= FSL information =

FSL is the FMRIB Software Library.  It is a C / C++ / Tcl/Tk package written by the Oxford analysis group.

For more information see:

 * Main page: http://www.fmrib.ox.ac.uk/fsl
 * FAQ: http://www.fmrib.ox.ac.uk/fslfaq/
 * FSL course notes: http://www.fmrib.ox.ac.uk/fslcourse/

On our system, the current version of FSL (that is, the version you get by typing 'fsl' at the command prompt) is the one pointed to by the link `/imaging/local/linux/fsl`.  At the time of writing this is the slightly outdated 3.2 version.

You can find the FSL example data set (http://www.fmrib.ox.ac.uk/fsl/feeds/doc/index.html) in `/imaging/local/fsl/feeds`.

The data for the FSL course is in `/imaging/local/fsl/fslcourse`.

Any problems, report them to MatthewBrett or RhodriCusack.

== Using a specific version of FSL on the CBU systems ==

If you need to use a specific version, rather than the one pointed to by `/imaging/local/linux/bin/fsl`, then define the path to the version of FSL you want, and put something like this at the end of your `~/.cshrc` file:

{{{
# FSL stuff
setenv FSLDIR /imaging/local/linux/bin/fsl-3.3.11
source ${FSLDIR}/etc/fslconf/fsl.csh
set path = (${FSLDIR}/bin $path)
}}}

In order for this to work when you login across linux machines, you will (I'm afraid) also need to put the same lines in your `~/.login` file.  Put these lines somewhere between the lines `#  Space for personal defaults` and `#  End space for personal defaults` in the `~/.login` file.

You can check which version of FSL you are getting by typing `fsl` at the unix prompt, and looking at the version number at the top of the FSL button window - for FSL 3.3.11 it should read FSL 3.3.  Oddly, you can't check which version of FSL you are getting by typing `which fsl` in unix - because, the version that you actually get depends on the `FSLDIR` environment variable, which can be mis-set, without the fixes above.