# Can't seem to get the skull out of a MRI scan of a brain

**URL:** <https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474>\
**Category:** Support\
**Created:** [July 9, 2023, 5:45pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474 "2023-07-09T17:45:09Z")\
**Posts on this page:** 9\
**Page:** 1

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**Author:** ![Sander\_Martens](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sander_martens/32/66722_2.png) [@Sander\_Martens](https://discourse.slicer.org/u/Sander_Martens)\
**Post date:** [July 9, 2023, 5:45pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/1 "2023-07-09T17:45:09Z")

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Hi, as a project I want to get a STL file from a skull, but when using my MRI scan I can’t seem to only get the skull. It’s either the whole head (with skin) or only the brain.

Could anyone help me with this issue?

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**Author:** ![cpinter](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/cpinter/32/7995_2.png) [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Post date:** [July 10, 2023, 11:28am UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/2 "2023-07-10T11:28:42Z")

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Are you asking about image segmentation? Can you describe _in detail_ what you tried already?

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**Author:** ![Sander\_Martens](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sander_martens/32/66722_2.png) [@Sander\_Martens](https://discourse.slicer.org/u/Sander_Martens)\
**Post date:** [July 10, 2023, 5:59pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/3 "2023-07-10T17:59:48Z")

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I tried using the Segment Editor and set a Threshold and tried different presets in the Volume Rendering module, but I have not been able to only show the skull. Each time I try it ends up looking something like this.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/2/52b449572b8bc3add4d608de15c1ab1259e4a0c4.jpeg)

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**Author:** ![rkikinis](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rkikinis/32/791_2.png) [@rkikinis](https://discourse.slicer.org/u/rkikinis)\
**Post date:** [July 10, 2023, 6:06pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/4 "2023-07-10T18:06:37Z")

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On MRI, you can see the bone as a black structure. Unfortunately, that is true for air and ligaments/tendons. Accordingly, you need to perform a significant amount of preparation on the data to get a partial skull rendering.

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**Author:** ![Sander\_Martens](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sander_martens/32/66722_2.png) [@Sander\_Martens](https://discourse.slicer.org/u/Sander_Martens)\
**Post date:** [July 10, 2023, 6:19pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/5 "2023-07-10T18:19:27Z")

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I see.

How would I go about achieving this? (I am fairly new to the program)

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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:** [July 10, 2023, 6:23pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/6 "2023-07-10T18:23:26Z")

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It’s not really about the program, it’s about the nature of CT vs MR scanning. Bones like the skull are hard to image in MR compared to CT.

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**Author:** ![Sander\_Martens](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sander_martens/32/66722_2.png) [@Sander\_Martens](https://discourse.slicer.org/u/Sander_Martens)\
**Post date:** [July 10, 2023, 6:27pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/7 "2023-07-10T18:27:39Z")

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In that case it would be very hard (if not impossible) to be able to export the skull with this data?

aka not possible?

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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:** [July 10, 2023, 6:28pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/8 "2023-07-10T18:28:45Z")

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Right - with just the data you have it would be very hard to segment the skull.

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**Author:** ![Sander\_Martens](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sander_martens/32/66722_2.png) [@Sander\_Martens](https://discourse.slicer.org/u/Sander_Martens)\
**Post date:** [July 10, 2023, 6:29pm UTC](https://discourse.slicer.org/t/cant-seem-to-get-the-skull-out-of-a-mri-scan-of-a-brain/30474/9 "2023-07-10T18:29:29Z")

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I understand. Thank all of you for you help!