Hi Steve, thanks for your reply!
Here is a screenshot of a sample CT with a minimal model of what we are able to do so far. I placed 5 fiducials, 3 of which are shown on the sagittal slice, just to illustrate a rough curve (blue). Ideally we want to have as many points as is reasonable because we want to measure the curvature at precise locations along the spinal cord for a ton of spine CTs.
The centerline function in the VMTK extension looks like it could be exactly what we need. Unfortunately, I’m not sure the best way to segment the isolated central canal. The adjacent tissue density is too uniform, so any of my attempts to threshold give pretty useless segmentations. This seems like an entirely separate problem than my original question about drawing a centerline (which seems to be solved). But do you have any suggestions for how we could get a reasonable segmentation of the central canal itself?
For now, it doesn’t really matter that the vertebrae are not entirely thresholded since the representation of the vertebral column is currently purely illustrative. I originally thought we could use it to extract a position within the hypodense canal, but that does not seem feasible.
We appreciate the help - thanks for looking after this forum, Steve! I’ll mark your original post as the solution to my original problem!