# Which is the best extension for Brain parcellation?

**URL:** <https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483>\
**Category:** Support\
**Tags:** segmentation, brain\
**Created:** [December 14, 2025, 9:57am UTC](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483 "2025-12-14T09:57:41Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Suhaim](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/suhaim/32/81421_2.png) [@Suhaim](https://discourse.slicer.org/u/Suhaim)\
**Post date:** [December 14, 2025, 9:57am UTC](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483/1 "2025-12-14T09:57:41Z")

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Hi,  
Is there any extension in 3D-Slicer which offers **automated brain segmentation** for parts such as - Amygdala, Hippocampus, Insula etc.? Which extension has the best accuracy?  
I was able to find [SlicerNeuroSegmentation](https://github.com/HOA-2/SlicerNeuroSegmentation/tree/main), but it seems to have a dependency on FreeSurfer and I was wondering if a more stand-alone module exists in 3d-Slicer.  
Thanks!

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [December 14, 2025, 2:49pm UTC](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483/2 "2025-12-14T14:49:58Z")

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I think FreeSurfer with [SlicerFreeSurfer](https://github.com/PerkLab/SlicerFreeSurfer) is your best bet, especially the new [SuperSynth](https://surfer.nmr.mgh.harvard.edu/fswiki/SuperSynth) tool to handle pretty much any brain scan. It’s not integrated directly with Slicer but it’s easy to install and use on it’s own.

Here’s an example applying SuperSynth to the MRHead SampleData that includes a color table to use if loading the nifti file directly.

> **[MRHead-SuperSynth.zip](https://drive.google.com/file/d/11DS7pSSIdOaT9zB0xJ4-kDHzAFuhIssI/view?usp=sharing)**
>
> Google Drive file.

The results look good to me, especially considering this is a scan from over 20 years ago.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/2/b2a090a3898181f248e6b87b1de89f0a3dfd908f.jpeg)

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**Author:** ![Suhaim](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/suhaim/32/81421_2.png) [@Suhaim](https://discourse.slicer.org/u/Suhaim)\
**Post date:** [December 15, 2025, 5:14am UTC](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483/3 "2025-12-15T05:14:55Z")

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Hi @pieper, thanks for the quick reply. I will use this extension and get back to you.  
It seems a standalone extension in 3D-Slicer doesn’t exist as of now for brain parcellation?

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**Author:** ![johny723](https://avatars.discourse-cdn.com/v4/letter/j/7ea924/32.png) [@johny723](https://discourse.slicer.org/u/johny723)\
**Post date:** [June 11, 2026, 9:28pm UTC](https://discourse.slicer.org/t/which-is-the-best-extension-for-brain-parcellation/45483/4 "2026-06-11T21:28:16Z")

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Hi, is there any module to do automatic brain segmentation without the need for writing scripts in python? Like total segmentator? If there is, could someone please make a video or a step by step tutorial for brain segmentation? Thank you. Jan