[ITK] CT liver segmentation

[Dženan Zukić]

Hi Jan,

that sounds like some silly simple mistake. If you provided a short
compilable example with the accompanying input, somebody will probably be
able to point out the problem.

Regards,
Dženan

On Sun, Dec 27, 2015 at 10:20 AM, Jan Witowski <
jan.witowski at student.uj.edu.pl> wrote:

> 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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