FSL Course

2017 FSL Course: UBC, Vancouver, Canada (19-23 June)

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

Register at the 2017 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.

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

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

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 (2016 Course)

All material copyright © 2000-2017, FMRIB Analysis Group & MGH, Boston.

Lectures and Practicals

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 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;
    

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


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/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/rest.tar.gz
    

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