[ITK] CT liver segmentation

[Jan Witowski]

Hello Dženan,

Thanks for your assistance.
Full code of my example is located here: https://gist.github.com/jwitos/9abe7124e28ce2e31b6e
I’ve also uploaded the DICOMs I’ve been using (30~MB, 152 .dcms inside) if you want to test them out: http://cm-uj.pl/files/cleaned.zip

Best,
Jan

On 27 grudnia 2015 at 17:35:24, Dženan Zukić (dzenanz at gmail.com<mailto:dzenanz at gmail.com>) wrote:

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<mailto: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

_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
http://public.kitware.com/mailman/listinfo/community


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/community/attachments/20151227/182d54f2/attachment.html>