12) = 0 

CORRECTING DEFECT 5 (vertices=25, convex hull=34)
After retessellation of defect 5, euler #=-11 (132635,397702,265056) : difference with theory (-11) = 0 

CORRECTING DEFECT 6 (vertices=41, convex hull=93)
After retessellation of defect 6, euler #=-10 (132650,397780,265120) : difference with theory (-10) = 0 

CORRECTING DEFECT 7 (vertices=22, convex hull=50)
After retessellation of defect 7, euler #=-9 (132657,397819,265153) : difference with theory (-9) = 0 

CORRECTING DEFECT 8 (vertices=5, convex hull=24)
After retessellation of defect 8, euler #=-8 (132659,397831,265164) : difference with theory (-8) = 0 

CORRECTING DEFECT 9 (vertices=91, convex hull=41)
After retessellation of defect 9, euler #=-7 (132668,397874,265199) : difference with theory (-7) = 0 

CORRECTING DEFECT 10 (vertices=128, convex hull=29)
After retessellation of defect 10, euler #=-6 (132676,397907,265225) : difference with theory (-6) = 0 

CORRECTING DEFECT 11 (vertices=22, convex hull=27)
After retessellation of defect 11, euler #=-5 (132679,397927,265243) : difference with theory (-5) = 0 

CORRECTING DEFECT 12 (vertices=8, convex hull=16)
After retessellation of defect 12, euler #=-4 (132681,397936,265251) : difference with theory (-4) = 0 

CORRECTING DEFECT 13 (vertices=71, convex hull=31)
After retessellation of defect 13, euler #=-3 (132688,397965,265274) : difference with theory (-3) = 0 

CORRECTING DEFECT 14 (vertices=7, convex hull=29)
After retessellation of defect 14, euler #=-2 (132689,397975,265284) : difference with theory (-2) = 0 

CORRECTING DEFECT 15 (vertices=160, convex hull=39)
After retessellation of defect 15, euler #=-1 (132698,398018,265319) : difference with theory (-1) = 0 

CORRECTING DEFECT 16 (vertices=13, convex hull=22)
After retessellation of defect 16, euler #=0 (132701,398035,265334) : difference with theory (0) = 0 

CORRECTING DEFECT 17 (vertices=134, convex hull=99)
After retessellation of defect 17, euler #=1 (132742,398203,265462) : difference with theory (1) = 0 

CORRECTING DEFECT 18 (vertices=16, convex hull=45)
After retessellation of defect 18, euler #=2 (132750,398244,265496) : difference with theory (2) = 0 
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.21 (0.12-->8.52) (max @ vno 121414 --> 133313)
face area 0.00 +- 0.00 (0.00-->0.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.21 (0.12-->8.52) (max @ vno 121414 --> 133313)
face area 0.00 +- 0.00 (0.00-->0.00)
tessellation finished, orienting corrected surface...
89 mutations (36.6%), 154 crossovers (63.4%), 8 vertices were eliminated
building final representation...
694 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=132750, nf=265496, ne=398244, g=0)
writing corrected surface to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.orig...

0.000 % of the vertices (0 vertices) exhibit an orientation change
topology fixing took 10.2 minutes
0 defective edges
removing intersecting faces
000: 101 intersecting

 mris_euler_number ../surf/rh.orig 

euler # = v-e+f = 2g-2: 132750 - 398244 + 265496 = 2 --> 0 holes
      F =2V-4:          265496 = 265500-4 (0)
      2E=3F:            796488 = 796488 (0)

total defect index = 0
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

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

intersection removal took 0.00 hours
removing intersecting faces
000: 27 intersecting
writing corrected surface to ../surf/rh.orig

 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Tue Jan 30 23:19:24 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs BPD0072_base 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/filled.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/brain.finalsurfs.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
11962 bright wm thresholded.
156 bright non-wm voxels segmented.
reading original surface position from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.orig...
computing class statistics...
border white:    242805 voxels (1.45%)
border gray      268383 voxels (1.60%)
WM (99.0): 99.4 +- 6.3 [70.0 --> 110.0]
GM (89.0) : 87.7 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
setting MAX_BORDER_WHITE to 112.3 (was 105)
setting MIN_BORDER_WHITE to 81.0 (was 85)
setting MAX_CSF to 61.2 (was 40)
setting MAX_GRAY to 99.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 76.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 51.3 (was 40)
repositioning cortical surface to gray/white boundary
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.83 +- 0.21 (0.03-->4.44) (max @ vno 121414 --> 132711)
face area 0.28 +- 0.12 (0.00-->1.48)
mean absolute distance = 0.80 +- 0.98
3143 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=81
mean inside = 99.1, mean outside = 85.3
smoothing surface for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
mean border=87.9, 21 (21) missing vertices, mean dist 0.4 [0.7 (%31.6)->0.8 (%68.4))]
%54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=e21.h, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.06-->3.89) (max @ vno 121414 --> 132711)
face area 0.28 +- 0.13 (0.00-->1.70)
mean absolute distance = 0.41 +- 0.62
2687 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4035078.0, rms=8.25
001: dt: 0.5000, sse=4340229.0, rms=5.855 (0.000%)
002: dt: 0.5000, sse=4413940.0, rms=4.292 (0.000%)
003: dt: 0.5000, sse=4503100.5, rms=3.282 (0.000%)
004: dt: 0.5000, sse=4575218.5, rms=2.659 (0.000%)
005: dt: 0.5000, sse=4585857.0, rms=2.315 (0.000%)
006: dt: 0.5000, sse=4606792.5, rms=2.130 (0.000%)
007: dt: 0.5000, sse=4608465.5, rms=2.045 (0.000%)
008: dt: 0.5000, sse=4626200.5, rms=1.989 (0.000%)
rms = 1.96, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=4605645.5, rms=1.964 (0.000%)
010: dt: 0.2500, sse=3005626.5, rms=1.421 (0.000%)
011: dt: 0.2500, sse=2872104.8, rms=1.351 (0.000%)
rms = 1.33, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=2822392.0, rms=1.334 (0.000%)
rms = 1.32, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=2796180.0, rms=1.322 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
mean border=90.8, 45 (3) missing vertices, mean dist -0.3 [0.5 (%74.3)->0.2 (%25.7))]
%71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=e21.h, 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 +- 0.24 (0.09-->4.20) (max @ vno 50981 --> 49745)
face area 0.35 +- 0.16 (0.00-->3.12)
mean absolute distance = 0.28 +- 0.37
3866 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3331759.0, rms=4.23
014: dt: 0.5000, sse=3463173.8, rms=2.693 (0.000%)
015: dt: 0.5000, sse=3620702.0, rms=2.057 (0.000%)
016: dt: 0.5000, sse=3751613.8, rms=1.688 (0.000%)
017: dt: 0.5000, sse=3989485.2, rms=1.619 (0.000%)
rms = 1.60, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=4118535.5, rms=1.598 (0.000%)
019: dt: 0.2500, sse=3262307.0, rms=1.179 (0.000%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=3134358.5, rms=1.138 (0.000%)
rms = 1.13, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=3104370.8, rms=1.130 (0.000%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
mean border=93.3, 27 (0) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=e21.h, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.10-->4.34) (max @ vno 50981 --> 49745)
face area 0.33 +- 0.16 (0.00-->2.97)
mean absolute distance = 0.19 +- 0.28
2722 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3294612.0, rms=3.16
022: dt: 0.5000, sse=3390104.2, rms=1.706 (0.000%)
023: dt: 0.5000, sse=3430253.2, rms=1.500 (0.000%)
024: dt: 0.5000, sse=3580348.8, rms=1.348 (0.000%)
rms = 1.49, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=3298427.5, rms=1.112 (0.000%)
026: dt: 0.2500, sse=3197690.5, rms=1.037 (0.000%)
rms = 1.04, time step reduction 2 of 3 to 0.125...
rms = 1.03, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=3185870.8, rms=1.032 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
mean border=94.1, 33 (0) missing vertices, mean dist -0.1 [0.2 (%59.9)->0.2 (%40.1))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=e21.h, 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
writing smoothed curvature to rh.curv
000: dt: 0.0000, sse=3193480.8, rms=1.39
028: dt: 0.5000, sse=3686528.8, rms=1.041 (0.000%)
rms = 1.25, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=3458785.0, rms=0.887 (0.000%)
rms = 0.86, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=3378764.0, rms=0.858 (0.000%)
rms = 0.85, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=3392926.5, rms=0.851 (0.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
generating cortex label...
8 non-cortical segments detected
only using segment with 2487 vertices
erasing segment 1 (vno[0] = 49713)
erasing segment 2 (vno[0] = 60003)
erasing segment 3 (vno[0] = 86824)
erasing segment 4 (vno[0] = 97619)
erasing segment 5 (vno[0] = 101336)
erasing segment 6 (vno[0] = 103028)
erasing segment 7 (vno[0] = 103086)
writing cortex label to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label/rh.cortex.label...
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.curv
writing smoothed area to rh.area
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.area
vertex spacing 0.88 +- 0.25 (0.06-->4.48) (max @ vno 50981 --> 49745)
face area 0.33 +- 0.15 (0.00-->2.93)
refinement took 5.2 minutes
#--------------------------------------------
#@# Smooth2 rh Tue Jan 30 23:24:38 EST 2018

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

/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Tue Jan 30 23:24:42 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

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

avg radius = 45.8 mm, total surface area = 79728 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc

step 000: RMS=0.107 (target=0.015)   
step 005: RMS=0.076 (target=0.015)   
step 010: RMS=0.054 (target=0.015)   
step 015: RMS=0.045 (target=0.015)   
step 020: RMS=0.037 (target=0.015)   
step 025: RMS=0.031 (target=0.015)   
step 030: RMS=0.026 (target=0.015)   
step 035: RMS=0.023 (target=0.015)   
step 040: RMS=0.020 (target=0.015)   
step 045: RMS=0.018 (target=0.015)   
step 050: RMS=0.016 (target=0.015)   
step 055: RMS=0.015 (target=0.015)   
inflation complete.
inflation took 0.5 minutes

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

normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
157 vertices thresholded to be in k1 ~ [-0.36 1.50], k2 ~ [-0.13 0.11]
total integrated curvature = 0.545*4pi (6.853) --> 0 handles
ICI = 1.6, FI = 11.1, variation=186.918
126 vertices thresholded to be in [-0.04 0.02]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
121 vertices thresholded to be in [-0.14 0.55]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.027
done.

#-----------------------------------------
#@# Curvature Stats rh Tue Jan 30 23:26:38 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm BPD0072_base 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 [ BPD0072_base/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                      [ 241 ]
Gb_filter = 0

WARN:    S lookup   min:                          -0.279365
WARN:    S explicit min:                          0.000000	vertex = 1914
#--------------------------------------------
#@# Sphere rh Tue Jan 30 23:26:43 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 0.295...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=e21.h, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 1234

--------------------
  mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %20.45
pass 1: epoch 2 of 3 starting distance error %20.39
unfolding complete - removing small folds...
starting distance error %20.35
removing remaining folds...
final distance error %20.37
MRISunfold() return, current seed 1234
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.79 hours
#--------------------------------------------
#@# Surf Reg rh Wed Jan 31 00:13:54 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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=e21.h, 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=e21.h, 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 = 0.596
curvature mean = 0.033, std = 0.931
curvature mean = 0.029, std = 0.855
Starting MRISrigidBodyAlignGlobal()
  d=64.00 min @ (16.00, 0.00, 0.00) sse = 384435.4, tmin=0.9512
  d=32.00 min @ (-8.00, 0.00, 8.00) sse = 304882.4, tmin=1.8988
  d=16.00 min @ (0.00, -4.00, 0.00) sse = 285400.0, tmin=2.8601
  d=4.00 min @ (1.00, 1.00, 0.00) sse = 283927.6, tmin=4.8176
  d=2.00 min @ (0.00, 0.00, -0.50) sse = 283771.8, tmin=5.8013
  d=1.00 min @ (0.00, -0.25, 0.25) sse = 283736.7, tmin=6.7738
  d=0.50 min @ (-0.12, 0.00, -0.12) sse = 283713.6, tmin=7.7585
tol=1.0e+00, sigma=0.5, host=e21.h, 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   7.76 min
curvature mean = 0.011, std = 0.941
curvature mean = 0.011, std = 0.936
curvature mean = 0.004, std = 0.949
curvature mean = 0.005, std = 0.970
curvature mean = 0.004, std = 0.950
curvature mean = 0.002, std = 0.986
2 Reading smoothwm
curvature mean = -0.027, std = 0.278
curvature mean = 0.006, std = 0.070
curvature mean = 0.067, std = 0.374
curvature mean = 0.006, std = 0.084
curvature mean = 0.022, std = 0.576
curvature mean = 0.006, std = 0.090
curvature mean = 0.012, std = 0.716
curvature mean = 0.006, std = 0.094
curvature mean = 0.003, std = 0.824
MRISregister() return, current seed 0
writing registered surface to ../surf/rh.sphere.reg...
expanding nbhd size to 1
#--------------------------------------------
#@# Jacobian white rh Wed Jan 31 00:39:04 EST 2018

 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 Wed Jan 31 00:39:06 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 Wed Jan 31 00:39:08 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 BPD0072_base 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...
1175 labels changed using aseg
relabeling using gibbs priors...
000:   2920 changed, 132750 examined...
001:    711 changed, 12552 examined...
002:    177 changed, 3958 examined...
003:     56 changed, 1071 examined...
004:     24 changed, 337 examined...
005:     15 changed, 143 examined...
006:      5 changed, 70 examined...
007:      3 changed, 29 examined...
008:      1 changed, 13 examined...
009:      0 changed, 4 examined...
135 labels changed using aseg
000: 92 total segments, 54 labels (309 vertices) changed
001: 39 total segments, 1 labels (2 vertices) changed
002: 38 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 39 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
966 vertices marked for relabeling...
966 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification took 1 minutes and 1 seconds.
#--------------------------------------------
#@# Make Pial Surf rh Wed Jan 31 00:40:10 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs BPD0072_base 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/filled.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/brain.finalsurfs.mgz...
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
11962 bright wm thresholded.
156 bright non-wm voxels segmented.
reading original surface position from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.orig...
computing class statistics...
border white:    242805 voxels (1.45%)
border gray      268383 voxels (1.60%)
WM (99.0): 99.4 +- 6.3 [70.0 --> 110.0]
GM (89.0) : 87.7 +- 9.9 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 71.1 (was 70)
setting MAX_BORDER_WHITE to 112.3 (was 105)
setting MIN_BORDER_WHITE to 81.0 (was 85)
setting MAX_CSF to 61.2 (was 40)
setting MAX_GRAY to 99.7 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 76.0 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 51.3 (was 40)
smoothing contralateral hemisphere...
using class modes intead of means, discounting robust sigmas....
intensity peaks found at WM=106,    GM=81
mean inside = 99.1, mean outside = 85.3
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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.mgz...
smoothing T1 volume with sigma = 2.000
vertex spacing 0.83 +- 0.21 (0.03-->4.44) (max @ vno 121414 --> 132711)
face area 0.28 +- 0.12 (0.00-->1.48)
mean absolute distance = 0.80 +- 0.99
3195 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
deleting segment 4 with 3 points - only 0.00% unknown
deleting segment 5 with 190 points - only 0.00% unknown
deleting segment 6 with 30 points - only 0.00% unknown
deleting segment 7 with 12 points - only 0.00% unknown
mean border=87.9, 21 (21) missing vertices, mean dist 0.4 [0.7 (%31.6)->0.8 (%68.4))]
%54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=2.0, host=e21.h, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0

smoothing T1 volume with sigma = 1.000
vertex spacing 0.92 +- 0.26 (0.06-->3.89) (max @ vno 121414 --> 132711)
face area 0.28 +- 0.13 (0.00-->1.70)
mean absolute distance = 0.41 +- 0.62
2689 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=4038813.2, rms=8.25
001: dt: 0.5000, sse=4346943.5, rms=5.851 (0.000%)
002: dt: 0.5000, sse=4420487.0, rms=4.289 (0.000%)
003: dt: 0.5000, sse=4508852.5, rms=3.280 (0.000%)
004: dt: 0.5000, sse=4580288.5, rms=2.657 (0.000%)
005: dt: 0.5000, sse=4591673.0, rms=2.313 (0.000%)
006: dt: 0.5000, sse=4611109.5, rms=2.129 (0.000%)
007: dt: 0.5000, sse=4612501.0, rms=2.044 (0.000%)
008: dt: 0.5000, sse=4630381.0, rms=1.988 (0.000%)
rms = 1.96, time step reduction 1 of 3 to 0.250...
009: dt: 0.5000, sse=4611225.5, rms=1.962 (0.000%)
010: dt: 0.2500, sse=3010494.5, rms=1.421 (0.000%)
011: dt: 0.2500, sse=2877152.5, rms=1.351 (0.000%)
rms = 1.33, time step reduction 2 of 3 to 0.125...
012: dt: 0.2500, sse=2827264.0, rms=1.334 (0.000%)
rms = 1.32, time step reduction 3 of 3 to 0.062...
013: dt: 0.1250, sse=2800963.0, rms=1.322 (0.000%)
positioning took 1.3 minutes
inhibiting deformation at non-cortical midline structures...
removing 4 vertex label from ripped group
deleting segment 0 with 4 points - only 0.00% unknown
removing 4 vertex label from ripped group
deleting segment 1 with 4 points - only 0.00% unknown
deleting segment 2 with 119 points - only 0.00% unknown
deleting segment 4 with 8 points - only 0.00% unknown
deleting segment 6 with 15 points - only 0.00% unknown
mean border=90.8, 45 (3) missing vertices, mean dist -0.3 [0.5 (%74.3)->0.2 (%25.7))]
%72 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=1.0, host=e21.h, 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 +- 0.24 (0.09-->4.20) (max @ vno 50981 --> 49745)
face area 0.35 +- 0.16 (0.00-->3.12)
mean absolute distance = 0.28 +- 0.37
3878 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3337676.8, rms=4.23
014: dt: 0.5000, sse=3469553.5, rms=2.693 (0.000%)
015: dt: 0.5000, sse=3625841.2, rms=2.057 (0.000%)
016: dt: 0.5000, sse=3757827.0, rms=1.688 (0.000%)
017: dt: 0.5000, sse=3996539.5, rms=1.618 (0.000%)
rms = 1.60, time step reduction 1 of 3 to 0.250...
018: dt: 0.5000, sse=4123952.0, rms=1.597 (0.000%)
019: dt: 0.2500, sse=3266277.5, rms=1.179 (0.000%)
rms = 1.14, time step reduction 2 of 3 to 0.125...
020: dt: 0.2500, sse=3138984.8, rms=1.138 (0.000%)
rms = 1.13, time step reduction 3 of 3 to 0.062...
021: dt: 0.1250, sse=3108638.5, rms=1.130 (0.000%)
positioning took 0.8 minutes
inhibiting deformation at non-cortical midline structures...
removing 3 vertex label from ripped group
removing 3 vertex label from ripped group
deleting segment 2 with 3 points - only 0.00% unknown
deleting segment 3 with 163 points - only 0.00% unknown
deleting segment 4 with 5 points - only 0.00% unknown
deleting segment 5 with 24 points - only 0.00% unknown
deleting segment 6 with 12 points - only 0.00% unknown
removing 3 vertex label from ripped group
mean border=93.3, 27 (0) missing vertices, mean dist -0.2 [0.3 (%78.3)->0.2 (%21.7))]
%86 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.5, host=e21.h, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
smoothing T1 volume with sigma = 0.250
vertex spacing 0.89 +- 0.24 (0.10-->4.34) (max @ vno 50981 --> 49745)
face area 0.33 +- 0.15 (0.00-->2.97)
mean absolute distance = 0.19 +- 0.28
2732 vertices more than 2 sigmas from mean.
averaging target values for 5 iterations...
000: dt: 0.0000, sse=3299719.2, rms=3.16
022: dt: 0.5000, sse=3395844.8, rms=1.705 (0.000%)
023: dt: 0.5000, sse=3436447.2, rms=1.499 (0.000%)
024: dt: 0.5000, sse=3586512.8, rms=1.348 (0.000%)
rms = 1.49, time step reduction 1 of 3 to 0.250...
025: dt: 0.2500, sse=3304354.2, rms=1.112 (0.000%)
026: dt: 0.2500, sse=3203545.8, rms=1.037 (0.000%)
rms = 1.04, time step reduction 2 of 3 to 0.125...
rms = 1.03, time step reduction 3 of 3 to 0.062...
027: dt: 0.1250, sse=3191720.5, rms=1.032 (0.000%)
positioning took 0.7 minutes
inhibiting deformation at non-cortical midline structures...
removing 2 vertex label from ripped group
deleting segment 0 with 2 points - only 0.00% unknown
deleting segment 1 with 174 points - only 0.00% unknown
deleting segment 2 with 5 points - only 0.00% unknown
deleting segment 3 with 25 points - only 0.00% unknown
deleting segment 4 with 12 points - only 0.00% unknown
mean border=94.1, 33 (0) missing vertices, mean dist -0.1 [0.2 (%59.9)->0.2 (%40.1))]
%90 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored
tol=1.0e-04, sigma=0.2, host=e21.h, 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=3199442.8, rms=1.39
028: dt: 0.5000, sse=3694505.2, rms=1.040 (0.000%)
rms = 1.25, time step reduction 1 of 3 to 0.250...
029: dt: 0.2500, sse=3466155.0, rms=0.887 (0.000%)
rms = 0.86, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=3385639.5, rms=0.858 (0.000%)
rms = 0.85, time step reduction 3 of 3 to 0.062...
031: dt: 0.1250, sse=3399590.0, rms=0.851 (0.000%)
positioning took 0.4 minutes
inhibiting deformation at non-cortical midline structures...
smoothing surface for 5 iterations...
mean border=71.3, 28 (28) missing vertices, mean dist 1.9 [0.4 (%0.0)->2.4 (%100.0))]
%26 local maxima, %51 large gradients and %19 min vals, 1287 gradients ignored
tol=1.0e-04, sigma=2.0, host=e21.h, 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=16525340.0, rms=23.58
001: dt: 0.5000, sse=13266039.0, rms=20.682 (0.000%)
002: dt: 0.5000, sse=10790590.0, rms=18.210 (0.000%)
003: dt: 0.5000, sse=9018370.0, rms=16.169 (0.000%)
004: dt: 0.5000, sse=7861258.5, rms=14.475 (0.000%)
005: dt: 0.5000, sse=7036907.5, rms=13.080 (0.000%)
006: dt: 0.5000, sse=6455089.5, rms=11.884 (0.000%)
007: dt: 0.5000, sse=6005321.0, rms=10.748 (0.000%)
008: dt: 0.5000, sse=5649843.0, rms=9.639 (0.000%)
009: dt: 0.5000, sse=5381446.5, rms=8.548 (0.000%)
010: dt: 0.5000, sse=5170878.5, rms=7.449 (0.000%)
011: dt: 0.5000, sse=5015553.0, rms=6.331 (0.000%)
012: dt: 0.5000, sse=4897943.5, rms=5.268 (0.000%)
013: dt: 0.5000, sse=4910591.0, rms=4.426 (0.000%)
014: dt: 0.5000, sse=4961158.5, rms=3.894 (0.000%)
015: dt: 0.5000, sse=5068974.5, rms=3.605 (0.000%)
016: dt: 0.5000, sse=5074809.0, rms=3.438 (0.000%)
017: dt: 0.5000, sse=5125969.0, rms=3.358 (0.000%)
018: dt: 0.5000, sse=5127124.5, rms=3.290 (0.000%)
rms = 3.25, time step reduction 1 of 3 to 0.250...
019: dt: 0.5000, sse=5151645.5, rms=3.251 (0.000%)
020: dt: 0.2500, sse=3415434.8, rms=2.402 (0.000%)
021: dt: 0.2500, sse=3243722.5, rms=2.176 (0.000%)
rms = 2.13, time step reduction 2 of 3 to 0.125...
022: dt: 0.2500, sse=3163531.0, rms=2.130 (0.000%)
023: dt: 0.1250, sse=3017307.8, rms=1.981 (0.000%)
rms = 1.96, time step reduction 3 of 3 to 0.062...
024: dt: 0.1250, sse=2995599.8, rms=1.964 (0.000%)
positioning took 2.3 minutes
mean border=68.4, 713 (3) missing vertices, mean dist 0.2 [0.2 (%38.0)->0.5 (%62.0))]
%50 local maxima, %31 large gradients and %14 min vals, 341 gradients ignored
tol=1.0e-04, sigma=1.0, host=e21.h, 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=3700246.8, rms=4.79
025: dt: 0.5000, sse=3757923.8, rms=3.446 (0.000%)
026: dt: 0.5000, sse=4617478.0, rms=3.376 (0.000%)
rms = 3.35, time step reduction 1 of 3 to 0.250...
027: dt: 0.5000, sse=4731854.5, rms=3.350 (0.000%)
028: dt: 0.2500, sse=3713500.5, rms=2.354 (0.000%)
029: dt: 0.2500, sse=3625543.5, rms=2.076 (0.000%)
rms = 2.07, time step reduction 2 of 3 to 0.125...
030: dt: 0.2500, sse=3550107.0, rms=2.067 (0.000%)
031: dt: 0.1250, sse=3417834.2, rms=1.872 (0.000%)
rms = 1.85, time step reduction 3 of 3 to 0.062...
032: dt: 0.1250, sse=3403934.8, rms=1.849 (0.000%)
positioning took 0.8 minutes
mean border=66.4, 758 (2) missing vertices, mean dist 0.1 [0.2 (%31.6)->0.3 (%68.4))]
%65 local maxima, %16 large gradients and %14 min vals, 364 gradients ignored
tol=1.0e-04, sigma=0.5, host=e21.h, 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=3579545.0, rms=3.13
033: dt: 0.5000, sse=3723383.5, rms=3.060 (0.000%)
rms = 3.38, time step reduction 1 of 3 to 0.250...
034: dt: 0.2500, sse=3498936.0, rms=2.275 (0.000%)
035: dt: 0.2500, sse=3555133.0, rms=1.941 (0.000%)
rms = 1.90, time step reduction 2 of 3 to 0.125...
036: dt: 0.2500, sse=3563408.8, rms=1.902 (0.000%)
037: dt: 0.1250, sse=3472251.2, rms=1.764 (0.000%)
rms = 1.75, time step reduction 3 of 3 to 0.062...
038: dt: 0.1250, sse=3460306.0, rms=1.749 (0.000%)
positioning took 0.6 minutes
mean border=65.5, 1762 (2) missing vertices, mean dist 0.0 [0.2 (%41.1)->0.2 (%58.9))]
%70 local maxima, %11 large gradients and %14 min vals, 263 gradients ignored
tol=1.0e-04, sigma=0.2, host=e21.h, 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
writing smoothed curvature to rh.curv.pial
000: dt: 0.0000, sse=3479408.0, rms=2.01
rms = 2.44, time step reduction 1 of 3 to 0.250...
039: dt: 0.2500, sse=3418159.8, rms=1.781 (0.000%)
040: dt: 0.2500, sse=3496446.5, rms=1.701 (0.000%)
rms = 1.69, time step reduction 2 of 3 to 0.125...
041: dt: 0.2500, sse=3518203.2, rms=1.688 (0.000%)
042: dt: 0.1250, sse=3464812.0, rms=1.633 (0.000%)
rms = 1.63, time step reduction 3 of 3 to 0.062...
043: dt: 0.1250, sse=3463950.5, rms=1.628 (0.000%)
positioning took 0.6 minutes
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.curv.pial
writing smoothed area to rh.area.pial
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.area.pial
vertex spacing 0.99 +- 0.41 (0.09-->7.18) (max @ vno 86881 --> 86882)
face area 0.39 +- 0.29 (0.00-->6.48)
measuring cortical thickness...
writing cortical thickness estimate to 'thickness' file.
0 of 132750 vertices processed
25000 of 132750 vertices processed
50000 of 132750 vertices processed
75000 of 132750 vertices processed
100000 of 132750 vertices processed
125000 of 132750 vertices processed
0 of 132750 vertices processed
25000 of 132750 vertices processed
50000 of 132750 vertices processed
75000 of 132750 vertices processed
100000 of 132750 vertices processed
125000 of 132750 vertices processed
thickness calculation complete, 508:860 truncations.
37158 vertices at 0 distance
92595 vertices at 1 distance
77021 vertices at 2 distance
32780 vertices at 3 distance
10786 vertices at 4 distance
2970 vertices at 5 distance
916 vertices at 6 distance
255 vertices at 7 distance
130 vertices at 8 distance
66 vertices at 9 distance
50 vertices at 10 distance
45 vertices at 11 distance
32 vertices at 12 distance
25 vertices at 13 distance
16 vertices at 14 distance
7 vertices at 15 distance
17 vertices at 16 distance
14 vertices at 17 distance
9 vertices at 18 distance
15 vertices at 19 distance
13 vertices at 20 distance
writing curvature file /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.thickness
positioning took 10.4 minutes
#--------------------------------------------
#@# Surf Volume rh Wed Jan 31 00:50:38 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 ]
#-----------------------------------------
#@# Parcellation Stats rh Wed Jan 31 00:50:39 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 BPD0072_base rh white 

computing statistics for each annotation in ../label/rh.aparc.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

 1234    874   2325  2.770 0.362     0.099     0.019        6     1.0  bankssts
  970    619   1704  2.643 0.755     0.132     0.033       14     1.1  caudalanteriorcingulate
 3104   2088   6045  2.529 0.563     0.127     0.033       35     4.2  caudalmiddlefrontal
 2798   1695   3631  1.912 0.449     0.148     0.073       53    10.8  cuneus
  332    233   1316  4.012 0.747     0.091     0.022        2     0.2  entorhinal
 5051   3365  10659  2.836 0.681     0.127     0.039       86     8.6  fusiform
 8355   5317  15888  2.685 0.595     0.127     0.038      138    13.0  inferiorparietal
 4429   2915  10032  2.914 0.596     0.129     0.042       68     6.7  inferiortemporal
 1395    893   2560  2.458 0.813     0.141     0.071       33     3.1  isthmuscingulate
 7272   4357  10905  2.289 0.527     0.140     0.050      127    14.3  lateraloccipital
 3653   2450   7663  2.733 0.687     0.145     0.056       68     8.1  lateralorbitofrontal
 4650   3017   6783  2.175 0.660     0.147     0.051       77     9.4  lingual
 2489   1710   4710  2.328 0.741     0.125     0.042       41     4.0  medialorbitofrontal
 4611   3076  11621  3.046 0.702     0.116     0.038       59     6.8  middletemporal
 1096    711   2395  3.060 0.709     0.103     0.030       11     1.2  parahippocampal
 1814   1145   2935  2.359 0.570     0.112     0.026       14     2.1  paracentral
 1999   1347   3908  2.515 0.567     0.120     0.032       26     2.6  parsopercularis
 1101    732   2890  2.986 0.656     0.142     0.044       20     1.9  parsorbitalis
 2140   1431   4023  2.461 0.530     0.128     0.035       30     3.0  parstriangularis
 2801   1728   2744  1.725 0.421     0.140     0.065       59     8.3  pericalcarine
 5883   3623   8490  2.072 0.668     0.105     0.029       76     7.4  postcentral
 1624   1059   2971  2.535 0.799     0.144     0.041       26     2.8  posteriorcingulate
 6932   4222  12293  2.635 0.652     0.106     0.058      100     9.4  precentral
 6085   4058  11043  2.468 0.597     0.135     0.058      374     9.1  precuneus
 1076    698   2437  2.952 0.641     0.131     0.041       17     1.7  rostralanteriorcingulate
 8168   5442  15120  2.353 0.667     0.144     0.067      323    15.1  rostralmiddlefrontal
 9573   6298  21440  2.895 0.676     0.127     0.042      124    14.7  superiorfrontal
 8534   5532  14305  2.302 0.529     0.125     0.033      106    11.6  superiorparietal
 4875   3195   9888  2.773 0.611     0.107     0.035       74     6.6  superiortemporal
 6065   3962  12095  2.712 0.574     0.118     0.032       74     8.7  supramarginal
  411    273    920  2.502 0.645     0.173     0.057       10     1.0  frontalpole
  482    342   2111  3.855 0.663     0.131     0.047        8     0.7  temporalpole
  547    335   1081  2.752 0.291     0.124     0.030        7     0.6  transversetemporal
 2917   1916   6189  3.302 0.754     0.114     0.039       31     4.6  insula
#-----------------------------------------
#@# Cortical Parc 2 rh Wed Jan 31 00:51:01 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 BPD0072_base 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...
13 labels changed using aseg
relabeling using gibbs priors...
000:   9358 changed, 132750 examined...
001:   2274 changed, 35736 examined...
002:    723 changed, 11695 examined...
003:    322 changed, 4034 examined...
004:    136 changed, 1775 examined...
005:     67 changed, 769 examined...
006:     28 changed, 357 examined...
007:     17 changed, 156 examined...
008:     10 changed, 109 examined...
009:      3 changed, 59 examined...
010:      3 changed, 18 examined...
011:      2 changed, 13 examined...
012:      1 changed, 10 examined...
013:      1 changed, 6 examined...
014:      0 changed, 5 examined...
4 labels changed using aseg
000: 302 total segments, 218 labels (2367 vertices) changed
001: 111 total segments, 29 labels (94 vertices) changed
002: 85 total segments, 3 labels (12 vertices) changed
003: 82 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 130 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
587 vertices marked for relabeling...
587 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classification took 1 minutes and 11 seconds.
#-----------------------------------------
#@# Parcellation Stats 2 rh Wed Jan 31 00:52:12 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 BPD0072_base rh white 

computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  992    652   1733  2.125 0.777     0.142     0.039       18     1.6  G_and_S_frontomargin
 1202    795   2139  2.409 0.619     0.129     0.035       15     1.7  G_and_S_occipital_inf
 1135    627   1677  2.269 0.572     0.120     0.039       13     2.0  G_and_S_paracentral
 1393    932   2885  2.697 0.555     0.133     0.032       19     1.8  G_and_S_subcentral
  901    601   1855  2.451 0.646     0.156     0.053       19     2.1  G_and_S_transv_frontopol
 2730   1802   5216  2.596 0.741     0.121     0.031       31     3.4  G_and_S_cingul-Ant
 1489   1010   2839  2.629 0.520     0.129     0.033       16     2.0  G_and_S_cingul-Mid-Ant
 1271    842   2363  2.706 0.663     0.136     0.039       16     2.0  G_and_S_cingul-Mid-Post
  407    267   1144  3.125 0.504     0.182     0.067       10     1.0  G_cingul-Post-dorsal
  269    160    652  2.975 0.794     0.146     0.045        5     0.4  G_cingul-Post-ventral
 2663   1596   3420  1.873 0.484     0.148     0.080       58    11.2  G_cuneus
 1118    744   2728  2.923 0.440     0.134     0.038       18     1.6  G_front_inf-Opercular
  303    194    763  2.849 0.479     0.135     0.045        5     0.5  G_front_inf-Orbital
 1029    675   2329  2.664 0.538     0.160     0.051       24     2.2  G_front_inf-Triangul
 4487   2956  10435  2.653 0.620     0.153     0.053       89     9.3  G_front_middle
 5830   3760  15372  3.131 0.620     0.141     0.052      100    10.9  G_front_sup
  370    247    947  3.942 0.681     0.135     0.048        6     0.7  G_Ins_lg_and_S_cent_ins
  621    365   1898  3.745 0.705     0.136     0.061       13     1.6  G_insular_short
 2640   1550   5340  2.746 0.497     0.158     0.060       64     6.6  G_occipital_middle
 1910   1170   3422  2.380 0.497     0.129     0.035       25     2.7  G_occipital_sup
 2194   1387   5036  2.921 0.548     0.141     0.053       56     4.9  G_oc-temp_lat-fusifor
 2957   1863   4714  2.246 0.687     0.158     0.058       58     6.6  G_oc-temp_med-Lingual
 1154    750   3352  3.509 0.784     0.116     0.041       15     1.8  G_oc-temp_med-Parahip
 2654   1766   7314  3.014 0.648     0.166     0.075       78     7.5  G_orbital
 3678   2257   8290  2.905 0.583     0.136     0.047       93     7.6  G_pariet_inf-Angular
 3316   2104   7869  2.982 0.504     0.131     0.041       53     5.9  G_pariet_inf-Supramar
 2637   1680   5575  2.607 0.517     0.141     0.044       46     4.7  G_parietal_sup
 1990   1087   3086  2.223 0.500     0.109     0.041       43     3.6  G_postcentral
 2929   1498   6241  3.037 0.506     0.106     0.106       74     5.5  G_precentral
 2801   1827   6115  2.597 0.551     0.157     0.094      349     5.5  G_precuneus
  671    485   1734  2.555 0.616     0.165     0.091       24     2.4  G_rectus
  242    162    451  2.682 0.842     0.059     0.016        1     0.1  G_subcallosal
  392    238    843  2.799 0.358     0.114     0.025        4     0.4  G_temp_sup-G_T_transv
 1622    996   4081  2.953 0.663     0.129     0.070       54     4.2  G_temp_sup-Lateral
  764    522   1861  3.088 0.508     0.065     0.012        2     0.3  G_temp_sup-Plan_polar
  840    581   1647  2.711 0.413     0.093     0.017        5     0.6  G_temp_sup-Plan_tempo
 2575   1641   7040  3.121 0.587     0.140     0.054       54     4.7  G_temporal_inf
 2876   1851   8464  3.272 0.647     0.122     0.050       46     5.5  G_temporal_middle
  271    180    408  2.413 0.473     0.106     0.021        2     0.2  Lat_Fis-ant-Horizont
  146    108    260  2.571 0.329     0.077     0.010        0     0.1  Lat_Fis-ant-Vertical
 1609   1100   2407  2.595 0.498     0.109     0.023       11     1.5  Lat_Fis-post
 3602   2039   4220  1.977 0.522     0.137     0.057       63     8.2  Pole_occipital
 1399    990   5103  3.525 0.840     0.145     0.044       26     2.3  Pole_temporal
 2653   1750   3198  1.964 0.651     0.134     0.055       44     6.8  S_calcarine
 2905   1949   3128  1.783 0.607     0.101     0.022       17     2.7  S_central
 1057    718   1566  2.181 0.466     0.107     0.021        7     1.0  S_cingul-Marginalis
  505    342    820  2.961 0.533     0.094     0.016        2     0.4  S_circular_insula_ant
 1095    713   1703  2.858 0.654     0.077     0.016        4     0.9  S_circular_insula_inf
 1289    893   2026  2.734 0.428     0.102     0.024        6     1.3  S_circular_insula_sup
 1087    749   1876  2.650 0.436     0.101     0.017        7     0.9  S_collat_transv_ant
  465    306    493  1.935 0.289     0.152     0.046        6     0.8  S_collat_transv_post
 2197   1469   3010  2.023 0.486     0.114     0.028       19     2.5  S_front_inf
 1645   1122   2634  2.281 0.572     0.130     0.141      200     2.2  S_front_middle
 2852   1916   4584  2.492 0.480     0.107     0.024       20     3.0  S_front_sup
  754    518   1164  2.346 0.491     0.093     0.018        4     0.6  S_interm_prim-Jensen
 3922   2606   5339  2.144 0.463     0.113     0.027       35     4.2  S_intrapariet_and_P_trans
  760    511   1044  2.192 0.403     0.130     0.032        7     1.0  S_oc_middle_and_Lunatus
 1606   1071   2209  2.199 0.469     0.113     0.026       14     1.6  S_oc_sup_and_transversal
  984    636   1468  2.606 0.440     0.117     0.031        9     1.2  S_occipital_ant
 1007    674   1569  2.520 0.337     0.113     0.028        9     1.3  S_oc-temp_lat
 2070   1440   3303  2.630 0.624     0.107     0.024       16     2.2  S_oc-temp_med_and_Lingual
  665    441    789  1.870 0.521     0.128     0.031        8     0.9  S_orbital_lateral
  704    514    940  1.680 0.711     0.098     0.014        4     0.4  S_orbital_med-olfact
 1483   1004   2739  2.685 0.577     0.128     0.037       14     2.4  S_orbital-H_Shaped
 2616   1709   3681  2.281 0.558     0.125     0.031       26     3.4  S_parieto_occipital
 1613   1013   1814  2.109 0.756     0.137     0.060       36     3.1  S_pericallosal
 1803   1209   2089  1.931 0.429     0.084     0.015        7     1.2  S_postcentral
 1486   1032   2239  2.283 0.394     0.105     0.022       12     1.2  S_precentral-inf-part
 1301    906   2000  2.346 0.579     0.104     0.025        8     1.1  S_precentral-sup-part
  304    202    468  2.386 0.637     0.139     0.030        3     0.4  S_suborbital
 1204    836   1996  2.360 0.533     0.107     0.021        7     1.0  S_subparietal
 1139    778   1579  2.495 0.440     0.117     0.020        8     1.1  S_temporal_inf
 4931   3379   7905  2.521 0.567     0.107     0.022       35     4.2  S_temporal_sup
  285    193    484  2.730 0.517     0.142     0.031        4     0.4  S_temporal_transverse
#-----------------------------------------
#@# Cortical Parc 3 rh Wed Jan 31 00:52:35 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/scripts

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 BPD0072_base 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...
1236 labels changed using aseg
relabeling using gibbs priors...
000:   2620 changed, 132750 examined...
001:    632 changed, 11330 examined...
002:    149 changed, 3422 examined...
003:     62 changed, 892 examined...
004:     28 changed, 366 examined...
005:     12 changed, 148 examined...
006:      5 changed, 72 examined...
007:      6 changed, 36 examined...
008:      4 changed, 35 examined...
009:      2 changed, 26 examined...
010:      2 changed, 13 examined...
011:      2 changed, 15 examined...
012:      2 changed, 14 examined...
013:      1 changed, 14 examined...
014:      1 changed, 7 examined...
015:      3 changed, 7 examined...
016:      3 changed, 13 examined...
017:      3 changed, 16 examined...
018:      5 changed, 15 examined...
019:      6 changed, 29 examined...
020:      4 changed, 25 examined...
021:      6 changed, 18 examined...
022:      6 changed, 28 examined...
023:      8 changed, 34 examined...
024:      5 changed, 35 examined...
025:      4 changed, 36 examined...
026:      2 changed, 27 examined...
027:      1 changed, 13 examined...
028:      0 changed, 7 examined...
153 labels changed using aseg
000: 56 total segments, 23 labels (96 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 46 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
636 vertices marked for relabeling...
636 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas40.annot...
classification took 1 minutes and 1 seconds.
#-----------------------------------------
#@# Parcellation Stats 3 rh Wed Jan 31 00:53:35 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 BPD0072_base rh white 

computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

 1010    640   1800  2.686 0.748     0.132     0.034       15     1.3  caudalanteriorcingulate
 3223   2174   6194  2.515 0.563     0.127     0.032       36     4.3  caudalmiddlefrontal
 3380   2092   4426  1.941 0.438     0.141     0.063       56    11.2  cuneus
  381    270   1437  4.019 0.712     0.101     0.023        2     0.3  entorhinal
 4531   2974   9039  2.789 0.613     0.126     0.040       79     7.7  fusiform
 8039   5108  15190  2.658 0.613     0.126     0.038      135    12.7  inferiorparietal
 4844   3220  11567  2.965 0.668     0.131     0.041       75     7.4  inferiortemporal
 1418    906   2577  2.452 0.811     0.140     0.070       33     3.1  isthmuscingulate
 7734   4656  11651  2.281 0.527     0.140     0.049      133    15.0  lateraloccipital
 4109   2749   8720  2.667 0.733     0.146     0.056       79     9.0  lateralorbitofrontal
 4663   3028   6814  2.181 0.663     0.146     0.050       76     9.3  lingual
 1991   1368   4099  2.367 0.761     0.134     0.049       41     3.8  medialorbitofrontal
 5483   3678  13270  3.024 0.665     0.116     0.036       65     7.8  middletemporal
 1064    692   2319  3.038 0.703     0.102     0.030       10     1.2  parahippocampal
 1894   1200   3193  2.391 0.586     0.113     0.026       15     2.1  paracentral
 2062   1391   3959  2.513 0.559     0.120     0.032       26     2.6  parsopercularis
 1199    793   2762  2.878 0.642     0.124     0.034       16     1.6  parsorbitalis
 2373   1582   4277  2.382 0.583     0.132     0.037       35     3.7  parstriangularis
 2796   1718   2744  1.732 0.421     0.142     0.066       60     8.5  pericalcarine
 6408   3963   9325  2.087 0.672     0.108     0.029       80     8.1  postcentral
 1645   1076   3013  2.539 0.794     0.145     0.041       26     2.9  posteriorcingulate
 6590   3986  11719  2.648 0.652     0.106     0.060       98     9.2  precentral
 6080   4038  11215  2.479 0.593     0.136     0.059      377     9.3  precuneus
 1268    820   2686  2.841 0.720     0.131     0.041       19     1.9  rostralanteriorcingulate
 5514   3656  10646  2.394 0.704     0.147     0.081      283    10.8  rostralmiddlefrontal
12264   8128  26148  2.779 0.682     0.129     0.041      161    18.9  superiorfrontal
 7252   4724  12496  2.335 0.541     0.125     0.034       92     9.9  superiorparietal
 6305   4186  13715  2.851 0.645     0.107     0.034       89     8.2  superiortemporal
 5647   3689  11167  2.723 0.545     0.117     0.033       67     8.1  supramarginal
  549    335   1065  2.739 0.294     0.125     0.030        7     0.6  transversetemporal
 2750   1813   5890  3.309 0.756     0.114     0.038       29     4.3  insula
#--------------------------------------------
#@# Cortical ribbon mask Wed Jan 31 00:53:57 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri

 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon BPD0072_base 

SUBJECTS_DIR is /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
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 = 14
writing volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/ribbon.mgz
 writing ribbon files
#--------------------------------------------
#@# ASeg Stats Wed Jan 31 01:06:23 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base

 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 BPD0072_base 

$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 BPD0072_base 
sysname  Linux
hostname e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze
UseRobust  0
atlas_icv (eTIV) = 1517774 mm^3    (det: 1.283528 )
Computing euler number
orig.nofix lheno =  -30, rheno = -12
orig.nofix lhholes =   16, rhholes = 7
Loading mri/aseg.mgz
Getting Brain Volume Statistics
lhCtxGM: 232391.093 232231.000  diff=  160.1  pctdiff= 0.069
rhCtxGM: 235434.067 235020.000  diff=  414.1  pctdiff= 0.176
lhCtxWM: 208129.754 208541.000  diff= -411.2  pctdiff=-0.198
rhCtxWM: 213280.339 213553.000  diff= -272.7  pctdiff=-0.128
SubCortGMVol  56969.000
SupraTentVol  954609.252 (953358.000) diff=1251.252 pctdiff=0.131
SupraTentVolNotVent  947588.252 (946337.000) diff=1251.252 pctdiff=0.132
BrainSegVol  1083202.000 (1080534.000) diff=2668.000 pctdiff=0.246
BrainSegVolNotVent  1072470.000 (1072246.252) diff=223.748 pctdiff=0.021
BrainSegVolNotVent  1072470.000
CerebellumVol 126019.000
VentChorVol    7021.000
3rd4th5thCSF   3711.000
CSFVol  1049.000, OptChiasmVol   108.000
MaskVol 1665485.000
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    2540    2539.990
  4     5                  Left-Inf-Lat-Vent     160     159.542
  5     7       Left-Cerebellum-White-Matter   14650   14649.776
  6     8             Left-Cerebellum-Cortex   48762   48761.859
  7    10               Left-Thalamus-Proper    7969    7969.008
  8    11                       Left-Caudate    3502    3502.274
  9    12                       Left-Putamen    5251    5250.815
 10    13                      Left-Pallidum    1211    1211.170
 11    14                      3rd-Ventricle     841     841.265
 12    15                      4th-Ventricle    1965    1965.158
 13    16                         Brain-Stem   17557   17557.410
 14    17                   Left-Hippocampus    4368    4368.167
 15    18                      Left-Amygdala    1285    1284.521
 16    24                                CSF    1045    1044.684
 17    26                Left-Accumbens-area     567     567.361
 18    28                     Left-VentralDC    3618    3618.393
 19    30                        Left-vessel      18      18.427
 20    31                Left-choroid-plexus     929     928.758
 23    43            Right-Lateral-Ventricle    2583    2582.648
 24    44                 Right-Inf-Lat-Vent      74      74.445
 25    46      Right-Cerebellum-White-Matter   15224   15223.554
 26    47            Right-Cerebellum-Cortex   48635   48635.230
 27    49              Right-Thalamus-Proper    7103    7103.464
 28    50                      Right-Caudate    3641    3641.229
 29    51                      Right-Putamen    5463    5462.941
 30    52                     Right-Pallidum    1445    1445.205
 31    53                  Right-Hippocampus    4520    4520.313
 32    54                     Right-Amygdala    1328    1328.188
 33    58               Right-Accumbens-area     691     691.022
 34    60                    Right-VentralDC    3764    3764.214
 35    62                       Right-vessel      25      25.226
 36    63               Right-choroid-plexus    1152    1152.425
 37    72                      5th-Ventricle       1       1.000
 38    77                 WM-hypointensities     949     949.426
 39    78            Left-WM-hypointensities       0       0.000
 40    79           Right-WM-hypointensities       0       0.000
 41    80             non-WM-hypointensities       5       5.473
 42    81        Left-non-WM-hypointensities       0       0.000
 43    82       Right-non-WM-hypointensities       0       0.000
 44    85                       Optic-Chiasm     105     105.060
 45   251                       CC_Posterior     773     772.600
 46   252                   CC_Mid_Posterior     396     395.527
 47   253                         CC_Central     662     661.891
 48   254                    CC_Mid_Anterior     612     611.698
 49   255                        CC_Anterior     666     666.474

Reporting on  45 segmentations
mri_segstats done
#-----------------------------------------
#@# AParc-to-ASeg Wed Jan 31 01:09:25 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base

 mri_aparc2aseg --s BPD0072_base --volmask 

SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
subject BPD0072_base
outvol /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white

Reading lh pial surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial

Loading lh annotations from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white

Reading rh pial surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial

Loading rh annotations from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 = 464861
Used brute-force search on 0 voxels
Writing output aseg to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aparc+aseg.mgz
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base

 mri_aparc2aseg --s BPD0072_base --volmask --a2009s 

SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
subject BPD0072_base
outvol /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aparc.a2009s+aseg.mgz
useribbon 0
baseoffset 10100
RipUnknown 0

Reading lh white surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white

Reading lh pial surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial

Loading lh annotations from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white

Reading rh pial surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial

Loading rh annotations from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 = 464861
Used brute-force search on 0 voxels
Writing output aseg to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aparc.a2009s+aseg.mgz
#-----------------------------------------
#@# WMParc Wed Jan 31 01:12:04 EST 2018
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base

 mri_aparc2aseg --s BPD0072_base --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 

SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
subject BPD0072_base
outvol mri/wmparc.mgz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 5.000000
RipUnknown 1
CtxSeg /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aparc+aseg.mgz

Reading lh white surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white

Reading lh pial surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial

Loading lh annotations from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white

Reading rh pial surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial

Loading rh annotations from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/ribbon.mgz
Loading filled from /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/filled.mgz
Ripping vertices labeled as unkown
Ripped 7843 vertices from left hemi
Ripped 8284 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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/aseg.mgz
Loading Ctx Seg File /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 = 886094
Used brute-force search on 330 voxels
Fixing Parahip LH WM
  Found 9 clusters
     0 k 1541.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 1.000000
     5 k 1.000000
     6 k 21.000000
     7 k 3.000000
     8 k 2.000000
Fixing Parahip RH WM
  Found 13 clusters
     0 k 3.000000
     1 k 1.000000
     2 k 1.000000
     3 k 1.000000
     4 k 2.000000
     5 k 1621.000000
     6 k 1.000000
     7 k 1.000000
     8 k 1.000000
     9 k 2.000000
     10 k 1.000000
     11 k 1.000000
     12 k 1.000000
Writing output aseg to mri/wmparc.mgz
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base

 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 BPD0072_base --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 BPD0072_base --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
sysname  Linux
hostname e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze
UseRobust  0
atlas_icv (eTIV) = 1517774 mm^3    (det: 1.283528 )
Loading mri/wmparc.mgz
Getting Brain Volume Statistics
lhCtxGM: 232391.093 232231.000  diff=  160.1  pctdiff= 0.069
rhCtxGM: 235434.067 235020.000  diff=  414.1  pctdiff= 0.176
lhCtxWM: 208129.754 208541.000  diff= -411.2  pctdiff=-0.198
rhCtxWM: 213280.339 213553.000  diff= -272.7  pctdiff=-0.128
SubCortGMVol  56969.000
SupraTentVol  954609.252 (953358.000) diff=1251.252 pctdiff=0.131
SupraTentVolNotVent  947588.252 (946337.000) diff=1251.252 pctdiff=0.132
BrainSegVol  1083202.000 (1080534.000) diff=2668.000 pctdiff=0.246
BrainSegVolNotVent  1072470.000 (1072246.252) diff=223.748 pctdiff=0.021
BrainSegVolNotVent  1072470.000
CerebellumVol 126019.000
VentChorVol    7021.000
3rd4th5thCSF   3711.000
CSFVol  1049.000, OptChiasmVol   108.000
MaskVol 1665485.000
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    2872    2871.635
  2   3002      wm-lh-caudalanteriorcingulate    2664    2663.670
  3   3003          wm-lh-caudalmiddlefrontal    6286    6286.157
  4   3004               wm-lh-corpuscallosum       0       0.000
  5   3005                       wm-lh-cuneus    2173    2173.292
  6   3006                   wm-lh-entorhinal     636     635.539
  7   3007                     wm-lh-fusiform    6663    6663.402
  8   3008             wm-lh-inferiorparietal    8358    8357.795
  9   3009             wm-lh-inferiortemporal    6055    6054.609
 10   3010             wm-lh-isthmuscingulate    3486    3486.328
 11   3011             wm-lh-lateraloccipital    8020    8019.912
 12   3012         wm-lh-lateralorbitofrontal    6874    6873.722
 13   3013                      wm-lh-lingual    5332    5331.795
 14   3014          wm-lh-medialorbitofrontal    2819    2818.503
 15   3015               wm-lh-middletemporal    4477    4476.781
 16   3016              wm-lh-parahippocampal    1650    1650.453
 17   3017                  wm-lh-paracentral    2936    2935.718
 18   3018              wm-lh-parsopercularis    3343    3343.165
 19   3019                wm-lh-parsorbitalis     797     796.532
 20   3020             wm-lh-parstriangularis    2967    2966.671
 21   3021                wm-lh-pericalcarine    3443    3442.863
 22   3022                  wm-lh-postcentral    6971    6971.488
 23   3023           wm-lh-posteriorcingulate    4090    4090.128
 24   3024                   wm-lh-precentral   11567   11567.408
 25   3025                    wm-lh-precuneus    9540    9540.124
 26   3026     wm-lh-rostralanteriorcingulate    2633    2632.905
 27   3027         wm-lh-rostralmiddlefrontal    9971    9971.325
 28   3028              wm-lh-superiorfrontal   17814   17814.281
 29   3029             wm-lh-superiorparietal   12687   12687.038
 30   3030             wm-lh-superiortemporal    7150    7150.454
 31   3031                wm-lh-supramarginal    8873    8872.587
 32   3032                  wm-lh-frontalpole     185     185.254
 33   3033                 wm-lh-temporalpole     569     569.477
 34   3034           wm-lh-transversetemporal     662     661.516
 35   3035                       wm-lh-insula    7839    7839.022
 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    2650    2650.001
120   4002      wm-rh-caudalanteriorcingulate    2821    2820.774
121   4003          wm-rh-caudalmiddlefrontal    5688    5687.524
122   4004               wm-rh-corpuscallosum       0       0.000
123   4005                       wm-rh-cuneus    2411    2411.219
124   4006                   wm-rh-entorhinal     424     424.414
125   4007                     wm-rh-fusiform    6816    6815.946
126   4008             wm-rh-inferiorparietal   11066   11065.925
127   4009             wm-rh-inferiortemporal    5458    5457.909
128   4010             wm-rh-isthmuscingulate    3374    3373.860
129   4011             wm-rh-lateraloccipital    8783    8782.511
130   4012         wm-rh-lateralorbitofrontal    6400    6399.954
131   4013                      wm-rh-lingual    5687    5687.447
132   4014          wm-rh-medialorbitofrontal    3489    3488.793
133   4015               wm-rh-middletemporal    5247    5246.976
134   4016              wm-rh-parahippocampal    1715    1714.775
135   4017                  wm-rh-paracentral    3683    3683.378
136   4018              wm-rh-parsopercularis    2731    2731.100
137   4019                wm-rh-parsorbitalis    1060    1059.713
138   4020             wm-rh-parstriangularis    2971    2970.574
139   4021                wm-rh-pericalcarine    3411    3410.571
140   4022                  wm-rh-postcentral    6528    6528.208
141   4023           wm-rh-posteriorcingulate    3946    3946.383
142   4024                   wm-rh-precentral   12158   12158.147
143   4025                    wm-rh-precuneus   10126   10126.370
144   4026     wm-rh-rostralanteriorcingulate    1778    1778.033
145   4027         wm-rh-rostralmiddlefrontal   11607   11607.267
146   4028              wm-rh-superiorfrontal   16642   16642.361
147   4029             wm-rh-superiorparietal   12443   12443.399
148   4030             wm-rh-superiortemporal    5833    5832.876
149   4031                wm-rh-supramarginal    9607    9607.415
150   4032                  wm-rh-frontalpole     265     265.234
151   4033                 wm-rh-temporalpole     486     485.505
152   4034           wm-rh-transversetemporal     548     547.648
153   4035                       wm-rh-insula    8086    8086.314
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   27051   27051.430
237   5002       Right-UnsegmentedWhiteMatter   29328   29328.346
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
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label
#--------------------------------------------
#@# BA Labels lh Wed Jan 31 01:21:29 EST 2018

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA1.label --trgsubject BPD0072_base --trglabel ./lh.BA1.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA1.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 289
Checking for and removing duplicates
Writing label file ./lh.BA1.label 4418
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA2.label --trgsubject BPD0072_base --trglabel ./lh.BA2.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA2.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 362
Checking for and removing duplicates
Writing label file ./lh.BA2.label 8271
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3a.label --trgsubject BPD0072_base --trglabel ./lh.BA3a.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3a.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4077 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 118
Checking for and removing duplicates
Writing label file ./lh.BA3a.label 4195
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3b.label --trgsubject BPD0072_base --trglabel ./lh.BA3b.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3b.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5983 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 345
Checking for and removing duplicates
Writing label file ./lh.BA3b.label 6328
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4a.label --trgsubject BPD0072_base --trglabel ./lh.BA4a.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4a.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5784 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 309
Checking for and removing duplicates
Writing label file ./lh.BA4a.label 6093
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4p.label --trgsubject BPD0072_base --trglabel ./lh.BA4p.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4p.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4070 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 181
Checking for and removing duplicates
Writing label file ./lh.BA4p.label 4251
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA6.label --trgsubject BPD0072_base --trglabel ./lh.BA6.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA6.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 13589 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 1030
Checking for and removing duplicates
Writing label file ./lh.BA6.label 14619
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA44.label --trgsubject BPD0072_base --trglabel ./lh.BA44.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA44.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4181 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 295
Checking for and removing duplicates
Writing label file ./lh.BA44.label 4476
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA45.label --trgsubject BPD0072_base --trglabel ./lh.BA45.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA45.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3422 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 660
Checking for and removing duplicates
Writing label file ./lh.BA45.label 4082
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V1.label --trgsubject BPD0072_base --trglabel ./lh.V1.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V1.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 1927
Checking for and removing duplicates
Writing label file ./lh.V1.label 6568
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V2.label --trgsubject BPD0072_base --trglabel ./lh.V2.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V2.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 2937
Checking for and removing duplicates
Writing label file ./lh.V2.label 11051
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.MT.label --trgsubject BPD0072_base --trglabel ./lh.MT.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.MT.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 329
Checking for and removing duplicates
Writing label file ./lh.MT.label 2347
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.perirhinal.label --trgsubject BPD0072_base --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.perirhinal.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1199 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 85
Checking for and removing duplicates
Writing label file ./lh.perirhinal.label 1284
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA1.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1014 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 63
Checking for and removing duplicates
Writing label file ./lh.BA1.thresh.label 1077
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA2.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2092 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 80
Checking for and removing duplicates
Writing label file ./lh.BA2.thresh.label 2172
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3a.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1504 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 29
Checking for and removing duplicates
Writing label file ./lh.BA3a.thresh.label 1533
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3b.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1996 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 187
Checking for and removing duplicates
Writing label file ./lh.BA3b.thresh.label 2183
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4a.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2319 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 138
Checking for and removing duplicates
Writing label file ./lh.BA4a.thresh.label 2457
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4p.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1549 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 50
Checking for and removing duplicates
Writing label file ./lh.BA4p.thresh.label 1599
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA6.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 7035 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 400
Checking for and removing duplicates
Writing label file ./lh.BA6.thresh.label 7435
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA44.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1912 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 128
Checking for and removing duplicates
Writing label file ./lh.BA44.thresh.label 2040
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA45.thresh.label --trgsubject BPD0072_base --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1151 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 341
Checking for and removing duplicates
Writing label file ./lh.BA45.thresh.label 1492
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V1.thresh.label --trgsubject BPD0072_base --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V1.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3405 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 1464
Checking for and removing duplicates
Writing label file ./lh.V1.thresh.label 4869
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V2.thresh.label --trgsubject BPD0072_base --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.V2.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3334 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 1393
Checking for and removing duplicates
Writing label file ./lh.V2.thresh.label 4727
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.MT.thresh.label --trgsubject BPD0072_base --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/lh.MT.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 513 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/lh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 129540
Number of reverse mapping hits = 102
Checking for and removing duplicates
Writing label file ./lh.MT.thresh.label 615
mri_label2label: Done

 mris_label2annot --s BPD0072_base --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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label
cmdline mris_label2annot --s BPD0072_base --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 e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze

subject BPD0072_base
hemi    lh
SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 89481 unhit vertices
Writing annot to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label/lh.BA.annot

 mris_label2annot --s BPD0072_base --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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label
cmdline mris_label2annot --s BPD0072_base --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 e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze

subject BPD0072_base
hemi    lh
SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 105739 unhit vertices
Writing annot to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label/lh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab BPD0072_base lh white 

computing statistics for each annotation in ./lh.BA.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

 1116    613   1992  2.443 0.478     0.118     0.037       14     1.6  BA1
 3459   2273   5473  2.315 0.491     0.103     0.024       26     3.5  BA2
  927    636    839  1.716 0.458     0.127     0.028        7     1.1  BA3a
 2420   1479   3419  1.987 0.689     0.112     0.046       29     3.4  BA3b
 1622    834   2764  2.672 0.589     0.101     0.039       19     3.0  BA4a
 1216    750   2080  2.808 0.487     0.082     0.019        5     1.0  BA4p
 8757   5497  20127  3.072 0.573     0.122     0.036      107    12.5  BA6
 2295   1537   4611  2.687 0.427     0.103     0.025       20     2.5  BA44
 3007   2022   5734  2.439 0.559     0.129     0.039       41     4.6  BA45
 4155   2555   4411  1.681 0.471     0.134     0.053      113     9.9  V1
 8316   5184  11719  2.080 0.546     0.151     0.060      147    21.3  V2
 1865   1189   3045  2.344 0.556     0.125     0.032       21     2.5  MT
  904    604   2769  3.674 0.840     0.095     0.025        5     0.9  perirhinal

 mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab BPD0072_base lh white 

computing statistics for each annotation in ./lh.BA.thresh.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  674    319   1246  2.592 0.354     0.126     0.042       11     1.1  BA1
 1382    903   2285  2.308 0.386     0.088     0.019        8     1.1  BA2
  772    530    665  1.693 0.434     0.131     0.029        6     1.0  BA3a
 1580    987   1758  1.691 0.486     0.104     0.047       16     1.8  BA3b
 1607    828   2748  2.695 0.568     0.090     0.035       16     2.8  BA4a
  964    624   1607  2.749 0.494     0.087     0.020        5     0.7  BA4p
 4753   2831  10626  3.095 0.485     0.116     0.037       57     6.6  BA6
 1452    972   3066  2.741 0.424     0.113     0.031       17     1.9  BA44
 1319    855   2888  2.694 0.483     0.144     0.052       25     2.4  BA45
 4441   2718   4845  1.712 0.482     0.134     0.054      118    10.6  V1
 4309   2644   5691  1.984 0.520     0.158     0.073       90    14.1  V2
  548    343    725  2.088 0.622     0.144     0.038        8     0.9  MT
#--------------------------------------------
#@# BA Labels rh Wed Jan 31 01:25:07 EST 2018

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA1.label --trgsubject BPD0072_base --trglabel ./rh.BA1.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA1.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 210
Checking for and removing duplicates
Writing label file ./rh.BA1.label 4172
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA2.label --trgsubject BPD0072_base --trglabel ./rh.BA2.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA2.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 214
Checking for and removing duplicates
Writing label file ./rh.BA2.label 6901
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3a.label --trgsubject BPD0072_base --trglabel ./rh.BA3a.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3a.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3980 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 155
Checking for and removing duplicates
Writing label file ./rh.BA3a.label 4135
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3b.label --trgsubject BPD0072_base --trglabel ./rh.BA3b.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3b.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4522 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 278
Checking for and removing duplicates
Writing label file ./rh.BA3b.label 4800
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4a.label --trgsubject BPD0072_base --trglabel ./rh.BA4a.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4a.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5747 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 457
Checking for and removing duplicates
Writing label file ./rh.BA4a.label 6204
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4p.label --trgsubject BPD0072_base --trglabel ./rh.BA4p.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4p.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4473 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 262
Checking for and removing duplicates
Writing label file ./rh.BA4p.label 4735
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA6.label --trgsubject BPD0072_base --trglabel ./rh.BA6.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA6.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 12256 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 828
Checking for and removing duplicates
Writing label file ./rh.BA6.label 13084
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA44.label --trgsubject BPD0072_base --trglabel ./rh.BA44.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA44.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6912 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 672
Checking for and removing duplicates
Writing label file ./rh.BA44.label 7584
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA45.label --trgsubject BPD0072_base --trglabel ./rh.BA45.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA45.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 5355 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 1041
Checking for and removing duplicates
Writing label file ./rh.BA45.label 6396
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V1.label --trgsubject BPD0072_base --trglabel ./rh.V1.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V1.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 2342
Checking for and removing duplicates
Writing label file ./rh.V1.label 7069
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V2.label --trgsubject BPD0072_base --trglabel ./rh.V2.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V2.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 3300
Checking for and removing duplicates
Writing label file ./rh.V2.label 11316
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.MT.label --trgsubject BPD0072_base --trglabel ./rh.MT.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.MT.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 643
Checking for and removing duplicates
Writing label file ./rh.MT.label 2575
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.perirhinal.label --trgsubject BPD0072_base --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.perirhinal.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 752 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 66
Checking for and removing duplicates
Writing label file ./rh.perirhinal.label 818
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA1.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA1.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 876 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 55
Checking for and removing duplicates
Writing label file ./rh.BA1.thresh.label 931
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA2.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA2.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2688 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 42
Checking for and removing duplicates
Writing label file ./rh.BA2.thresh.label 2730
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3a.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3a.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1698 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 20
Checking for and removing duplicates
Writing label file ./rh.BA3a.thresh.label 1718
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3b.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA3b.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 2183 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 177
Checking for and removing duplicates
Writing label file ./rh.BA3b.thresh.label 2360
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4a.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4a.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1388 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 33
Checking for and removing duplicates
Writing label file ./rh.BA4a.thresh.label 1421
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4p.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA4p.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1489 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 82
Checking for and removing duplicates
Writing label file ./rh.BA4p.thresh.label 1571
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA6.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA6.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 6959 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 420
Checking for and removing duplicates
Writing label file ./rh.BA6.thresh.label 7379
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA44.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA44.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1012 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 200
Checking for and removing duplicates
Writing label file ./rh.BA44.thresh.label 1212
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA45.thresh.label --trgsubject BPD0072_base --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.BA45.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 1178 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 195
Checking for and removing duplicates
Writing label file ./rh.BA45.thresh.label 1373
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V1.thresh.label --trgsubject BPD0072_base --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V1.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3232 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 1731
Checking for and removing duplicates
Writing label file ./rh.V1.thresh.label 4963
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V2.thresh.label --trgsubject BPD0072_base --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.V2.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 3437 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 1630
Checking for and removing duplicates
Writing label file ./rh.V2.thresh.label 5067
mri_label2label: Done

 mri_label2label --srcsubject fsaverage --srclabel /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.MT.thresh.label --trgsubject BPD0072_base --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface 

srclabel = /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/label/rh.MT.thresh.label
srcsubject = fsaverage
trgsubject = BPD0072_base
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    /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
FREESURFER_HOME /opt/freesurfer/5.3.0
Loading source label.
Found 268 points in source label.
Starting surface-based mapping
Reading source registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/fsaverage/surf/rh.sphere.reg
Rescaling ...  original radius = 100
Reading target surface 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white
Reading target registration 
 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.sphere.reg
Rescaling ...  original radius = 99.9999
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 132750
Number of reverse mapping hits = 136
Checking for and removing duplicates
Writing label file ./rh.MT.thresh.label 404
mri_label2label: Done

 mris_label2annot --s BPD0072_base --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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label
cmdline mris_label2annot --s BPD0072_base --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 e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze

subject BPD0072_base
hemi    rh
SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA
nlables 13
LabelThresh 0 0.000000
Loading /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 92394 unhit vertices
Writing annot to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label/rh.BA.annot

 mris_label2annot --s BPD0072_base --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 /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label
cmdline mris_label2annot --s BPD0072_base --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 e21.hpcc.dartmouth.edu
machine  x86_64
user     zbasgoze

subject BPD0072_base
hemi    rh
SUBJECTS_DIR /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces
ColorTable /opt/freesurfer/5.3.0/average/colortable_BA.txt
AnnotName  BA.thresh
nlables 12
LabelThresh 0 0.000000
Loading /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 110007 unhit vertices
Writing annot to /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label/rh.BA.thresh.annot

 mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab BPD0072_base rh white 

computing statistics for each annotation in ./rh.BA.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  877    414   1458  2.461 0.370     0.118     0.060       27     2.4  BA1
 2606   1695   3527  2.047 0.480     0.089     0.019       20     2.2  BA2
  929    657    851  1.661 0.494     0.146     0.039        9     1.6  BA3a
 1995   1225   2323  1.669 0.583     0.101     0.023       19     2.0  BA3b
 1493    745   2503  2.764 0.478     0.102     0.174       51     3.6  BA4a
 1155    736   1719  2.411 0.441     0.084     0.019        5     0.8  BA4p
 7422   4689  16345  2.940 0.649     0.117     0.039       87    10.0  BA6
 3283   2234   5948  2.429 0.592     0.117     0.028       35     3.6  BA44
 4274   2822   8525  2.518 0.668     0.136     0.040       66     6.8  BA45
 4804   2902   5375  1.795 0.468     0.141     0.074      102    18.1  V1
 8643   5329  12092  2.142 0.570     0.144     0.050      138    16.9  V2
 2268   1477   3631  2.464 0.512     0.127     0.037       27     3.6  MT
  607    404   2064  3.755 0.782     0.093     0.032        4     0.8  perirhinal

 mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab BPD0072_base rh white 

computing statistics for each annotation in ./rh.BA.thresh.annot.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  573    235    895  2.510 0.314     0.121     0.071       23     1.9  BA1
 1469    968   2085  2.037 0.495     0.081     0.017       13     1.1  BA2
  792    561    672  1.583 0.375     0.138     0.036        6     1.2  BA3a
 1635   1042   1628  1.470 0.411     0.094     0.020       12     1.4  BA3b
  790    407   1312  2.703 0.515     0.108     0.058       11     2.5  BA4a
  983    628   1508  2.469 0.439     0.086     0.018        5     0.7  BA4p
 4748   2967  10256  2.875 0.655     0.117     0.031       51     5.9  BA6
  988    678   2001  2.502 0.541     0.129     0.035       15     1.4  BA44
 1076    707   2471  2.759 0.560     0.146     0.047       21     1.9  BA45
 4631   2786   5061  1.792 0.470     0.142     0.077      105    18.1  V1
 4664   2810   6315  2.066 0.584     0.149     0.056       80    10.2  V2
  394    236    781  2.776 0.383     0.158     0.068       10     1.1  MT
/dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label lh Wed Jan 31 01:28:49 EST 2018

 mris_spherical_average -erode 1 -orig white -t 0.4 -o BPD0072_base label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 

painting output onto subject BPD0072_base.
processing subject lh.EC_average...
reading output surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 971 points to lh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label BPD0072_base lh white 

limiting computations to label ./lh.entorhinal_exvivo.label.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/lh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  390    225   1219  3.238 0.909     0.114     0.055        8     0.9  ./lh.entorhinal_exvivo.label
#--------------------------------------------
#@# Ex-vivo Entorhinal Cortex Label rh Wed Jan 31 01:29:03 EST 2018

 mris_spherical_average -erode 1 -orig white -t 0.4 -o BPD0072_base label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 

painting output onto subject BPD0072_base.
processing subject rh.EC_average...
reading output surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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 791 points to rh.entorhinal_exvivo.label...

 mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label BPD0072_base rh white 

limiting computations to label ./rh.entorhinal_exvivo.label.
reading volume /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/mri/wm.mgz...
reading input surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.white...
reading input pial surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/surf/rh.pial...
reading input white surface /dartfs-hpc/rc/lab/C/CooperE/Zeynep/freesurfer_surfaces/BPD0072_base/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

  279    179   1085  3.644 0.870     0.088     0.032        3     0.3  ./rh.entorhinal_exvivo.label

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

Started at Tue Jan 30 14:41:25 EST 2018 
Ended   at Wed Jan 31 01:29:17 EST 2018
#@#%# recon-all-run-time-hours 10.798
recon-all -s BPD0072_base finished without error at Wed Jan 31 01:29:17 EST 2018