I am using a probabilistic mask for my ROI in DTI space but when Ia pply my mask to DTI, it does not fit well. This is the case for several brains.
If I want to repeat the non-linear registration between structural and standard spaces, what options in the fnirt command can I use?
I tried: fnirt --ref=<MNI image> --in=<structural BET image>
But it did not produce the highres2standard_warp images.
My question: what options do I need to add to this fnirt command? Can I use FEAT or MELODIC for this registration without the functional?