Hello again.
I dug into the code and could locate the problem (I don't have a solution, though. My coding skills are quite amateurish.) I think the problem somehow lies in the format of my bvecs file.
flip4fsl is not able to read it correctly: ------- if (-e $inbvecs) then echo "INFO: found $inbvecs, converting to FSL format" if $fslflipx then set sign = `echo $inorient | sed "s/[RAS]/+\ /g; s/[LPI]/-\ /g"` endif cp /dev/null $outbvecs foreach j (1 2 3) foreach k (1 2 3) if ($order[$k] == $j) then printf '%s ' `cat $inbvecs | awk -v sgn=$sign[$k]1 -v n=$k '{print sgn*$n}'` \ >> $outbvecs printf '\n' >> $outbvecs endif end end endif -------
I tried awk '{ print $1 }' bvecs (with my original bvecs file) this printed: 0
This has something to do with the file's carriage return. I then produced a new bvecs file by manually typing values into a new text file. Now awk '{ print $1 }' bvecs delivers one column with 33 lines.
Nevertheless, the bvecs output of flip4fsl is weird (full of zeros; 3 x 66; see attachment). I don't really get how this printf & awk command works.
Any comments are very much appreciated. Franz
Am 05.07.2011 um 15:19 schrieb Franz Liem:
Dear Freesurfers.
I am trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries. I checked the dmri/bvals and dmri/bvecs. There seems to be a problem at the -corr stage (-corr alone finishes without error).
My input file is one 4d .nii.gz file (with a total of 33 images, with the first being a b0 image).
(I have attached the files from the dmri folder)
The dmri/bvecs file only contains: 0,0000000 0,0000000 0,0000000
The original bvecs contains 3 columns and 33 lines.
The dmri/bvals seems to be ok (1 column and 33 lines).
eddy_correct processes 33 files (dmri/dwi_tmp0000 ... dmri/dwi_tmp0032).
I am running FSL(4.6.1) and Freesurfer v5.1.0 on Mac (10.6.4) (although the recon was done with 5.0.0, but I guess this not important at this stage, is it?)
My Configuration File:
set dtroot = $SUBJECTS_DIR/DTI set subjlist = (s02x)
set dcmroot = $SUBJECTS_DIR/DTI set dcmlist = (s02x/dti4d.nii.gz)
set bvalfile = /Users/.../DTI/bvals/bvals set bvecfile = /Users/.../DTI/bvals/bvecs set nb0 = 1
set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0
Thanks, Franz
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