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FSL Course

Learn the theory and practice of using FSL for structural, functional and diffusion image analysis. The course is designed for people at all skill levels, from those with little or no experience through to intermediate users of FSL. It is based around a set of self-paced, hands-on practicals, supported by a broad set of accessible lectures.

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Organised Courses

There are usually one or two organised FSL courses a year and they can be either in-person (1 week) or online (2 weeks). At these courses, expert tutors are available throughout the course, to answer any questions you might have about FSL.

Further information is also available regarding both upcoming and previous courses.

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Course Materials

All course materials are available freely, including:

  • recorded lectures (video)
  • recorded practical overviews (video)
  • practical instructions (written)
  • practical data

The most important parts of the course are the self-paced practicals. Both these and the lectures are suitable for users from a wide range of backgrounds, such as psychology, medicine, biology, engineering and physics.


You can use all of our online course materials to learn about FSL outside of our organised courses.

Recommended Steps

  1. Install FSL (on a Windows, Mac or Linux machine) of your own machine or use an Amazon workspace
  2. Work through the preparatory material
  3. For each section of the main course material
    • Download the practical data
    • Watch the set of lectures on this topic (4-7 videos each)
    • Watch the practical overview video
    • Work through the self-paced practical (using instructions and downloaded data)

Note that later sections often rely on earlier sections, especially registration (secton 1) and the GLM statistics (sections 3 and 4). Therefore, please make sure you do not skip these, even if you are just interested in the resting-state fMRI or diffusion practicals.

Course Data

All course data is provided for educational use only, not for research.

We have created a simple installation script for our course data (to be used after you've installed FSL). To use it simply download the fsldl script, move it to your Desktop and then open a terminal and paste in the following command (and don't forget to press return after pasting in order to run the command):

						fslpython ~/Desktop/fsldl.py

It will then ask you which dataset you wish to install.

For users who would prefer to install data directly themselves, there are alternative instructions here for accessing the data.


You should allow around 2 hours to watch the lectures for each section and between 2 to 4 hours per practical. The preparatory lecture and practicals are similar. The introduction to UNIX should take around 2 to 3 hours to go through yourself.


If you have questions at any point then start by having a look at the FSL wiki. This contains the full documentation for each tool, and you can find detailed instructions and frequently asked questions. If you have further questions at any point then have a look at the FSL email list, as others may have asked the same question before. If you cannot find an answer there then please subscribe to the mailing list and ask your own question.

Preparatory Material

In the main sections of the course we will be covering a lot of material. Whether you are enrolled in an organised course or you are using the material for self-study, it is important to complete the preparatory material before attempting the rest of the course if you are relatively new to FSL.

The preparatory material consists of:

  1. An introductory lecture (2 videos)
  2. Introduction to UNIX practicals (5 video walkthroughs)
    • It is very important to do these (including using data and running through the exercises yourself, not just watching the video walkthroughs) if you are not comfortable with basic UNIX (e.g. using commands like ls, cd, mv, pwd). If you are comfortable then feel free to skip these.
    • These are aimed at people with zero previous experience of UNIX or Linux.
  3. Three introductory FSL practicals: Image Viewer (FSLeyes), Brain Extraction (BET), and Command-line FSL Utils
  4. A scripting tutorial (optional)

Please download and install the data for the Introductory Practicals or the Introduction to UNIX Practicals and use that on a machine with FSL installed.

In the main sections of the course it is assumed that the preparatory materials listed above have been completed.

Chinese/English Version

A version of the written course materials with Chinese translations of the English, as used in the 2019 Beijing course, can be found here.

Additional Resources

For those that are entirely new to neuroimaging this course will feel like a lot of new information at a rapid pace. Therefore, for those with little or no prior experience, we strongly recommend the Introduction to Neuroimaging Analysis Primer as a very useful introduction.

The Oxford Neuroimaging Primers is a bookseries published by Oxford University Press that contains several short textbooks and currently includes: 'Introduction to Neuroimaging Analysis', 'Introduction to Perfusion Quantification using Arterial Spin Labelling' and 'Introduction to Resting State fMRI Functional Connectivity'. These primers have been specifically written with the target audience of the FSL Course in mind.

Intro Primer
ASL Primer
Resting-State Primer

In addition, several free short introductions (15-35 pages) that are linked to the main primers are also available. These are aimed at a very introductory level, for those that are new to the GLM, MRI Physics or Brain Anatomy, as we recognise that people come from a wide range of backgrounds. Visit the Neuroimaging Primers website to see these, and more, or click on the images below for a PDF version.

For more MRI Physics there are also additional lectures (slides only) that are available, as presented in previous courses.


We are extremely grateful to all members of the FMRIB Analysis Group and the FSL Course team, past and present, that have prepared material and helped to shape the course into what it is today. What you see in this course is the combined effort of a large number of researchers over a long period of time, and was voluntarily done on top of their research work, in order to promote the use of FSL and make sure it is being used to its best.