# Segmentation of trabeculal and corticalis from HRpQCT images

**URL:** <https://discourse.slicer.org/t/segmentation-of-trabeculal-and-corticalis-from-hrpqct-images/40640>\
**Category:** Development\
**Tags:** segmentation, python\
**Created:** [December 11, 2024, 5:09pm UTC](https://discourse.slicer.org/t/segmentation-of-trabeculal-and-corticalis-from-hrpqct-images/40640 "2024-12-11T17:09:33Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![nikkos](https://avatars.discourse-cdn.com/v4/letter/n/f0a364/32.png) [@nikkos](https://discourse.slicer.org/u/nikkos)\
**Post date:** [December 11, 2024, 5:09pm UTC](https://discourse.slicer.org/t/segmentation-of-trabeculal-and-corticalis-from-hrpqct-images/40640/1 "2024-12-11T17:09:34Z")

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Hello dear Slicer Community,

I wonder if there is an extension that allows me to automatically segment the corticalis of the femur and the trabeculae ?

Best regards  
Niklas

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**Author:** ![jamesobutler](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/jamesobutler/32/7511_2.png) [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Post date:** [December 11, 2024, 8:16pm UTC](https://discourse.slicer.org/t/segmentation-of-trabeculal-and-corticalis-from-hrpqct-images/40640/2 "2024-12-11T20:16:16Z")

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The following are likely relevant to what you are interested in however the mentioned Slicer [BoneTextureExtension](https://github.com/Kitware/BoneTextureExtension) has had issues recently. @muratmaga whenever you reached out about this extension what was the conclusion about whether it would be updated to work with latest Slicer?

> [@Separating Cortical and trabecular region of Talus bone](https://discourse.slicer.org/t/separating-cortical-and-trabecular-region-of-talus-bone/19049):
>
> I am interested in separating cortical and trabecular region of Talus bone and generate individual STL file. There is one add-on in Analyze Direct software named Bone Microarchitecture Analysis (BMA). Is there any similar function in Slicer as well? Thanking You

> [@Is BoneTexture Extension abandoned?](https://discourse.slicer.org/t/is-bonetexture-extension-abandoned/39711):
>
> A colleague of mine needs to use this extension, and it appears that it hasn’t been functioning since v5.0.3. I tried to download that specific release, but the extension catalogue is empty (no extensions are shown). There are bunch of issues on the repo, some of which are couple years old. This is listed under Kitware, so I am not sure who is responsible for it…

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [December 12, 2024, 2:18am UTC](https://discourse.slicer.org/t/segmentation-of-trabeculal-and-corticalis-from-hrpqct-images/40640/3 "2024-12-12T02:18:02Z")

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I think the major blocking issues of expecting labelmaps as input (as opposed to segmentation) are fixed now. Though I haven’t tried it personally. @bpaniagua is the person who knows best.