Hi Anthony,
>
> I am not sure how fnirted_A (output image from fnirt) should look
> like for it appears as a mixture of squares of different
> intensities. It doesn't look like a brain image but does seem to
> cover the shape of a brain.
It is not see easy to interpret fnirted_A, since it is a 4D file of
spline coefficients. If you want to check if fnirt did OK you are
better off looking at what the warped image looks like. You can do
that with
applywarp --ref=MNI152_T1_2mm --in=A --warp=fnirted_A --
out=A_InSpaceOf_MNI
and then use fslview to look at A_InSpaceOf_MNI. If that looks good
fnirt probably did alright.
Good luck Jesper
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