Remove islands inside the resulting STL from a segment

anon29823344
Wed, 02 Feb 2022 13:24:34 +0000
Support

Operating system: Windows 10 Pro. Version: 21H2. Build: 19044.1466
Slicer version: 4.11.20210226 r29738 / 7a593c8

Hello all.

This is my first question in the forum, so I hope this topic is not repeated (at least I couldn’t find it).

I need to solve a problem that I found during multiple segmentation tasks of CBCT dental scans by using the Segment Editor module. In particular, I am segmenting the teeth, mandible and the maxilla, and inside all of them, there are multiple “islands” that I can’t remove with the Islands method. I tried the following:
- remove islands smaller than a fixed number of voxels (with different voxel sizes),
- keep the largest island (both for mandible and maxilla),
- split islands into segments,
but in any case, I could not remove these parts.

I attach some images of that problem (images are snapshots from MeshLab software due to I don’t know how I can see those islands with slicer in an easy way) where I hope you can see the islands inside the STL resulting from the segmentations done.

Can somebody help me with this problem? How can I remove these islands inside the STL? These islands are really considered “islands” by Slicer? Is there a way to check them in Slicer instead of using MeshLab or other software?

I take this opportunity to ask the Slicer community what methodology each of you uses to segment these types of images, with the goal of both improving my work and contributing to a piece of shared knowledge in this type of segmentation. In my case, I use to apply a Grow From Seeds for tooth segmentation but it is a very rough segmentation and I have to invest a lot of time in debugging it. For the jaw segmentation, I usually apply a threshold between the maximum value of HU and a value around 500 HU, this way I remove the air and much of the soft tissue and then, after manual cleaning, I subtract the segmentation made by the teeth. If you want I can upload photos of how I do it.

I hope I have explained it well. Thanks in advance for your time.

Best regards.

3 posts - 2 participants