I would like to 3D print a CT of a skull. The problem is, there are a lot of holes and islands in the scan. Is there any automatic tool to help?

Support
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Other than manually filling the holes with “Paint” and removing the easy islands with “Islands”.

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In this picture you can see the part above the nose (sorry not for using medical terms, I’m not from that field) and in the eye socket. They have a few holes. The actual bone is continuous, so I assume that issue is that the scan is not perfect. I tried playing around with smoothing (fill holes) but I’m looking for something more automatic, if exists. In addition, I want to remove the spine.

Previously, when I wanted to isolate the brain, it was pretty easy with Overview | 3D Slicer segmentation recipes . And when I had an MRI, I was able to get a really good image of just the brain using freesurfer’s recon-all (and even with 3D slicer using SlicerSwissSkullStripper, although with some more manual fixing). Does something somewhat automatic exit for a skull CT?

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It seems that this scan is highly anisotropic and voxel spacing is quite large. You would be able to get smoother surface and less holes if you crop and resample the source volume before you start segmentation.

You can fill holes using SurfaceWrapSolidify extension.

You can also give the NNInteractive extension a try, which should be able to provide a smooth, no-hole segmentation by a few clicks on the skull.

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Thanks!
I tried SurfaceWrapSolidify and it worked relatively well. I want the skull to be empty, but I can later process that. I will have to wait for NNInteractive until I have access to a strong server.