# segmentation of brain from CT 

**URL:** <https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217>\
**Category:** Support\
**Created:** [March 1, 2018, 1:56pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217 "2018-03-01T13:56:43Z")\
**Posts on this page:** 15\
**Page:** 1

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**Author:** ![iplneuro](https://avatars.discourse-cdn.com/v4/letter/i/7ba0ec/32.png) [@iplneuro](https://discourse.slicer.org/u/iplneuro)\
**Post date:** [March 1, 2018, 1:56pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/1 "2018-03-01T13:56:43Z")

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Hi,  
I am just trying to segment brain from CT. Is there a way to segment brain from CT data or it is possible to segment brain from only MRI. Anyone can help me with this issue.

Thanks in advance,  
Suba

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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:** [March 1, 2018, 2:19pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/2 "2018-03-01T14:19:27Z")

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Do you mean you would like to remove the skull? [Swiss Skull Stripper extension](https://github.com/lorensen/SwissSkullStripperExtension) should be able to do that completely automatically. The built-in atlas is optimal for MRI, but if you segment a CT manually then you can use that as atlas and may get better results.

See for example the result it gave for the CTBrain sample data set:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/7/474074be252056ba018d75067b8ea72102ab5770.jpeg)

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**Author:** ![iplneurosurgery](https://avatars.discourse-cdn.com/v4/letter/i/e56c9b/32.png) [@iplneurosurgery](https://discourse.slicer.org/u/iplneurosurgery)\
**Post date:** [March 3, 2018, 5:47am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/3 "2018-03-03T05:47:05Z")

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Hi,

Thank you for your valuable reply.

I have attached the screen shot of the brain segmented from MRI. Will I be able to segment the brain with those grooves and more detail from CT data.

Thanks and regards,

Suba

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/e/5/e51a488de3ec88631d3470c4463886453e7f5130.png)

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<div class="post-metadata">

**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:** [March 3, 2018, 1:17pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/4 "2018-03-03T13:17:07Z")

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You will not get the same level of detail from CT as from MRI - see below MRI and CT image of the same patient, showing the same image slice:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/b/cbe94b7ed37102896dbacb7e2646e74efa575626.jpeg)

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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:** [September 9, 2019, 4:52am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/5 "2019-09-09T04:52:37Z")

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Hi andras,  
Is it possible to get the brain portion automatically without the cerebellum part of the brain(the back lower brain portion)

thank you

Regards,  
Saima Safdar

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<div class="post-metadata">

**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:** [September 9, 2019, 5:41pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/6 "2019-09-09T17:41:13Z")

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Contrast between cerebellum and other parts of the brain is not very good but you can try to modify the atlas that the skull stripper module uses and see if it can provide the region you need.

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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:** [September 16, 2019, 2:47pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/7 "2019-09-16T14:47:45Z")

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How can i modify the atlas. I do not understand this. Could you please tell me how can I change it.

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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:** [September 17, 2019, 12:25am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/8 "2019-09-17T00:25:37Z")

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You can import the atlas labelmap volume node into a segmentation node using Segmentations module, then edit it using Segment Editor module, finally export the segmentation to a labelmap volume node. See segmentation tutorials [here](https://www.slicer.org/wiki/Documentation/Nightly/Training#Segmentation).

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**Author:** ![AbnerxzHe](https://avatars.discourse-cdn.com/v4/letter/a/439d5e/32.png) [@AbnerxzHe](https://discourse.slicer.org/u/AbnerxzHe)\
**Post date:** [November 2, 2019, 2:34am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/9 "2019-11-02T02:34:23Z")

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Hello,  
have you realized the brain extraction on CT? If you can, can you introduce how you do it?  
Thank you

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<div class="post-metadata">

**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:** [November 3, 2019, 5:04am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/10 "2019-11-03T05:04:01Z")

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What do you mean by extraction of brain on CT? Would you like to remove the skin and skull from the image?

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<div class="post-metadata">

**Author:** ![AbnerxzHe](https://avatars.discourse-cdn.com/v4/letter/a/439d5e/32.png) [@AbnerxzHe](https://discourse.slicer.org/u/AbnerxzHe)\
**Post date:** [November 3, 2019, 6:56am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/11 "2019-11-03T06:56:38Z")

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Hello,  
Yes, when I do brain CT, I can remove the bone, but I don’t know how to remove the soft tissue and skin .if you have any good way to deal with it?  
Thank you

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<div class="post-metadata">

**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:** [November 4, 2019, 12:05am UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/12 "2019-11-04T00:05:22Z")

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> [@AbnerxzHe](#):
>
> I can remove the bone, but I don’t know how to remove the soft tissue and skin

Yes, this should be quite straightforward by segmenting the brain by thresholding then separating other soft tissues by margin shrinking, island removal, and margin growing.  
See step-by-step instructions in CT skull stripping segmentation recipe here: [Segmentation recipes for 3D Slicer | 3D Slicer segmentation recipes](https://lassoan.github.io/SlicerSegmentationRecipes/)

You can find more segmentation tutorials here: [Documentation/Nightly/Training - Slicer Wiki](https://www.slicer.org/wiki/Documentation/Nightly/Training#Segmentation)

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<div class="post-metadata">

**Author:** ![AbnerxzHe](https://avatars.discourse-cdn.com/v4/letter/a/439d5e/32.png) [@AbnerxzHe](https://discourse.slicer.org/u/AbnerxzHe)\
**Post date:** [November 4, 2019, 12:51pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/13 "2019-11-04T12:51:15Z")

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Thank you very much for your help!

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<div class="post-metadata">

**Author:** ![KateDelb](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/katedelb/32/14981_2.png) [@KateDelb](https://discourse.slicer.org/u/KateDelb)\
**Post date:** [July 8, 2022, 12:10pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/14 "2022-07-08T12:10:04Z")

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Dear Andras,

The recipe for CT skull stripping is very helpful, I was wondering if this is implemented in python code as well?

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<div class="post-metadata">

**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:** [July 9, 2022, 4:05pm UTC](https://discourse.slicer.org/t/segmentation-of-brain-from-ct/2217/15 "2022-07-09T16:05:37Z")

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I’ve implemented the procedure in Python, but then the [SurfaceWrapSolidify](https://github.com/sebastianandress/Slicer-SurfaceWrapSolidify) extension was developed, which does a much better job. Both the old and new method is made available by SlicerMorph extension developers in their [Segment Endocranium module](https://github.com/SlicerMorph/SlicerMorph/blob/master/SegmentEndocranium/SegmentEndocranium.py).