Extract sub-segment from segmentation based on seed and volume (in Python)

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1

Hi everyone,

I’m currently having a segmented image, but now I want to create a new (sub-)segmentation from the segmented image based on an initial seed point (x,y,z) and with a given volume threshold, e.g. max 20 cc. I want to implement it in Python.
Has anyone ever done this or any idea what the easiest way is to do this?
Thanks in advance!

Kylie

2

This is exactly what Fast Marching segment editor effect does. It is provided by SegmentEditorExtraEffects extension.

I don’t think that this is effect can take into account masking during the region growing operation. But you can blank out the volume (set it to a very different intensity) outside the mask before applying Fast Marching.

3

Thank you for the fast reply! I’ll look into it :grinning_face_with_smiling_eyes:

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4

So I’m currently still struggling with it. The situation is that I already have a segmentation result, so I should set the output data of the vtkPichonFastMarching() either with setOutData() or SetOutput(), right? And add the seed point with either addSeed() or addSeedIJK()? So I can then perform the fm.show() operation with the given fraction? Or is there still additional information that I need to provide for the vtkPichonFastMarching?

Thanks in advance!

5

I would recommend to first just use the GUI. Once you confirmed that everything works as expected you can start Python scripting to automate everything.

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