[Insight-users] Filling big 3D holes

[Richard Beare]

Hi,
There is a fillholes filter that is part of the binary attribute
morphology contribution. Alternatively, you can build a hole filler
using either connected component labelling or reconstruction
approaches. If you start with your binary image, label the non edge
intensity. Then throw away the label touching the image edge. The
remaining blobs should be the interior or your arteries. Combine these
with the original binary image to fill the holes.

On Thu, Feb 3, 2011 at 2:28 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> 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
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