We had very similar problem when segmenting thin orbital bone. Couple of things that helped:
- Crop and resample your volume to make the structures that you want to segment at least 4-5 voxel wide. Otherwise all the region-growing based method will fail, as due to random noise a few voxels may be missed and your structure may break to parts.
- Apply filtering, which enhances thin structures. We have found that unsharp masking helped.
- If the structure that you need to represent is a surface then instead of a volumetric representation, you may try to reconstruct a surface from points. See this complete example that works in Slicer as is, See also these additional VTK examples: Poisson surface reconstruction, comparison of 3 surface reconstruction methods that are available in VTK. If this approach works well then let me know and I can make a segment editor effect from it.
- You may paint the structure manually on a couple of (non-neighbor) slices and use
Fill between sliceseffect to create a complete segmentation out of it.