Hi Matt,
Thank you very much!! Could you please elaborate on what you mean by fMRI timeseries not having isotropic organisation? (I'm not smoothing fMRI timeseries, but am curious what this means.)
All the best,
Luke.
On 11/07/2019, 00:53, "FSL - FMRIB's Software Library on behalf of Glasser, Matthew" <[log in to unmask] on behalf of [log in to unmask]> wrote:
1) Smooth brain masked image.
2) Smooth brain mask.
3) Divide smoothed brain mask image by smoothed brain mask
4) Remask the result.
This sort of thing works well for doing stuff like computing 3D intensity bias fields from particular tissue classes. Obviously you wouldn't want to smooth things in 3D that don't have isotropic organization in 3D space like fMRI timeseries.
Matt.
On 7/10/19, 6:15 PM, "FSL - FMRIB's Software Library on behalf of Luke Baxter" <[log in to unmask] on behalf of [log in to unmask]> wrote:
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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