After threshold-based bone segmentation in CT structure filled with holes

Hi all,

I am segmenting the geometries of flatfoot skeleton from a CT scan using Threshold effect.
What is the better way to fill the holes inside the segmented flatfoot skeleton (see picture below)?
Thanks!

You can try dilate and erode same amount (e.g., dilate 5mm and shrink 5mm) each of the segments one by one. This will take care most of the holes inside segments. But for the ones on the surface, you may have to play with your threshold.

There is an excellent extension (that will be available in Slicer within days) to fill holes in cancellous bone: https://github.com/sebastianandress/Slicer-SegmentEditorSRSFilter.

You may also try the approach described in the Skin surface extraction segmentation recipe.