Automatic segmentation of the ventricles (brain)

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Hello everyone,

I am currently working on hydrocephalus . I wanted to automatically segment the ventricles (brain) and use the volume statistics for research purposes. I tried MONAI Auto3Dseg and nnUnet but I couldn’t find any specific module for ventricles . Can anyone please help me with this

Thanks in advance

Regards,

Preetham S.D.

Fellow in pediatric neurosurgery, Amrita institute, Kochi,India

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I don’t think there is any model specific to the ventricles, but are probably many brain segmentation models that do provide ventricles as part of the output.

Having said that, I highly encourage you to try the [NNInteractive extension](GitHub - coendevente/SlicerNNInteractive: A 3D Slicer extension for efficient segmentation with nnInteractive.). It is very simple prompt based AI-segmentation tool. It will probably work very well in your case.

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Hi Preetham,

Great research focus, ventricular segmentation in hydrocephalus is a genuinely tricky problem because the enlarged, irregular ventricles fall outside the training distribution of most standard models including the ones you’ve tried. That’s not a user error, it’s a fundamental limitation of those pipelines for this pathology.

Getting volumetric statistics that are accurate and reproducible enough for research purposes requires a more targeted approach.

I work with medical image segmentation and have a clinical background in neurology, so this kind of problem is something I can help with properly. DM me and we can talk through your data and what you need.

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Thanks for your suggestion Muratmaga. I tried NNinteractive. I couldn’t get it working as it required me to do a lot in the terminal. I am a non technical person and have zero coding knowledge. Thanks again for the help.

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Thanks lollypoppink, I will DM you

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If semi-automatic approach is acceptable for you, the you can try the “Grow from seed” in the Segment Editor.

We used that module in one of work studying the ventricle volume in children after hydrocephalus treatment at:

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Thanks Mr.Yi Gao, I had actually gone through your article and found it very interesting. I was probably not very thorough as I was under the impression that you had done automatic segmentation. Thanks for your reply . I will try growing from seeds as you results seem excellent

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let me know if there’s anything i could of help.