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
bvecs
Description: Binary data
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 > > <bvals><bvecs><bvecs.norot><dwi_orig.mghdti.bvals><dwi_orig.mghdti.bvecs>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
