# Recommendations for segmenting internal cavities 

**URL:** <https://discourse.slicer.org/t/recommendations-for-segmenting-internal-cavities/19505>\
**Category:** Community\
**Tags:** segmentation\
**Created:** [September 3, 2021, 9:14pm UTC](https://discourse.slicer.org/t/recommendations-for-segmenting-internal-cavities/19505 "2021-09-03T21:14:57Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Ale](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ale/32/67086_2.png) [@Ale](https://discourse.slicer.org/u/Ale)\
**Post date:** [September 3, 2021, 9:14pm UTC](https://discourse.slicer.org/t/recommendations-for-segmenting-internal-cavities/19505/1 "2021-09-03T21:14:57Z")

</div>

Hi, I’m working with a microCT of bone osteoderms. I need to segment internal cavities and external compact bone. I started with threshold tool to segment compact bone and went successful. But the internal cavities is a lot more complex and some are connected with the exterior. I started segmenting full manually using the painting tool, but it take a LOT of time (2 - 3 days only 1 osteoderms). I’m asking for advice to follow some strategy to fill those cavities in a more automatic or semiautomatic way. Thanks in advance.

Below is and screenshot of the osteoderm:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/4/544d612a27eb0d48b1d9f0cde01b894b42f8cbf1.png)

---

<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 3, 2021, 9:32pm UTC](https://discourse.slicer.org/t/recommendations-for-segmenting-internal-cavities/19505/2 "2021-09-03T21:32:19Z")

</div>

Yes, we have several automated tools that could segment these structures effortlessly. The key is to prevent leaking through small holes.

From a single image slice it is hard to tell which method will work the best, but I would recommend to start with trying cavity extraction using SurfaceWrapSolidify extension. See this [segmentation recipe](https://lassoan.github.io/SlicerSegmentationRecipes/CTSkullStripping/) for step-by-step instructions.