Operating system: 3D slicer
Slicer version: 5.8.1
Expected behavior: I am trying to segment the occipital bone of a Head CT. I set the initial threshold to 226-3071 in order to capture the skull bone. I think use the cutoff of 700 HU for the cortical and subtract that from my occipital total to get the bone marrow. However, the bone marrow region is coming out on the outside of the cortical region. I assume this is an issue with my initial threshold. If anyone has any advice that would be greatly appreciated!
Actual behavior:
If you have access to a GPU, you may want to start by segmenting the skull using TotalSegmentator.
To isolate the occipital bone, I would first manually correct the skull segment generated by TotalSegmentator as needed. You could then duplicate the corrected skull segment and edit the copy using tools such as Scissors or Erase to separate the occipital bone.
The next step would be to distinguish cortical bone from trabecular bone. However, cortical and trabecular bone are structurally continuous, with a gradual transition rather than a sharp boundary between two discrete layers. In other words, they cannot be separated as neatly as the cookie and cream layers of an Oreo.
In practice, one possible approach would be to define voxels above a certain HU threshold within the occipital bone segment as cortical bone and classify the remaining region as trabecular bone. However, the selection and validation of the HU threshold are directly related to the methodology of the study, so I cannot comment on that point in detail.
I apologize that this is only a rough suggestion, but I hope it is helpful.