FSL Course

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.

Upcoming Courses

The details of the 2017 FSL Course are not yet finalised. It will probably take place in spring or summer 2017. 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.

Past Courses

2016 - Sicily, Italy     2011 - Montreal, Canada     
2015 - Honolulu, USA      2010 - Heidelberg, Germany     2005 - Waltham, USA
2014 - Oxford, UK 2009 - San Francisco, USA2004 - Würzburg, Germany
2013 - Redmond, USA 2008 - Brisbane, Australia2003 - Los Angeles, USA
2012 - Bristol, UK 2007 - Cardiff, UK 2002 - Oxford, UK
2012 - Auckland, New Zealand 2006 - Siena, Italy 2002 - Melbourne, Australia

Lecture Slides & Practical Data (2015 Course)

All material copyright © 2000-2015, FMRIB Analysis Group & MGH, Boston.

Lectures and Practicals

Documentation for FSL can be found at the FSL wiki

FreeSurfer material can be found here.


People with no previous experience of UNIX would benefit greatly from spending a few hours working through at least the first 5 sections of A Basic UNIX Tutorial.


Data Files

The data for the course is divided into 6 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:

      tar zxf fdt1.tar.gz; tar zxf fdt2.tar.gz; tar zxvf fmri.nii.gz
      tar zxf intro.tar.gz; tar zxf registration.tar.gz; tar zxvf rest.nii.gz
      tar zxf scripting.tar.gz; tar zxf seg_struc.tar.gz; tar zxvf tbss.nii.gz
    

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'.


2014 Physics / Applications


2013 Physics / Applications


2012 Physics / Applications


2011/2010 Physics


2007 Physics / Applications


2006 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:

      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/fmri.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/intro.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/registration.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/scripting.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/seg_struc.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz
      wget -c http://fsl.fmrib.ox.ac.uk/fslcourse/rest.tar.gz
    

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:

      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/fdt1.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/fdt2.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/fmri.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/intro.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/registration.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/scripting.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/seg_struc.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/tbss.tar.gz
      curl -# -O -C - http://fsl.fmrib.ox.ac.uk/fslcourse/rest.tar.gz
    

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