Liver segmentation from CT

(Marco Festugato) #1

Hi guys, I’m very new to 3D slicer…I have to segment the liver from 199 DICOM images of the same patient…do u have any example I could use to do this? I cant find much on the internet…
Thank u!

(Andras Lasso) #2

Do you mean you have a volume that consists of 199 slices? What is the purpose of the segmentation? What structures you would like to obtain?

To get started, you need to learn anatomy of liver and surrounding tissues and how they appear on CT. You should be able to find anatomic atlases and probably even tutorials for liver contouring on the web. There are also data sets with expert liver segmentation that you can learn from.

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(Marco Festugato) #3

Ty Andras for your kind answer. Yes, I have a volume that consists of 199 dicom slices (axial). My purpose is to segment the liver in these slices and save those 199 slices ONLY with the liver segmented (segmentation doesnt need to be perfect though) in dicom format.

(Marco Festugato) #4

I’ve managed to roughly segment the liver liver

how can i save the original dicom series in order to ‘‘contain’’ only the liver? So, I started with 199 dicom images and now i want 199 dicom images containing only the segmented liver…thanks in advance!

(Andras Lasso) #5

Would you like to blank out voxels outside the segment? You can use Mask Volume effect for that (provided by SegmentEditorExtraEffects extension).

You can then export the masked image as a CT image by right-clicking on the image in Data module and choose DICOM export.

(Marco Festugato) #6

Thank you again Andras for your kind answer. Yes, I want to keep the segmentation in grey levels and then put everything else to 0 (black). Then, I want to save my 199 segmented slices in DICOM format.