Jesper,
Thank you so much for your help!
One question that I still have about FNIRT registration is once I register
the FA (without the rim) to the cropped T1 using fnirt, can I use invwarp to
perform the inverse transformation? In other words, if a mask is drawn on a
T1 and I would like to use fnirt to register it to the dwi space, would the
inverse transform work? From what I understand, DWI and FA images are in the
same space, but would the removal of the rim of the FA image change this?
Sincerely,
Anastasia
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