FSL is available precompiled for various different operating systems (Linux, Mac OS X, Windows, SunOS). The sources are also available if you want to compile it yourself.
To unpack a distribution, you need gunzip and tar. First cd to the directory where you want FSL installed (for example /usr/local). Then uncompress and untar the distribution - for example, if you have downloaded the Redhat 9 distribution to your home directory, type
gunzip ~/fsl-3.2-redhat9.tar.gz tar xvf ~/fsl-3.2-redhat9.tar
Put the following somewhere in your shell setup file (.bashrc, .profile, .cshrc etc., depending on what shell you use), setting the "/usr/local/fsl" to wherever you have installed FSL:
bash / sh / ksh
FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
tcsh / csh
setenv FSLDIR /usr/local/fsl
source ${FSLDIR}/etc/fslconf/fsl.csh
setenv PATH ${FSLDIR}/bin:${PATH}
To run the FSL tools from the command line, you can find the tools in $FSLDIR/bin. In general command-line programs are lower case (e.g. 'bet'). In general the GUI version is capitalised (e.g. 'Bet'), except on Mac/Windows, where '_gui' is appended because those file systems can't tell the difference between upper and lower case (e.g. 'Bet_gui').
To bring up a simple GUI which is just a menu of the main
individual FSL GUI tools, just type fsl.
There are several environment variables which FSL uses to determine certain user preferences, such as the output file format (NIFTI, Analyze, etc). The defaults for these are set when you source the setup file as shown above (i.e., ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.csh). If you wish to change these defaults then you need to:
cd mkdir .fslconf cd .fslconfand in this directory create a file called fsl.sh or fsl.csh, depending on the shell that you use, setting any or all of the variables that appear in the central ${FSLDIR}/etc/fslconf/fsl.sh or ${FSLDIR}/etc/fslconf/fsl.csh files.
DO NOT copy the central files into ~/.fslconf/ as it will cause a loop that will stop your login from working.
It is recommended that the files ~/.fslconf/fsl.sh or ~/.fslconf/fsl.csh only include a few variable definitions and nothing more. Note that whoever installs FSL can also edit the central files in $FSLDIR/etc/fslconf to change the preferences for all users.