Can I quantifiy signal intensity with the SCT?

Dear SCT Team,

We came across this amazing tool while looking for ways to quantitative analyze the signal intensity in relevant regions on the spinal cord. Specifically, we would like to quantify the degree of “increased signal” of grey matter lesions on T2w-images (i.e. mild, moderate or severe increase in signal intensity)
We have thought of manually drawing our ROI (i.e. the grey matter lesion) and analyzing the maximum or average voxel intensity in imageJ or similar, but we were wondering if the SCT has a tool that could potentially give us similar data in a more objective and reproducible way.

Thank you!

Andrea Salazar
Research Fellow
Deparmtent of Neurology
Johns Hopkins School of Medicine


Thank you for reaching out. Yes, with SCT you would be able to automatize some of the processes, including e.g.:

  • segmentation of the spinal cord: sct_deepseg_sc
  • segmentation of the spinal cord gray matter: sct_deepseg_gm
  • vertebral labeling: sct_label_vertebrae
  • lesion detection: sct_detect_lesion
  • analyse lesion morphometry and statistics: sct_analyze_lesion

There are other tools, e.g. to register your data to a template, in order to use pre-existing regions of interest (e.g., cuneatus, corticospinal tract, etc.) for quantifying the lesion location wrt. specific tracts.

A good starting point would be to look at the latest SCT course, and then we would be happy to support you with, e.g., custom batch script to analyze your data.


Dear Julien,

Thank you for your answer! We will definitely look into it with more detail.

Unfortunately, our cohort has some limitations. Mainly, they are clinically acquired MRIs with variable parameters, as well as remarkable intramedullary T2 hyperintensity that could hinder the automated SC segmentation.

We will investigate it further and give it a try.

Once again, thank you for this great tool,

Kind regards,

Worst case scenario, is that you could do the manual segmentation of lesions and semi-automatic segmentation of the spinal cord (automatic followed by manual correction), then we can help you with setting up automatic quantification of e.g. lesion volume fraction across individuals