I have run my functional data through fmriprep, and I understand that it does not automatically skull strip, and rather provides a mask to do so in further processing.
My question is, if I’m using a standard MNI mask, is that sufficient? Or do i need to apply the fmriprep skull stripping mask first?
Should be okay, but to be sure you should try simply visualizing the mask overlaid the data. You can also just make a consensus mask with all of the MNI masks across subject. nilearn.masking.intersect_masks - Nilearn