Hello FSL experts,
I was wondering if someone could please help me with this registration problem that I seem to be having.
After running single-session FSL and using the rsfMRI as input data and brain extracted T1 image as main structural image, I obtain the results seen in the two screenshots.
It looks like the registration should be the other way around since the brain extracted image (second row) should have the red lines in the first row (which include the cerebellum).
I have used nonlinear registration with 12 DOF in both cases. Do you think the registration hasn't been performed correctly?
I tried to change the main structural image to a non brain extracted one since it seems like the results are the opposite. However, FSL did not let me since it should indeed be the brain extracted image.
Is there something I can do to fix this or is this normal?
Thank you very much.
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