I am segmenting the skull from a head CT and there are very little slices (ranging form 50-65) with pixel dimensions in the z-direction rangin from 2.5-3.5. I've attached a picture of what my current mesh looks like after applying isosurface to my binary array. I've tried smoothing with the sgolayfilt function in the second dimension as shown in my code below. If anyone has ever encountered this issue before, what did you to address it? I need the smoothing to happen on the mask rather than the image as my segmentation method isn't designed for large datasets in the third dimension.
Code and Image:
for i = 1:size(skull_mask,2)
current_slice_skull = squeeze(double(skull_mask(:,i,:)));
y1 = sgolayfilt(current_slice_skull,3,11);
new_resized_skull(:,i,:) = y1;