Hi Jesper,
following up on the FNIRT issue, if I want to FNIRT using the gui, some things are not 100% clear to me.
I understand the instructions on the FEAT site that I feed in my brain extracted T1 (say "T1_bet") as the main structural image and then the MNI space as the template, as I would do when using FLIRT only, since FLIRT is running first in any event. In addition, then, I need to have a non brain extracted T1 ("T1_brain" or "T1_bet_brain"?, first unclear point) in the same directory that my "T1_bet" is in. However, when I do that, I still get an error message from the gui. So I am assuming this is not correct. So, which image do I need to feed in where, which one does need to be brain extracted and how do they need to be called. I guess, part of my confusion stems from, that in the tutorial for BET, the bet-ed images are called "brain".
Thanks a lot! And best regards,
Hannah
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