[Insight-users] Filling big 3D holes

[Gib Bogle]

I'm working with a volume image that was generated by labelling the laminae of 
blood vessels.  My aim is to segment out the vasculature.  There are many 
difficulties, and the particular issue I'm addressing at the moment is filling 
in the vessels.  The intensity of the labelling of the walls is variable, with 
patches that are indistinguishable from background.  The vessel diameters vary 
widely, from about 4 to about 60 voxels.  After some preprocessing I have a 
binary image, on which the ITK hole-filling function works well with the 
small-diameter vessels, but the big vessels present a problem, even when the 
walls are "watertight" (i.e. without holes).

My best idea so far is to send probes out in all 26 directions (all neighbours 
of a voxel) and count the number of probes that hit a wall within a specified 
radius.  It's tricky to specify both the radius and the critical number of hits, 
without getting too many false positives (voxels outside the vessels showing up 
as inside).  (The filter is of course applied iteratively.)

I'm wondering if anyone else here has addressed a similar problem.

Thanks
Gib