Online FSL Course

8-18 September 2020


Learn the theory and practice of functional and structural brain image analysis. We have hosted the FSL course for nearly 20 years, and trained thousands of users in that time. We welcome all skill levels, and we have self-paced primer material to get you started before attending.

Attend Remotely

All FSL course material will be delivered remotely. Lecture videos will be online. We will be providing machines to work on in the cloud, complete with all the data and software you will need. You will interact with expert tutors and other course attendees through Zoom, or equivalent. We will support you through all the practical, hands-on sessions.

Global Community

FSL is used all over the world. This year's online FSL course will offer a unique opportunity for those that may not normally travel to a course. We will be inclusive, supporting users in all countries, and we want to support our diverse users at all career stages.


Both courses are now sold out and the waiting list is full.

Registration (in UK pounds) is £125 for PhD/MSc students (this includes anyone who is currently registered as a student with your university or institution), £150 for postdocs and other non-student attendees, and £250 for commercial attendees. Only a 9-day full registration is available - no partial registration options are available.

Course registration includes access to recorded lectures, live practical sessions with expert tutors (via Zoom or equivalent), and remote desktop machines in the cloud (via Amazon or equivalent) with all the necessary software and data already setup. All course materials (online lectures, practical instructions and data) will be available in electronic format during and after the course.
The number of attendees are strictly limited and are available on a first-come-first-served basis.


This two-week course covers both the theory and practice of functional and structural brain image analysis. Live, guided practicals will be supported across a wide range of time zones.

Each daily practical session will last half a day, with an additional online lecture to watch beforehand on your own. The course will last for nine days, spread across the two week time period (no weekends).

Background concepts and the practicalities of analyses are taught in hands-on practical sessions, supported by online lectures. Attendees will learn how to carry out analysis for themselves on real data, with a remote desktop computer in the cloud that we provide access to. Each attendee will need to have their own computer (Mac, Windows, Linux) in order to access the cloud based desktop and for video conferencing with tutors in the guided practical sessions. After completing the course, attendees should be able to analyse their own structural, functional and diffusion MRI data sets.

The course is aimed at both new and existing users of FSL and will cover both basic and advanced features. The methods covered are primarily aimed at applications in basic science and clinical research (not clinical practice) and include:

Functional MRI: GLM analysis, including Bayesian multi-subject statistics (FEAT), ICA Model-free analysis, functional connectivity (MELODIC)

Structural MRI: Image registration and unwarping (FLIRT/FNIRT/FUGUE & BBR), Brain extraction and tissue-type segmentation (BET/FAST), Structural spatial statistical analysis e.g. atrophy (SIENA/FSL-VBM), Automatic subcortical segmentation / alignment (FIRST), white matter hyperintensities (BIANCA).

Diffusion MRI: Probabilistic diffusion modelling and tractography, including crossing-fibres (FDT) Diffusion tensor fitting and voxelwise multi-subject analysis (DTIFIT/TBSS), Correction for motion, distortions and eddy-current effects (TOPUP/EDDY)

Resting-State Networks and Connectivity: Resting-State functional MRI analysis (dual regression), Functional and structural connectivity analysis

All lectures and practical material will be in English.

This course does not provide any CME credits and we will cover neuroimaging analysis for basic science and clinical research but not clinical practice.


Each attendee will need to have their own computer (Mac, Windows, Linux) in order to access the cloud based desktop and for video conferencing with tutors in the guided practical sessions. It is therefore essential that you have a reasonable internet connection - one that will allow video conferencing - so most home internet will be fine.  It does not need to be super-fast but we will be relying on it during the practical sessions, and we cannot be responsible for any internet outages or speed problems during the course, although we will do whatever is within our power to provide you with the best service.

We are committed to supporting all users, from all countries, and we will provide alternative options to certain platforms (e.g. zoom) if they are not available in your country. We need to know where you will be connecting from (and not what your country of origin/residence is) in order to setup the appropriate platforms, in the appropriate geographic regions to maximise your experience.


The course organisers for this course are: Jesper Andersson, Janine Bijsterbosch, Sean Fitzgibbon, Ludovica Griffanti, Taylor Hanayik, Mark Jenkinson, Kamila Szulc-Lerch and Michele Veldsman

Tutors on the course have all been trained in FSL at the University of Oxford, and include those currently still there as well as those now at other universities. The list of tutors is: Jesper Andersson, Matteo Bastiani, Luke Baxter, Christian Beckmann, Janine Bijsterbosch, Michiel Cottaar, Nicola Dinsdale, Eugene Duff, Hanna Nowicka, Rezvan Farahibozorg, Liv Harrison (née Faull), Sean Fitzgibbon, Sezgi Goksan, Ludo Griffanti, Taylor Hanayik, Sam Harrison, Saad Jbabdi, Mark Jenkinson, Rick Lange, Marieke Martens, Paul McCarthy, Clare O'Donoghue, Emma Robinson, Steve Smith, Natalie Voets, Matthew Webster, Anderson Winkler and Moss Zhao.


Two separate courses will be run, in order to cater for different timezones. The content for the two courses will be identical. Each attendee will need to choose one course to register for and then stick with those times.  The times for the live practical sessions with the tutors are:

Course A: 9am-12noon (UK) / 10am-1pm (Europe) / 11am-2pm (Israel) / 12:30pm-3:30pm (Iran) / 1:30-4:30pm (India) / 4pm-7pm (China/Singapore) / 6pm-9pm (Melbourne) / 8pm-11pm (New Zealand)

Course B: 3pm-6pm (UK) / 10am-1pm (East Coast USA) / 7am-10am (West Coast USA)

Each day of the course covers a different topic (what would normally have been covered in one morning or afternoon of the traditional course). The topics and dates are as follows:

Day Date Topic
Tuesday 8 Sep. Registration and Distortion Correction
Wednesday 9 Sep. Segmentation and Structural Analysis
Thursday 10 Sep. Statistics & Task fMRI: Basic GLM and Single-Subject Analysis
Friday 11 Sep. Statistics & Task fMRI: Inference and Group Analysis
Monday 14 Sep. Statistics & Task fMRI: Advanced GLM and Noise Correction
Tuesday 15 Sep. Resting-State fMRI: ICA and Dual Regression
Wednesday 16 Sep. Resting-State fMRI: Network Analysis with FSLNETS
Thursday 17 Sep. Diffusion Tensor Imaging and TBSS
Friday 18 Sep. Diffusion Tractography

Recorded lectures associated with each topic will be available and should be watched before the practical session (ideally no more than 48 hours before the practical session, so that it is fresh in your mind).

There will also be an online social networking event early in the course. More details will be provided at the beginning of the course.

Preparatory Material (before the course)

During the FSL Course, we will be covering a lot of material in a short period of time. To make the most of our time together, we have put together some preparatory material that we ask you to complete before attending the FSL Course.

This consists of a lecture set of three short introductory FSL practicals on FSLeyes, BET, and FSL Utils.

There is also a set of five videos on "Introduction to UNIX". The Introduction to UNIX videos are optional. However, if you do not have experience using a terminal, then these are extremely useful to watch before the course.

Links to all the videos and accompanying data and instructions can be found on the FSL Course Material website.

Please allow at least three hours to go through the material on a computer that has FSL installed. If you do not have FSL installed you can still watch the videos to learn some basics before the course. During the course it will be expected that the preparatory materials listed above have been completed. If you are entirely new to neuroimaging the course will feel like a lot of new information in a very short time. Therefore, for those with little or no prior experience, we strongly recommend the Introduction to Neuroimaging Analysis Primer as a very useful introduction.

If you are looking for additional materials before or after the course, we recommend the Oxford Neuroimaging Primers. This bookseries published by Oxford University Press contains several short introductions and currently includes: 'Introduction to Neuroimaging Analysis' and, 'Introduction to Resting State fMRI Functional Connectivity'. These primers have been specifically written with the target audience of the FSL Course in mind.