# Anatomical brain segmentation

**URL:** <https://discourse.slicer.org/t/anatomical-brain-segmentation/17778>\
**Category:** Support\
**Tags:** segmentation, brain\
**Created:** [May 24, 2021, 10:49pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778 "2021-05-24T22:49:01Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Miglius\_Mikalauskas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/miglius_mikalauskas/32/11046_2.png) [@Miglius\_Mikalauskas](https://discourse.slicer.org/u/Miglius_Mikalauskas)\
**Post date:** [May 24, 2021, 10:49pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778/1 "2021-05-24T22:49:01Z")

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Hi. Is there a way to automatically segment human brain in mri by anatomical structures?

 ![smegenu anatomija](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/f/ffd1c82cd89d67b40536d73046d4fe3e514dd577.jpeg)  
So that i could automatically see the human brain segmented by either lobes (frontal, temporal etc) or by gyri?  
The photo is from a video in youtube.

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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:** [May 25, 2021, 11:34am UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778/2 "2021-05-25T11:34:04Z")

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We usually suggest you use freesurfer for that:  
[https://surfer.nmr.mgh.harvard.edu/](https://surfer.nmr.mgh.harvard.edu/)

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [May 25, 2021, 11:54am UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778/3 "2021-05-25T11:54:47Z")

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You may also try more modern and faster methods, such as [FastSurfer](https://www.sciencedirect.com/science/article/pii/S1053811920304985). Let us know which one you end up using.

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**Author:** ![Miglius\_Mikalauskas](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/miglius_mikalauskas/32/11046_2.png) [@Miglius\_Mikalauskas](https://discourse.slicer.org/u/Miglius_Mikalauskas)\
**Post date:** [May 25, 2021, 12:17pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778/4 "2021-05-25T12:17:22Z")

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Thank you for your answers. I have tried running FreeSurfer in linux on VirtualBox, but failed. Never heard of FastSurfer. The problem is that I only have access to microsoft windows. Therefore i was wondering whether there is a method suitable for plain microsoft windows.

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [May 26, 2021, 5:05pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778/5 "2021-05-26T17:05:30Z")

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FastSurfer and other modern brain segmentation tools should run fine on any operating systems (because the deep learning frameworks support all operating systems). If FastSurfer does not work well enough for you then you need to do some web searching, there are several other upcoming competitors.

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**Author:** ![dokay1](https://avatars.discourse-cdn.com/v4/letter/d/b4bc9f/32.png) [@dokay1](https://discourse.slicer.org/u/dokay1)\
**Post date:** [July 21, 2022, 3:49pm UTC](https://discourse.slicer.org/t/anatomical-brain-segmentation/17778/6 "2022-07-21T15:49:27Z")

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Depending on the level of detail you need the SAMSEG module of FreeSurfer7+ can do a volume based brain segmentation in 5-10 minutes. It generates WM, GM, basal ganglia, ventricles, etc, and has a pretty high tolerance for surface defects or mass lesions.