CSA and warping field per IV level normal values

SCT
1

Hello SC toolbox team,
I am trying to compare the percentage decrease in the spinal cord tissue area in individuals with spinal cord injury.
Based on the PAM50 template, is there a normal value(s) per inter-vertebral disc label data that I can use to quantify the percentage damage to the spinal cord following an injury?
Similarly, are there normative cross-sectional area values for the per level gray and white matter?

Thank you,
Pawan

2

Hi Pawan,

Great question. Yes, there are normative values that you can extract from the PAM50 template. You can use the exact same command that you use for your images to get those normative values. For example, to compute spinal cord CSA at C2-C3 and C3-C4 discs, you can do this:

 sct_process_segmentation -i $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -vertfile $SCT_DIR/data/PAM50/template/PAM50_label_disc.nii.gz -vert 3,4 -perlevel 1 -o CSA_spinalcord.csv

It should output this file: CSA_spinalcord.csv (1018 Bytes)

Similarly, to get gray matter CSA, you can do this:

 sct_process_segmentation -i $SCT_DIR/data/PAM50/template/PAM50_gm.nii.gz -vertfile $SCT_DIR/data/PAM50/template/PAM50_label_disc.nii.gz -vert 3,4 -perlevel 1 -o CSA_graymatter.csv
1 Like
3

Great. Thank you!

Pawan