Quality loss in segments

Support
1

Hello everyone,

I am working with a micro-CT dataset of a snake skull in 3D Slicer (v5.8) and I am experiencing some difficulty with the segmentation workflow.

When I visualize the dataset using Volume Rendering, the skull appears very detailed and the surface structures (such as teeth and thin bones) look sharp. However, when I create a segmentation using Segment Editor → Threshold, the resulting segment already seems to lose some surface detail. The 3D model generated from the segment appears slightly smoother and less detailed compared to the original volume rendering.

This loss of detail seems to occur during the creation of the segment itself, rather than during later steps like removing artifacts.

My goal is to:

  • isolate the skull from the CT volume

  • remove small floating artifacts around it

  • preserve as much surface detail as possible in the final 3D model

I would like to know if there is a recommended workflow or settings in Slicer to preserve higher surface resolution when creating a segmentation.

Thank you very much!

2

A good way to do this is to increase the resolution of the segmentation with respect to the source data (change this with the segmentation geometry dialog).

If you paste your question and this answer into google you’ll no doubt get more details from the AI.

1 Like
3

It worked here, thank you very much! I was having trouble finding this information, as I’m learning to use the software on my own. I really appreciate your help.

4

Given that you are working with microCT you’ll probably benefit from reviewing our SlicerMorph Tutorials GitHub - SlicerMorph/Tutorials: SlicerMorph module tutorials · GitHub