Hi Saad,
thanks for your answer. I did check with fslstats and the range is [0,0]
but my bvals seem fine. bedpostx_datacheck also does not show any
errors. My bvals file looks like this:
0 700 700 700 700 700 700 0 700 700 700 700 700 700 0 700 700 700 700
700 700 ...
A repetition of 40 times 6 dwi images and 1 unweighted image. I also
tried to evaluate the averaged images, because I thought the b=0 in
between the b=700 might cause problems but here also fslstats gives a
range of [0,0].
Any other suggestions?
Sarah
Saad Jbabdi schrieb:
> Hi Sarah,
> DTIFIT works perfectly on single slice data.
>
> I suppose you have checked the range in your output files using
> fslstats -R
> If this range is [0 0], then you it might be a problem with your bvals
> file.
>
> Can you rename your mask file to "nodif_brain_mask.nii" and then run
> bedpostx_datacheck on the directory containing the data/mask/bvecs/bvals?
>
> Saad.
>
>
>
> On 29 Aug 2008, at 13:04, Sarah Mang wrote:
>
>> Hi,
>>
>> I am trying to run dti evaluation of a single slice with DTI fit. I
>> get no errors but all resulting maps (FA, MD, ...) are all zeros.
>>
>> I checked the binary mask and recomputed it with
>> fslmaths <data> -div <data> mask.nii
>> as previously suggested in this list. The mask.nii file is one
>> everywhere.
>>
>> The dtifit protocol looks like this:
>> dtifit --verbose --data=average_data.nii.gz --out=average_spine_dti
>> --mask=mask.nii --bvecs=bvecs --bvals=bvals
>> data file average_data.nii.gz
>> mask file mask.nii
>> bvecs bvecs
>> bvals bvals
>> reading data
>> reading mask
>> ok
>> 0 64 0 32 0 1
>> setting up vols
>> copying input properties to output volumes
>> zeroing output volumes
>> ok
>> Forming A matrix
>> starting the fits
>> 0 slices processed
>>
>> Is it possible that dtifit does not work on single slice data? The
>> slice is tilted. Is that a problem?
>> I would appreciate any suggestions.
>>
>> Cheers,
>> Sarah
>>
>> --
>> Dr. rer. nat. Dipl.-Inform. Sarah Mang
>>
>> Section Exp. MR of the CNS
>> Department of Neuroradiology
>> University of Tuebingen
>> Hoppe-Seyler-Str. 3
>> D-72076 Tuebingen
>>
>> Phone (+49) 7071/29 87753
>> Fax (+49) 7071/294371
>> [log in to unmask]
>>
>
> ---------------------------------------------------------------------------
>
> Saad Jbabdi,
> Postdoctoral Research Assistant,
> Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222545 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad
> ---------------------------------------------------------------------------
>
>
--
Dr. rer. nat. Dipl.-Inform. Sarah Mang
Section Exp. MR of the CNS
Department of Neuroradiology
University of Tuebingen
Hoppe-Seyler-Str. 3
D-72076 Tuebingen
Phone (+49) 7071/29 87753
Fax (+49) 7071/294371
[log in to unmask]
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