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Hi Stefano, You can run tractography with masks in MNI space, as long as you provide the diffusion-> MNI transformations, there is no need to transform the data. If you feel that these transformations are not good enough you should try to improve them rather than applying them to the data (as they will result to imperfectly co-registered data). Do you use a structural image as an intermediate step in the registration, i.e. diffusion->structural->MNI? Have you tried nonlinear registration with FNIRT? Finally, have you corrected for distortions the diffusion images? Large residual distortions can result to misalignments. Cheers Stam On 9 Oct 2013, at 10:23, Stefano wrote: > Hi list, > > I'm running probtrackX for hard segmentation of subcortical structure. > > I'd like to run this command with seed and target masks in MNI space. > > I'm noting some errors in co-registration, and I can not solve them. > > For this reason, I'd like to trasform the data.nii.gz. form diffusion to MNI space. > > After I'd like to run bedpostX directly in MNI space. > > Is it possible? When I run FLIRT I obtained nodif with 1 volume? Where is the other 15? In this way the bedpostX produces empty files. > > Please, give me a responce. > > Thank you very much. > > > Stefano >