FSL mini-Course Downunder

17-21 November 2017
Adelaide, Australia

Organised by the Wellcome Centre For Integrative Neuroimaging, University of Oxford

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Learn the theory and practice of functional and structural brain image analysis

We are pleased to announce the FSL mini-Course Downunder, to be held at Adelaide Health & Medical Sciences Building, University of Adelaide, Australia (17-21 November). This is the week before the 2017 Australasian Cognitive Neuroscience Society in Adelaide.

This intensive 4-day course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data. After completing the course, attendees should be able to analyse their own FMRI and 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)
  • 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.


Registration (in UK pounds) is £350 for PhD/MSc students (this includes anyone who is currently registered as a student with your University or Institution), £500 for postdocs and other non-student attendees, and £1200 for commercial attendees.

Course registration includes lectures, computer practical sessions, and coffee/tea breaks. Course materials (lecture slide PDFs, and practical instructions) will be available in electronic format during the course.

All course material and practical datasets will also be available online after the course.

The registration fee does not include accommodation (see below), or lunches; there are plenty of local shops, cafes and restaurants where course attendees will be able to get lunch.

We are only able to take payment by credit card. To register and pay, visit the on-line registration page. Please note that your registration is not complete until you have finalised the payment (going to the shopping basket and then to checkout and payment).

Accommodation & Location Information

The course will take place at the Adelaide Health & Medical Sciences Building, University of Adelaide, North Terrace, Adelaide SA 5000, Australia.

You will need to organise your own accommodation for the course. There are many accomodation options within the city of Adelaide. Please see the map below for hotels (in blue) and backpackers/hostels (in green) that are within walking distance of the Adelaide Health & Medical Sciences Building. All of the listed options have ratings of at least 3 out of 5 on Google and TripAdvisor, and if you click on a venue the description includes a link to the TripAdvisor review. There are also a number of Airbnb's available within the city.

Preparatory Material - Important

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 in Adelaide, we have put together some preparatory material that we ask you to complete before attending the FSL Course. This consists of: i) a lecture, ii) a set of three short introductory FSL practicals, and iii) 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 website: the FSL Course website. Please allow at least three hours to go through the material on a computer that has FSL installed.


Mark Jenkinson, Sean Fitzgibbon, Olivia Faull, Sam Harrison, Paul McCarthy

Preliminary Timetable: November 2017

Please note that there may be some minor changes to the timetable.

Contact Details

If you have any queries about the course, please email fslcourse@fmrib.ox.ac.uk