[Insight-users] CT Lung Segmentation: Extract Outer Contours

[frédéric salvador]

Dear all,


So as to segment lungs in CT volume, I implemented the following steps:
   - low-pass smoothing,
   - binary thresolding,
   - connected component analysis,
   - (eventually some objects relabelling).

So now I get a good binary mask of the lung volume.

Though, there are numerous veins and arteries in the lungs volume (appearing
in black in my binary mask) that I would like to fill.

I tried a rolling-ball operator consisting of a morphological closing
followed by a hole filling filter. But as my image is 512*512*605 it takes
too long computation time for my application. Besides, the kernel should be
pretty big so as to fill big holes.

So here comes my question:
Is it possible:
   - to extract the outer surface, by using marching cubes for instance, and
fill inside the surface?
OR
   - to extract and operate on 2D slice to extract the outer contours, by
using some itk or vtk contour filter, and of course fill inside the outer
contours?


I have been struggling a few hours on this, so your help would be highly
appreciated.

Thanks a lot in advance for your answer.

Fred
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