Dear Freesurfer community,
Whenever i try to launch the tracula preprocessing, using "set dob0 = 1 " and
the following command line:
trac-all -prep -no-isrunning -c
'/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config
It stops, giving me errors like these:
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
ERROR: reading
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
While setting "dob0 = 0" everything runs smoothly.
Can you help me please? I'll attach the log + dmrirc (tracula.config)
Best,Elia.
--------------------------------------------------------------------------------------------------------------
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS
Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct
23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
INFO: SUBJECTS_DIR is /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D INFO: Diffusion root is /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D Actual FREESURFER_HOME /home/alberto/Desktop/freesurfer trac-preproc -c /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/dmrirc.local -log /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/trac-all.log -cmd /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/trac-all.cmd -no-isrunning #------------------------------------- /home/alberto/Desktop/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Jun 12 12:07:07 CEST 2014 mri_convert /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000353.dcm /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz mri_convert /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000353.dcm /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000353.dcm... Getting Series No INFO: Found 2245 files in /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1 INFO: Scanning for Series Number 6 Scanning Directory INFO: found 2240 files in series INFO: loading series header info.
RunNo = 5
INFO: sorting.
INFO: (128 128 64), nframes = 35, ismosaic=0
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;
This looks like an MGH DTI volume
DTI is in non-moasic form, so cannot extract bvals/bvects
FileName
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000385.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName 5-001-11-MRDTI-PT-001-T00-000
Date and time
StudyDate 20111223
StudyTime 120731.359000
SeriesTime 124439.515000
AcqTime 123906.902499
Acquisition parameters
PulseSeq ep_b0#0
Protocol DTI 2x2x2 b700 5b0
PhEncDir COL
EchoNo 0
FlipAngle 90
EchoTime 87
InversionTime -1
RepetitionTime 9300
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 5
SeriesNo 6
ImageNo 1
NImageRows 128
NImageCols 128
NFrames 35
SliceArraylSize 64
IsMosaic 0
ImgPos 128.3131 134.4756 -57.2379
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 64
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 -0.0087
Vs -0.0000 -0.0087 1.0000
VolCenter 0.3131 5.9220 5.6427
TransferSyntaxUID 1.2.840.10008.1.2
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=9300.00, TE=87.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 8.67362e-19)
j_ras = (-0, -0.999962, -0.00872654)
k_ras = (-0, -0.00872654, 0.999962)
writing to
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz...
mri_probedicom --i
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000353.dcm
>
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dcminfo.dat
cp /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/bvecs.txt
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.mghdti.bvecs
cp /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/bvals.txt
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.mghdti.bvals
mv -f
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvecs.tmp
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.mghdti.bvecs
mv -f
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvals.tmp
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.mghdti.bvals
flip4fsl
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
fslswapdim
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz
x -y z
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig_flip.nii.gz
INFO: found
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv -f
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig_flip.mghdti.bvecs
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvecs
mv -f
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig_flip.mghdti.bvals
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvals
eddy_correct
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig_flip.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
0
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0000
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0001
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0002
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0003
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0004
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0005
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0006
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0007
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0008
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0009
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0010
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0011
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0012
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0013
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0014
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0015
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0016
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0017
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0018
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0019
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0020
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0021
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0022
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0023
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0024
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0025
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0026
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0027
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0028
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0029
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0030
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0031
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0032
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0033
processing
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_tmp0034
mv -f
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvecs
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvecs.norot
xfmrot
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.ecclog
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvecs.norot
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/bvecs
mv -f
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_eddy.nii.gz
mri_convert
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0mag/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
mri_convert
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0mag/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0mag/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm...
Getting Series No
INFO: Found 85 files in
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0mag/timePoint1
INFO: Scanning for Series Number 3
Scanning Directory
INFO: found 80 files in series
INFO: loading series header info.
RunNo = 2
INFO: sorting.
INFO: ( 64 64 40), nframes = 2, ismosaic=0
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
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0mag/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000245.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName 5-001-11-MRIB0-PT-001-T00-000
Date and time
StudyDate 20111223
StudyTime 120731.359000
SeriesTime 123242.187000
AcqTime 123124.222490
Acquisition parameters
PulseSeq *fm2d2
Protocol gre_field_mapping
PhEncDir COL
EchoNo 0
FlipAngle 55
EchoTime 2.78
InversionTime -1
RepetitionTime 541
PhEncFOV 192
ReadoutFOV 192
Image information
RunNo 2
SeriesNo 3
ImageNo 1
NImageRows 64
NImageCols 64
NFrames 2
SliceArraylSize 40
IsMosaic 0
ImgPos 96.0000 102.1185 -50.1544
VolRes 3.0000 3.0000 3.4500
VolDim 64 64 40
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -0.9963 -0.0854
Vs -0.0000 -0.0854 0.9963
VolCenter 0.0000 0.5755 10.3934
TransferSyntaxUID 1.2.840.10008.1.2
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=541.00, TE=2.78, TI=-1.00, flip angle=55.00
i_ras = (-1, -0, 0)
j_ras = (-0, -0.996345, -0.0854169)
k_ras = (-0, -0.0854169, 0.996345)
writing to
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz...
flip4fsl
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 31.05
fslswapdim
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
x -y z
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
mri_convert
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0phase/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
mri_convert
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0phase/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0phase/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm...
Getting Series No
INFO: Found 85 files in
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0phase/timePoint1
INFO: Scanning for Series Number 3
Scanning Directory
INFO: found 80 files in series
INFO: loading series header info.
RunNo = 2
INFO: sorting.
INFO: ( 64 64 40), nframes = 2, ismosaic=0
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
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0phase/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000245.dcm
Identification
NumarisVer syngo MR 2004A 4VA25A
ScannerModel Allegra
PatientName 5-001-11-MRIB0-PT-001-T00-000
Date and time
StudyDate 20111223
StudyTime 120731.359000
SeriesTime 123242.187000
AcqTime 123124.222490
Acquisition parameters
PulseSeq *fm2d2
Protocol gre_field_mapping
PhEncDir COL
EchoNo 0
FlipAngle 55
EchoTime 2.78
InversionTime -1
RepetitionTime 541
PhEncFOV 192
ReadoutFOV 192
Image information
RunNo 2
SeriesNo 3
ImageNo 1
NImageRows 64
NImageCols 64
NFrames 2
SliceArraylSize 40
IsMosaic 0
ImgPos 96.0000 102.1185 -50.1544
VolRes 3.0000 3.0000 3.4500
VolDim 64 64 40
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -0.9963 -0.0854
Vs -0.0000 -0.0854 0.9963
VolCenter 0.0000 0.5755 10.3934
TransferSyntaxUID 1.2.840.10008.1.2
UseSliceScaleFactor 0 (slice 0: 1)
INFO: no Siemens slice order reversal detected (good!).
TR=541.00, TE=2.78, TI=-1.00, flip angle=55.00
i_ras = (-1, -0, 0)
j_ras = (-0, -0.996345, -0.0854169)
k_ras = (-0, -0.0854169, 0.996345)
writing to
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz...
flip4fsl
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 31.05
fslswapdim
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
x -y z
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
mri_probedicom --i
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/B0phase/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm
>
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0info.dat
fslroi
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_eddy.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/lowb.nii.gz
0 1
epidewarp.fsl --mag
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0mag.nii.gz
--ph
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/b0pha.nii.gz
--exf
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/lowb.nii.gz
--epi
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_eddy.nii.gz
--tediff 2.46000000000000000000 --esp 0.7 --vsm
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/vsm.nii.gz
--epidw
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
FSLVersion 5.0.6
FSLVerMaj 5
FSL Version is 5.0.6, must be 3.X or 4.X
ln -sf
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/data.nii.gz
mri_convert --frame 0
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
mri_convert --frame 0
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz...
mri_convert --frame 1
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame1.nii.gz
mri_convert --frame 1
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame1.nii.gz
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz...
mri_convert --frame 2
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame2.nii.gz
mri_convert --frame 2
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame2.nii.gz
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz...
mri_convert --frame 3
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame3.nii.gz
mri_convert --frame 3
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame3.nii.gz
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz...
mri_convert --frame 4
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame4.nii.gz
mri_convert --frame 4
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame4.nii.gz
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz...
mri_concat --i
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame1.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame2.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame3.nii.gz
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame4.nii.gz
--mean --o
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/lowb.nii.gz
niiRead(): error opening file
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
ninputs = 5
Checking inputs
ERROR: reading
/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz
tracula.config
Description: Binary data
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