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Hi again, > thank you Jesper for your reply, i have just to inform you that i will use the transformation matrix i produced using flirt (12 dof) between the diffusion space and the T1 space as an affine starting guess, but for the other parameters (subsamp, warpre, lambda ...), i want ask if you have an optimised script for such situations (registering diffusion volume of 256x256x56 to T1 256x256x256) > I'm sorry. I didn't read your original message carefully enough. I didn't realise you were registering diffusion to structural within same subject. My bad. In this situation my guess is that your problem is due to the distortions in the diffusion data. The brainstem can often be displaced quite a lot. The remedy for this is to either use a fieldmap (which means you need to have acquired one) or to use something like topup (which again means you must have acquired the right kind of data). Maybe Jon Brooks has some tips on what to do if you haven't acquired any of those as he has worked a lot with the brainstem. Jon? Jesper