That is correct, yes, but you need to keep in mind that if the spinal cord deformation only occurs at the disc level and that is what you’d like to capture, then it is suboptimal to aggregate CSA values across the entire vertebral level, because it will average out the effect you’d like to capture.
Alternatively, it might be more appropriate to only compute CSA at the disc level. In that case, you simply need to select the labeled disc file (output of
sct_label_vertebrae) when running
sct_process_segmentation. Example below:
sct_process_segmentation -i t2_seg.nii.gz -vertfile t2_seg_labeled_discs.nii.gz -vert 2:5 -perlevel 1 -o csa_disc.csv
Here’s the output: csa_disc.csv (1.6 KB)
Where each line gives you the CSA at a specific disc level (notice the single slice selection). For example, a value of ‘3’ under the row ‘VertLevel’ corresponds to disc C2/C3, according to this convention.