Thank you for your previous help with “funky” thoracic warping and improving the functionality of the center line viewer.
In all of my thoracic datasets, I have identified the most rostral and caudal vertebral levels and also identified the center line manually. However, despite manually entering control points and identifying the center line, there are still issues with accurately warping to the spinal cord template in about 1/3 of the data sets. The attached figure summarizes what I am seeing. I’m really not sure what happened in [a] (sheering and stretching), [b] exhibits compression equal to almost an entire vertebral level, [c] exhibits compression and sheering, and [d] exhibits sheering despite having nice contrast between the cord and CSF. In addition to manually labeling vertebral levels and identifying the center line, are there other things that I can do to help the function