Start using SCT and can use your help with general questions

Hi there.
I just started new position at the Multiple Sclerosis center in Tel-Hashomer hospital, Israel.
My position is to assimilation SCT for research purpose.

After installing the SCT on my linux OS I’ve got some trouble with understanding the working flow and the platform.

Does the main use of the software goes through the terminal?
(At first I expected a graphic platform or something similar).

Is there a list of the commands which can give me guidelines for using the SCT functionality?

How can I view images with the FSLeyes viewer?

what do I need to change inside the for different subjects data?

The SCT support comparing multiple MRI scans from different dates, or different patients, simultaneously, and analysis differences or some progress, for statistical conclusions?

In general, how can I get started using this amazing tool?

I am a student, studying Computer science and Brain science. I have experience with linux OS, nevertheless, find the SCT tool very complex and challenging. I am the first one to use SCT in the MS center, so I have no one for teaching me.

I hope I have provided a clear picture for my situation and current state as SCT user.

Thanks a lot.

Dear Yuval,

Thank you for reaching out. As a starting point, I would recommend you read the latest SCT course material and try the hands-on session. If you have any question we will be happy to help.


I shall do.
Thank you for your prompt reply.

Yuval :slight_smile:

Hi Yuval,

Sorry for stating the obvious, but make sure you install FSL too - There is a nice installer for macOS, it’s a big download.

I think it would be worth getting to grips with fsleyes before venturing into the SCT teaching material, as you need this essential tool to visually assess whether things are working as expected in SCT. There is online course material to help with learning FSL (, and Andrew Jahn has created some very useful youtube vids:

Best wishes,


1 Like

That’s ok. I actually expected for this advice. I already started with london 2019 tuturial. Yet something graphic is missing. I’ll start with the recommanded software and maybe this will orgenize my confusion.
Thank you very much. Your support is really comfort. I will write you if I have a more specific question.

Have a great day.