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Hi - you can load in dyads1 (analogous to V1 from dtifit) on FSLView, on top of mean_f1samples (analogous to FA, kind of...) and then change the view options for dyads1 to see the "lines" to check that they look reasonably aligned with the tracts. Cheers. On 31 Mar 2009, at 05:15, Shantanu Majumdar wrote: > Hello, > > I am performing DTI experiments with b=1000 s/mm2 and 30 diffusion > encoding > gradients. The scanner is GE 3T Signa HDx MR scanner. In the post- > processing > stage, I ran 'bedpostx' using gradients from the scanner and finally > 'probtrackx'. I noticed that the tracking results were not correct > for standard > brain structures. While fixing this problem, I found out that my > Nifti dataset > was not in radiological orientation. So, I changed it using the > commands > > fslswapdim input -x y z output > fslorient -swaporient output > > But, I also had to change signs of 'y' values in the 'bvecs' (ie, > y=-y) to get > correct tracking in 'probtrackx'. My questions are: what is the > proper way to > verify the directions in 'bvecs' ? Does 'bedpostx' and 'probtrackx' > assume > certain convention in 'bvecs'? Your suggestions are welcome. > > Thanks in advance. > > Shantanu > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------