We created that model using “Grow from seeds” effect, similarly to how @dzenanz described above, with two additions for CT:
- On CT images you can see the facet joints as well, and there usually no clear separation between the vertebrae, so it is important to set an “Editable intensity range” (from about 150-250HU to maximum) using Threshold effect, to restrict region growing to bone region. The editable intensity range makes painting the seeds easier (you don’t need to worry about painting into soft tissue) and must be done before starting Grow from seeds.
- Cancellous bone inside vertebrae have the same density as soft tissues, therefore the bones will appear hollow after segmentation. You can fill all internal holes using this code snippet (after clicking “Apply” in Grow from seeds effect).
I captured a screen capture video of how I do this:
The goal of the video was to keep it short. As always, you can get more accurate segmentation by spending more time with reviewing and correcting automatic segmentation results.