Hi, I am having to register a fMRI scan with only a few slices to a full brain structural scan. I have no other scan, just these two. Usually I have more, but for some, I have only these. Registration by usual methods usually get the translation in the z direction (the direction which I only have a few slices) wrong. The method I tried was to use a two stage registration: a 3 dof (translations only) then a limited 2D, 6 dof. Another one I tried but also not so good was to use the schedule which limits only translations in z direction.
I am thinking that by shifting the fMRI images in the z direction a pre-determined distance (known and accurate, in mm) can solve the problem. So the question is which utility of FSL can help me do that?
Best regards.
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