Downloading

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 (including all necessary third-party software) 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.

Download FSL



Unpacking

To unpack a distribution, you need gunzip and tar. Type

gunzip ???whatever???.tar.gz
tar xvf ???whatever???.tar




Compiling the source distribution

If you have not taken a precompiled version, you will require:

Then cd into the top level (fsl) and type BUILD.



Running

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. Where there is a choice between GUI and non-GUI version of a tool, the non-GUI version is fully lower case (e.g. 'bet'), whilst the GUI version is capitalised (e.g. 'Bet'). "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).

Quick start

(If you don't know what shell you are using, try both of the following)
bash users: export FSLDIR=/usr/local/fsl; export PATH=$PATH:$FSLDIR/bin; $FSLDIR/bin/fsl
tcsh users: setenv FSLDIR /usr/local/fsl; setenv PATH ${PATH}:$FSLDIR/bin; rehash; $FSLDIR/bin/fsl



Running FSL on Apple Mac

The binary distribution of FSL for Apple Mac requires Mac OS X (tested under 10.1 and 10.2). If you are happy to run FSL tools from the command line, then you need install NO other software on your Mac (simply set FSLDIR to the top fsl directory name as described above and include ${FSLDIR}/bin in your path). If you want to use the FSL GUIs then you will need to install X windows on top of Mac OS X (by default Mac OS X comes with a different window system - Aqua - which can work alongside X but which cannot on its own run X windows programs such as the FSL GUIs). Installing X on Mac OS X is easy:


Windows program for viewing AVW images

There is a nice tool (separate from FSL), for viewing AVW images (including colour AVW images generated by FSL) - go to 3D VisionWorks.