# Automatic segmentation of the ventricles (brain)

**URL:** <https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915>\
**Category:** Support\
**Tags:** segmentation, mri, monai-auto3dseg, nnunet\
**Created:** [January 26, 2026, 10:34am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915 "2026-01-26T10:34:44Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![Preetham\_Dange](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/preetham_dange/32/81825_2.png) [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\
**Post date:** [January 26, 2026, 10:34am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/1 "2026-01-26T10:34:45Z")

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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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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [January 27, 2026, 1:50am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/2 "2026-01-27T01:50:39Z")

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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.](https://github.com/coendevente/SlicerNNInteractive)). It is very simple prompt based AI-segmentation tool. It will probably work very well in your case.

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**Author:** ![drnoorfatima](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drnoorfatima/32/81980_2.png) [@drnoorfatima](https://discourse.slicer.org/u/drnoorfatima)\
**Post date:** [February 17, 2026, 9:35am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/3 "2026-02-17T09:35:55Z")

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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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**Author:** ![Preetham\_Dange](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/preetham_dange/32/81825_2.png) [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\
**Post date:** [February 17, 2026, 3:36pm UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/4 "2026-02-17T15:36:47Z")

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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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**Author:** ![Preetham\_Dange](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/preetham_dange/32/81825_2.png) [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\
**Post date:** [February 17, 2026, 3:37pm UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/5 "2026-02-17T15:37:31Z")

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Thanks lollypoppink, I will DM you

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**Author:** ![gaoyi.cn](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/gaoyi.cn/32/1422_2.png) [@gaoyi.cn](https://discourse.slicer.org/u/gaoyi.cn)\
**Post date:** [March 4, 2026, 12:36pm UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/6 "2026-03-04T12:36:46Z")

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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:

> **[Relationship between the volume of ventricles, brain parenchyma and...](https://link.springer.com/article/10.1007/s00381-024-06674-4)**
>
> Purpose The treatment of hydrocephalus aims to facilitate optimal brain development and improve the overall condition of patients. To further evaluate the postoperative recovery process in individuals undergoing hydrocephalus treatment, we...

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**Author:** ![Preetham\_Dange](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/preetham_dange/32/81825_2.png) [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\
**Post date:** [March 5, 2026, 6:06am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/7 "2026-03-05T06:06:47Z")

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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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**Author:** ![gaoyi.cn](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/gaoyi.cn/32/1422_2.png) [@gaoyi.cn](https://discourse.slicer.org/u/gaoyi.cn)\
**Post date:** [March 5, 2026, 8:11am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915/8 "2026-03-05T08:11:07Z")

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