Skull Stripping Nilearn

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Hi All,

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?

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Hi @NordicNarwhal,

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

Best,
Steven

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I have but I’ve gotten some weird results so am trying to figure out what the cause may be.

Thank you!