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]
>
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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
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