Hi again Jesper,
I don't know if you had a chance to look at this, but I found today that if I FLIRT the "inmask" image to the "in" image using the identity matrix and nearest neighbour interpolation, I get (apparently) the same image as "inmask", but FNIRT does not complain about it. So there must be something very subtly different with the headers between the "in" image and the original "inmask" image.
Is there some way that the user can access the header information that FNIRT is checking, given that the output of fslhd does not reveal the problem in this case? I tried AFNI's 3dinfo as well, but the headers also appeared identical based on its output. Or perhaps the requirements of FNIRT for the images to have identical dimensions can be relaxed, to match the requirements of fslmaths?
Thanks again,
Erin
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