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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 ---------------------------------------------------------------------------