I am using the following command to help the SCT identify the thoracic spinal cord, which, as you know, can be more challenging in a handful of subjects:
sct_deepseg_sc -i t2.nii -c t2 -centerline viewer -brain 0 -kernel 2d
By default this viewer is in “Mode Auto”, which automatically initializes the first point a fair distance from the superior edge of the imaging volume (see above pic). I tried to fix this by switching to “Mode Custom”, but doing so then deletes(!) all the points defined during auto mode. And then if you define some point in custom mode and then switch back to auto mode, it deletes all the points again.
I have used this functionality a fair bit, and while it works well, I would like to suggest some simple potential enhancements:
- switching between custom mode and auto mode does not delete points previously defined.
- auto mode starts closer to the superior edge of the imaging volume… maybe a few mm from the top.
- if it could be helpful to the code in problematic (i.e, low SNR) regions(?), make the S-I step side in auto mode a parameter that the user can tweak (i.e., define 50% more control points).
The most important suggestion is #1 because doing a first pass in auto mode and then adding a few extra points in manual mode would be a terrifically awesome enhancement.