= 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/

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 RhodriCusack.

== Using the latest version of FSL ==

Before running fsl you need to run 

{{{
fsl_4.1.0_setup
}}}

which is the latest version of fsl at the moment. By running this command you are also using load sharing with any fsl command. If you want to check if you are using the latest version try 
{{{
which fsl
}}}

== 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. By using this method load sharing is not used automatically.