Wed May 24 17:03:23 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-prep -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD/surfaces
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-2.local
Linux compute-0-2.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   41890008   24166740        196     155480   37730548
-/+ buffers/cache:    4003980   62052768
Swap:     32767996     921244   31846752

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:03:23-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-2.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-preproc

ksimon
compute-0-2.local
Linux compute-0-2.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   41930892   24125856        196     155480   37769776
-/+ buffers/cache:    4005636   62051112
Swap:     32767996     921244   31846752

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed May 24 17:03:23 EDT 2017
mri_convert --bvec-voxel /data/picsl/mackey_group/BPD/surfaces//dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces//BPD0067A/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /data/picsl/mackey_group/BPD/surfaces//dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces//BPD0067A/dmri/dwi_orig.nii.gz 
ERROR: file /data/picsl/mackey_group/BPD/surfaces//dicoms//BPD0067A/001_000011_000001.dcm does not exist
Linux compute-0-2.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed May 24 17:03:23 EDT 2017

New invocation of trac-all

Wed May 24 17:05:03 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-prep -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-15.local
Linux compute-0-15.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   45232372   20824376        188     139088   33253820
-/+ buffers/cache:   11839464   54217284
Swap:     32767996     108164   32659832

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:05:03-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-15.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-preproc

ksimon
compute-0-15.local
Linux compute-0-15.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   45318544   20738204        188     139088   33292988
-/+ buffers/cache:   11886468   54170280
Swap:     32767996     108164   32659832

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed May 24 17:05:04 EDT 2017
mri_convert --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm...
Getting Series No 
INFO: Found 914 files in /data/picsl/mackey_group/BPD/dicoms//BPD0067A
INFO: Scanning for Series Number 14
Scanning Directory 
INFO: found 72 files in series
INFO: loading series header info.

RunNo = 13
WARNING: Run 1 appears to be truncated
  Files Found: 72, Files Expected (lRep+1): 1
FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            1075.9100 1019.7200 -105.5320 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (140 140  92), nframes = 72, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR D13D 
found in dicom tag 18,1020 (len = 4 != 6)
Repetition Time = 3420, TR = 3420 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 0.99891   0.02885  -0.03668   0.86231;
-0.02938   0.99947  -0.01399   0.43169;
 0.03626   0.01506   0.99923   11.70969;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            104.6823 102.9802 -57.0400 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter          -0.7012   2.0860  17.2948 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 0, correv =0, trarev = 0
Vs = 0.0366819 0.0139935 0.999229
INFO: no Siemens slice order reversal detected (good!). 
TR=3420.00, TE=97.80, TI=-1.00, flip angle=90.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
mri_probedicom --i /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm > /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dcminfo.dat
cp /data/picsl/mackey_group/BPD/niftis/dti.bvec /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvecs
cp: cannot stat `/data/picsl/mackey_group/BPD/niftis/dti.bvec': No such file or directory
Linux compute-0-15.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed May 24 17:06:14 EDT 2017

New invocation of trac-all

Wed May 24 17:07:58 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-prep -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-7.local
Linux compute-0-7.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   51855212   14201536        188     119356   40562096
-/+ buffers/cache:   11173760   54882988
Swap:     32767996    1227984   31540012

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:07:58-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-7.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-preproc

ksimon
compute-0-7.local
Linux compute-0-7.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   51896072   14160676        188     119356   40601832
-/+ buffers/cache:   11174884   54881864
Swap:     32767996    1227984   31540012

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed May 24 17:07:58 EDT 2017
mri_convert --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm...
Getting Series No 
INFO: Found 914 files in /data/picsl/mackey_group/BPD/dicoms//BPD0067A
INFO: Scanning for Series Number 14
Scanning Directory 
INFO: found 72 files in series
INFO: loading series header info.

RunNo = 13
WARNING: Run 1 appears to be truncated
  Files Found: 72, Files Expected (lRep+1): 1
FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            1075.9100 1019.7200 -105.5320 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (140 140  92), nframes = 72, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR D13D 
found in dicom tag 18,1020 (len = 4 != 6)
Repetition Time = 3420, TR = 3420 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 0.99891   0.02885  -0.03668   0.86231;
-0.02938   0.99947  -0.01399   0.43169;
 0.03626   0.01506   0.99923   11.70969;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            104.6823 102.9802 -57.0400 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter          -0.7012   2.0860  17.2948 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 0, correv =0, trarev = 0
Vs = 0.0366819 0.0139935 0.999229
INFO: no Siemens slice order reversal detected (good!). 
TR=3420.00, TE=97.80, TI=-1.00, flip angle=90.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
mri_probedicom --i /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm > /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dcminfo.dat
cp /data/picsl/mackey_group/BPD/0067A/niftis/0067A/dti.bvec /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvecs
cp: cannot stat `/data/picsl/mackey_group/BPD/0067A/niftis/0067A/dti.bvec': No such file or directory
Linux compute-0-7.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed May 24 17:08:45 EDT 2017

New invocation of trac-all

Wed May 24 17:14:11 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-prep -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-20.local
Linux compute-0-20.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      1550744 

             total       used       free     shared    buffers     cached
Mem:     397013288  192450328  204562960        192     329268   96578168
-/+ buffers/cache:   95542892  301470396
Swap:     32767996      39500   32728496

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:14:11-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-20.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-preproc

ksimon
compute-0-20.local
Linux compute-0-20.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      1550744 

             total       used       free     shared    buffers     cached
Mem:     397013288  192451260  204562028        192     329268   96578168
-/+ buffers/cache:   95543824  301469464
Swap:     32767996      39500   32728496

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed May 24 17:14:11 EDT 2017
mri_convert --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm...
Getting Series No 
INFO: Found 914 files in /data/picsl/mackey_group/BPD/dicoms//BPD0067A
INFO: Scanning for Series Number 14
Scanning Directory 
INFO: found 72 files in series
INFO: loading series header info.

RunNo = 13
WARNING: Run 1 appears to be truncated
  Files Found: 72, Files Expected (lRep+1): 1
FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            1075.9100 1019.7200 -105.5320 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (140 140  92), nframes = 72, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR D13D 
found in dicom tag 18,1020 (len = 4 != 6)
Repetition Time = 3420, TR = 3420 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 0.99891   0.02885  -0.03668   0.86231;
-0.02938   0.99947  -0.01399   0.43169;
 0.03626   0.01506   0.99923   11.70969;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            104.6823 102.9802 -57.0400 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter          -0.7012   2.0860  17.2948 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 0, correv =0, trarev = 0
Vs = 0.0366819 0.0139935 0.999229
INFO: no Siemens slice order reversal detected (good!). 
TR=3420.00, TE=97.80, TI=-1.00, flip angle=90.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
mri_probedicom --i /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm > /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dcminfo.dat
cp /data/picsl/mackey_group/BPD/niftis/0067A/dti.bvec /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvecs
cp: cannot stat `/data/picsl/mackey_group/BPD/niftis/0067A/dti.bvec': No such file or directory
Linux compute-0-20.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Wed May 24 17:15:03 EDT 2017

New invocation of trac-all

Wed May 24 17:16:56 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-prep -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   37330992   94919116        188     716788   33344992
-/+ buffers/cache:    3269212  128980896
Swap:     32767996      28440   32739556

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/24-21:16:56-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-preproc

ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   37365620   94884488        188     716788   33377752
-/+ buffers/cache:    3271080  128979028
Swap:     32767996      28440   32739556

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Wed May 24 17:16:56 EDT 2017
mri_convert --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm...
Getting Series No 
INFO: Found 914 files in /data/picsl/mackey_group/BPD/dicoms//BPD0067A
INFO: Scanning for Series Number 14
Scanning Directory 
INFO: found 72 files in series
INFO: loading series header info.

RunNo = 13
WARNING: Run 1 appears to be truncated
  Files Found: 72, Files Expected (lRep+1): 1
FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            1075.9100 1019.7200 -105.5320 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (140 140  92), nframes = 72, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR D13D 
found in dicom tag 18,1020 (len = 4 != 6)
Repetition Time = 3420, TR = 3420 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 0.99891   0.02885  -0.03668   0.86231;
-0.02938   0.99947  -0.01399   0.43169;
 0.03626   0.01506   0.99923   11.70969;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            104.6823 102.9802 -57.0400 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter          -0.7012   2.0860  17.2948 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 0, correv =0, trarev = 0
Vs = 0.0366819 0.0139935 0.999229
INFO: no Siemens slice order reversal detected (good!). 
TR=3420.00, TE=97.80, TI=-1.00, flip angle=90.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
mri_probedicom --i /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm > /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dcminfo.dat
cp /data/picsl/mackey_group/BPD/niftis/BPD0067A/dti.bvec /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvecs
cp /data/picsl/mackey_group/BPD/niftis/BPD0067A/dti.bval /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvals
mv -f /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs.tmp /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvecs
mv -f /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvals.tmp /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvals
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 3.375
mri_convert -oni 140 -onj 140 -onk 92 -oid -0.998911 0.0293779 0.0362588 -ojd 0.0288478 0.99947 -0.0150559 -okd 0.0366819 0.0139935 0.999229 -oc -0.657976 3.58525 17.2722 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 140 -onj 140 -onk 92 -oid -0.998911 0.0293779 0.0362588 -ojd 0.0288478 0.99947 -0.0150559 -okd 0.0366819 0.0139935 0.999229 -oc -0.657976 3.58525 17.2722 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz 
normalizing out_i_direction: (-0.998911, 0.0293779, 0.0362588) -> (-0.998911, 0.0293779, 0.0362588)
normalizing out_j_direction: (0.0288478, 0.99947, -0.0150559) -> (0.0288478, 0.99947, -0.0150559)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
TR=3420.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz...
INFO: found /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvals, copying
INFO: found /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.bvecs, converting to LAS
mv -f /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.bvecs /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs
mv -f /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.bvals /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvals
eddy_correct /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz 0
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0000
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0001
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0002
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0003
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0004
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0005
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0006
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0007
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0008
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0009
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0010
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0011
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0012
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0013
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0014
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0015
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0016
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0017
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0018
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0019
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0020
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0021
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0022
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0023
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0024
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0025
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0026
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0027
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0028
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0029
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0030
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0031
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0032
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0033
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0034
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0035
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0036
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0037
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0038
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0039
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0040
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0041
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0042
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0043
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0044
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0045
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0046
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0047
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0048
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0049
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0050
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0051
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0052
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0053
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0054
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0055
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0056
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0057
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0058
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0059
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0060
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0061
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0062
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0063
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0064
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0065
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0066
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0067
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0068
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0069
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0070
processing /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_tmp0071
mv -f /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs.norot
xfmrot /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.ecclog /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs.norot /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs
ln -sf /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/data.nii.gz
mri_convert --frame 0 1 12 23 36 47 58 71 /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 12 23 36 47 58 71 /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (0.0288478, 0.99947, -0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
keeping frames 0 1 12 23 36 47 58 71
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz...
mri_concat --i /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz --mean --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 8
Allocing output
Done allocing
nframes = 8
Computing mean across frames
Writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz
bet /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb_brain_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff
#-------------------------------------
#@# Image quality assessment Wed May 24 17:35:06 EDT 2017
/share/apps/freesurfer/6.0.0/bin/dmri_motion --dwi /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz --mat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.ecclog --bval /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvals --T 1571.375000 --out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_motion.txt

cwd /home/ksimon
cmdline /share/apps/freesurfer/6.0.0/bin/dmri_motion --dwi /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_orig.nii.gz --mat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.ecclog --bval /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvals --T 1571.375000 --out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_motion.txt 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon
Output motion measure file: /data/picsl/mackey_group/BPD/surfaces/surfaces/BPD0067A/dmri/dwi_motion.txt
Input transform file: /data/picsl/mackey_group/BPD/surfaces/surfaces/BPD0067A/dmri/dwi.ecclog
Input DWI file: /data/picsl/mackey_group/BPD/surfaces/surfaces/BPD0067A/dmri/dwi_orig.nii.gz
Input b-value table: /data/picsl/mackey_group/BPD/surfaces/surfaces/BPD0067A/dmri/bvals
Low-b image intensity threshold: 1571.38
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 72 volumes
Loading DWI volume series from /data/picsl/mackey_group/BPD/surfaces/surfaces/BPD0067A/dmri/dwi_orig.nii.gz
Loading b-value table from /data/picsl/mackey_group/BPD/surfaces/surfaces/BPD0067A/dmri/bvals
Computing within-volume head motion measures
Done in 9.726 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Wed May 24 17:35:16 EDT 2017
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brain.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brain.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brain.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz...
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz...
tkregister2 --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz --targ /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2anat.mat --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2anatorig.dat
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
target  volume /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz
movable volume /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz
reg file       /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2anatorig.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.00000   0.00000  -0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000  -0.00000   1.00000   1.00000;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
 1.00000   0.00000  -0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000  -0.00000   1.00000   1.00000;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
 1.00000  -0.00000   0.00000   0.00000;
-0.00000  -0.00000  -1.00000   0.00000;
 0.00000   1.00000  -0.00000   1.00000;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2anatorig.mat -inverse /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2anat.mat
tmp /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843
Log file is /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.log
Wed May 24 17:35:20 EDT 2017

setenv SUBJECTS_DIR /data/picsl/mackey_group/BPD
cd /home/ksimon
/share/apps/freesurfer/6.0.0/bin/bbregister --s surfaces/BPD0067A --init-fsl --dti --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --fslmat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /share/apps/freesurfer/6.0.0
mri_convert /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (0.0288478, 0.99947, -0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii...
fslregister --s surfaces/BPD0067A --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat --niters 1 --maxangle 90 --tmp /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov

Log file is /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat.fslregister.log

Wed May 24 17:35:32 EDT 2017
--s surfaces/BPD0067A --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat --niters 1 --maxangle 90 --tmp /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/ksimon
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/refvol.fslregister.nii
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/ksimon
mri_convert /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii --frame 0
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (0.0288478, 0.99947, -0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
keeping frame 0
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii...
Mov determinant is -3.375
/home/ksimon
tkregister2_cmdl --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/reg0.41884.dat --regheader --fslregout /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat.fsl.mat0 --s surfaces/BPD0067A --noedit
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii
reg file       /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/reg0.41884.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.50000   0.00000   0.00000   105.00000;
 0.00000   0.00000   1.50000  -69.00000;
 0.00000  -1.50000   0.00000   105.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 0.99891  -0.02938  -0.03626  -0.38435;
 0.03668   0.01399   0.99923  -5.62213;
-0.02885  -0.99947   0.01506   3.93708;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
 0.99891  -0.02938  -0.03626  -0.38435;
 0.03668   0.01399   0.99923  -5.62213;
-0.02885  -0.99947   0.01506   3.93708;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = surfaces/BPD0067A
RegMat ---------------------------
 0.99891  -0.02938  -0.03626  -0.38435;
 0.03668   0.01399   0.99923  -5.62213;
-0.02885  -0.99947   0.01506   3.93708;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -3.375, ref det = -1
Wed May 24 17:35:40 EDT 2017
/home/ksimon
flirt.fsl -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/refvol.fslregister.nii -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/fslmat0.trans.mat -schedule /share/apps/freesurfer/6.0.0/bin/fsl.5.0.2.xyztrans.sch -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat.fsl.mat0
Wed May 24 17:35:52 EDT 2017
/home/ksimon
flirt.fsl -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/refvol.fslregister.nii -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat.fsl.mat -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/fslregister/fslmat0.trans.mat -schedule /share/apps/freesurfer/6.0.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s surfaces/BPD0067A --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat --fslreg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat.fsl.mat --noedit
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.99939  -0.02925  -0.01891   26.75490;
-0.01932  -0.01398  -0.99972   192.78999;
 0.02897   0.99947  -0.01453   23.97390;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii
reg file       /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii
Tmov: --------------------
-1.50000   0.00000   0.00000   105.00000;
 0.00000   0.00000   1.50000  -69.00000;
 0.00000  -1.50000   0.00000   105.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -3.375, ref det = -1
---- Input registration matrix (computed) --------
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = surfaces/BPD0067A
RegMat ---------------------------
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;
(standard_in) 1: illegal character: P
(standard_in) 1: syntax error
 
Started at Wed May 24 17:35:32 EDT 2017 
Ended   at Wed May 24 17:36:17 EDT 2017
 
fslregister Done
 
To check results, run:
tkregister2 --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat --surf orig
 
mri_segreg --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --init-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat --out-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /data/picsl/mackey_group/BPD
cd /home/ksimon
mri_segreg --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --init-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat --out-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon
movvol /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii
regfile /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.init.dat
subject surfaces/BPD0067A
dof 6
outregfile /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1496207019
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;

Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
 0  -25.0 -25.0 -25.0   1.030488
 1  -25.0 -25.0  25.0   1.041796
 2  -25.0  25.0 -25.0   1.058652
 3  -25.0  25.0  25.0   1.014194
 4   25.0 -25.0 -25.0   1.029777
 5   25.0 -25.0  25.0   1.020985
 6   25.0  25.0 -25.0   1.025319
 7   25.0  25.0  25.0   1.071559
REL:  8  0.632523    8.292770  1.036596 rel = 0.610192 
Initial costs ----------------
Number of surface hits 2830
WM  Intensity  2099.6731 +/- 624.1202
Ctx Intensity  2384.4033 +/- 812.5299
Pct Contrast     10.1893 +/-  33.9558
Cost   0.6325
RelCost   0.6102

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0130   1.0130  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9919   0.9919  0.0
     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      0.9758   0.9758  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9544   0.9544  0.0
    10  -4.0000  -4.0000  -4.0000   0.0000  -4.0000   0.0000      0.9468   0.9468  0.0
    36  -4.0000  -4.0000   0.0000   0.0000  -4.0000  -4.0000      0.9376   0.9376  0.0
    63  -4.0000  -4.0000   4.0000   0.0000  -4.0000  -4.0000      0.9217   0.9217  0.0
   111  -4.0000   0.0000   0.0000  -4.0000   0.0000  -4.0000      0.9015   0.9015  0.0
   114  -4.0000   0.0000   0.0000  -4.0000   4.0000  -4.0000      0.8562   0.8562  0.0
   273   0.0000  -4.0000   0.0000  -4.0000   0.0000  -4.0000      0.8493   0.8493  0.0
   274   0.0000  -4.0000   0.0000  -4.0000   0.0000   0.0000      0.8399   0.8399  0.0
   275   0.0000  -4.0000   0.0000  -4.0000   0.0000   4.0000      0.8286   0.8286  0.0
   292   0.0000  -4.0000   0.0000   4.0000   0.0000   0.0000      0.8242   0.8242  0.0
   352   0.0000   0.0000   0.0000  -4.0000  -4.0000   0.0000      0.8164   0.8164  0.0
   354   0.0000   0.0000   0.0000  -4.0000   0.0000  -4.0000      0.7041   0.7041  0.0
   355   0.0000   0.0000   0.0000  -4.0000   0.0000   0.0000      0.4603   0.4603  0.0
Brute Force --------------------------
Min cost was 0.460342
Number of iterations   729
Search time 1.467000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000 -4.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 -4
4 0
5 0
fs_powell::minimize
  nparams 6
  maxfev 36
  ftol   0.000100
  linmin_xtol_   0.001000
  powell nthiter 0: fret = 0.460342
   6  0.382  0.000  0.000 -4.000  0.000  0.000   0.4503623457
   7  0.488  0.000  0.000 -4.000  0.000  0.000   0.4481819818
   9  0.505  0.000  0.000 -4.000  0.000  0.000   0.4478228227
  11  0.527  0.000  0.000 -4.000  0.000  0.000   0.4477052927
  12  0.522  0.000  0.000 -4.000  0.000  0.000   0.4477048904
  15  0.521  0.000  0.000 -4.000  0.000  0.000   0.4477008926
  16  0.519  0.000  0.000 -4.000  0.000  0.000   0.4476979544
  18  0.520  0.000  0.000 -4.000  0.000  0.000   0.4476978542
  23  0.520 -0.618  0.000 -4.000  0.000  0.000   0.4387041388
  31  0.520 -0.608  0.000 -4.000  0.000  0.000   0.4386491695
  35  0.520 -0.608  1.000 -4.000  0.000  0.000   0.4318433972
  39  0.520 -0.608  0.618 -4.000  0.000  0.000   0.4283188727
  40  0.520 -0.608  0.697 -4.000  0.000  0.000   0.4277513315
  41  0.520 -0.608  0.724 -4.000  0.000  0.000   0.4276373319
  43  0.520 -0.608  0.760 -4.000  0.000  0.000   0.4274670667
  44  0.520 -0.608  0.786 -4.000  0.000  0.000   0.4273745874
  46  0.520 -0.608  0.787 -4.000  0.000  0.000   0.4273741094
  49  0.520 -0.608  0.787 -3.000  0.000  0.000   0.3859234384
  54  0.520 -0.608  0.787 -2.982  0.000  0.000   0.3858166663
  55  0.520 -0.608  0.787 -2.891  0.000  0.000   0.3854610930
  56  0.520 -0.608  0.787 -2.696  0.000  0.000   0.3853046571
  58  0.520 -0.608  0.787 -2.669  0.000  0.000   0.3852194326
  61  0.520 -0.608  0.787 -2.660  0.000  0.000   0.3851954465
  62  0.520 -0.608  0.787 -2.655  0.000  0.000   0.3851918781
  63  0.520 -0.608  0.787 -2.654  0.000  0.000   0.3851907252
  65  0.520 -0.608  0.787 -2.650  0.000  0.000   0.3851899220
  66  0.520 -0.608  0.787 -2.651  0.000  0.000   0.3851898483
  73  0.520 -0.608  0.787 -2.651  0.382  0.000   0.3836315622
  74  0.520 -0.608  0.787 -2.651  0.222  0.000   0.3800454301
  83  0.520 -0.608  0.787 -2.651  0.222 -0.618   0.3791830439
  85  0.520 -0.608  0.787 -2.651  0.222 -0.325   0.3744647402
  88  0.520 -0.608  0.787 -2.651  0.222 -0.339   0.3744256129
  powell nthiter 1: fret = 0.374426
  98  0.338 -0.608  0.787 -2.651  0.222 -0.339   0.3726944352
  99  0.354 -0.608  0.787 -2.651  0.222 -0.339   0.3725681962
 100  0.383 -0.608  0.787 -2.651  0.222 -0.339   0.3723403826
 102  0.404 -0.608  0.787 -2.651  0.222 -0.339   0.3722631347
 103  0.406 -0.608  0.787 -2.651  0.222 -0.339   0.3722622875
 104  0.407 -0.608  0.787 -2.651  0.222 -0.339   0.3722617982
 116  0.407 -0.633  0.787 -2.651  0.222 -0.339   0.3721286587
 123  0.407 -0.633  0.169 -2.651  0.222 -0.339   0.3597261592
 125  0.407 -0.633  0.364 -2.651  0.222 -0.339   0.3594666868
 126  0.407 -0.633  0.280 -2.651  0.222 -0.339   0.3582456977
 127  0.407 -0.633  0.271 -2.651  0.222 -0.339   0.3582098867
 128  0.407 -0.633  0.257 -2.651  0.222 -0.339   0.3582047679
 130  0.407 -0.633  0.263 -2.651  0.222 -0.339   0.3581965336
 131  0.407 -0.633  0.264 -2.651  0.222 -0.339   0.3581959706
 133  0.407 -0.633  0.265 -2.651  0.222 -0.339   0.3581958723
 140  0.407 -0.633  0.265 -2.893  0.222 -0.339   0.3521449663
 141  0.407 -0.633  0.265 -2.892  0.222 -0.339   0.3521322432
 142  0.407 -0.633  0.265 -2.852  0.222 -0.339   0.3518342636
 146  0.407 -0.633  0.265 -2.855  0.222 -0.339   0.3518298603
 155  0.407 -0.633  0.265 -2.855  0.258 -0.339   0.3509177158
 156  0.407 -0.633  0.265 -2.855  0.322 -0.339   0.3503983734
 157  0.407 -0.633  0.265 -2.855  0.313 -0.339   0.3502887235
 158  0.407 -0.633  0.265 -2.855  0.301 -0.339   0.3502568410
 159  0.407 -0.633  0.265 -2.855  0.304 -0.339   0.3502535651
 160  0.407 -0.633  0.265 -2.855  0.303 -0.339   0.3502534988
 168  0.407 -0.633  0.265 -2.855  0.303 -0.380   0.3497468822
 170  0.407 -0.633  0.265 -2.855  0.303 -0.428   0.3495399502
 171  0.407 -0.633  0.265 -2.855  0.303 -0.429   0.3495333872
 173  0.407 -0.633  0.265 -2.855  0.303 -0.440   0.3494942248
  powell nthiter 2: fret = 0.349494
 183  0.248 -0.633  0.265 -2.855  0.303 -0.440   0.3479176126
 184  0.278 -0.633  0.265 -2.855  0.303 -0.440   0.3476460272
 185  0.293 -0.633  0.265 -2.855  0.303 -0.440   0.3476144701
 187  0.299 -0.633  0.265 -2.855  0.303 -0.440   0.3476098703
 189  0.324 -0.633  0.265 -2.855  0.303 -0.440   0.3475735395
 190  0.314 -0.633  0.265 -2.855  0.303 -0.440   0.3475661594
 191  0.317 -0.633  0.265 -2.855  0.303 -0.440   0.3475659506
 193  0.316 -0.633  0.265 -2.855  0.303 -0.440   0.3475658977
 200  0.316 -0.523  0.265 -2.855  0.303 -0.440   0.3460904847
 201  0.316 -0.525  0.265 -2.855  0.303 -0.440   0.3460527541
 202  0.316 -0.556  0.265 -2.855  0.303 -0.440   0.3458943936
 204  0.316 -0.546  0.265 -2.855  0.303 -0.440   0.3458585747
 206  0.316 -0.545  0.265 -2.855  0.303 -0.440   0.3458578901
 216  0.316 -0.545  0.305 -2.855  0.303 -0.440   0.3455042667
 217  0.316 -0.545  0.327 -2.855  0.303 -0.440   0.3454915902
 218  0.316 -0.545  0.318 -2.855  0.303 -0.440   0.3454750873
 219  0.316 -0.545  0.317 -2.855  0.303 -0.440   0.3454748921
 228  0.316 -0.545  0.317 -2.876  0.303 -0.440   0.3453336155
 239  0.316 -0.545  0.317 -2.876  0.348 -0.440   0.3451054356
 240  0.316 -0.545  0.317 -2.876  0.342 -0.440   0.3451039470
 241  0.316 -0.545  0.317 -2.876  0.344 -0.440   0.3451034910
 252  0.316 -0.545  0.317 -2.876  0.345 -0.461   0.3450723869
 253  0.316 -0.545  0.317 -2.876  0.345 -0.454   0.3450602663
 254  0.316 -0.545  0.317 -2.876  0.345 -0.453   0.3450597468
 255  0.316 -0.545  0.317 -2.876  0.345 -0.452   0.3450594515
  powell nthiter 3: fret = 0.345059
 267  0.291 -0.545  0.317 -2.876  0.345 -0.452   0.3449960229
 269  0.286 -0.545  0.317 -2.876  0.345 -0.452   0.3449950251
 270  0.287 -0.545  0.317 -2.876  0.345 -0.452   0.3449946648
 281  0.287 -0.544  0.317 -2.876  0.345 -0.452   0.3449916170
 282  0.287 -0.542  0.317 -2.876  0.345 -0.452   0.3449915183
 292  0.287 -0.542  0.338 -2.876  0.345 -0.452   0.3448964416
 293  0.287 -0.542  0.333 -2.876  0.345 -0.452   0.3448939371
 305  0.287 -0.542  0.333 -2.875  0.345 -0.452   0.3448936654
 315  0.287 -0.542  0.333 -2.875  0.342 -0.452   0.3448804786
 316  0.287 -0.542  0.333 -2.875  0.334 -0.452   0.3448572855
 318  0.287 -0.542  0.333 -2.875  0.333 -0.452   0.3448562948
 319  0.287 -0.542  0.333 -2.875  0.332 -0.452   0.3448560469
 320  0.287 -0.542  0.333 -2.875  0.331 -0.452   0.3448558272
 329  0.287 -0.542  0.333 -2.875  0.331 -0.454   0.3448488205
 331  0.287 -0.542  0.333 -2.875  0.331 -0.468   0.3448156409
 332  0.287 -0.542  0.333 -2.875  0.331 -0.469   0.3448153320
 334  0.259 -0.538  0.350 -2.874  0.316 -0.486   0.3447411738
 340  0.270 -0.540  0.343 -2.874  0.322 -0.480   0.3447168733
 341  0.267 -0.539  0.345 -2.874  0.320 -0.481   0.3447157082
 342  0.268 -0.540  0.345 -2.874  0.321 -0.481   0.3447156507
 343  0.267 -0.539  0.345 -2.874  0.321 -0.481   0.3447155441
 344  0.267 -0.539  0.345 -2.874  0.321 -0.481   0.3447154998
  powell nthiter 4: fret = 0.344716
 357  0.263 -0.539  0.345 -2.874  0.321 -0.481   0.3447030074
 359  0.262 -0.539  0.345 -2.874  0.321 -0.481   0.3447014764
 368  0.262 -0.525  0.345 -2.874  0.321 -0.481   0.3446041203
 369  0.262 -0.516  0.345 -2.874  0.321 -0.481   0.3445716776
 371  0.262 -0.514  0.345 -2.874  0.321 -0.481   0.3445671887
 373  0.262 -0.512  0.345 -2.874  0.321 -0.481   0.3445651740
 374  0.262 -0.511  0.345 -2.874  0.321 -0.481   0.3445649912
 384  0.262 -0.511  0.345 -2.874  0.321 -0.510   0.3444097122
 385  0.262 -0.511  0.345 -2.874  0.321 -0.507   0.3444005134
 386  0.262 -0.511  0.345 -2.874  0.321 -0.504   0.3443997341
 388  0.262 -0.511  0.345 -2.874  0.321 -0.505   0.3443996220
 408  0.262 -0.511  0.345 -2.874  0.326 -0.505   0.3443876652
 416  0.251 -0.510  0.351 -2.873  0.321 -0.512   0.3443483564
 418  0.254 -0.510  0.349 -2.874  0.322 -0.510   0.3443410934
 419  0.254 -0.510  0.350 -2.874  0.322 -0.510   0.3443409416
 424  0.254 -0.510  0.350 -2.874  0.322 -0.510   0.3443408754
  powell nthiter 5: fret = 0.344341
 438  0.250 -0.510  0.350 -2.874  0.322 -0.510   0.3443332149
 439  0.249 -0.510  0.350 -2.874  0.322 -0.510   0.3443331265
 449  0.249 -0.505  0.350 -2.874  0.322 -0.510   0.3443326281
 450  0.249 -0.507  0.350 -2.874  0.322 -0.510   0.3443275661
 451  0.249 -0.508  0.350 -2.874  0.322 -0.510   0.3443265705
 460  0.249 -0.508  0.350 -2.874  0.322 -0.507   0.3443258823
 462  0.249 -0.508  0.350 -2.874  0.322 -0.508   0.3443255047
 472  0.249 -0.508  0.350 -2.878  0.322 -0.508   0.3443206126
 474  0.249 -0.508  0.350 -2.877  0.322 -0.508   0.3443201413
 475  0.249 -0.508  0.350 -2.876  0.322 -0.508   0.3443198599
 485  0.249 -0.508  0.350 -2.876  0.328 -0.508   0.3443155843
 486  0.249 -0.508  0.350 -2.876  0.326 -0.508   0.3443133669
 496  0.251 -0.508  0.349 -2.876  0.326 -0.507   0.3443123848
 499  0.250 -0.508  0.349 -2.876  0.326 -0.507   0.3443123247
 500  0.251 -0.508  0.349 -2.876  0.326 -0.507   0.3443122576
Powell done niters = 5
Computing relative cost
 0  -25.0 -25.0 -25.0   1.056450
 1  -25.0 -25.0  25.0   1.018935
 2  -25.0  25.0 -25.0   1.066527
 3  -25.0  25.0  25.0   1.023565
 4   25.0 -25.0 -25.0   1.028076
 5   25.0 -25.0  25.0   1.020587
 6   25.0  25.0 -25.0   1.011766
 7   25.0  25.0  25.0   1.071534
REL:  8  0.344312    8.297440  1.037180 rel = 0.33197 
Number of iterations     5
Min cost was 0.344312
Number of FunctionCalls   501
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.908000 sec
Parameters at optimum (transmm)  0.25050 -0.50842  0.34885
Parameters at optimum (rotdeg) -2.87594  0.32624 -0.50719 
Final costs ----------------
Number of surface hits 2830
WM  Intensity  1945.1389 +/- 565.7964
Ctx Intensity  2410.6197 +/- 772.3697
Pct Contrast     19.0085 +/-  30.1341
Cost   0.3443
RelCost   0.6102
Reg at min cost was 
 0.99932  -0.03522  -0.01086  -0.24567;
 0.00857  -0.06435   0.99789  -7.99476;
-0.03585  -0.99731  -0.06401   3.81550;
 0.00000   0.00000   0.00000   1.00000;

Writing optimal reg to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat, type = 14 
Original Reg 
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;

Original Reg - Optimal Reg
 0.00007   0.00625  -0.00847  -0.20395;
 0.01034   0.04982   0.00183   0.33995;
 0.00660  -0.00217   0.05003  -0.73153;
 0.00000   0.00000   0.00000   0.00000;

Computing change in lh position
LH rmsDiffMean 2.274471
Computing change in rh position
Surface-RMS-Diff-mm 2.233650 0.885490 4.513099
mri_segreg done
mri_segreg --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --init-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat --out-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /data/picsl/mackey_group/BPD
cd /home/ksimon
mri_segreg --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii --init-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat --out-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon
movvol /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/template.nii
regfile /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.41843/bbr.pass1.dat
subject surfaces/BPD0067A
dof 6
outregfile /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1496627971
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.99932  -0.03522  -0.01086  -0.24567;
 0.00857  -0.06435   0.99789  -7.99476;
-0.03585  -0.99731  -0.06401   3.81550;
 0.00000   0.00000   0.00000   1.00000;

Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
 0  -25.0 -25.0 -25.0   1.035950
 1  -25.0 -25.0  25.0   1.019012
 2  -25.0  25.0 -25.0   1.039914
 3  -25.0  25.0  25.0   1.016318
 4   25.0 -25.0 -25.0   1.018113
 5   25.0 -25.0  25.0   1.021250
 6   25.0  25.0 -25.0   1.020098
 7   25.0  25.0  25.0   1.060903
REL:  8  0.348651    8.231559  1.028945 rel = 0.338843 
Initial costs ----------------
Number of surface hits 284302
WM  Intensity  1945.6313 +/- 567.8147
Ctx Intensity  2401.5899 +/- 743.6584
Pct Contrast     18.9836 +/-  29.8793
Cost   0.3487
RelCost   0.3388

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.3543   0.3543  0.0
     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.3512   0.3512  0.0
     2  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.3490   0.3490  0.0
     5  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.1000      0.3466   0.3466  0.0
    85  -0.1000   0.0000  -0.1000  -0.1000   0.0000   0.0000      0.3454   0.3454  0.0
   197  -0.1000   0.1000   0.0000  -0.1000   0.1000   0.1000      0.3452   0.3452  0.0
   355   0.0000   0.0000   0.0000  -0.1000   0.0000   0.0000      0.3451   0.3451  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3443   0.3443  0.0
Brute Force --------------------------
Min cost was 0.344312
Number of iterations   729
Search time 1.332000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
  nparams 6
  maxfev 36
  ftol   0.000000
  linmin_xtol_   0.001000
  powell nthiter 0: fret = 0.348651
   7 -0.163  0.000  0.000  0.000  0.000  0.000   0.3473319131
   8 -0.144  0.000  0.000  0.000  0.000  0.000   0.3472677347
   9 -0.132  0.000  0.000  0.000  0.000  0.000   0.3472482649
  10 -0.124  0.000  0.000  0.000  0.000  0.000   0.3472461832
  11 -0.126  0.000  0.000  0.000  0.000  0.000   0.3472458877
  19 -0.126  0.137  0.000  0.000  0.000  0.000   0.3455951855
  21 -0.126  0.149  0.000  0.000  0.000  0.000   0.3455873880
  23 -0.126  0.146  0.000  0.000  0.000  0.000   0.3455861942
  32 -0.126  0.146 -0.026  0.000  0.000  0.000   0.3455512700
  41 -0.126  0.146 -0.026 -0.050  0.000  0.000   0.3452146545
  42 -0.126  0.146 -0.026 -0.080  0.000  0.000   0.3451707705
  44 -0.126  0.146 -0.026 -0.090  0.000  0.000   0.3451703237
  46 -0.126  0.146 -0.026 -0.085  0.000  0.000   0.3451690267
  56 -0.126  0.146 -0.026 -0.085  0.014  0.000   0.3451571311
  58 -0.126  0.146 -0.026 -0.085  0.015  0.000   0.3451570697
  66 -0.126  0.146 -0.026 -0.085  0.015  0.058   0.3450178559
  68 -0.126  0.146 -0.026 -0.085  0.015  0.069   0.3450128236
  70 -0.126  0.146 -0.026 -0.085  0.015  0.073   0.3450121685
  powell nthiter 1: fret = 0.345012
  81 -0.123  0.146 -0.026 -0.085  0.015  0.073   0.3450110642
  82 -0.122  0.146 -0.026 -0.085  0.015  0.073   0.3450110353
  90 -0.122  0.104 -0.026 -0.085  0.015  0.073   0.3449908999
  91 -0.122  0.123 -0.026 -0.085  0.015  0.073   0.3449475176
  92 -0.122  0.124 -0.026 -0.085  0.015  0.073   0.3449472959
 100 -0.122  0.124 -0.015 -0.085  0.015  0.073   0.3449412418
 101 -0.122  0.124 -0.014 -0.085  0.015  0.073   0.3449411679
 110 -0.122  0.124 -0.014 -0.080  0.015  0.073   0.3449345106
 111 -0.122  0.124 -0.014 -0.076  0.015  0.073   0.3449336226
 112 -0.122  0.124 -0.014 -0.077  0.015  0.073   0.3449335032
 113 -0.122  0.124 -0.014 -0.078  0.015  0.073   0.3449333321
 121 -0.122  0.124 -0.014 -0.078  0.017  0.073   0.3449314121
 122 -0.122  0.124 -0.014 -0.078  0.022  0.073   0.3449309506
 124 -0.122  0.124 -0.014 -0.078  0.020  0.073   0.3449307337
 132 -0.122  0.124 -0.014 -0.078  0.020  0.067   0.3449277545
  powell nthiter 2: fret = 0.344928
 152 -0.122  0.123 -0.014 -0.078  0.020  0.067   0.3449272980
 153 -0.122  0.122 -0.014 -0.078  0.020  0.067   0.3449272185
 171 -0.122  0.122 -0.014 -0.076  0.020  0.067   0.3449269063
 173 -0.122  0.122 -0.014 -0.077  0.020  0.067   0.3449268393
  powell nthiter 3: fret = 0.344927
Powell done niters = 3
Computing relative cost
 0  -25.0 -25.0 -25.0   1.036336
 1  -25.0 -25.0  25.0   1.016882
 2  -25.0  25.0 -25.0   1.039153
 3  -25.0  25.0  25.0   1.015118
 4   25.0 -25.0 -25.0   1.018326
 5   25.0 -25.0  25.0   1.021311
 6   25.0  25.0 -25.0   1.019585
 7   25.0  25.0  25.0   1.062072
REL:  8  0.344927    8.228782  1.028598 rel = 0.335337 
Number of iterations     3
Min cost was 0.344927
Number of FunctionCalls   245
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 21.629000 sec
Parameters at optimum (transmm) -0.12195  0.12172 -0.01413
Parameters at optimum (rotdeg) -0.07710  0.02017  0.06694 
Final costs ----------------
Number of surface hits 284302
WM  Intensity  1946.1155 +/- 565.7939
Ctx Intensity  2402.4475 +/- 738.8626
Pct Contrast     19.0318 +/-  29.6346
Cost   0.3449
RelCost   0.3388
Reg at min cost was 
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;

Writing optimal reg to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat, type = 14 
Original Reg 
 0.99932  -0.03522  -0.01086  -0.24567;
 0.00857  -0.06435   0.99789  -7.99476;
-0.03585  -0.99731  -0.06401   3.81550;
 0.00000   0.00000   0.00000   1.00000;

Original Reg - Optimal Reg
 0.00002   0.00027   0.00119   0.11127;
-0.00112   0.00138   0.00010  -0.12658;
 0.00036  -0.00010   0.00134   0.00329;
 0.00000   0.00000   0.00000   0.00000;

Computing change in lh position
LH rmsDiffMean 0.170767
Computing change in rh position
Surface-RMS-Diff-mm 0.193013 0.042866 0.277485
mri_segreg done
MinCost: 0.344927 1946.115540 2402.447482 19.031843 
tkregister2_cmdl --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz
reg file       /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;
float2int = 0
---------------------------------------
INFO: loading target /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz
Tmov: --------------------
-1.50000   0.00000   0.00000   105.00000;
 0.00000   0.00000   1.50000  -69.00000;
 0.00000  -1.50000   0.00000   105.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = surfaces/BPD0067A
RegMat ---------------------------
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -3.375, ref det = -1
Cleaning up
 
Started at Wed May 24 17:35:20 EDT 2017 
Ended   at Wed May 24 17:37:13 EDT 2017
BBR-Run-Time-Sec 113
 
bbregister Done
To check results, run:
tkregisterfv --mov /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz --reg /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --surfs 
 
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.mat -inverse /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -concat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.mat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2anat.bbr.mat -inverse /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat
#-------------------------------------
#@# Inter-subject registration Wed May 24 17:37:13 EDT 2017
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_mni.nii.gz -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/mni2anat.mat -inverse /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat -concat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/mni2diff.bbr.mat -inverse /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2mni.mat -concat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/mni2anatorig.mat -inverse /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks Wed May 24 17:39:21 EDT 2017
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz
Binarizing based on matching values
nMatch 5
 0     2
 1     7
 2    41
 3    46
 4    77
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 504761 values in range
Counting number of voxels in first frame
Found 504761 voxels in final mask
Count: 504761 504761.000000 16777216 3.008610
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz
Binarizing based on matching values
nMatch 8
 0     2
 1     7
 2    41
 3    46
 4    77
 5    28
 6    60
 7    16
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 534965 values in range
Counting number of voxels in first frame
Found 534965 voxels in final mask
Count: 534965 534965.000000 16777216 3.188640
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
 0     4
 1    43
binval        0
binvalnot     1
fstart = 0, fend = 0, nframes = 1
Found 12097 values in range
Counting number of voxels in first frame
Found 12097 voxels in final mask
Count: 12097 12097.000000 16777216 0.072104
mri_binarize done
mri_aparc2aseg --s surfaces/BPD0067A --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /data/picsl/mackey_group/BPD
subject surfaces/BPD0067A
outvol /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 2.000000
RipUnknown 0

Reading lh white surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/lh.white

Reading lh pial surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/lh.pial

Loading lh annotations from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/rh.white

Reading rh pial surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/rh.pial

Loading rh annotations from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/ribbon.mgz
Loading filled from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/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 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 979063
Used brute-force search on 0 voxels
Fixing Parahip LH WM
  Found 9 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 3.000000
     3 k 1.000000
     4 k 2.000000
     5 k 2.000000
     6 k 2.000000
     7 k 1.000000
     8 k 692.000000
Fixing Parahip RH WM
  Found 5 clusters
     0 k 2.000000
     1 k 766.000000
     2 k 2.000000
     3 k 1.000000
     4 k 1.000000
Writing output aseg to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min        1000
max        2999
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 501678 values in range
Counting number of voxels in first frame
Found 501678 voxels in final mask
Count: 501678 501678.000000 16777216 2.990234
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min        1000
max        4999
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 798545 values in range
Counting number of voxels in first frame
Found 798545 voxels in final mask
Count: 798545 798545.000000 16777216 4.759699
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 16 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 16 --o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
 0    16
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 22059 values in range
Counting number of voxels in first frame
Found 22059 voxels in final mask
Count: 22059 22059.000000 16777216 0.131482
mri_binarize done
fslmaths /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz -add /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz...
fslmaths /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz -mul /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz...
fslmaths /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/White-Matter.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/notventricles.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/cortex.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz...
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz -k /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi_snr.txt
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/lowb_brain_mask.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/lowb_brain_mask.nii.gz -ref /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Wed May 24 17:44:30 EDT 2017
dtifit -k /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dwi.nii.gz -m /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvecs -b /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/bvals -o /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit
0 140 0 140 0 92
0 slices processed
1 slices processed
2 slices processed
3 slices processed
4 slices processed
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91 slices processed
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_FA.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_FA.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_L1.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_L1.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_L2.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_L2.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_L3.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_L3.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_MD.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_MD.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_MO.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_MO.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/dtifit_S0.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/mni/dtifit_S0.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD/surfaces//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
#-------------------------------------
#@# Priors Wed May 24 17:44:55 EDT 2017

New invocation of trac-all

Thu May 25 13:21:22 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-bedp -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   58083088   74167020        188     717936   52857056
-/+ buffers/cache:    4508096  127742012
Swap:     32767996      28428   32739568

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/05/25-17:21:22-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri
subjectdir is /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
Queuing post processing stage

Type /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri.bedpostX/monitor to show progress.
Type /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri.bedpostX/cancel to terminate all the queued tasks.

You will get an email at the end of the post-processing stage.

New invocation of trac-all

Thu Jun  1 13:52:27 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-path -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   31081612  101168496        188     734524   25945148
-/+ buffers/cache:    4401940  127848168
Swap:     32767996      28376   32739620

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/01-17:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/01-17:52:28-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-paths

ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   31082616  101167492        188     734524   25945156
-/+ buffers/cache:    4402936  127847172
Swap:     32767996      28376   32739620

New invocation of trac-all

Thu Jun  1 13:54:37 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-path -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   31129772  101120336        188     734548   26033592
-/+ buffers/cache:    4361632  127888476
Swap:     32767996      28376   32739620

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/01-17:54:37-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-19.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-paths

ksimon
compute-0-19.local
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      516513 

             total       used       free     shared    buffers     cached
Mem:     132250108   31130564  101119544        188     734548   26033660
-/+ buffers/cache:    4362356  127887752
Swap:     32767996      28376   32739620

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-paths 
#-------------------------------------
#@# Path reconstruction Thu Jun  1 13:54:37 EDT 2017
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr
/share/apps/freesurfer/6.0.0/bin/dmri_paths --outdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --grad /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --mask /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat --init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt

cwd /home/ksimon
cmdline /share/apps/freesurfer/6.0.0/bin/dmri_paths --outdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --grad /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --mask /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat --init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt 
sysname  Linux
hostname compute-0-19.local
machine  x86_64
user     ksimon
Output directory: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr
DWIs: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Gradients: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
B-values: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
Mask: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
BEDPOST directory: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX
Max number of tracts per voxel: 2
Tract volume fraction threshold: 0.05
Initial control point file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt
End ROI 1: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz
End ROI 2: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz
Neighbor aseg prior: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all
Neighbor aseg label ID list: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all
Neighbor aseg prior set: 14
Local aseg prior: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all
Local aseg label ID list: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all
Local aseg prior set: 15
Segmentation map:  /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz
DWI-to-atlas affine registration: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
Number of burn-in samples: 200
Number of post-burn-in samples: 7500
Keep every: 5-th sample
Update proposal every: 0-th sample
Initial proposal SD file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Loading DWIs from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Loading mask from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX
Loading b-values from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
Loading gradients from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
INFO: Found 8 baseline images (b = 5) out of a total of 72 frames
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Linux compute-0-19.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Thu Jun  1 13:55:29 EDT 2017

New invocation of trac-all

Thu Jun  1 15:49:33 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-path -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-12.local
Linux compute-0-12.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   7340032 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   40217512   25839236        188     183704   17657008
-/+ buffers/cache:   22376800   43679948
Swap:     32767996     191020   32576976

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-19:49:33-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-19:49:33-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-19:49:34-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/01-19:49:34-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-19:49:34-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/01-19:49:34-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/01-19:49:34-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-12.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-paths

ksimon
compute-0-12.local
Linux compute-0-12.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   7340032 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   40053032   26003716        188     183704   17694596
-/+ buffers/cache:   22174732   43882016
Swap:     32767996     191020   32576976

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-paths 
#-------------------------------------
#@# Path reconstruction Thu Jun  1 15:49:34 EDT 2017
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr
/share/apps/freesurfer/6.0.0/bin/dmri_paths --outdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --grad /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --mask /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat --init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt

cwd /home/ksimon
cmdline /share/apps/freesurfer/6.0.0/bin/dmri_paths --outdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --grad /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --mask /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat --init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt 
sysname  Linux
hostname compute-0-12.local
machine  x86_64
user     ksimon
Output directory: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr
DWIs: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Gradients: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
B-values: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
Mask: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
BEDPOST directory: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX
Max number of tracts per voxel: 2
Tract volume fraction threshold: 0.05
Initial control point file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt
End ROI 1: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz
End ROI 2: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz
Neighbor aseg prior: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all
Neighbor aseg label ID list: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all
Neighbor aseg prior set: 14
Local aseg prior: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all
Local aseg label ID list: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all
Local aseg prior set: 15
Segmentation map:  /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz
DWI-to-atlas affine registration: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
Number of burn-in samples: 200
Number of post-burn-in samples: 7500
Keep every: 5-th sample
Update proposal every: 0-th sample
Initial proposal SD file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Loading DWIs from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Loading mask from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX
Loading b-values from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
Loading gradients from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
INFO: Found 8 baseline images (b = 5) out of a total of 72 frames
INFO: Found 422094 voxels in brain mask
INFO: Resolution of DWI space relative to base space is (1, 1, 1)
Loading atlas reference volume from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
niiRead(): error opening file /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
ERROR: Could not read /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
Linux compute-0-12.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Thu Jun  1 15:50:35 EDT 2017

New invocation of trac-all

Fri Jun  2 15:45:42 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-prep -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257189 

             total       used       free     shared    buffers     cached
Mem:      65863332   33109856   32753476        180     321064   31814292
-/+ buffers/cache:     974500   64888832
Swap:      8191996      17412    8174584

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-19:45:44-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-19:45:45-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-19:45:45-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/02-19:45:46-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-19:45:46-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-19:45:46-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/02-19:45:47-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-preproc

ksimon
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257189 

             total       used       free     shared    buffers     cached
Mem:      65863332   33145200   32718132        180     321096   31849480
-/+ buffers/cache:     974624   64888708
Swap:      8191996      17412    8174584

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Fri Jun  2 15:46:02 EDT 2017
mri_convert --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm...
Getting Series No 
INFO: Found 914 files in /data/picsl/mackey_group/BPD/dicoms//BPD0067A
INFO: Scanning for Series Number 14
Scanning Directory 
INFO: found 72 files in series
INFO: loading series header info.

RunNo = 13
WARNING: Run 1 appears to be truncated
  Files Found: 72, Files Expected (lRep+1): 1
FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            1075.9100 1019.7200 -105.5320 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (140 140  92), nframes = 72, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR D13D 
found in dicom tag 18,1020 (len = 4 != 6)
Repetition Time = 3420, TR = 3420 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 0.99891   0.02885  -0.03668   0.86231;
-0.02938   0.99947  -0.01399   0.43169;
 0.03626   0.01506   0.99923   11.70969;
 0.00000   0.00000   0.00000   1.00000;

FileName 		/data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm
Identification
	NumarisVer        syngo MR D13D 
	ScannerModel      Prisma
	PatientName       825656_BPD0067A_359666
Date and time
	StudyDate         20170521
	StudyTime         132535.435000 
	SeriesTime        135432.217000 
	AcqTime           135419.750000 
Acquisition parameters
	PulseSeq          ep_b5#1 
	Protocol          DTI_64dir_7b0_mb4 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          97.8
	InversionTime     -1
	RepetitionTime    3420
	PhEncFOV          210
	ReadoutFOV        210
Image information
	RunNo             13
	SeriesNo          14
	ImageNo           1
	NImageRows        1400
	NImageCols        1400
	NFrames           72
	SliceArraylSize   92
	IsMosaic          1
	ImgPos            104.6823 102.9802 -57.0400 
	VolRes              1.5000   1.5000   1.5000 
	VolDim            140      140       92 
	Vc                 -0.9989   0.0294   0.0363 
	Vr                 -0.0288  -0.9995   0.0151 
	Vs                  0.0367   0.0140   0.9992 
	VolCenter          -0.7012   2.0860  17.2948 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
sagrev = 0, correv =0, trarev = 0
Vs = 0.0366819 0.0139935 0.999229
INFO: no Siemens slice order reversal detected (good!). 
TR=3420.00, TE=97.80, TI=-1.00, flip angle=90.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
mri_probedicom --i /data/picsl/mackey_group/BPD/dicoms//BPD0067A/001_000011_000001.dcm > /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dcminfo.dat
cp /data/picsl/mackey_group/BPD/niftis/BPD0067A/dti.bvec /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.bvecs
cp /data/picsl/mackey_group/BPD/niftis/BPD0067A/dti.bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.bvals
mv -f /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs.tmp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.bvecs
mv -f /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals.tmp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.bvals
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 3.375
mri_convert -oni 140 -onj 140 -onk 92 -oid -0.998911 0.0293779 0.0362588 -ojd 0.0288478 0.99947 -0.0150559 -okd 0.0366819 0.0139935 0.999229 -oc -0.657976 3.58525 17.2722 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 140 -onj 140 -onk 92 -oid -0.998911 0.0293779 0.0362588 -ojd 0.0288478 0.99947 -0.0150559 -okd 0.0366819 0.0139935 0.999229 -oc -0.657976 3.58525 17.2722 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz 
normalizing out_i_direction: (-0.998911, 0.0293779, 0.0362588) -> (-0.998911, 0.0293779, 0.0362588)
normalizing out_j_direction: (0.0288478, 0.99947, -0.0150559) -> (0.0288478, 0.99947, -0.0150559)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz...
TR=3420.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (-0.0288478, -0.99947, 0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz...
INFO: found /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.bvals, copying
INFO: found /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.bvecs, converting to LAS
mv -f /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.bvecs /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
mv -f /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.bvals /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
eddy_correct /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig_las.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz 0
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0000
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0001
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0002
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0003
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0004
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0005
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0006
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0007
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0008
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0009
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0010
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0011
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0012
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0013
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0014
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0015
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0016
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0017
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0018
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0019
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0020
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0021
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0022
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0023
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0024
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0025
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0026
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0027
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0028
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0029
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0030
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0031
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0032
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0033
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0034
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0035
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0036
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0037
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0038
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0039
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0040
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0041
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0042
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0043
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0044
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0045
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0046
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0047
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0048
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0049
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0050
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0051
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0052
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0053
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0054
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0055
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0056
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0057
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0058
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0059
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0060
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0061
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0062
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0063
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0064
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0065
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0066
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0067
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0068
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0069
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0070
processing /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_tmp0071
mv -f /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs.norot
xfmrot /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.ecclog /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs.norot /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
ln -sf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/data.nii.gz
mri_convert --frame 0 1 12 23 36 47 58 71 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 12 23 36 47 58 71 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (0.0288478, 0.99947, -0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
keeping frames 0 1 12 23 36 47 58 71
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz...
mri_concat --i /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz --mean --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 8
Allocing output
Done allocing
nframes = 8
Computing mean across frames
Writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz
bet /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb_brain_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff
#-------------------------------------
#@# Image quality assessment Fri Jun  2 16:04:22 EDT 2017
/share/apps/freesurfer/6.0.0/bin/dmri_motion --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz --mat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.ecclog --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --T 1571.375000 --out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_motion.txt

cwd /home/ksimon
cmdline /share/apps/freesurfer/6.0.0/bin/dmri_motion --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_orig.nii.gz --mat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.ecclog --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --T 1571.375000 --out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_motion.txt 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon
Output motion measure file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/dwi_motion.txt
Input transform file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/dwi.ecclog
Input DWI file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/dwi_orig.nii.gz
Input b-value table: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/bvals
Low-b image intensity threshold: 1571.38
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 72 volumes
Loading DWI volume series from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/dwi_orig.nii.gz
Loading b-value table from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/bvals
Computing within-volume head motion measures
Done in 7.553 sec.
dmri_motion done
#-------------------------------------
#@# Intra-subject registration Fri Jun  2 16:04:30 EDT 2017
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brain.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brain.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brain.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz...
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz...
tkregister2 --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz --targ /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2anat.mat --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2anatorig.dat
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
target  volume /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz
movable volume /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz
reg file       /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2anatorig.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.00000   0.00000  -0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000  -0.00000   1.00000   1.00000;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
 1.00000   0.00000  -0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000  -0.00000   1.00000   1.00000;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
 1.00000  -0.00000   0.00000   0.00000;
-0.00000  -0.00000  -1.00000   0.00000;
 0.00000   1.00000  -0.00000   1.00000;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2anatorig.mat -inverse /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2anat.mat
tmp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558
Log file is /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.log
Fri Jun  2 16:04:32 EDT 2017

setenv SUBJECTS_DIR /data/picsl/mackey_group/BPD
cd /home/ksimon
/share/apps/freesurfer/6.0.0/bin/bbregister --s surfaces/BPD0067A --init-fsl --dti --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --fslmat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat

$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /share/apps/freesurfer/6.0.0
mri_convert /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii
mri_convert.bin /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (0.0288478, 0.99947, -0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii...
fslregister --s surfaces/BPD0067A --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat --niters 1 --maxangle 90 --tmp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov

Log file is /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat.fslregister.log

Fri Jun  2 16:04:45 EDT 2017
--s surfaces/BPD0067A --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat --niters 1 --maxangle 90 --tmp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: fslregister,v 1.40 2016/02/12 21:43:15 zkaufman Exp $
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/home/ksimon
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/refvol.fslregister.nii
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/refvol.fslregister.nii...
--------------------------------------
/home/ksimon
mri_convert /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii --frame 0
mri_convert.bin /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.998911, 0.0293779, 0.0362588)
j_ras = (0.0288478, 0.99947, -0.0150559)
k_ras = (0.0366819, 0.0139935, 0.999229)
keeping frame 0
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii...
Mov determinant is -3.375
/home/ksimon
tkregister2_cmdl --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/reg0.111599.dat --regheader --fslregout /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat.fsl.mat0 --s surfaces/BPD0067A --noedit
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii
reg file       /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/reg0.111599.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.50000   0.00000   0.00000   105.00000;
 0.00000   0.00000   1.50000  -69.00000;
 0.00000  -1.50000   0.00000   105.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 0.99891  -0.02938  -0.03626  -0.38435;
 0.03668   0.01399   0.99923  -5.62213;
-0.02885  -0.99947   0.01506   3.93708;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
 0.99891  -0.02938  -0.03626  -0.38435;
 0.03668   0.01399   0.99923  -5.62213;
-0.02885  -0.99947   0.01506   3.93708;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = surfaces/BPD0067A
RegMat ---------------------------
 0.99891  -0.02938  -0.03626  -0.38435;
 0.03668   0.01399   0.99923  -5.62213;
-0.02885  -0.99947   0.01506   3.93708;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -3.375, ref det = -1
Fri Jun  2 16:04:52 EDT 2017
/home/ksimon
flirt.fsl -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/refvol.fslregister.nii -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/fslmat0.trans.mat -schedule /share/apps/freesurfer/6.0.0/bin/fsl.5.0.2.xyztrans.sch -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat.fsl.mat0
Fri Jun  2 16:05:00 EDT 2017
/home/ksimon
flirt.fsl -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/refvol.fslregister.nii -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat.fsl.mat -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/fslregister/fslmat0.trans.mat -schedule /share/apps/freesurfer/6.0.0/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s surfaces/BPD0067A --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat --fslreg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat.fsl.mat --noedit
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.99939  -0.02925  -0.01891   26.75490;
-0.01932  -0.01398  -0.99972   192.78999;
 0.02897   0.99947  -0.01453   23.97390;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii
reg file       /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
INFO: loading target /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii
Tmov: --------------------
-1.50000   0.00000   0.00000   105.00000;
 0.00000   0.00000   1.50000  -69.00000;
 0.00000  -1.50000   0.00000   105.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -3.375, ref det = -1
---- Input registration matrix (computed) --------
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;
---------------------------------------
---- Input registration matrix --------
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = surfaces/BPD0067A
RegMat ---------------------------
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;
(standard_in) 1: illegal character: P
(standard_in) 1: syntax error
 
Started at Fri Jun 2 16:04:45 EDT 2017 
Ended   at Fri Jun  2 16:05:13 EDT 2017
 
fslregister Done
 
To check results, run:
tkregister2 --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat --surf orig
 
mri_segreg --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --init-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat --out-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /data/picsl/mackey_group/BPD
cd /home/ksimon
mri_segreg --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --init-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat --out-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon
movvol /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii
regfile /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.init.dat
subject surfaces/BPD0067A
dof 6
outregfile /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 100
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000100
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1496890441
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;

Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
 0  -25.0 -25.0 -25.0   1.030488
 1  -25.0 -25.0  25.0   1.041796
 2  -25.0  25.0 -25.0   1.058652
 3  -25.0  25.0  25.0   1.014194
 4   25.0 -25.0 -25.0   1.029777
 5   25.0 -25.0  25.0   1.020985
 6   25.0  25.0 -25.0   1.025319
 7   25.0  25.0  25.0   1.071559
REL:  8  0.632523    8.292770  1.036596 rel = 0.610192 
Initial costs ----------------
Number of surface hits 2830
WM  Intensity  2099.6731 +/- 624.1202
Ctx Intensity  2384.4033 +/- 812.5299
Pct Contrast     10.1893 +/-  33.9558
Cost   0.6325
RelCost   0.6102

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0130   1.0130  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9919   0.9919  0.0
     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      0.9758   0.9758  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9544   0.9544  0.0
    10  -4.0000  -4.0000  -4.0000   0.0000  -4.0000   0.0000      0.9468   0.9468  0.0
    36  -4.0000  -4.0000   0.0000   0.0000  -4.0000  -4.0000      0.9376   0.9376  0.0
    63  -4.0000  -4.0000   4.0000   0.0000  -4.0000  -4.0000      0.9217   0.9217  0.0
   111  -4.0000   0.0000   0.0000  -4.0000   0.0000  -4.0000      0.9015   0.9015  0.0
   114  -4.0000   0.0000   0.0000  -4.0000   4.0000  -4.0000      0.8562   0.8562  0.0
   273   0.0000  -4.0000   0.0000  -4.0000   0.0000  -4.0000      0.8493   0.8493  0.0
   274   0.0000  -4.0000   0.0000  -4.0000   0.0000   0.0000      0.8399   0.8399  0.0
   275   0.0000  -4.0000   0.0000  -4.0000   0.0000   4.0000      0.8286   0.8286  0.0
   292   0.0000  -4.0000   0.0000   4.0000   0.0000   0.0000      0.8242   0.8242  0.0
   352   0.0000   0.0000   0.0000  -4.0000  -4.0000   0.0000      0.8164   0.8164  0.0
   354   0.0000   0.0000   0.0000  -4.0000   0.0000  -4.0000      0.7041   0.7041  0.0
   355   0.0000   0.0000   0.0000  -4.0000   0.0000   0.0000      0.4603   0.4603  0.0
Brute Force --------------------------
Min cost was 0.460342
Number of iterations   729
Search time 0.814000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000 -4.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 -4
4 0
5 0
fs_powell::minimize
  nparams 6
  maxfev 36
  ftol   0.000100
  linmin_xtol_   0.001000
  powell nthiter 0: fret = 0.460342
   6  0.382  0.000  0.000 -4.000  0.000  0.000   0.4503623457
   7  0.488  0.000  0.000 -4.000  0.000  0.000   0.4481819818
   9  0.505  0.000  0.000 -4.000  0.000  0.000   0.4478228227
  11  0.527  0.000  0.000 -4.000  0.000  0.000   0.4477052927
  12  0.522  0.000  0.000 -4.000  0.000  0.000   0.4477048904
  15  0.521  0.000  0.000 -4.000  0.000  0.000   0.4477008926
  16  0.519  0.000  0.000 -4.000  0.000  0.000   0.4476979544
  18  0.520  0.000  0.000 -4.000  0.000  0.000   0.4476978542
  23  0.520 -0.618  0.000 -4.000  0.000  0.000   0.4387041388
  31  0.520 -0.608  0.000 -4.000  0.000  0.000   0.4386491695
  35  0.520 -0.608  1.000 -4.000  0.000  0.000   0.4318433972
  39  0.520 -0.608  0.618 -4.000  0.000  0.000   0.4283188727
  40  0.520 -0.608  0.697 -4.000  0.000  0.000   0.4277513315
  41  0.520 -0.608  0.724 -4.000  0.000  0.000   0.4276373319
  43  0.520 -0.608  0.760 -4.000  0.000  0.000   0.4274670667
  44  0.520 -0.608  0.786 -4.000  0.000  0.000   0.4273745874
  46  0.520 -0.608  0.787 -4.000  0.000  0.000   0.4273741094
  49  0.520 -0.608  0.787 -3.000  0.000  0.000   0.3859234384
  54  0.520 -0.608  0.787 -2.982  0.000  0.000   0.3858166663
  55  0.520 -0.608  0.787 -2.891  0.000  0.000   0.3854610930
  56  0.520 -0.608  0.787 -2.696  0.000  0.000   0.3853046571
  58  0.520 -0.608  0.787 -2.669  0.000  0.000   0.3852194326
  61  0.520 -0.608  0.787 -2.660  0.000  0.000   0.3851954465
  62  0.520 -0.608  0.787 -2.655  0.000  0.000   0.3851918781
  63  0.520 -0.608  0.787 -2.654  0.000  0.000   0.3851907252
  65  0.520 -0.608  0.787 -2.650  0.000  0.000   0.3851899220
  66  0.520 -0.608  0.787 -2.651  0.000  0.000   0.3851898483
  73  0.520 -0.608  0.787 -2.651  0.382  0.000   0.3836315622
  74  0.520 -0.608  0.787 -2.651  0.222  0.000   0.3800454301
  83  0.520 -0.608  0.787 -2.651  0.222 -0.618   0.3791830439
  85  0.520 -0.608  0.787 -2.651  0.222 -0.325   0.3744647402
  88  0.520 -0.608  0.787 -2.651  0.222 -0.339   0.3744256129
  powell nthiter 1: fret = 0.374426
  98  0.338 -0.608  0.787 -2.651  0.222 -0.339   0.3726944352
  99  0.354 -0.608  0.787 -2.651  0.222 -0.339   0.3725681962
 100  0.383 -0.608  0.787 -2.651  0.222 -0.339   0.3723403826
 102  0.404 -0.608  0.787 -2.651  0.222 -0.339   0.3722631347
 103  0.406 -0.608  0.787 -2.651  0.222 -0.339   0.3722622875
 104  0.407 -0.608  0.787 -2.651  0.222 -0.339   0.3722617982
 116  0.407 -0.633  0.787 -2.651  0.222 -0.339   0.3721286587
 123  0.407 -0.633  0.169 -2.651  0.222 -0.339   0.3597261592
 125  0.407 -0.633  0.364 -2.651  0.222 -0.339   0.3594666868
 126  0.407 -0.633  0.280 -2.651  0.222 -0.339   0.3582456977
 127  0.407 -0.633  0.271 -2.651  0.222 -0.339   0.3582098867
 128  0.407 -0.633  0.257 -2.651  0.222 -0.339   0.3582047679
 130  0.407 -0.633  0.263 -2.651  0.222 -0.339   0.3581965336
 131  0.407 -0.633  0.264 -2.651  0.222 -0.339   0.3581959706
 133  0.407 -0.633  0.265 -2.651  0.222 -0.339   0.3581958723
 140  0.407 -0.633  0.265 -2.893  0.222 -0.339   0.3521449663
 141  0.407 -0.633  0.265 -2.892  0.222 -0.339   0.3521322432
 142  0.407 -0.633  0.265 -2.852  0.222 -0.339   0.3518342636
 146  0.407 -0.633  0.265 -2.855  0.222 -0.339   0.3518298603
 155  0.407 -0.633  0.265 -2.855  0.258 -0.339   0.3509177158
 156  0.407 -0.633  0.265 -2.855  0.322 -0.339   0.3503983734
 157  0.407 -0.633  0.265 -2.855  0.313 -0.339   0.3502887235
 158  0.407 -0.633  0.265 -2.855  0.301 -0.339   0.3502568410
 159  0.407 -0.633  0.265 -2.855  0.304 -0.339   0.3502535651
 160  0.407 -0.633  0.265 -2.855  0.303 -0.339   0.3502534988
 168  0.407 -0.633  0.265 -2.855  0.303 -0.380   0.3497468822
 170  0.407 -0.633  0.265 -2.855  0.303 -0.428   0.3495399502
 171  0.407 -0.633  0.265 -2.855  0.303 -0.429   0.3495333872
 173  0.407 -0.633  0.265 -2.855  0.303 -0.440   0.3494942248
  powell nthiter 2: fret = 0.349494
 183  0.248 -0.633  0.265 -2.855  0.303 -0.440   0.3479176126
 184  0.278 -0.633  0.265 -2.855  0.303 -0.440   0.3476460272
 185  0.293 -0.633  0.265 -2.855  0.303 -0.440   0.3476144701
 187  0.299 -0.633  0.265 -2.855  0.303 -0.440   0.3476098703
 189  0.324 -0.633  0.265 -2.855  0.303 -0.440   0.3475735395
 190  0.314 -0.633  0.265 -2.855  0.303 -0.440   0.3475661594
 191  0.317 -0.633  0.265 -2.855  0.303 -0.440   0.3475659506
 193  0.316 -0.633  0.265 -2.855  0.303 -0.440   0.3475658977
 200  0.316 -0.523  0.265 -2.855  0.303 -0.440   0.3460904847
 201  0.316 -0.525  0.265 -2.855  0.303 -0.440   0.3460527541
 202  0.316 -0.556  0.265 -2.855  0.303 -0.440   0.3458943936
 204  0.316 -0.546  0.265 -2.855  0.303 -0.440   0.3458585747
 206  0.316 -0.545  0.265 -2.855  0.303 -0.440   0.3458578901
 216  0.316 -0.545  0.305 -2.855  0.303 -0.440   0.3455042667
 217  0.316 -0.545  0.327 -2.855  0.303 -0.440   0.3454915902
 218  0.316 -0.545  0.318 -2.855  0.303 -0.440   0.3454750873
 219  0.316 -0.545  0.317 -2.855  0.303 -0.440   0.3454748921
 228  0.316 -0.545  0.317 -2.876  0.303 -0.440   0.3453336155
 239  0.316 -0.545  0.317 -2.876  0.348 -0.440   0.3451054356
 240  0.316 -0.545  0.317 -2.876  0.342 -0.440   0.3451039470
 241  0.316 -0.545  0.317 -2.876  0.344 -0.440   0.3451034910
 252  0.316 -0.545  0.317 -2.876  0.345 -0.461   0.3450723869
 253  0.316 -0.545  0.317 -2.876  0.345 -0.454   0.3450602663
 254  0.316 -0.545  0.317 -2.876  0.345 -0.453   0.3450597468
 255  0.316 -0.545  0.317 -2.876  0.345 -0.452   0.3450594515
  powell nthiter 3: fret = 0.345059
 267  0.291 -0.545  0.317 -2.876  0.345 -0.452   0.3449960229
 269  0.286 -0.545  0.317 -2.876  0.345 -0.452   0.3449950251
 270  0.287 -0.545  0.317 -2.876  0.345 -0.452   0.3449946648
 281  0.287 -0.544  0.317 -2.876  0.345 -0.452   0.3449916170
 282  0.287 -0.542  0.317 -2.876  0.345 -0.452   0.3449915183
 292  0.287 -0.542  0.338 -2.876  0.345 -0.452   0.3448964416
 293  0.287 -0.542  0.333 -2.876  0.345 -0.452   0.3448939371
 305  0.287 -0.542  0.333 -2.875  0.345 -0.452   0.3448936654
 315  0.287 -0.542  0.333 -2.875  0.342 -0.452   0.3448804786
 316  0.287 -0.542  0.333 -2.875  0.334 -0.452   0.3448572855
 318  0.287 -0.542  0.333 -2.875  0.333 -0.452   0.3448562948
 319  0.287 -0.542  0.333 -2.875  0.332 -0.452   0.3448560469
 320  0.287 -0.542  0.333 -2.875  0.331 -0.452   0.3448558272
 329  0.287 -0.542  0.333 -2.875  0.331 -0.454   0.3448488205
 331  0.287 -0.542  0.333 -2.875  0.331 -0.468   0.3448156409
 332  0.287 -0.542  0.333 -2.875  0.331 -0.469   0.3448153320
 334  0.259 -0.538  0.350 -2.874  0.316 -0.486   0.3447411738
 340  0.270 -0.540  0.343 -2.874  0.322 -0.480   0.3447168733
 341  0.267 -0.539  0.345 -2.874  0.320 -0.481   0.3447157082
 342  0.268 -0.540  0.345 -2.874  0.321 -0.481   0.3447156507
 343  0.267 -0.539  0.345 -2.874  0.321 -0.481   0.3447155441
 344  0.267 -0.539  0.345 -2.874  0.321 -0.481   0.3447154998
  powell nthiter 4: fret = 0.344716
 357  0.263 -0.539  0.345 -2.874  0.321 -0.481   0.3447030074
 359  0.262 -0.539  0.345 -2.874  0.321 -0.481   0.3447014764
 368  0.262 -0.525  0.345 -2.874  0.321 -0.481   0.3446041203
 369  0.262 -0.516  0.345 -2.874  0.321 -0.481   0.3445716776
 371  0.262 -0.514  0.345 -2.874  0.321 -0.481   0.3445671887
 373  0.262 -0.512  0.345 -2.874  0.321 -0.481   0.3445651740
 374  0.262 -0.511  0.345 -2.874  0.321 -0.481   0.3445649912
 384  0.262 -0.511  0.345 -2.874  0.321 -0.510   0.3444097122
 385  0.262 -0.511  0.345 -2.874  0.321 -0.507   0.3444005134
 386  0.262 -0.511  0.345 -2.874  0.321 -0.504   0.3443997341
 388  0.262 -0.511  0.345 -2.874  0.321 -0.505   0.3443996220
 408  0.262 -0.511  0.345 -2.874  0.326 -0.505   0.3443876652
 416  0.251 -0.510  0.351 -2.873  0.321 -0.512   0.3443483564
 418  0.254 -0.510  0.349 -2.874  0.322 -0.510   0.3443410934
 419  0.254 -0.510  0.350 -2.874  0.322 -0.510   0.3443409416
 424  0.254 -0.510  0.350 -2.874  0.322 -0.510   0.3443408754
  powell nthiter 5: fret = 0.344341
 438  0.250 -0.510  0.350 -2.874  0.322 -0.510   0.3443332149
 439  0.249 -0.510  0.350 -2.874  0.322 -0.510   0.3443331265
 449  0.249 -0.505  0.350 -2.874  0.322 -0.510   0.3443326281
 450  0.249 -0.507  0.350 -2.874  0.322 -0.510   0.3443275661
 451  0.249 -0.508  0.350 -2.874  0.322 -0.510   0.3443265705
 460  0.249 -0.508  0.350 -2.874  0.322 -0.507   0.3443258823
 462  0.249 -0.508  0.350 -2.874  0.322 -0.508   0.3443255047
 472  0.249 -0.508  0.350 -2.878  0.322 -0.508   0.3443206126
 474  0.249 -0.508  0.350 -2.877  0.322 -0.508   0.3443201413
 475  0.249 -0.508  0.350 -2.876  0.322 -0.508   0.3443198599
 485  0.249 -0.508  0.350 -2.876  0.328 -0.508   0.3443155843
 486  0.249 -0.508  0.350 -2.876  0.326 -0.508   0.3443133669
 496  0.251 -0.508  0.349 -2.876  0.326 -0.507   0.3443123848
 499  0.250 -0.508  0.349 -2.876  0.326 -0.507   0.3443123247
 500  0.251 -0.508  0.349 -2.876  0.326 -0.507   0.3443122576
Powell done niters = 5
Computing relative cost
 0  -25.0 -25.0 -25.0   1.056450
 1  -25.0 -25.0  25.0   1.018935
 2  -25.0  25.0 -25.0   1.066527
 3  -25.0  25.0  25.0   1.023565
 4   25.0 -25.0 -25.0   1.028076
 5   25.0 -25.0  25.0   1.020587
 6   25.0  25.0 -25.0   1.011766
 7   25.0  25.0  25.0   1.071534
REL:  8  0.344312    8.297440  1.037180 rel = 0.33197 
Number of iterations     5
Min cost was 0.344312
Number of FunctionCalls   501
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 0.560000 sec
Parameters at optimum (transmm)  0.25050 -0.50842  0.34885
Parameters at optimum (rotdeg) -2.87594  0.32624 -0.50719 
Final costs ----------------
Number of surface hits 2830
WM  Intensity  1945.1389 +/- 565.7964
Ctx Intensity  2410.6197 +/- 772.3697
Pct Contrast     19.0085 +/-  30.1341
Cost   0.3443
RelCost   0.6102
Reg at min cost was 
 0.99932  -0.03522  -0.01086  -0.24567;
 0.00857  -0.06435   0.99789  -7.99476;
-0.03585  -0.99731  -0.06401   3.81550;
 0.00000   0.00000   0.00000   1.00000;

Writing optimal reg to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat, type = 14 
Original Reg 
 0.99939  -0.02897  -0.01932  -0.44962;
 0.01891  -0.01453   0.99972  -7.65481;
-0.02925  -0.99948  -0.01398   3.08396;
 0.00000   0.00000   0.00000   1.00000;

Original Reg - Optimal Reg
 0.00007   0.00625  -0.00847  -0.20395;
 0.01034   0.04982   0.00183   0.33995;
 0.00660  -0.00217   0.05003  -0.73153;
 0.00000   0.00000   0.00000   0.00000;

Computing change in lh position
LH rmsDiffMean 2.274471
Computing change in rh position
Surface-RMS-Diff-mm 2.233650 0.885490 4.513099
mri_segreg done
mri_segreg --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --init-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat --out-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /data/picsl/mackey_group/BPD
cd /home/ksimon
mri_segreg --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii --init-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat --out-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon
movvol /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/template.nii
regfile /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/tmp.bbregister.111558/bbr.pass1.dat
subject surfaces/BPD0067A
dof 6
outregfile /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat
UseMask 0
UseLH 1
UseRH 1
nsubsamp 1
PenaltySign  -1
PenaltySlope 0.500000
PenaltyCenter 0.000000
surfname white
GMProjFrac 0.500000
WMProjAbs 2.000000
lhcostfile (null)
rhcostfile (null)
interp  trilinear (1)
frame  0
TolPowell 0.000000
nMaxItersPowell 36
n1dmin  3
Profile   0
Gdiag_no  -1
AddNoise  0 (0)
SynthSeed 1496551262
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.99932  -0.03522  -0.01086  -0.24567;
 0.00857  -0.06435   0.99789  -7.99476;
-0.03585  -0.99731  -0.06401   3.81550;
 0.00000   0.00000   0.00000   1.00000;

Loading mov
Extracting frame 0
Projecting LH Surfs
Loading lh.white surf
Loading lh.thickness for GM
GM Proj: 1 0.500000 2.000000
WM Proj: 0 0.500000 2.000000
Projecting RH Surfs
Loading rh.white surf
Loading rh.thickness for GM
Projecting RH Surfs
Using lh.cortex.label
Using rh.cortex.label
Computing relative cost
 0  -25.0 -25.0 -25.0   1.035950
 1  -25.0 -25.0  25.0   1.019012
 2  -25.0  25.0 -25.0   1.039914
 3  -25.0  25.0  25.0   1.016318
 4   25.0 -25.0 -25.0   1.018113
 5   25.0 -25.0  25.0   1.021250
 6   25.0  25.0 -25.0   1.020098
 7   25.0  25.0  25.0   1.060903
REL:  8  0.348651    8.231559  1.028945 rel = 0.338843 
Initial costs ----------------
Number of surface hits 284302
WM  Intensity  1945.6313 +/- 567.8147
Ctx Intensity  2401.5899 +/- 743.6584
Pct Contrast     18.9836 +/-  29.8793
Cost   0.3487
RelCost   0.3388

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.3543   0.3543  0.0
     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.3512   0.3512  0.0
     2  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.3490   0.3490  0.0
     5  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.1000      0.3466   0.3466  0.0
    85  -0.1000   0.0000  -0.1000  -0.1000   0.0000   0.0000      0.3454   0.3454  0.0
   197  -0.1000   0.1000   0.0000  -0.1000   0.1000   0.1000      0.3452   0.3452  0.0
   355   0.0000   0.0000   0.0000  -0.1000   0.0000   0.0000      0.3451   0.3451  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3443   0.3443  0.0
Brute Force --------------------------
Min cost was 0.344312
Number of iterations   729
Search time 0.811000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
fs_powell::minimize
  nparams 6
  maxfev 36
  ftol   0.000000
  linmin_xtol_   0.001000
  powell nthiter 0: fret = 0.348651
   7 -0.163  0.000  0.000  0.000  0.000  0.000   0.3473319131
   8 -0.144  0.000  0.000  0.000  0.000  0.000   0.3472677347
   9 -0.132  0.000  0.000  0.000  0.000  0.000   0.3472482649
  10 -0.124  0.000  0.000  0.000  0.000  0.000   0.3472461832
  11 -0.126  0.000  0.000  0.000  0.000  0.000   0.3472458877
  19 -0.126  0.137  0.000  0.000  0.000  0.000   0.3455951855
  21 -0.126  0.149  0.000  0.000  0.000  0.000   0.3455873880
  23 -0.126  0.146  0.000  0.000  0.000  0.000   0.3455861942
  32 -0.126  0.146 -0.026  0.000  0.000  0.000   0.3455512700
  41 -0.126  0.146 -0.026 -0.050  0.000  0.000   0.3452146545
  42 -0.126  0.146 -0.026 -0.080  0.000  0.000   0.3451707705
  44 -0.126  0.146 -0.026 -0.090  0.000  0.000   0.3451703237
  46 -0.126  0.146 -0.026 -0.085  0.000  0.000   0.3451690267
  56 -0.126  0.146 -0.026 -0.085  0.014  0.000   0.3451571311
  58 -0.126  0.146 -0.026 -0.085  0.015  0.000   0.3451570697
  66 -0.126  0.146 -0.026 -0.085  0.015  0.058   0.3450178559
  68 -0.126  0.146 -0.026 -0.085  0.015  0.069   0.3450128236
  70 -0.126  0.146 -0.026 -0.085  0.015  0.073   0.3450121685
  powell nthiter 1: fret = 0.345012
  81 -0.123  0.146 -0.026 -0.085  0.015  0.073   0.3450110642
  82 -0.122  0.146 -0.026 -0.085  0.015  0.073   0.3450110353
  90 -0.122  0.104 -0.026 -0.085  0.015  0.073   0.3449908999
  91 -0.122  0.123 -0.026 -0.085  0.015  0.073   0.3449475176
  92 -0.122  0.124 -0.026 -0.085  0.015  0.073   0.3449472959
 100 -0.122  0.124 -0.015 -0.085  0.015  0.073   0.3449412418
 101 -0.122  0.124 -0.014 -0.085  0.015  0.073   0.3449411679
 110 -0.122  0.124 -0.014 -0.080  0.015  0.073   0.3449345106
 111 -0.122  0.124 -0.014 -0.076  0.015  0.073   0.3449336226
 112 -0.122  0.124 -0.014 -0.077  0.015  0.073   0.3449335032
 113 -0.122  0.124 -0.014 -0.078  0.015  0.073   0.3449333321
 121 -0.122  0.124 -0.014 -0.078  0.017  0.073   0.3449314121
 122 -0.122  0.124 -0.014 -0.078  0.022  0.073   0.3449309506
 124 -0.122  0.124 -0.014 -0.078  0.020  0.073   0.3449307337
 132 -0.122  0.124 -0.014 -0.078  0.020  0.067   0.3449277545
  powell nthiter 2: fret = 0.344928
 152 -0.122  0.123 -0.014 -0.078  0.020  0.067   0.3449272980
 153 -0.122  0.122 -0.014 -0.078  0.020  0.067   0.3449272185
 171 -0.122  0.122 -0.014 -0.076  0.020  0.067   0.3449269063
 173 -0.122  0.122 -0.014 -0.077  0.020  0.067   0.3449268393
  powell nthiter 3: fret = 0.344927
Powell done niters = 3
Computing relative cost
 0  -25.0 -25.0 -25.0   1.036336
 1  -25.0 -25.0  25.0   1.016882
 2  -25.0  25.0 -25.0   1.039153
 3  -25.0  25.0  25.0   1.015118
 4   25.0 -25.0 -25.0   1.018326
 5   25.0 -25.0  25.0   1.021311
 6   25.0  25.0 -25.0   1.019585
 7   25.0  25.0  25.0   1.062072
REL:  8  0.344927    8.228782  1.028598 rel = 0.335337 
Number of iterations     3
Min cost was 0.344927
Number of FunctionCalls   245
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 16.261000 sec
Parameters at optimum (transmm) -0.12195  0.12172 -0.01413
Parameters at optimum (rotdeg) -0.07710  0.02017  0.06694 
Final costs ----------------
Number of surface hits 284302
WM  Intensity  1946.1155 +/- 565.7939
Ctx Intensity  2402.4475 +/- 738.8626
Pct Contrast     19.0318 +/-  29.6346
Cost   0.3449
RelCost   0.3388
Reg at min cost was 
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;

Writing optimal reg to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat, type = 14 
Original Reg 
 0.99932  -0.03522  -0.01086  -0.24567;
 0.00857  -0.06435   0.99789  -7.99476;
-0.03585  -0.99731  -0.06401   3.81550;
 0.00000   0.00000   0.00000   1.00000;

Original Reg - Optimal Reg
 0.00002   0.00027   0.00119   0.11127;
-0.00112   0.00138   0.00010  -0.12658;
 0.00036  -0.00010   0.00134   0.00329;
 0.00000   0.00000   0.00000   0.00000;

Computing change in lh position
LH rmsDiffMean 0.170767
Computing change in rh position
Surface-RMS-Diff-mm 0.193013 0.042866 0.277485
mri_segreg done
MinCost: 0.344927 1946.115540 2402.447482 19.031843 
tkregister2_cmdl --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat
tkregister_tcl /share/apps/freesurfer/6.0.0/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
reg file       /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;
float2int = 0
---------------------------------------
INFO: loading target /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/orig.mgz
Ttarg: --------------------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
INFO: loading movable /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Tmov: --------------------
-1.50000   0.00000   0.00000   105.00000;
 0.00000   0.00000   1.50000  -69.00000;
 0.00000  -1.50000   0.00000   105.00000;
 0.00000   0.00000   0.00000   1.00000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;
Determinant 1
subject = surfaces/BPD0067A
RegMat ---------------------------
 0.99930  -0.03550  -0.01205  -0.35694;
 0.00969  -0.06574   0.99779  -7.86818;
-0.03621  -0.99721  -0.06535   3.81220;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -3.375, ref det = -1
Cleaning up
 
Started at Fri Jun 2 16:04:32 EDT 2017 
Ended   at Fri Jun  2 16:05:54 EDT 2017
BBR-Run-Time-Sec 81
 
bbregister Done
To check results, run:
tkregisterfv --mov /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.dat --surfs 
 
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.mat -inverse /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -concat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2diff.bbr.mat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2anat.bbr.mat -inverse /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat
#-------------------------------------
#@# Inter-subject registration Fri Jun  2 16:05:54 EDT 2017
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_mni.nii.gz -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/mni2anat.mat -inverse /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat -concat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/mni2diff.bbr.mat -inverse /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2mni.mat -concat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/mni2anatorig.mat -inverse /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks Fri Jun  2 16:07:25 EDT 2017
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz
Binarizing based on matching values
nMatch 5
 0     2
 1     7
 2    41
 3    46
 4    77
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 504761 values in range
Counting number of voxels in first frame
Found 504761 voxels in final mask
Count: 504761 504761.000000 16777216 3.008610
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz
Binarizing based on matching values
nMatch 8
 0     2
 1     7
 2    41
 3    46
 4    77
 5    28
 6    60
 7    16
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 534965 values in range
Counting number of voxels in first frame
Found 534965 voxels in final mask
Count: 534965 534965.000000 16777216 3.188640
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
 0     4
 1    43
binval        0
binvalnot     1
fstart = 0, fend = 0, nframes = 1
Found 12097 values in range
Counting number of voxels in first frame
Found 12097 voxels in final mask
Count: 12097 12097.000000 16777216 0.072104
mri_binarize done
mri_aparc2aseg --s surfaces/BPD0067A --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /data/picsl/mackey_group/BPD
subject surfaces/BPD0067A
outvol /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
useribbon 0
baseoffset 0
labeling wm
labeling hypo-intensities as wm
dmaxctx 2.000000
RipUnknown 0

Reading lh white surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/lh.white

Reading lh pial surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/lh.pial

Loading lh annotations from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/rh.white

Reading rh pial surface 
 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/surf/rh.pial

Loading rh annotations from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/ribbon.mgz
Loading filled from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/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 /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 979063
Used brute-force search on 0 voxels
Fixing Parahip LH WM
  Found 9 clusters
     0 k 1.000000
     1 k 2.000000
     2 k 3.000000
     3 k 1.000000
     4 k 2.000000
     5 k 2.000000
     6 k 2.000000
     7 k 1.000000
     8 k 692.000000
Fixing Parahip RH WM
  Found 5 clusters
     0 k 2.000000
     1 k 766.000000
     2 k 2.000000
     3 k 1.000000
     4 k 1.000000
Writing output aseg to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min        1000
max        2999
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 501678 values in range
Counting number of voxels in first frame
Found 501678 voxels in final mask
Count: 501678 501678.000000 16777216 2.990234
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min        1000
max        4999
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 798545 values in range
Counting number of voxels in first frame
Found 798545 voxels in final mask
Count: 798545 798545.000000 16777216 4.759699
mri_binarize done
mri_binarize --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 16 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/ksimon
cmdline mri_binarize.bin --i /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz --match 16 --o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon

input      /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
 0    16
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 22059 values in range
Counting number of voxels in first frame
Found 22059 voxels in final mask
Count: 22059 22059.000000 16777216 0.131482
mri_binarize done
fslmaths /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz -add /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/Brain-Stem.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/brainmask.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz...
fslmaths /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz -mul /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert.bin /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD/surfaces/BPD0067A/mri/aparc+aseg.mgz...
TR=2530.00, TE=3.11, TI=1250.00, flip angle=7.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz...
fslmaths /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/White-Matter.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/White-Matter++.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/White-Matter++.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/notventricles.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/notventricles.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/notventricles.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/cortex.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/cortex+2mm+bs.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/cortex+2mm+bs.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg+2mm.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/aparc+aseg_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/aparc+aseg_mask.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
orientLAS /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
mri_convert -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz
mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 1.86265e-09 3.72529e-09 -ojd 0 1 1.04774e-09 -okd 3.72529e-09 -9.31323e-10 1 -oc -1.36173 -0.417114 12.7276 -rt nearest /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/anat_brain_mask-vent.nii.gz...
TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 1.86265e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 9.31323e-10, -1)
k_ras = (0, 1, 1.04774e-09)
Reslicing using nearest 
writing to /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz...
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/lowb.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz -k /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi_snr.txt
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lowb_brain_mask.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lowb_brain_mask.nii.gz -ref /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/brain_anat_orig.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Fri Jun  2 16:11:07 EDT 2017
dtifit -k /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz -m /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs -b /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals -o /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit
0 140 0 140 0 92
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91 slices processed
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_FA.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_FA.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_L1.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_L1.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_L2.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_L2.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_L3.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_L3.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_MD.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_MD.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_MO.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_MO.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
flirt -in /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dtifit_S0.nii.gz -ref /share/apps/fsl/5.0.8/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/mni/dtifit_S0.bbr.nii.gz -applyxfm -init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
#-------------------------------------
#@# Priors Fri Jun  2 16:11:25 EDT 2017

New invocation of trac-all

Fri Jun  2 16:15:14 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-bedp -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-0-17.local
Linux compute-0-17.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257945 

             total       used       free     shared    buffers     cached
Mem:      66056748   40137744   25919004        188     366068   29661608
-/+ buffers/cache:   10110068   55946680
Swap:     32767996      30548   32737448

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-20:15:14-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-20:15:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-20:15:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/02-20:15:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-20:15:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/02-20:15:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/02-20:15:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-0-17.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri
subjectdir is /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
Queuing post processing stage

Type /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri.bedpostX/monitor to show progress.
Type /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri.bedpostX/cancel to terminate all the queued tasks.

You will get an email at the end of the post-processing stage.

New invocation of trac-all

Sat Jun  3 11:10:15 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-path -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257189 

             total       used       free     shared    buffers     cached
Mem:      65863332    8412696   57450636        180     338944    7132816
-/+ buffers/cache:     940936   64922396
Swap:      8191996      17360    8174636

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/03-15:10:15-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-paths

ksimon
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257189 

             total       used       free     shared    buffers     cached
Mem:      65863332    8413568   57449764        180     338944    7132816
-/+ buffers/cache:     941808   64921524
Swap:      8191996      17360    8174636

New invocation of trac-all

Sat Jun  3 11:11:10 EDT 2017
/home/ksimon
/share/apps/freesurfer/6.0.0/bin/trac-all
-path -c /data/picsl/mackey_group/BPD/scripts/config.txt
Subject surfaces/BPD0067A
SUBJECTS_DIR /data/picsl/mackey_group/BPD
FREESURFER_HOME /share/apps/freesurfer/6.0.0
Actual FREESURFER_HOME /share/apps/freesurfer/6.0.0
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
ksimon
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257189 

             total       used       free     shared    buffers     cached
Mem:      65863332    8413108   57450224        180     338976    7132964
-/+ buffers/cache:     941168   64922164
Swap:      8191996      17360    8174636

########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2017/06/03-15:11:10-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: ksimon  Machine: compute-gpu-0.local  Platform: Linux  PlatformVersion: 2.6.32-642.15.1.el6.x86_64  CompilerName: GCC  CompilerVersion: 40400 

New invocation of trac-paths

ksimon
compute-gpu-0.local
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    125000 kbytes
coredumpsize 400 kbytes
memoryuse    unlimited
vmemoryuse   3072000 kbytes
descriptors  1024 
memorylocked 64 kbytes
maxproc      257189 

             total       used       free     shared    buffers     cached
Mem:      65863332    8413932   57449400        180     338976    7132964
-/+ buffers/cache:     941992   64921340
Swap:      8191996      17360    8174636

#-------------------------------------
/share/apps/freesurfer/6.0.0/bin/trac-paths 
#-------------------------------------
#@# Path reconstruction Sat Jun  3 11:11:10 EDT 2017
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr
rm -rf /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr
/share/apps/freesurfer/6.0.0/bin/dmri_paths --outdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --grad /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --mask /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat --init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt

cwd /home/ksimon
cmdline /share/apps/freesurfer/6.0.0/bin/dmri_paths --outdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr --dwi /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz --grad /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs --bval /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals --mask /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz --bpdir /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX --ntr 2 --fmin 0.05 --roi1 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz --roi2 /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz --reg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat --init /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt --nprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all --lprior /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all --seg /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 --sdp /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt 
sysname  Linux
hostname compute-gpu-0.local
machine  x86_64
user     ksimon
Output directory: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cst_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ilf_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.unc_AS_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fmajor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/fminor_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.atr_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.cab_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.ccg_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slfp_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/lh.slft_PP_avg33_mni_bbr /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dpath/rh.slft_PP_avg33_mni_bbr
DWIs: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Gradients: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
B-values: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
Mask: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
BEDPOST directory: /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX
Max number of tracts per voxel: 2
Tract volume fraction threshold: 0.05
Initial control point file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt
End ROI 1: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz
End ROI 2: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz
Neighbor aseg prior: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all
Neighbor aseg label ID list: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsnnids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsnnids_all
Neighbor aseg prior set: 14
Local aseg prior: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsprior_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsprior_all
Local aseg label ID list: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cst_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.unc_AS_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fmajor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/fminor_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.atr_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.cab_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.ccg_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slfp_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/lh.slft_PP_avg33_mni_bbr_fsids_all /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/rh.slft_PP_avg33_mni_bbr_fsids_all
Local aseg prior set: 15
Segmentation map:  /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/mni/aparc+aseg.nii.gz
DWI-to-atlas affine registration: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dmri/xfms/diff2mni.bbr.mat
Number of burn-in samples: 200
Number of post-burn-in samples: 7500
Keep every: 5-th sample
Update proposal every: 0-th sample
Initial proposal SD file: /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.cab_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.ccg_PP_avg33_mni_bbr_cpts_4_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt /data/picsl/mackey_group/BPD/surfaces/BPD0067A/dlabel/diff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt
Loading DWIs from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/dwi.nii.gz
Loading mask from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
Loading BEDPOST parameter samples from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri.bedpostX
Loading b-values from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvals
Loading gradients from /data/picsl/mackey_group/BPD//surfaces/BPD0067A/dmri/bvecs
INFO: Found 8 baseline images (b = 5) out of a total of 72 frames
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Linux compute-gpu-0.local 2.6.32-642.15.1.el6.x86_64 #1 SMP Fri Feb 24 14:31:22 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

trac-paths exited with ERRORS at Sat Jun  3 11:11:49 EDT 2017