The objective is to generate a surface model from the bone segmentation
It would be useful to know the end goal, as requirements for the generated surface are very different for each clinical application. If you need to generate bone surface models for 3D printing then you want to minimize internal holes, while if you need surface for ultrasound or surface-scan based registration then you want to have good-quality posterior bone surfaces; if work on artificial disk planning then accurate separation of vertebrae is very important, etc. The choice of method also depends on accuracy requirements and available time for performing the segmentation.
Anyway, these tutorials and tips should help in finding a good workflow for your segmentation:
- Fill holes after threshold-based bone segmentation in CT - #2 by lassoan
- Bone segmentation to create 3D-printable STL
- Documentation/Nightly/Training - Slicer Wiki
If you figure out a good workflow or cannot figure out an acceptable solution then let us know.