FSL is available as a single package. As well as the FSL source distribution, which needs compiling before it can be used, FSL is available precompiled for some platforms. If you want to just run certain tools then the easiest thing to do is take the appropriate precompiled distribution and find the relevant program in fsl/bin.
To unpack a distribution, you need gunzip and tar. Type
gunzip ???whatever???.tar.gz tar xvf ???whatever???.tar
First, set environment variable FSLDIR to the top fsl directory name, e.g. /usr/local/fsl . Next, include ${FSLDIR}/bin in your path.
To run the FSL tools from the command line, you can find the tools in fsl/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 (e.g. 'Bet_gui'). 'fsl' is a simple GUI which will start up the main individual FSL GUI tools - you probably want to start with this.
All programs use Analyze (AVW) format files, as used by Analyze, MEDx, SPM etc.
Some of the tools are separately compiled for each
image data type (8-bit unsigned, 16-bit signed, etc.) named e.g.,
bet_8UI, bet_16SI, etc. Note that there is a mechanism in place to
choose which to call automatically; e.g., bet detects which data type
is being processed, and then calls the appropriate binary name on the
basis of the original program name (e.g. bet) and the data type
(e.g. 16SI).