Hi Franz, Sorry I just saw your previous email now. The problem could be due to the variable decimal places you've used in your input bvecs file. I've modified your bvecs file from the previous email to 3 decimal places constantly for all the gradient values (See Attached!!). Can you check to see if this solves the problem?
Thanks,
Priti
> 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
>>
>> <bvals><bvecs><bvecs.norot><dwi_orig.mghdti.bvals><dwi_orig.mghdti.bvecs>_______________________________________________
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modified_bvecs
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