Dear FSL Experts,
I was trying to use fslmaths to smooth a brain masked epi image and I am running into a problem where the masked image has shrunk. The degree of the shrinking seems to depend on the sigma value I choose, with larger sigma values resulting in more shrinkage.
I think this may be because the epi image I am smoothing has a zero background (e.g. brain masked). If a use a raw epi (unmasked) everything works fine.
Here is an example of the syntax I used:
fslmaths input_epi.nii.gz -kernel gauss 5 -fmean smoothed_epi.nii.gz
Is there a way to resolve this without resulting to smoothing the unmasked image?
Any thoughts?
Many Thanks in Advance,
Evgeny
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