How to start for the beginners

Dear Experts,
I have successfully installed SCT on Ubuntu. I need the software for segmenting cross-sectional areas. Please simply tell me how to start working with the software. I mean that I really appreciate it if you give me a ““step by step”” procedure.

Thaaaaaank you so much.

Hi @Hedieh_Toofany,

thank you for posting! We are currently updating our documentation, here is the working version pointing to the step-by-step commands. If you scroll down, you will see the “t2” section, which starts with segmenting the cord, labeling and then computing CSA. Let us know if this helps,


Hi @jcohenadad , I wrote / but didn´t start. I have to write another additional code?

Hi Marco,

what do you mean by “didn´t start”?

one thing you can do, is copy/paste each line of the, so you can get familiar with the Terminal environment and what each line is doing.