[Insight-users] Filling big 3D holes

[Dawood Masslawi]

Hi Gib,
In addition to what Brian and Richard said, maybe using a different segmentation method
can improve the results altogether since you have no problems with small-diameter vessels
and your problem is with the vessels of large diameter, even when they would have no
holes. You haven't mentioned what segmentation method you use in your preprocessing
step, my suggestion is to incorporate a priori in the segmentation based on a initial
estimation of a binary edge image with its gaps filled (which would be easier than filling the
gaps in a binary image). I think there are two segmentation methods already implemented
in ITK with the ability to incorporate a priori, geodesic active contour with shape guidance
and shape prior level set. Also, the Canny edge detector gives a good estimation of the
edges.
Regards,
Dawood

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On Wed, Feb 2, 2011 at 10:28 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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