Hi Anastasia
Thanks for your quick reply. I’ve changed the command and I got one step
further. Now I get another error:
mv -f
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs
mv: rename
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such
file or directory
Darwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3
21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Mon Aug 25 14:23:03 CEST 2014
Somehow the folder bvecs was not created?
Regards,
Robby
Hi Robby - It looks like in your config file "setbveclist" is one word, instead
of "set bveclist". This may be why you're getting the "Badly placed ()'s."
error at the very beginning of your trac-all output. And it would explain why
it can't find the files.
Hope this helps,
a.y
On Thu, 21 Aug 2014, Robby De Pauw wrote:
Dear FreeSurfer,
When I try to use TRACULA I keep getting the following error:
mv -f
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs
mv: rename
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such
file or directory
after entering the following command:
$ trac-all -prep -c dmrirc.preproc
I tried to specify my bval and bvec in the config file, but that doesn’t seem
to help.
My data was assessed using a Siemens-scanner. Attached you can find the
config-file.
Thank you in advance,
Best regards,
Robby
—————————————
the complete output can be found here:
~/Desktop/SUBJECTS_FS $ trac-all -prep -c dmrirc.preproc
Badly placed ()'s.
INFO: SUBJECTS_DIR is /Users/rdpauw/Desktop/SUBJECTS_FS/T1
INFO: Diffusion root is /Users/rdpauw/Desktop/SUBJECTS_FS/T1
Actual FREESURFER_HOME /Applications/freesurfer
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /Applications/freesurfer
Previous: /apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64
trac-preproc -c
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/dmrirc.local -log
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.log -cmd
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/scripts/trac-all.cmd
#-------------------------------------
/Applications/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Thu Aug 21 15:59:52 CEST 2014
mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz
mri_convert /Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA...
INFO: this looks like a dicom, not an old Siemens .ima file, so I'm going to
unpack it as a dicom.
If this fails, run mri_convert with -it dicom
Getting Series No
INFO: Found 71 files in
/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 4
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName
/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName Sabbe^Linde
Date and time
StudyDate 20140422
StudyTime 164616.578000
SeriesTime 171854.765000
AcqTime 171832.007500
Acquisition parameters
PulseSeq *ep_b0
Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 83
InversionTime -1
RepetitionTime 10800
PhEncFOV 240
ReadoutFOV 240
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 60
IsMosaic 1
ImgPos 961.3685 959.9193 107.7635
VolRes 2.5000 2.5000 2.5000
VolDim 96 96 60
Vc -1.0000 -0.0011 0.0062
Vr 0.0000 -0.9841 -0.1774
Vs 0.0063 -0.1774 0.9841
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: ( 96 96 60), nframes = 65, ismosaic=1
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 10800, TR = 10800 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
/Users/rdpauw/Desktop/SUBJECTS_FS/Diffusion/INP_080_LISA_V_1/1.IMA
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName Sabbe^Linde
Date and time
StudyDate 20140422
StudyTime 164616.578000
SeriesTime 171854.765000
AcqTime 171832.007500
Acquisition parameters
PulseSeq *ep_b0
Protocol DTI64dir_1av_b1200_2.5x2.5x2.5_sfs
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 83
InversionTime -1
RepetitionTime 10800
PhEncFOV 240
ReadoutFOV 240
Image information
RunNo 4
SeriesNo 5
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 60
IsMosaic 1
ImgPos 121.3850 132.3092 -36.0742
VolRes 2.5000 2.5000 2.5000
VolDim 96 96 60
Vc -1.0000 -0.0011 0.0062
Vr 0.0000 -0.9841 -0.1774
Vs 0.0063 -0.1774 0.9841
VolCenter 1.8567 0.7748 17.1866
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = 0.0062587 -0.177391 0.98412
INFO: no Siemens slice order reversal detected (good!).
TR=10800.00, TE=83.00, TI=-1.00, flip angle=90.00
i_ras = (-0.99998, -0.00111026, 0.00615943)
j_ras = (3.52518e-09, -0.98414, -0.177395)
k_ras = (0.0062587, -0.177391, 0.98412)
writing to
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz...
flip4fsl
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 15.625
fslswapdim
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig.nii.gz x -y
z
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.nii.gz
mv -f
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs
mv: rename
/Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/dwi_orig_flip.mghdti.bvecs
to /Users/rdpauw/Desktop/SUBJECTS_FS/T1/INP_080_LISA_V_1/dmri/bvecs: No such
file or directory
Darwin ge24p176.ugent.be 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3
21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64
trac-preproc exited with ERRORS at Thu Aug 21 16:00:45 CEST 2014
Robby De Pauw, dra.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent
robby.dep...@ugent.be
____________________________________
Robby De Pauw, dra.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent
robby.dep...@ugent.be
_______________________________________________
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