The provisional dates for the next FSL Course are September 15th to 26th, 2025.
This course will be held online and will be the only FSL course in 2025.
Registration for the next course will open soon!
Learn the theory and practice of functional and structural brain image analysis. We have hosted the FSL course for over 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.
The course will take place at the Sky Building in Osaka, Japan. All FSL course material will be delivered via in-person lectures and guided practical exercises. There will be no hybrid or remote attendence option. We will be providing cloud desktops for attendees, complete with all the data and software you will need. Attendees just need to provide their own laptop during the course. You will interact with expert tutors and other course attendees. We will support you through all the practical, hands-on sessions.
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.
FSL is used in 250+ countries. We aim to be inclusive, supporting our users across the world at all career stages.
Places are limited and will be allocated on a first-come, first-served basis. Please register early to reserve your place. Click here to register (opens a new page)
Registration for the next course will open soon!
Students are classified as PhD, MSc or undergraduate students. Commercial attendees are those from industry or other commercial organisations. Academic attendees include postdocs at any level, faculty, and other academic staff.
| Student/Pre-PhD Research Assistants | Postdoc/Faculty/Other Non-student Academic | Commercial |
|---|---|---|
Pricing will be available when the registration opens.
Attendees must arrange their own accomodation during the course. Accomodation is not included in the course fee.
There are many hotels near the Sky Building in Osaka. We suggest using one of the many hotel booking websites to find a hotel close to the course venue.
You can use this google maps link to explore hotels near the Sky Building in Osaka: Hotels near the Sky Building in Osaka
Attendees must arrange their own travel to and from the course. Travel is not included in the course fee.
We suggest flying into Osaka International Airport (ITM) or Kansai International Airport (KIX). There are public transport
options from both airports to the course venue. If you fly into a different airport, there are usually public transport options to get to Osaka.
Visa info: Depending on where you live or your nationality, you will need to meet certain entry requirements to visit Japan. More information on who can travel to Japan can be found here.
Attendees from low/middle income countries may be eligible for Imagining 4 All
funding. Please note we have no affiliation with the organisation and the link is presented for
information purposes only.
Contact us if you require a letter of invitation to attend the course.
The course will take place at the Sky Building in Osaka, Japan. We have reserved large meeting rooms for lectures and practical sessions for analysing data. We will provide cloud desktops for attendees to use during the course. Attendees just need to provide their own laptop, which they use to log into their FSL course desktop environment.
A Google Maps link to Stella Hall can be found here
| Time | Monday 17 June | Tuesday 18 June | Wednesday 19 June | Thursday 20 June | Friday 21 June |
|---|---|---|---|---|---|
| 8:00 - 8:30 | Course registration | ||||
| 8:30 - 9:15 | Registration (Frederik Lange) |
fMRI Preprocessing (Taylor Hanayik) |
Pipeline overview (Ludovica Griffanti) |
Resting state FSLNETS (Janine Bijsterbosch) |
Diffusion MRI (tractography) (Shaun Warrington) |
| 9:15 - 9:45 | Coffee/tea break | ||||
| 9:45 - 10:30 | Unwarping (Frederik Lange) |
GLM stats (Janine Bijsterbosch) |
Advanced fMRI (Michiel Cottaar) |
Resting state FSLNETS (Janine Bijsterbosch) |
Diffusion MRI (tractography) (Shaun Warrington) |
| 10:30 - 12:15 | Practical session | ||||
| 12:15 - 13:45 | Lunch (not provided) | ||||
| 13:45 - 14:30 | Segmentation (Ludovica Griffanti) |
Multi-subject stats (Janine Bijsterbosch) |
Resting state ICA (Seyedehrezvan Farahibozorg) |
Diffusion MRI (DTI) (Michiel Cottaar) |
Demos: New and upcoming FSL features and pipelines (multiple speakers) |
| 14:30 - 15:00 | Coffee/tea break | ||||
| 15:00 - 15:45 | Segmentation (Ludovica Griffanti) |
Inference (Frederik Lange) |
Resting state ICA (Seyedehrezvan Farahibozorg) |
Diffusion MRI (DTI) (Michiel Cottaar) |
Final day early close (3pm) |
| 15:45 - 17:30 | Practical session | ||||
| 17:45 - 18:00+ | Welcome reception (36F Sky Room, Tower East) |
This one week in-person course covers both the theory and
practice of
functional and structural brain image analysis. We will offer live lectures and guided practicals with
expert tutors. Since this is an in-person course, coffee/tea will be provided during breaks to all registered
attendees. Lunch is not provided, but there are many restaurants and cafes near the course venue.
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. 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.
Please note this is a provisional timetable for the 2025 Online Course and is subject to change!
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.
Each day of the course covers a different topic (what would normally
have been covered
in one morning or afternoon of the traditional course).
Recorded lectures associated with each topic will be available and should be watched before the practical session. You should account for 90-120 mins each day to watch the lectures, outside the practical session.
It is essential for attendees to watch the recorded lectures before the practical session (ideally less than 48 hours before) as otherwise you will not be able to understand the practical session. Tutors cannot be expected to explain the practical to you if you have not watched the lectures.
Each day, the first 30 minutes of the practical session will include a Q&A session with tutors and lecturers to answer the questions you may have on the lectures. It will also be possible to submit your questions in advance. We will then show a short introductory video presenting the content of the practical.
The remaining 2 hours (3 on the first day) are reserved for self-paced work through practicals with access to tutors on Zoom.
| Region | 15 Sep | 16 Sep | 17 Sep | 18 Sep | 19 Sep | 22 Sep | 23 Sep | 24 Sep | 25 Sep | 26 Sep |
|---|
| Region | 15 Sep | 16 Sep | 17 Sep | 18 Sep | 19 Sep | 22 Sep | 23 Sep | 24 Sep | 25 Sep | 26 Sep |
|---|
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 2h (3h on the first day), with an additional online lecture to watch beforehand. The course will last for ten
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 laptop computer (Mac, Windows, or Linux) in order to access the cloud based desktop in the guided practical sessions. Please be sure to bring your own charging cable. We cannot provide laptops for attendees, and we do not recommend using a small tablet or mobile device to access the cloud desktop environment.
Each attendee will need to have their own computer (Mac, Windows, Linux) in order to access the cloud based desktop in the guided practical sessions.
The organisers for this course are:
Fidel Alfaro-Almagro, Christian Beckmann, Renato Besenczi, Janine Bijsterbosch, Michiel Cottaar, Ludovica Griffanti, Kaitlin Krebs, Steve Smith, Rezvan Farahibozorg, and Matthew Webster
The teaching faculty for this course are: Fidel Alfaro-Almagro,
Janine Bijsterbosch (Washington University in St. Louis), Michiel Cottaar, Seyedehrezvan Farahibozorg, Masaki Fukunaga (National Institute for Physiological Sciences), Grace Gillis, Ludovica Griffanti,
Taylor Hanayik, Joe Kong (Chinese Academy of Sciences), Frederik Lange, Kiyotaka Nemoto (University of Tsukuba) and Shaun Warrington (University of Nottingham).
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.
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.