Is it possible to label all 29 levels of spinal cord?


I know that sct_label_vertebrae is using sct_5.3.0/data/PAM50/spinal_levels in order to label first 20 levels of spinal cord (C1:C8 and T1:T12). But, is it possible to label Lumbal and/or Sacral spinal segments as well (L1:L5 and/or S1:S5)?

Could I add information to label_info.txt and corresponding .nifi.gz files. If so, how?

Hi @Stefan_Radonjic,

As you rightfully mentioned it is currently not possible to label the lumbar and sacral spinal levels “out-of-the-box”. However, if you are confident about the location of these spinal levels, you can re-generate the file spinal_levels.nii.gz with the additional levels. To do so, I would start by reading this section of the documentation, which explains the context of how these labels were generated. Then, you can modify this script to extend the generation of spinal levels to the lumbar and sacral levels.

The reason we did not do it at the first place, is because we did not have that information. The only probabilistic information we had was at the cervical level (ie: correspondance between vertebral and spinal levels manually identified from high resolution T2w scans), and then we extrapolated it to the thoracic level. But we felt it was too far fetched to extrapolate it further to the lumbar and sacral cord. That being said, if you do have that information, then you can modify the script so that the extrapolation is more accurate.

I hope that helps,