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Reducing jagged appearance of head CT mesh

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Hi Everyone,
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:outside_skull_mesh.png
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;
end

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Accepted Answer

Sean de Wolski
Sean de Wolski on 13 Aug 2019
Look at using smooth3 on the volume first before calling isosurface().

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Katherine Beaulieu
Katherine Beaulieu on 13 Aug 2019
That seems to be working - thanks for the quick response! I've attached a picture of the result with the parameters that worked for my case for anyone looking at this after-the-fact!
W = smooth3(outer_boundary_mask,'box',25);

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