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

[Richard Beare]

If the holes are cavities - i.e. not connected to the surface - then
you can fill them with connected component operations - the
binaryattributemorphology package, most of which is in the review part
of ITK, has filters to do hole filling. If you are after a large
closing with a flat structuring element then the
consolidatedMorphology (also in review section) package will give you
quick 3D rectangular options of any size you like. If you really want
spheres then the parabolicMorphology package (latest version at
voxel.jouy.inra.fr/darcs/contrib-itk) has some preliminary code for
fast binary erosions and dilations.

It may be that the best way to go is to start with a connected
operation - region growing or watershed transform from markers - which
won't produce holes in the first place. I've had success in the past
with CT images and watershed and very basic manual marker creation.



2010/1/20 frédéric salvador <frederic.salvador at gmail.com>:
> 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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