# Fill holes after threshold-based bone segmentation in CT

**URL:** <https://discourse.slicer.org/t/fill-holes-after-threshold-based-bone-segmentation-in-ct/2478>\
**Category:** Support\
**Created:** [March 30, 2018, 6:16pm UTC](https://discourse.slicer.org/t/fill-holes-after-threshold-based-bone-segmentation-in-ct/2478 "2018-03-30T18:16:15Z")\
**Posts on this page:** 1\
**Showing post:** 2

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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 31, 2018, 1:45am UTC](https://discourse.slicer.org/t/fill-holes-after-threshold-based-bone-segmentation-in-ct/2478/2 "2018-03-31T01:45:57Z")

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If you are lucky then with “Smoothing” effect you can fill the gaps and then you can fill cavities using “Flood filling” effect (in SegmentEditorExtraEffects extension).

Unfortunately, often you cannot make your mesh watertight easily. In such cases, follow these instructions:

> [@Bone segmentation to create 3D-printable STL](https://discourse.slicer.org/t/how-to-edit-stl-file/960/2):
>
> In the STL that you linked, large portions of the bone is missing, so I don’t think it make sense to “fix” it. Instead, I would recommend to redo the segmentation. I would recommend to use the latest nightly version of Slicer and perform the following steps: reduce image noise: use Cast Scalar Volume' module to convert input volume to Float type; use Simple Filtersmodule withGradientAnisotropicDiffusionImageFilter` on the converted volume go to Segment Editor module, use the noise-reduced vol…

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_[View the full topic](https://discourse.slicer.org/t/fill-holes-after-threshold-based-bone-segmentation-in-ct/2478)._