[ITK] CT liver segmentation

[Jan Witowski]

Hello,

I am working with CT abdomen images and trying to segmentate the liver (liver itself, vessels and the HCC tumor). I managed to do it using OsiriX which was rather manual segmentation, and now I am working to do the same using more accurate and semi-automatic algorithms with usage of SimpleITK. I don’t really have much experience with ITK and image manipulation which is why I ask you guys for some help.

Currently, I want to try the watershed method. I loaded my DICOM series, ran the GradientMagnitude filter and proceeded with MorphologicalWatershed (using arg Level=17, value chosen manually). I got pretty nice output image, I guess:
http://jwitowski.com/content/images/2015/12/WSsegmentation-4469-0.jpg

But now, the question is - how do I take that liver out of the image above? My best guess is, I should run a region growing segmentation.
I tried to do that, but - no matter what parameters I choose - I always get the all-black image as an output. The whole image is black. I tried different thresholds and other starting seeds, but… no result.
Here is a gist of my segmentation part:
https://gist.github.com/jwitos/4b953b3ef873fee3965c

I would really appreciate any help or tip


Best,
Jan Witowski
Collegium Medicum Jagiellonian University in Krakow
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