 |
 |
Hi Sarah, Could you upload your tar-zipped subject directory that contains your data and bvecs/bvals onto: www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and send the 6-digits ref number? Cheers, Saad. On 1 Sep 2008, at 09:09, Sarah Mang wrote: > 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] > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------