Mon Jul 29 16:17:47 CEST 2013
/data/physics/florian/fs/1020000485074_20080319
/usr/local/freesurfer/bin/trac-all
-prep -c /data/physics/florian/dmrirc.flo_single_1
Subject 1020000485074_20080319
SUBJECTS_DIR /data/physics/florian/fs
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
neurophysics
pu02neu003
Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      192270 
maxlocks     unlimited
maxsignal    192270 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:      24679544   24446236     233308          0     441344   12119440
-/+ buffers/cache:   11885452   12794092
Swap:            0          0          0

########################################
Program versions:
$Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $
mri_convert --all-info 
ProgramName: mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/07/29-14:17:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $  User: neurophysics  Machine: pu02neu003  Platform: Linux  PlatformVersion: 3.5.0-34-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
$Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/07/29-14:17:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS:   User: neurophysics  Machine: pu02neu003  Platform: Linux  PlatformVersion: 3.5.0-34-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/07/29-14:17:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS:   User: neurophysics  Machine: pu02neu003  Platform: Linux  PlatformVersion: 3.5.0-34-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/07/29-14:17:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS:   User: neurophysics  Machine: pu02neu003  Platform: Linux  PlatformVersion: 3.5.0-34-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable5 $  TimeStamp: 2013/07/29-14:17:47-GMT  BuildTimeStamp: May 13 2013 16:24:28  CVS:   User: neurophysics  Machine: pu02neu003  Platform: Linux  PlatformVersion: 3.5.0-34-generic  CompilerName: GCC  CompilerVersion: 40400 


New invocation of trac-preproc


neurophysics
pu02neu003
Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
cputime      unlimited
filesize     unlimited
datasize     unlimited
stacksize    8192 kbytes
coredumpsize 0 kbytes
memoryuse    unlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc      192270 
maxlocks     unlimited
maxsignal    192270 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

             total       used       free     shared    buffers     cached
Mem:      24679544   24467084     212460          0     441344   12119440
-/+ buffers/cache:   11906300   12773244
Swap:            0          0          0

#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc 
#-------------------------------------
#@# Image corrections Mon Jul 29 16:17:47 CEST 2013
mri_convert /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz
mri_convert /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM...
Getting Series No 
INFO: Found 58 files in /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2
INFO: Scanning for Series Number 9
Scanning Directory 
INFO: found 56 files in series
INFO: loading series header info.

RunNo = 8
WARNING: Run 1 appears to be truncated
  Files Found: 56, Files Expected (lRep+1): 8
FileName 		/data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM
Identification
	NumarisVer        syngo MR B15
	ScannerModel      TrioTim 
	PatientName       AAAAAA 
Date and time
	StudyDate         20080319
	StudyTime         093334.578000 
	SeriesTime        100726.484000 
	AcqTime           100548.362500 
Acquisition parameters
	PulseSeq          *ep_b0
	Protocol          ep2d_diff_2b_6d_grpa2 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          81
	InversionTime     -1
	RepetitionTime    4900
	PhEncFOV          240
	ReadoutFOV        240
Image information
	RunNo             8
	SeriesNo          9
	ImageNo           1
	NImageRows        896
	NImageCols        896
	NFrames           56
	SliceArraylSize   40
	IsMosaic          1
	ImgPos            843.6656 853.4301 -62.8985 
	VolRes              1.8750   1.8750   3.0000 
	VolDim            128      128       40 
	Vc                 -0.9996  -0.0017  -0.0295 
	Vr                  0.0000  -0.9983   0.0581 
	Vs                 -0.0295   0.0581   0.9979 
	VolCenter           0.0000   0.0000   0.0000 
	TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128  40), nframes = 56, ismosaic=1
Could not parse NUMARIS version string syngo MR B15
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 4900, TR = 4900 ms
PE Dir COL COL
AutoAlign matrix detected 
AutoAlign Matrix --------------------- 
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

FileName 		/data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM
Identification
	NumarisVer        syngo MR B15
	ScannerModel      TrioTim 
	PatientName       AAAAAA 
Date and time
	StudyDate         20080319
	StudyTime         093334.578000 
	SeriesTime        100726.484000 
	AcqTime           100548.362500 
Acquisition parameters
	PulseSeq          *ep_b0
	Protocol          ep2d_diff_2b_6d_grpa2 
	PhEncDir          COL
	EchoNo            1
	FlipAngle         90
	EchoTime          81
	InversionTime     -1
	RepetitionTime    4900
	PhEncFOV          240
	ReadoutFOV        240
Image information
	RunNo             8
	SeriesNo          9
	ImageNo           1
	NImageRows        896
	NImageCols        896
	NFrames           56
	SliceArraylSize   40
	IsMosaic          1
	ImgPos            123.9795 133.4112 -42.2885 
	VolRes              1.8750   1.8750   3.0000 
	VolDim            128      128       40 
	Vc                 -0.9996  -0.0017  -0.0295 
	Vr                  0.0000  -0.9983   0.0581 
	Vs                 -0.0295   0.0581   0.9979 
	VolCenter           2.2603  16.8925  21.0191 
	TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = -0.029525 0.0580748 0.997876
INFO: no Siemens slice order reversal detected (good!). 
TR=4900.00, TE=81.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (3.5909e-08, -0.998311, 0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz...
mri_probedicom --i /data/physics/florian/20080319_1020000485074__1/ep2d_diff_2b_6d_grpa2/AAAAAA0901030001000100010001.DCM > /data/physics/florian/nii/1020000485074_20080319/dmri/dcminfo.dat
cp /data/physics/florian/nii/1020000485074_20080319/data/1020000485074_20080319_diff_oriented.bvec /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvecs
cp /data/physics/florian/nii/1020000485074_20080319/data/1020000485074_20080319_diff_oriented.bval /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvals
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 10.5469
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz x -y z /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz
mv -f /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.mghdti.bvecs /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs
mv: der Aufruf von stat für »/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.mghdti.bvecs“ ist nicht möglich: Datei oder Verzeichnis nicht gefunden //cannot find file or directory
mv -f /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.mghdti.bvals /data/physics/florian/nii/1020000485074_20080319/dmri/bvals
mv: der Aufruf von stat für »/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.mghdti.bvals“ ist nicht möglich: Datei oder Verzeichnis nicht gefunden //cannot find file or directory
eddy_correct /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz 0
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0000
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0001
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0002
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0003
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0004
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0005
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0006
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0007
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0008
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0009
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0010
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0011
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0012
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0013
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0014
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0015
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0016
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0017
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0018
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0019
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0020
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0021
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0022
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0023
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0024
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0025
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0026
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0027
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0028
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0029
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0030
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0031
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0032
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0033
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0034
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0035
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0036
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0037
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0038
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0039
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0040
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0041
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0042
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0043
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0044
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0045
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0046
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0047
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0048
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0049
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0050
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0051
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0052
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0053
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0054
processing /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_tmp0055
mv -f /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs.norot
mv: der Aufruf von stat für »/data/physics/florian/nii/1020000485074_20080319/dmri/bvecs“ ist nicht möglich: Datei oder Verzeichnis nicht gefunden  //cannot find file or directory
xfmrot /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.ecclog /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs.norot /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs
awk: Kommandozeile:1: Fatal: Die Datei »/data/physics/florian/nii/1020000485074_20080319/dmri/bvecs.norot« kann nicht zum Lesen geöffnet werden (Datei oder Verzeichnis nicht gefunden)  //cannot open file to read, cannot find file or directory
awk: Kommandozeile:1: Fatal: Die Datei »/data/physics/florian/nii/1020000485074_20080319/dmri/bvecs.norot« kann nicht zum Lesen geöffnet werden (Datei oder Verzeichnis nicht gefunden)  //cannot open file to read, cannot find file or directory
ERROR: Gradient file needs to have 3 rows or 3 columns of coordinates
ln -sf /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/data.nii.gz
mri_convert --frame 0 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame0.nii.gz
mri_convert --frame 0 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame0.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 0
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame0.nii.gz...
mri_convert --frame 7 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame7.nii.gz
mri_convert --frame 7 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame7.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 7
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame7.nii.gz...
mri_convert --frame 14 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame14.nii.gz
mri_convert --frame 14 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame14.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 14
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame14.nii.gz...
mri_convert --frame 21 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame21.nii.gz
mri_convert --frame 21 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame21.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 21
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame21.nii.gz...
mri_convert --frame 28 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame28.nii.gz
mri_convert --frame 28 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame28.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 28
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame28.nii.gz...
mri_convert --frame 35 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame35.nii.gz
mri_convert --frame 35 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame35.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 35
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame35.nii.gz...
mri_convert --frame 42 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame42.nii.gz
mri_convert --frame 42 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame42.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 42
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame42.nii.gz...
mri_convert --frame 49 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame49.nii.gz
mri_convert --frame 49 /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame49.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 49
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame49.nii.gz...
mri_concat --i /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame0.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame7.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame14.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame21.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame28.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame35.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame42.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_frame49.nii.gz --mean --o /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz
ninputs = 8
Checking inputs
nframestot = 8
Allocing output
Done allocing
nframes = 8
Computing mean across frames
Writing to /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz
bet /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /data/physics/florian/nii/1020000485074_20080319/dmri/lowb_brain_mask.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/diff
#-------------------------------------
#@# Intra-subject registration Mon Jul 29 16:35:08 CEST 2013
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brain.mgz /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brain.mgz /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/fs/1020000485074_20080319/mri/brain.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.07122e-08, -4.65661e-10)
j_ras = (-9.31323e-10, 5.82077e-11, -1)
k_ras = (1.45138e-08, 1, -5.82077e-11)
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz...
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat.nii.gz
tkregister2 --mov /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz --targ /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2anat.mat --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2anatorig.dat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
target  volume /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat.nii.gz
movable volume /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz
reg file       /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2anatorig.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /data/physics/florian/nii/1020000485074_20080319/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: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz
Tmov: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.000  -0.000  -0.000   0.000;
-0.000   1.000   0.000   0.000;
-0.000   0.000   1.000   1.000;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.000  -0.000  -0.000   0.000;
-0.000   1.000   0.000   0.000;
-0.000   0.000   1.000   1.000;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = subject-unknown
RegMat ---------------------------
 1.000  -0.000  -0.000  -0.000;
 0.000  -0.000  -1.000   0.000;
 0.000   1.000   0.000   1.000;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -1, ref det = -1
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2anatorig.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2anat.mat
Log file is /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.log
Mon Jul 29 16:35:10 CEST 2013

setenv SUBJECTS_DIR /data/physics/florian/fs
cd /data/physics/florian/fs/1020000485074_20080319
/usr/local/freesurfer/bin/bbregister --s 1020000485074_20080319 --init-fsl --dti --mov /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --fslmat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat

$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
mri_convert /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii
mri_convert /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii...
fslregister --s 1020000485074_20080319 --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister --dof 6 --fsvol brainmask.mgz

Log file is /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat.fslregister.log

Mon Jul 29 16:35:16 CEST 2013
--s 1020000485074_20080319 --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister --dof 6 --fsvol brainmask.mgz
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
pu02neu003
Linux pu02neu003 3.5.0-34-generic #55~precise1-Ubuntu SMP Fri Jun 7 16:25:50 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--------------------------------------
/data/physics/florian/fs/1020000485074_20080319
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/refvol.fslregister.nii
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/refvol.fslregister.nii 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.07122e-08, -4.65661e-10)
j_ras = (-9.31323e-10, 5.82077e-11, -1)
k_ras = (1.45138e-08, 1, -5.82077e-11)
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/refvol.fslregister.nii...
--------------------------------------
/data/physics/florian/fs/1020000485074_20080319
mri_convert /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii --frame 0
mri_convert /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii --frame 0 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999564, -0.00171544, -0.0294751)
j_ras = (-3.5909e-08, 0.998311, -0.0581001)
k_ras = (-0.029525, 0.0580748, 0.997876)
keeping frame 0
writing to /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii...
Mov determinant is -10.5469
/data/physics/florian/fs/1020000485074_20080319
tkregister2_cmdl --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/reg0.30841.dat --regheader --fslregout /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat.fsl.mat0 --s 1020000485074_20080319 --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii
reg file       /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/reg0.30841.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /data/physics/florian/fs/1020000485074_20080319/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii
Tmov: --------------------
-1.875   0.000   0.000   120.000;
 0.000   0.000   3.000  -60.000;
 0.000  -1.875   0.000   120.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
 1.000   0.002   0.029   1.940;
-0.030   0.058   0.998  -46.564;
 0.000  -0.998   0.058  -6.142;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 1.000   0.002   0.029   1.940;
-0.030   0.058   0.998  -46.564;
 0.000  -0.998   0.058  -6.142;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = 1020000485074_20080319
RegMat ---------------------------
 1.000   0.002   0.029   1.940;
-0.030   0.058   0.998  -46.564;
 0.000  -0.998   0.058  -6.142;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI 
tkreg2FSL: mov det = -10.5469, ref det = -1
Mon Jul 29 16:35:26 CEST 2013
/data/physics/florian/fs/1020000485074_20080319
flirt.fsl -ref /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/refvol.fslregister.nii -in /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat.fsl.mat0
Mon Jul 29 16:35:42 CEST 2013
/data/physics/florian/fs/1020000485074_20080319
flirt.fsl -ref /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/refvol.fslregister.nii -in /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat.fsl.mat -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch
tkregister2_cmdl --s 1020000485074_20080319 --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat --fslreg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat.fsl.mat --noedit
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
---- FSL registration matrix --------
 0.998  -0.062   0.004   15.806;
 0.009   0.091  -0.996   132.589;
 0.062   0.994   0.091  -6.436;
 0.000   0.000   0.000   1.000;
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii
reg file       /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target /data/physics/florian/fs/1020000485074_20080319/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii
Tmov: --------------------
-1.875   0.000   0.000   120.000;
 0.000   0.000   3.000  -60.000;
 0.000  -1.875   0.000   120.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI 
fsl2TkReg: mov det = -10.5469, ref det = -1
---- Input registration matrix (computed) --------
 0.998  -0.062   0.009  -0.256;
-0.004   0.091   0.996  -42.794;
-0.062  -0.994   0.091  -6.192;
 0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
 0.998  -0.062   0.009  -0.256;
-0.004   0.091   0.996  -42.794;
-0.062  -0.994   0.091  -6.192;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = 1020000485074_20080319
RegMat ---------------------------
 0.998  -0.062   0.009  -0.256;
-0.004   0.091   0.996  -42.794;
-0.062  -0.994   0.091  -6.192;
 0.000   0.000   0.000   1.000;
(standard_in) 1: illegal character: _
(standard_in) 1: syntax error
 
Started at Mon Jul 29 16:35:16 CEST 2013 
Ended   at Mon Jul 29 16:36:13 CEST 2013
 
fslregister Done
 
To check results, run:
tkregister2 --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat --surf orig
 
mri_segreg --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --init-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat --out-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /data/physics/florian/fs
cd /data/physics/florian/fs/1020000485074_20080319
mri_segreg --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --init-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat --out-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/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 pu02neu003
machine  x86_64
user     neurophysics
movvol /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii
regfile /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.init.dat
subject 1020000485074_20080319
dof 6
outregfile /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/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 1375182701
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.998  -0.062   0.009  -0.256;
-0.004   0.091   0.996  -42.794;
-0.062  -0.994   0.091  -6.192;
 0.000   0.000   0.000   1.000;

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
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   1.016056
 1  -25.0 -25.0  25.0   1.056254
 2  -25.0  25.0 -25.0   1.031998
 3  -25.0  25.0  25.0   0.978608
 4   25.0 -25.0 -25.0   1.023124
 5   25.0 -25.0  25.0   0.991830
 6   25.0  25.0 -25.0   1.025478
 7   25.0  25.0  25.0   1.021861
REL:  8  0.352095    8.145208  1.018151 rel = 0.345818 
Initial costs ----------------
Number of surface hits 2851
WM  Intensity   230.3028 +/-  52.2290
Ctx Intensity   285.4129 +/-  77.4484
Pct Contrast     19.7018 +/-  25.2371
Cost   0.3521
RelCost   0.3458

------------------------------------
Brute force preopt -4 4 4, n = 729
     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0101   1.0101  0.0
     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9933   0.9933  0.0
     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      0.9469   0.9469  0.0
     6  -4.0000  -4.0000  -4.0000  -4.0000   4.0000  -4.0000      0.9307   0.9307  0.0
     7  -4.0000  -4.0000  -4.0000  -4.0000   4.0000   0.0000      0.9214   0.9214  0.0
    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8861   0.8861  0.0
    33  -4.0000  -4.0000   0.0000  -4.0000   4.0000  -4.0000      0.8641   0.8641  0.0
    36  -4.0000  -4.0000   0.0000   0.0000  -4.0000  -4.0000      0.8106   0.8106  0.0
   117  -4.0000   0.0000   0.0000   0.0000  -4.0000  -4.0000      0.8102   0.8102  0.0
   120  -4.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.7949   0.7949  0.0
   135  -4.0000   0.0000   4.0000  -4.0000  -4.0000  -4.0000      0.7932   0.7932  0.0
   273   0.0000  -4.0000   0.0000  -4.0000   0.0000  -4.0000      0.7038   0.7038  0.0
   274   0.0000  -4.0000   0.0000  -4.0000   0.0000   0.0000      0.6770   0.6770  0.0
   361   0.0000   0.0000   0.0000   0.0000  -4.0000   0.0000      0.6388   0.6388  0.0
   363   0.0000   0.0000   0.0000   0.0000   0.0000  -4.0000      0.5524   0.5524  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.3521   0.3521  0.0
Brute Force --------------------------
Min cost was 0.352095
Number of iterations   729
Search time 3.297000 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
   8  0.026  0.000  0.000  0.000  0.000  0.000   0.3517391285
  10  0.062  0.000  0.000  0.000  0.000  0.000   0.3514171795
  13  0.061  0.000  0.000  0.000  0.000  0.000   0.3514158609
  17  0.060  0.000  0.000  0.000  0.000  0.000   0.3514157290
  21  0.060 -1.618  0.000  0.000  0.000  0.000   0.3437549856
  22  0.060 -0.861  0.000  0.000  0.000  0.000   0.3098969405
  27  0.060 -0.736  0.000  0.000  0.000  0.000   0.3086304333
  29  0.060 -0.773  0.000  0.000  0.000  0.000   0.3085731376
  31  0.060 -0.757  0.000  0.000  0.000  0.000   0.3084895104
  33  0.060 -0.753  0.000  0.000  0.000  0.000   0.3084886592
  35  0.060 -0.754  0.000  0.000  0.000  0.000   0.3084878444
  38  0.060 -0.754  1.000  0.000  0.000  0.000   0.2909187916
  42  0.060 -0.754  0.618  0.000  0.000  0.000   0.2891661964
  43  0.060 -0.754  0.724  0.000  0.000  0.000   0.2888843421
  45  0.060 -0.754  0.736  0.000  0.000  0.000   0.2888593270
  47  0.060 -0.754  0.775  0.000  0.000  0.000   0.2887694663
  48  0.060 -0.754  0.799  0.000  0.000  0.000   0.2886919698
  54  0.060 -0.754  0.799 -1.618  0.000  0.000   0.2567588000
  55  0.060 -0.754  0.799 -1.138  0.000  0.000   0.2537133667
  58  0.060 -0.754  0.799 -1.321  0.000  0.000   0.2507861058
  60  0.060 -0.754  0.799 -1.286  0.000  0.000   0.2505768888
  62  0.060 -0.754  0.799 -1.294  0.000  0.000   0.2505564550
  70  0.060 -0.754  0.799 -1.294 -0.618  0.000   0.2170934457
  72  0.060 -0.754  0.799 -1.294 -0.791  0.000   0.2146627176
  74  0.060 -0.754  0.799 -1.294 -0.782  0.000   0.2146366979
  76  0.060 -0.754  0.799 -1.294 -0.758  0.000   0.2145553436
  77  0.060 -0.754  0.799 -1.294 -0.743  0.000   0.2145514596
  78  0.060 -0.754  0.799 -1.294 -0.749  0.000   0.2145455729
  85  0.060 -0.754  0.799 -1.294 -0.749 -0.618   0.1984095648
  87  0.060 -0.754  0.799 -1.294 -0.749 -0.566   0.1979268609
  90  0.060 -0.754  0.799 -1.294 -0.749 -0.576   0.1978693603
  92  0.060 -0.754  0.799 -1.294 -0.749 -0.579   0.1978626748
 102  0.110 -0.754  0.799 -1.294 -0.749 -0.579   0.1962734742
 103  0.178 -0.754  0.799 -1.294 -0.749 -0.579   0.1961273772
 105  0.148 -0.754  0.799 -1.294 -0.749 -0.579   0.1958774299
 116  0.148 -0.850  0.799 -1.294 -0.749 -0.579   0.1941877832
 117  0.148 -0.862  0.799 -1.294 -0.749 -0.579   0.1941598499
 120  0.148 -0.863  0.799 -1.294 -0.749 -0.579   0.1941597745
 127  0.148 -0.863  0.919 -1.294 -0.749 -0.579   0.1932016811
 128  0.148 -0.863  0.910 -1.294 -0.749 -0.579   0.1931750502
 129  0.148 -0.863  0.899 -1.294 -0.749 -0.579   0.1931730176
 131  0.148 -0.863  0.904 -1.294 -0.749 -0.579   0.1931678091
 143  0.148 -0.863  0.904 -1.312 -0.749 -0.579   0.1931539615
 144  0.148 -0.863  0.904 -1.304 -0.749 -0.579   0.1931407002
 146  0.148 -0.863  0.904 -1.303 -0.749 -0.579   0.1931405523
 155  0.148 -0.863  0.904 -1.303 -0.772 -0.579   0.1928932790
 158  0.148 -0.863  0.904 -1.303 -0.789 -0.579   0.1928597573
 159  0.148 -0.863  0.904 -1.303 -0.788 -0.579   0.1928593585
 160  0.148 -0.863  0.904 -1.303 -0.787 -0.579   0.1928590006
 163  0.148 -0.863  0.904 -1.303 -0.786 -0.579   0.1928587911
 172  0.148 -0.863  0.904 -1.303 -0.786 -0.622   0.1925105807
 173  0.148 -0.863  0.904 -1.303 -0.786 -0.641   0.1925052286
 174  0.148 -0.863  0.904 -1.303 -0.786 -0.633   0.1924958439
 186  0.152 -0.863  0.904 -1.303 -0.786 -0.633   0.1924950815
 187  0.151 -0.863  0.904 -1.303 -0.786 -0.633   0.1924947492
 199  0.151 -0.845  0.904 -1.303 -0.786 -0.633   0.1923555701
 211  0.151 -0.845  0.901 -1.303 -0.786 -0.633   0.1923545073
 224  0.151 -0.845  0.901 -1.306 -0.786 -0.633   0.1923525921
 233  0.151 -0.845  0.901 -1.306 -0.787 -0.633   0.1923480346
 234  0.151 -0.845  0.901 -1.306 -0.814 -0.633   0.1923413105
 236  0.151 -0.845  0.901 -1.306 -0.802 -0.633   0.1923240081
 237  0.151 -0.845  0.901 -1.306 -0.803 -0.633   0.1923233972
 249  0.151 -0.845  0.901 -1.306 -0.803 -0.641   0.1923193185
 250  0.151 -0.845  0.901 -1.306 -0.803 -0.638   0.1923179454
 262  0.146 -0.845  0.901 -1.306 -0.803 -0.638   0.1923079026
 263  0.144 -0.845  0.901 -1.306 -0.803 -0.638   0.1923071840
 276  0.144 -0.842  0.901 -1.306 -0.803 -0.638   0.1923011322
 277  0.144 -0.841  0.901 -1.306 -0.803 -0.638   0.1923006558
 287  0.144 -0.841  0.906 -1.306 -0.803 -0.638   0.1922918301
 289  0.144 -0.841  0.909 -1.306 -0.803 -0.638   0.1922900609
 290  0.144 -0.841  0.908 -1.306 -0.803 -0.638   0.1922899120
 301  0.144 -0.841  0.908 -1.312 -0.803 -0.638   0.1922827654
 302  0.144 -0.841  0.908 -1.311 -0.803 -0.638   0.1922820482
 312  0.144 -0.841  0.908 -1.311 -0.804 -0.638   0.1922818466
 325  0.144 -0.841  0.908 -1.311 -0.804 -0.639   0.1922816453
 336  0.143 -0.841  0.908 -1.311 -0.804 -0.639   0.1922806019
 337  0.141 -0.841  0.908 -1.311 -0.804 -0.639   0.1922798580
 360  0.141 -0.841  0.907 -1.311 -0.804 -0.639   0.1922797260
 371  0.141 -0.841  0.907 -1.312 -0.804 -0.639   0.1922796376
 381  0.141 -0.841  0.907 -1.312 -0.803 -0.639   0.1922795310
 394  0.141 -0.841  0.907 -1.312 -0.803 -0.638   0.1922793603
Powell done niters = 4
Computing relative cost
 0  -25.0 -25.0 -25.0   1.008197
 1  -25.0 -25.0  25.0   1.040647
 2  -25.0  25.0 -25.0   1.013724
 3  -25.0  25.0  25.0   0.971294
 4   25.0 -25.0 -25.0   1.014794
 5   25.0 -25.0  25.0   0.989281
 6   25.0  25.0 -25.0   1.001577
 7   25.0  25.0  25.0   1.039681
REL:  8  0.192279    8.079195  1.009899 rel = 0.190395 
Number of iterations     4
Min cost was 0.192279
Number of FunctionCalls   396
TolPowell 0.000100
nMaxItersPowell 36
OptimizationTime 2.032000 sec
Parameters at optimum (transmm)  0.14101 -0.84064  0.90749
Parameters at optimum (rotdeg) -1.31205 -0.80316 -0.63848 
Final costs ----------------
Number of surface hits 2851
WM  Intensity   221.3414 +/-  50.2306
Ctx Intensity   283.7556 +/-  68.7123
Pct Contrast     23.7100 +/-  21.9804
Cost   0.1923
RelCost   0.3458
Reg at min cost was 
 0.999  -0.047   0.019  -0.520;
-0.016   0.069   0.998  -43.760;
-0.048  -0.997   0.068  -4.306;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/bbr.pass1.dat, type = 14 
Original Reg 
 0.998  -0.062   0.009  -0.256;
-0.004   0.091   0.996  -42.794;
-0.062  -0.994   0.091  -6.192;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
-0.001  -0.015  -0.010   0.264;
 0.013   0.022  -0.002   0.966;
-0.014   0.003   0.023  -1.886;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 1.249894
Computing change in rh position
Surface RMS Diff (mm) 1.588729 3.420876
mri_segreg done
mri_segreg --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --init-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/bbr.pass1.dat --out-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $
setenv SUBJECTS_DIR /data/physics/florian/fs
cd /data/physics/florian/fs/1020000485074_20080319
mri_segreg --mov /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii --init-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/bbr.pass1.dat --out-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics
movvol /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/template.nii
regfile /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/tmp.bbregister.28999/bbr.pass1.dat
subject 1020000485074_20080319
dof 6
outregfile /data/physics/florian/nii/1020000485074_20080319/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 1375975948
TransRandMax 0.000000
RotRandMax 0.000000
Translations 0.000000 0.000000 0.000000
Rotations   0.000000 0.000000 0.000000
Input reg
 0.999  -0.047   0.019  -0.520;
-0.016   0.069   0.998  -43.760;
-0.048  -0.997   0.068  -4.306;
 0.000   0.000   0.000   1.000;

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
Projecting RH Surfs
Computing relative cost
 0  -25.0 -25.0 -25.0   0.989194
 1  -25.0 -25.0  25.0   1.022331
 2  -25.0  25.0 -25.0   1.004167
 3  -25.0  25.0  25.0   1.004099
 4   25.0 -25.0 -25.0   1.022683
 5   25.0 -25.0  25.0   1.013470
 6   25.0  25.0 -25.0   1.032700
 7   25.0  25.0  25.0   1.029271
REL:  8  0.189212    8.117914  1.014739 rel = 0.186464 
Initial costs ----------------
Number of surface hits 282618
WM  Intensity   221.7666 +/-  53.6626
Ctx Intensity   286.1719 +/-  70.9834
Pct Contrast     24.3679 +/-  22.5488
Cost   0.1892
RelCost   0.1865

------------------------------------
Brute force preopt -0.1 0.1 0.1, n = 729
     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.1996   0.1996  0.0
     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.1994   0.1994  0.0
     2  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.1000      0.1994   0.1994  0.0
     3  -0.1000  -0.1000  -0.1000  -0.1000   0.0000  -0.1000      0.1976   0.1976  0.0
     4  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.0000      0.1964   0.1964  0.0
     7  -0.1000  -0.1000  -0.1000  -0.1000   0.1000   0.0000      0.1963   0.1963  0.0
    11  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.1000      0.1961   0.1961  0.0
    14  -0.1000  -0.1000  -0.1000   0.0000   0.0000   0.1000      0.1959   0.1959  0.0
    19  -0.1000  -0.1000  -0.1000   0.1000  -0.1000   0.0000      0.1956   0.1956  0.0
    20  -0.1000  -0.1000  -0.1000   0.1000  -0.1000   0.1000      0.1948   0.1948  0.0
    35  -0.1000  -0.1000   0.0000  -0.1000   0.1000   0.1000      0.1944   0.1944  0.0
    71  -0.1000  -0.1000   0.1000   0.0000   0.1000   0.1000      0.1935   0.1935  0.0
   361   0.0000   0.0000   0.0000   0.0000  -0.1000   0.0000      0.1934   0.1934  0.0
   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1923   0.1923  0.0
Brute Force --------------------------
Min cost was 0.192279
Number of iterations   729
Search time 2.462000 sec
Parameters at best (transmm, rotdeg)
  0.000   0.000   0.000  0.000  0.000  0.000 
--------------------------------------------

Starting Powell Minimization
Init Powel Params dof = 6
0 0
1 0
2 0
3 0
4 0
5 0
   7 -0.069  0.000  0.000  0.000  0.000  0.000   0.1890082835
  17 -0.069 -0.199  0.000  0.000  0.000  0.000   0.1870176707
  18 -0.069 -0.192  0.000  0.000  0.000  0.000   0.1870080001
  19 -0.069 -0.184  0.000  0.000  0.000  0.000   0.1870063682
  20 -0.069 -0.186  0.000  0.000  0.000  0.000   0.1870058285
  29 -0.069 -0.186  0.129  0.000  0.000  0.000   0.1860621580
  30 -0.069 -0.186  0.128  0.000  0.000  0.000   0.1860596670
  31 -0.069 -0.186  0.118  0.000  0.000  0.000   0.1860547369
  33 -0.069 -0.186  0.119  0.000  0.000  0.000   0.1860546142
  41 -0.069 -0.186  0.119  0.070  0.000  0.000   0.1860523839
  42 -0.069 -0.186  0.119  0.035  0.000  0.000   0.1859824018
  51 -0.069 -0.186  0.119  0.035  0.189  0.000   0.1837879222
  53 -0.069 -0.186  0.119  0.035  0.177  0.000   0.1837780918
  55 -0.069 -0.186  0.119  0.035  0.176  0.000   0.1837779804
  63 -0.069 -0.186  0.119  0.035  0.176 -0.068   0.1837022363
  65 -0.069 -0.186  0.119  0.035  0.176 -0.067   0.1837019786
  66 -0.069 -0.186  0.119  0.035  0.176 -0.063   0.1837012229
  70 -0.069 -0.186  0.119  0.035  0.176 -0.062   0.1837011201
  78 -0.118 -0.186  0.119  0.035  0.176 -0.062   0.1834568021
  79 -0.132 -0.186  0.119  0.035  0.176 -0.062   0.1834356938
  81 -0.136 -0.186  0.119  0.035  0.176 -0.062   0.1834349396
  90 -0.136 -0.168  0.119  0.035  0.176 -0.062   0.1834116931
  92 -0.136 -0.169  0.119  0.035  0.176 -0.062   0.1834116102
 101 -0.136 -0.169  0.072  0.035  0.176 -0.062   0.1833532905
 103 -0.136 -0.169  0.085  0.035  0.176 -0.062   0.1833456969
 104 -0.136 -0.169  0.084  0.035  0.176 -0.062   0.1833456100
 112 -0.136 -0.169  0.084  0.101  0.176 -0.062   0.1833279433
 113 -0.136 -0.169  0.084  0.072  0.176 -0.062   0.1832859421
 114 -0.136 -0.169  0.084  0.071  0.176 -0.062   0.1832855420
 115 -0.136 -0.169  0.084  0.065  0.176 -0.062   0.1832851617
 117 -0.136 -0.169  0.084  0.067  0.176 -0.062   0.1832848932
 125 -0.136 -0.169  0.084  0.067  0.205 -0.062   0.1832307504
 126 -0.136 -0.169  0.084  0.067  0.207 -0.062   0.1832302186
 127 -0.136 -0.169  0.084  0.067  0.208 -0.062   0.1832302112
 137 -0.136 -0.169  0.084  0.067  0.208 -0.058   0.1832298440
 153 -0.147 -0.169  0.084  0.067  0.208 -0.058   0.1832234933
 154 -0.145 -0.169  0.084  0.067  0.208 -0.058   0.1832232199
 155 -0.144 -0.169  0.084  0.067  0.208 -0.058   0.1832231658
 163 -0.144 -0.165  0.084  0.067  0.208 -0.058   0.1832197255
 164 -0.144 -0.161  0.084  0.067  0.208 -0.058   0.1832197206
 166 -0.144 -0.162  0.084  0.067  0.208 -0.058   0.1832195502
 167 -0.144 -0.163  0.084  0.067  0.208 -0.058   0.1832194546
 176 -0.144 -0.163  0.082  0.067  0.208 -0.058   0.1832191918
 185 -0.144 -0.163  0.082  0.082  0.208 -0.058   0.1832080525
 186 -0.144 -0.163  0.082  0.083  0.208 -0.058   0.1832078853
 187 -0.144 -0.163  0.082  0.085  0.208 -0.058   0.1832078376
 197 -0.144 -0.163  0.082  0.085  0.213 -0.058   0.1832069926
 199 -0.144 -0.163  0.082  0.085  0.212 -0.058   0.1832069913
 208 -0.144 -0.163  0.082  0.085  0.212 -0.072   0.1832055322
 209 -0.144 -0.163  0.082  0.085  0.212 -0.067   0.1832050130
 220 -0.151 -0.163  0.082  0.085  0.212 -0.067   0.1832038174
 221 -0.149 -0.163  0.082  0.085  0.212 -0.067   0.1832035188
 230 -0.149 -0.160  0.082  0.085  0.212 -0.067   0.1831993064
 231 -0.149 -0.149  0.082  0.085  0.212 -0.067   0.1831961775
 233 -0.149 -0.152  0.082  0.085  0.212 -0.067   0.1831954893
 244 -0.149 -0.152  0.078  0.085  0.212 -0.067   0.1831946724
 254 -0.149 -0.152  0.078  0.086  0.212 -0.067   0.1831941678
 255 -0.149 -0.152  0.078  0.090  0.212 -0.067   0.1831931876
 276 -0.149 -0.152  0.078  0.090  0.213 -0.072   0.1831923553
 277 -0.149 -0.152  0.078  0.090  0.213 -0.071   0.1831922945
 285 -0.151 -0.148  0.077  0.092  0.213 -0.073   0.1831908587
 286 -0.151 -0.148  0.076  0.092  0.213 -0.073   0.1831907604
 287 -0.151 -0.147  0.076  0.092  0.213 -0.074   0.1831907577
 288 -0.151 -0.147  0.076  0.092  0.213 -0.073   0.1831907558
 289 -0.151 -0.147  0.076  0.092  0.213 -0.073   0.1831907131
 290 -0.151 -0.147  0.076  0.092  0.213 -0.073   0.1831906667
 293 -0.151 -0.147  0.076  0.092  0.213 -0.073   0.1831906385
 302 -0.155 -0.147  0.076  0.092  0.213 -0.073   0.1831897565
 303 -0.156 -0.147  0.076  0.092  0.213 -0.073   0.1831897540
 312 -0.156 -0.147  0.076  0.092  0.213 -0.083   0.1831893758
 313 -0.156 -0.147  0.076  0.092  0.213 -0.079   0.1831888529
 325 -0.156 -0.147  0.077  0.092  0.213 -0.079   0.1831888103
 343 -0.156 -0.147  0.077  0.092  0.212 -0.079   0.1831887119
 351 -0.156 -0.146  0.077  0.093  0.212 -0.079   0.1831884896
 352 -0.156 -0.146  0.077  0.093  0.212 -0.079   0.1831884663
 355 -0.156 -0.146  0.077  0.093  0.212 -0.079   0.1831884634
 369 -0.157 -0.146  0.077  0.093  0.212 -0.079   0.1831884330
 379 -0.157 -0.146  0.077  0.093  0.212 -0.080   0.1831884133
 408 -0.157 -0.146  0.077  0.093  0.211 -0.080   0.1831883556
 417 -0.157 -0.146  0.077  0.093  0.211 -0.080   0.1831883204
 481 -0.157 -0.146  0.077  0.093  0.211 -0.080   0.1831883183
Powell done niters = 6
Computing relative cost
 0  -25.0 -25.0 -25.0   0.988170
 1  -25.0 -25.0  25.0   1.022487
 2  -25.0  25.0 -25.0   1.006132
 3  -25.0  25.0  25.0   1.002057
 4   25.0 -25.0 -25.0   1.022293
 5   25.0 -25.0  25.0   1.013936
 6   25.0  25.0 -25.0   1.033168
 7   25.0  25.0  25.0   1.028554
REL:  8  0.183188    8.116796  1.014600 rel = 0.180552 
Number of iterations     6
Min cost was 0.183188
Number of FunctionCalls   488
TolPowell 0.000000
nMaxItersPowell 36
OptimizationTime 61.206000 sec
Parameters at optimum (transmm) -0.15732 -0.14580  0.07683
Parameters at optimum (rotdeg)  0.09270  0.21076 -0.08045 
Final costs ----------------
Number of surface hits 282618
WM  Intensity   221.2824 +/-  54.0193
Ctx Intensity   285.6875 +/-  69.6304
Pct Contrast     24.5458 +/-  22.3053
Cost   0.1832
RelCost   0.1865
Reg at min cost was 
 0.998  -0.051   0.021  -0.755;
-0.017   0.070   0.997  -43.898;
-0.052  -0.996   0.069  -4.298;
 0.000   0.000   0.000   1.000;

Writing optimal reg to /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat, type = 14 
Original Reg 
 0.999  -0.047   0.019  -0.520;
-0.016   0.069   0.998  -43.760;
-0.048  -0.997   0.068  -4.306;
 0.000   0.000   0.000   1.000;

Original Reg - Optimal Reg
 0.000   0.004  -0.002   0.235;
 0.001  -0.002   0.000   0.138;
 0.004  -0.000  -0.002  -0.008;
 0.000   0.000   0.000   0.000;

Computing change in lh position
LH rmsDiffMean 0.305245
Computing change in rh position
Surface RMS Diff (mm) 0.298596 0.478660
mri_segreg done
tkregister2_cmdl --mov /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat
tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz
reg file       /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat
LoadVol        0
ZeroCRAS       0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
---- Input registration matrix --------
 0.998  -0.051   0.021  -0.755;
-0.017   0.070   0.997  -43.898;
-0.052  -0.996   0.069  -4.298;
 0.000   0.000   0.000   1.000;
float2int = 0
---------------------------------------
INFO: loading target /data/physics/florian/fs/1020000485074_20080319/mri/orig.mgz
Ttarg: --------------------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
INFO: loading movable /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz
Tmov: --------------------
-1.875   0.000   0.000   120.000;
 0.000   0.000   3.000  -60.000;
 0.000  -1.875   0.000   120.000;
 0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0
---- Input registration matrix --------
 0.998  -0.051   0.021  -0.755;
-0.017   0.070   0.997  -43.898;
-0.052  -0.996   0.069  -4.298;
 0.000   0.000   0.000   1.000;
Determinant 1
subject = 1020000485074_20080319
RegMat ---------------------------
 0.998  -0.051   0.021  -0.755;
-0.017   0.070   0.997  -43.898;
-0.052  -0.996   0.069  -4.298;
 0.000   0.000   0.000   1.000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = -10.5469, ref det = -1
Cleaning up
 
Started at Mon Jul 29 16:35:10 CEST 2013 
Ended   at Mon Jul 29 16:37:50 CEST 2013
BBR-Run-Time-Sec 160
 
bbregister Done
To check results, run:
tkregister2 --mov /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.dat --surf
 
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -concat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2diff.bbr.mat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anat.bbr.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat
#-------------------------------------
#@# Inter-subject registration Mon Jul 29 16:37:50 CEST 2013
flirt -in /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_mni.nii.gz -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2anat.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2mni.flt.mat -concat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anat.flt.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2diff.flt.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2mni.flt.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2mni.bbr.mat -concat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2mni.mat -concat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2anatorig.mat -inverse /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anatorig2mni.mat
#-------------------------------------
#@# Masks Mon Jul 29 16:40:46 CEST 2013
mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/physics/florian/fs/1020000485074_20080319
cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics

input      /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/physics/florian/nii/1020000485074_20080319/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
Found 582742 values in range
Counting number of voxels
Found 582742 voxels in final mask
mri_binarize done
mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/physics/florian/fs/1020000485074_20080319
cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics

input      /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/physics/florian/nii/1020000485074_20080319/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
Found 613368 values in range
Counting number of voxels
Found 613368 voxels in final mask
mri_binarize done
mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/physics/florian/fs/1020000485074_20080319
cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics

input      /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz
Binarizing based on matching values
nMatch 2
 0     4
 1    43
binval        0
binvalnot     1
Found 7114 values in range
Counting number of voxels
Found 7114 voxels in final mask
mri_binarize done
mri_aparc2aseg --s 1020000485074_20080319 --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz
SUBJECTS_DIR /data/physics/florian/fs
subject 1020000485074_20080319
outvol /data/physics/florian/nii/1020000485074_20080319/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/physics/florian/fs/1020000485074_20080319/surf/lh.white

Reading lh pial surface 
 /data/physics/florian/fs/1020000485074_20080319/surf/lh.pial

Loading lh annotations from /data/physics/florian/fs/1020000485074_20080319/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /data/physics/florian/fs/1020000485074_20080319/surf/rh.white

Reading rh pial surface 
 /data/physics/florian/fs/1020000485074_20080319/surf/rh.pial

Loading rh annotations from /data/physics/florian/fs/1020000485074_20080319/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /data/physics/florian/fs/1020000485074_20080319/mri/ribbon.mgz
Loading filled from /data/physics/florian/fs/1020000485074_20080319/mri/filled.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/physics/florian/fs/1020000485074_20080319/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000   0.000   0.000   128.000;
 0.000   0.000   1.000  -128.000;
 0.000  -1.000   0.000   128.000;
 0.000   0.000   0.000   1.000;
-------------------------

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19 
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39 
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59 
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99 
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1041158
Used brute-force search on 0 voxels
Fixing Parahip LH WM
  Found 1 clusters
     0 k 1202.000000
Fixing Parahip RH WM
  Found 4 clusters
     0 k 1.000000
     1 k 1.000000
     2 k 1190.000000
     3 k 1.000000
Writing output aseg to /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/physics/florian/fs/1020000485074_20080319
cmdline mri_binarize --i /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics

input      /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz
Binarizing based on threshold
min        1000
max        2999
binval        1
binvalnot     0
Found 483708 values in range
Counting number of voxels
Found 483708 voxels in final mask
mri_binarize done
mri_binarize --i /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/physics/florian/fs/1020000485074_20080319
cmdline mri_binarize --i /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics

input      /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz
frame      0
nErode3d   0
nErode2d   0
output     /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz
Binarizing based on threshold
min        1000
max        4999
binval        1
binvalnot     0
Found 808514 values in range
Counting number of voxels
Found 808514 voxels in final mask
mri_binarize done
mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 16 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz

$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
cwd /data/physics/florian/fs/1020000485074_20080319
cmdline mri_binarize --i /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz --match 16 --o /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics

input      /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz
frame      0
nErode3d   0
nErode2d   0
output     /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz
Binarizing based on matching values
nMatch 1
 0    16
binval        1
binvalnot     0
Found 22404 values in range
Counting number of voxels
Found 22404 voxels in final mask
mri_binarize done
fslmaths /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz -add /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/Brain-Stem.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/fs/1020000485074_20080319/mri/brainmask.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.07122e-08, -4.65661e-10)
j_ras = (-9.31323e-10, 5.82077e-11, -1)
k_ras = (1.45138e-08, 1, -5.82077e-11)
writing to /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz...
fslmaths /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz -mul /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz
mri_convert /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /data/physics/florian/fs/1020000485074_20080319/mri/aparc+aseg.mgz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.07122e-08, -4.65661e-10)
j_ras = (-9.31323e-10, 5.82077e-11, -1)
k_ras = (1.45138e-08, 1, -5.82077e-11)
writing to /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz...
fslmaths /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg_mask.nii.gz
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/White-Matter.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/White-Matter.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/White-Matter++.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/White-Matter++.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/White-Matter++.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/notventricles.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/notventricles.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/notventricles.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/notventricles.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/notventricles.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/notventricles.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/notventricles.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/notventricles.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/notventricles.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/cortex.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/cortex.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/cortex+2mm.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm+bs.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/cortex+2mm+bs.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/cortex+2mm+bs.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg+2mm.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg+2mm.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg_mask.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/aparc+aseg_mask.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/anat_brain_mask.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask-vent.nii.gz /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz
INFO: input image orientation is LIA
INFO: input image determinant is -1
fslswapdim /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/anat_brain_mask-vent.nii.gz x z -y /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz
fslorient -forceradiological /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/anat_brain_mask-vent.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/lowb.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz -k /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_snr.txt
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/lowb_brain_mask.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2mni.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/lowb_brain_mask.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/lowb_brain_mask.flt.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anatorig.flt.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/lowb_brain_mask.nii.gz -ref /data/physics/florian/nii/1020000485074_20080319/dmri/brain_anat_orig.nii.gz -out /data/physics/florian/nii/1020000485074_20080319/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /data/physics/florian/nii/1020000485074_20080319/dmri/nodif_brain_mask.nii.gz
#-------------------------------------
#@# Tensor fit Mon Jul 29 16:50:04 CEST 2013
dtifit -k /data/physics/florian/nii/1020000485074_20080319/dmri/dwi.nii.gz -m /data/physics/florian/nii/1020000485074_20080319/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs -b /data/physics/florian/nii/1020000485074_20080319/dmri/bvals -o /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit
Could not open matrix file /data/physics/florian/nii/1020000485074_20080319/dmri/bvecs
Could not open matrix file /data/physics/florian/nii/1020000485074_20080319/dmri/bvals
Error: bvecs must be either 3xN or Nx3
#-------------------------------------
#@# Priors Mon Jul 29 16:50:04 CEST 2013
/usr/local/freesurfer/bin/dmri_train --outdir /data/physics/florian/nii/1020000485074_20080319/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.1020000485074_20080319.17152.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz --fa /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit_FA.nii.gz --cptdir /data/physics/florian/nii/1020000485074_20080319/dlabel/diff --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat --ncpts 5 --trunc


cwd /data/physics/florian/fs/1020000485074_20080319
cmdline /usr/local/freesurfer/bin/dmri_train --outdir /data/physics/florian/nii/1020000485074_20080319/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.1020000485074_20080319.17152.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz --fa /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit_FA.nii.gz --cptdir /data/physics/florian/nii/1020000485074_20080319/dlabel/diff --reg /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat --ncpts 5 --trunc 
sysname  Linux
hostname pu02neu003
machine  x86_64
user     neurophysics
Output directory: /data/physics/florian/nii/1020000485074_20080319/dlabel/mni
Output directory in test subject's space: /data/physics/florian/nii/1020000485074_20080319/dlabel/diff
Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr
Training subject directory list: /tmp/subj33.1020000485074_20080319.17152.txt
Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk
Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz
Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz
Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz
Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0
Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz
Brain mask for output subject: /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz
FA map for output subject: /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit_FA.nii.gz
Affine registration from atlas to base for output subject: /data/physics/florian/nii/1020000485074_20080319/dmri/xfms/mni2diff.bbr.mat
Number of control points for initial spline: 5
Exclude previously chosen center streamlines: 0
Use truncated streamlines: 1
Loading brain mask of output subject from /data/physics/florian/nii/1020000485074_20080319/dlabel/mni/aparc+aseg_mask.nii.gz
Loading FA map of output subject from /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit_FA.nii.gz
niiRead(): error opening file /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit_FA.nii.gz
ERROR: Could not read /data/physics/florian/nii/1020000485074_20080319/dmri/dtifit_FA.nii.gz
#-------------------------------------
trac-preproc finished without error at Mon Jul 29 16:50:05 CEST 2013
