FSL Course

2017 FSL mini-Course Downunder: Adelaide, Australia (17-21 November)

We are pleased to announce that the 2017 mini-course downunder is now open.

Register at the course website

The FSL Course is an intensive course that 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.

The details of the 2018 FSL Course are not yet finalised. It will probably take place in spring or summer 2018. However, until times and venues are finalised, and officially announced, nothing is guaranteed.

Full details will be posted on this website and on the FSL list as soon as they have been finalised.

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

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 (2017 Course)

All material copyright © 2017, FMRIB Analysis Group.

Introductory lecture

video part 1, video part 2 / slides

Practicals

Unix section

video playlist / handout

Data Files

Data for FSL practicals

Data for UNIX practicals

Additional UNIX help

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


Lecture Slides & Practical Data (2017 Course)

All material copyright © 2000-2017, 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. 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
  3. Model-Free FMRI Analysis  (MELODIC)  lecture / practical
  4. Resting-State and Connectivity Analysis  (dual regression) lecture / practical
  5. Diffusion MRI Analysis  (FDT, TBSS)  lecture / practical
  6. Diffusion Tractography  (FDT)  lecture / practical
  7. Segmentation & Structural Statistics  (FAST, FIRST, SIENA, FSL-VBM) lecture / practical
  8. 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

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.