i am trying to set up a bids-compatible data structure. As I understand, bids currently is primarily geared to raw data (unprocessed) - and that is fine since I want to i) have a clean archive and ii) later share it.
My question: I want to deface the T1s right away, but using the https://github.com/poldracklab/pydeface tool cut off part of the brain. After I normalized the T1 into MNI space, it was fine. However, I want to do deface raw data - so normalizing is not good. I could try to just reorient them slightly to coarsely match, but before I spend too much time I thought perhaps sb who has done this before has a recommendation.
Thanks and best, Ralf.
PS: sidequestion: how can I add tags here? It wouldln'd accept the "deface" in the field below.