Image SCT course


Course on the Spinal Cord Toolbox (SCT) software.

The general aim of this 2-day course is to learn how to analyse spinal cord quantitative MRI data. There will first be an introduction presenting the challenges/solutions of spinal cord MRI, followed by a general overview of the Spinal Cord Toolbox (SCT) and its applications in various diseases. Then, the course will dive into the various processes of spinal cord MRI analysis, from segmentation, to the registration to a template, to the extraction of quantitative metrics (diffusion MRI, magnetization transfer). We will also touch base on various “niche” applications, such as the quantification of compression in spinal cord injured patients, fMRI analysis, etc. We will also discuss “best practice” for running reproducible analyses using batch scripts, for processing multiple subjects at once, for doing quality control and manual corrections.

This is a “hands-on” workshop: you will actively participate by running SCT commands at the same time as the presenters. So please make sure to have the latest version of SCT installed before the workshop.

Registration and pricing

The workshop is free 🙂

👉 Please register here so we have an idea about the number of attendees.

How to connect

🎥 Zoom link

Please note that the meeting will be recorded and uploaded on the SCT website.

🗒 Miro board. This board is used as a visual communication platform. If you have questions/ideas/suggestions to share, please contribute to the board (you will need to create an account and log in).


If you are unable to connect to the meeting, or if you have any trouble installing SCT v6.1, please email and one of SCT’s developers will be happy to help.


This is a two-day workshop. Times are Eastern Time Zone (UTC-05:00):

November 20th

10:00 Welcome speech
10:15 SCT course (course material)
12:00 Lunch Break
12:30 Resume course
14:00 Adjourn meeting

November 21th

10:00 SCT course (course material)
12:00 Lunch Break
12:30 Resume course
13:00 Feedback from users, suggestions for new features
14:00 Adjourn meeting

Minutes of the meeting

To come.


SCT team.