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Hi Looking at the corpus callosum on the coronal, it looks like you need to flip z (z->-z) Looking at the axial section (splenium CC), it looks like you need to flip y (y->-y) These two operations are equivalent to flipping x (x->-x). Cheers, Saad. On 7 Sep 2011, at 10:07, Herve Lemaitre wrote: > Dear FSL users, > > we are using probtrackx to do tractography from a seed located in the corpus callosum. It is working pretty well for the majority of the subjects coming from different sites. But for one site, the tracks are completely wrong as they go in the ventricles. I think it is a problem with the bvec or the orientation of the image but I do not know how to diagnose the problem. > > I checked the dyads1 images after bedpostx and it seems ok for me: > http://hpics.li/0bedff1 > > I checked the transformations from FA to target and from target to FA and they seem ok too. > > You can see the result of the probtrackx on this image: > http://hpics.li/bbf9093 > - FA map in the target space > - fdt_paths in red > - seed in green > > Any ideas on what can cause that and how I can solve this issue? > > Thanks for your help, > > Herve Lemaitre > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad