# Perform cortical and  trabecular bone segmentation of a Talus bone to generate a 2body STL file

**URL:** <https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950>\
**Category:** Support\
**Created:** [June 4, 2021, 1:35pm UTC](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950 "2021-06-04T13:35:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Manav\_Kothari](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/manav_kothari/32/11104_2.png) [@Manav\_Kothari](https://discourse.slicer.org/u/Manav_Kothari)\
**Post date:** [June 4, 2021, 1:35pm UTC](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950/1 "2021-06-04T13:35:39Z")

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I apologise for being extremely naive in the field of biomechanics and radiology but I need to extract a 3D model of Talus bone from a CT scan of a foot. So far I have been successful in segmenting the outer structure of Talus bone from the DICOM file which has provided me with a 1 body 3D CAD model. However, as you might be aware, the Talus bone comprises the outer cortical bone with an inner Trabecular bone. So I would like to get a 3D CAD model containing 2 different bodies (one of each bone) with a considerable amount of accuracy. Kindly help me understand the steps that I need to follow in Slicer software to achieve the same.  
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:** [June 8, 2021, 11:47pm UTC](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950/2 "2021-06-08T23:47:14Z")

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You can easily create a fixed-thickness segment to represent the cortical bone:

- create a new segment
- click Logical operators effect, Copy operation, choose the first segment to copy from, and click Apply
- click Margin effect, Shrink operation, type the thickness into Margin size, then click Apply

An alternative approach is to create a volumetric mesh (using SegmentMesher extension), and set CT density values as point data in each point of the mesh (using Probe Volume with Model volume). I think FEBio Studio can load these meshes and use the CT density values to vary material properties across the mesh.

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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:** [July 18, 2021, 3:15am UTC](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950/3 "2021-07-18T03:15:22Z")

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You can use the [“fill holes inside bones” Python script](https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html#use-segment-editor-effects-from-script-qmrmlsegmenteditorwidget) to fill these holes fully automatically.