# Brain Segmentation in MR

**URL:** <https://discourse.slicer.org/t/brain-segmentation-in-mr/36924>\
**Category:** Support\
**Tags:** segmentation, brain\
**Created:** [June 20, 2024, 7:48pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924 "2024-06-20T19:48:50Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![BDhoth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bdhoth/32/78752_2.png) [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Post date:** [June 20, 2024, 7:48pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/1 "2024-06-20T19:48:50Z")

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Operating system: Windows  
Slicer version:5.6.2  
Expected behavior: I have been trying to get a good brain segmentation for quite a while and have attempted the skull stripping without much success. I have watched several other videos as well, but still can’t get it to look complete or without the face/dura/etc. Any tips for this? Thank you!  
Actual behavior:

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**Author:** ![JASON](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason/32/13419_2.png) [@JASON](https://discourse.slicer.org/u/JASON)\
**Post date:** [July 17, 2024, 4:27am UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/2 "2024-07-17T04:27:42Z")

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@BDhoth Have you tried HDBET? I’ve had success with the 3D Slicer extension on MRI  
[https://extensions.slicer.org/view/HDBrainExtraction/32919/win](https://extensions.slicer.org/view/HDBrainExtraction/32919/win)

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<div class="post-metadata">

**Author:** ![BDhoth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bdhoth/32/78752_2.png) [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Post date:** [July 19, 2024, 1:48pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/3 "2024-07-19T13:48:12Z")

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I have not tried that. I installed it. I really wish there were better instructions of how to use these extensions.

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**Author:** ![JASON](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason/32/13419_2.png) [@JASON](https://discourse.slicer.org/u/JASON)\
**Post date:** [July 19, 2024, 1:55pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/4 "2024-07-19T13:55:01Z")

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HDBET is pretty easy. It asks for input volume that you want to skull strip, and you can set two outputs for the new stripped volume and the new  
brain mask segmentation. Set both of these outputs to “Create New…” and hit ‘Apply’.

![HDBET](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/4/64d48e18779ca00ee5d24edb4d66013ea33eb9cb.jpeg)

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<div class="post-metadata">

**Author:** ![BDhoth](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bdhoth/32/78752_2.png) [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Post date:** [July 19, 2024, 3:22pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/5 "2024-07-19T15:22:14Z")

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Weird, that was what I did the first time and it came up with a weird “torch” error and failed. It worked this second time; however, how do I handle it in segment editor to have just the brain and no skull/face?  
Thank you so much for your help!

> **(attachments)**
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> ![Screenshot 2024-07-19 102043.png](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/c/5c8b3e705256938a4109a52d2d7849ef215a5e13.png)

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<div class="post-metadata">

**Author:** ![JASON](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jason/32/13419_2.png) [@JASON](https://discourse.slicer.org/u/JASON)\
**Post date:** [July 19, 2024, 7:00pm UTC](https://discourse.slicer.org/t/brain-segmentation-in-mr/36924/6 "2024-07-19T19:00:19Z")

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It looks like you correctly created a brain mask segmentation in white, and a new skull-stripped volume. The green segment looks like it is from a different segmentation node created from threshold of the image before skull stripping.

If you go back to the data view, you can turn off the node named ‘Segmentation’ with the green head label to see only the brain mask label in white.