# Brain and skull segmentation

**URL:** <https://discourse.slicer.org/t/brain-and-skull-segmentation/15859>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 4, 2021, 7:38am UTC](https://discourse.slicer.org/t/brain-and-skull-segmentation/15859 "2021-02-04T07:38:34Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [February 4, 2021, 7:38am UTC](https://discourse.slicer.org/t/brain-and-skull-segmentation/15859/1 "2021-02-04T07:38:34Z")

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Hi Andras,  
I segmented the brain and removed the skull. I now need to get some extra layer on top of the brain extracted assuming that it is a skull how can I do it. and another layer for the scalp as well on top of skull.

Thank you

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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:** [February 5, 2021, 4:10am UTC](https://discourse.slicer.org/t/brain-and-skull-segmentation/15859/2 "2021-02-05T04:10:32Z")

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Please describe in more detail what you would like to achieve and include a few annotated screenshots or sketches.

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [February 8, 2021, 7:30am UTC](https://discourse.slicer.org/t/brain-and-skull-segmentation/15859/3 "2021-02-08T07:30:39Z")

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Hi,  
I have a single brain segmentation. I now need to get the skull segmentation and scalp segmentation without any gaps between the three segmentations. how can i get this. Can I grow a segmentation and then subtract it from brain segmentation. How can I grow a brain segmentation so it covers the skull and scalp as well.

Thank you

Regards,  
Saima safdar

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [February 8, 2021, 8:29am UTC](https://discourse.slicer.org/t/brain-and-skull-segmentation/15859/4 "2021-02-08T08:29:33Z")

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Have you used the swiss skull stripper module

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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:** [February 8, 2021, 9:12pm UTC](https://discourse.slicer.org/t/brain-and-skull-segmentation/15859/5 "2021-02-08T21:12:48Z")

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Yes, Swiss Skull Stripper can provide the brain segment. Skin surface extraction is easy (see for example [this segmentation recipe](https://lassoan.github.io/SlicerSegmentationRecipes/SkinSurface2/)). Bone segmentation on general T2 MRI images is hard (bone is essentially not visible), but if you don’t want to have gaps between the 3 segments then you can consider “skull” to be anything that is inside the skin and not brain (and generate it using “Logical operators” effect in Segment Editor).