FSL Course

Upcoming Courses:

2018 FSL Course: San Diego, 29 October - 2nd November 2018

2019 Mini FSL Course: Dunedin, New Zealand, 18 - 22 February 2019

2019 FSL Course: Croatia, 17-21 June 2019 ( Save the date )

The main 2019 FSL Course will take place in Croatia 17-21 June 2019 (the week after the OHBM conference in Rome), and will have a substantially larger capacity. More information about the larger main course will become available in early 2019, when registration for this course will also open. Please note that the location for this course is to be confirmed, so we recommend that you do not book any travel until the course is announced.

Contact

If you have a query about the FSL course please contact us on fslcourse@fmrib.ox.ac.uk

Note that, as stated above, we will not have any more information about future course dates or locations until arrangements are finalised, at which time the information will immediately appear on this website.

Past Courses

2018 - Oxford, UK
2017 - Vancouver, Canada     2012 - Auckland, New Zealand     2006 - Siena, Italy
2016 - Sicily, Italy2011 - Montreal, Canada2005 - Waltham, USA
2015 - Honolulu, USA2010 - Heidelberg, Germany2004 - Würzburg, Germany
2014 - Oxford, UK2009 - San Francisco, USA2003 - Los Angeles, USA
2013 - Redmond, USA2008 - Brisbane, Australia2002 - Oxford, UK
2012 - Bristol, UK2007 - Cardiff, UK2002 - Melbourne, Australia
     

Preparatory material

All material copyright © 2017-2018, FMRIB Analysis Group.

Introductory lecture

video part 1, video part 2 / slides

Practicals

Unix section

video playlist / handout

Data Files

Data for FSL practicals

To follow along directly with the tutorial videos the two folders contained in preCourse.tar.gz need to be copied into a folder in your home directory called fsl_course_data ( referred to as ~/fsl_course_data in the videos ).

Data for UNIX practicals

Additional UNIX help

Additonal UNIX help can be found in:A Basic UNIX Tutorial.


Lecture Slides & Practical Data (2018 Course)

All material copyright © 2000-2018, FMRIB Analysis Group & MGH, Boston.

Lectures and Practicals

  1. Brain Extraction, Registration, Motion Correction and EPI Distortion   (BET, FLIRT, MCFLIRT, PRELUDE & FUGUE)   lecture / practical
  2. Segmentation & Structural Statistics  (FAST, FIRST, SIENA, FSL-VBM) lecture / practical
  3. FMRI Preprocessing and Model-Based Analysis  (FEAT)
    1. Preprocesing and Simple Single-Session Stats   lecture part 1, part 2 / practical
    2. Permutation Testing (Randomise) and Multi-Subject Stats    lecture part 1, part 2 / practical
    3. Advanced FMRI Analysis    lecture / practical
  4. Resting-State Analysis, ICA  (MELODIC, dual regression)  lecture / practical
  5. Resting-State Analysis, Network Modelling  (FSLNets) lecture / practical
  6. Diffusion MRI Analysis  (FDT, TBSS)  lecture / practical
  7. Diffusion Tractography  (FDT)  lecture / practical
  8. Arterial spin labelling  (ASL) lecture / practical
  9. Scripting  lecture & practical. This is not a formal part of the course, but can be carried out on your own during the course if you have time to spare. Within the lecture web pages, to find the interleaved practical instructions, click on the e symbols when they appear in the lecture slides, or go to the lecture index (via the up arrow in the bottom right) and find the green links.

Documentation for FSL can be found at the FSL wiki

FreeSurfer material can be found here.


Data Files

The data for the course is divided into a number of parts due to the size of the data and can be downloaded using the links below, or using wget [Linux] or curl [Mac OS X]. If you are working at the FMRIB Centre then please see these instructions for information on following the course inside FMRIB.

Once you have downloaded the files they need to be uncompressed before you can begin the course. To do this, open a terminal, change into the folder where you downloaded the course files to and run the following commands:


    
    

NB If you downloaded the files using Safari on Mac OS X, then they may already have been uncompressed, ie missing the .gz extension. In this case, change the tar commands above to 'tar xf'.


Evening/Additional Lectures

2018 Physics

2014 Physics / Applications


2013 Physics / Applications


2012 Physics / Applications


2011/2010 Physics


2007 Physics / Applications


All material copyright © 2006-2014 held by talk/practical authors

Using wget to download the course data

As the course data files are large, Linux users may find that using the wget command to download the course data files is more reliable. In a terminal, change to the folder you wish to download the data to and issue the following commands:


    
    

If, for some reason your wget downloads are interrupted, you can restart any incomplete downloads by running that wget command again.

Using curl to download the course data

As the course data files are large, Mac users may find that using the curl command to download the course data files is more reliable. In a terminal, change to the folder you wish to download the data to and issue the following commands:


    
    

If, for some reason your curl downloads are interrupted, you can restart any incomplete downloads by running that curl command again.