How to exclude area through thresholding?

Hi there,

I’m trying to segment out a CT w/ contrast of the L hip. I’m trying to use a threshold to segment just the bone but the contrast has the same intensity as the bone and I’m unable to effectively separate out the two. I was able to set the threshold to just include the contrast and I was wondering if there was a way to exclude this and paint over the bone or a way to inverse it? I’m still new to slicer and could use any tips or tricks! Thank you!

Screenshot 2024-06-11 103519

You can use tools in the Segment Editor to separate bones from contrasted vessels. Easiest is to use Islands effect, choose Keep selected island mode, and click on the component you want to keep. You can also remove islands using the same effect, or use Scissors effect, etc.

However, normally you don’t need to do any of these manually anymore. AI segmentation tools, such as MONAI Auto3DSeg and TotalSegmentator extensions in Slicer can segment all major bones and vessels fully automatically in a few minutes.

Thank you for that. I have been trying out MONAI Auto3D and for some reason after I run it and hit apply- it doesn’t seem to be working. Does that software only work for the sample data it comes with?

MONAI Auto3DSeg and TotalSegmentator are very robust and work well with any CT images.