Compute CSA in corticospinal tract


When I compute the area of white matter and gray matter, Can SCT compute the area of a particular tract, for example, the corticospinal tract. Just like DTI value.


Hi @chang,

You can specify the CST file directly, eg:

sct_process_segmentation -i label/atlas/PAM50_atlas_04.nii.gz -o csa_cst_left.csv
sct_process_segmentation -i label/atlas/PAM50_atlas_05.nii.gz -o csa_cst_right.csv

To know the ID of each label, you can type:

sct_extract_metric -list-labels

:warning: It is important to understand that this measure is not a true measure of the corticospinal tract CSA for a specific subject, but it corresponds to the corticospinal tract CSA from the PAM50 template, scaled to the spinal cord of that subject. As you know, the CST is not visible on standard MRI contrast, hence the only possible thing to do is to use both the information from the spinal cord contour (and gray matter if available) of that subject, and the CSA of the CST from the PAM50 template, and scale the latter to the former.

P.S. I’ve also renamed this topic from “Compute CSA Problem” to “Compute CSA in corticospinal tract”, in order to be more specific to your request and help other researchers find the answer if they have the same question.

Thank you very much for your help!

1 Like