Hi,
Possibly silly question here, but can't figure it out. I'm applying spatial smoothing to a nifti image using fslmaths and the -s flag. However, I'm getting unwanted effects at the boundaries of the brain, I'm presuming because the smoothing is averaging brain voxels with non-brain voxels across the brain boundary. Since these non-brain voxels are all zeros, the smoothing is really dragging down the values at the edges of the brain. Is there a way to limit the spatial smoothing to brain voxels only? I have a mask of the brain regions, so is there a way of providing this info the fslmaths in order to limit the smoothing to within the mask only?
Cheers,
Luke.
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