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').
To bring up a simple GUI which is just a menu of the main
individual FSL GUI tools, just type fsl.