| FSL - The FMRIB Software LibraryRelease 1.3, June 2001FMRIB Image Analysis Group, Oxford University | ![]() ![]() |
The FMRIB Software Library (FSL) is a collection of functional and structural brain image analysis tools, written mainly by members of the Image Analysis Group in FMRIB, Oxford University.
FSL is completely self-contained. Most of the tools can be run both from the unix command line and as GUIs (easy to use "point-and-click" graphical user interfaces).
You do not need any other software in order to use FSL. However, if you have MEDx, you can configure it to seamlessly access the FSL GUIs. MEDx is a GUI-driven commercial image analysis and display package, available from Sensor Systems. The latest version of MEDx (3.4) comes with FSL release 1.2a built in.
For up-to-date information regarding FSL see the FSL home page. For support relating to FSL or related theory, email the FSL email list or, even better, join the FSL email list.
Tools which can be run from the unix command line are ticked under CL and tools which can be run as a graphical user interface are ticked under GUI.
CL | GUI | |||
---|---|---|---|---|
Structural tools | ||||
BET | Brain Extraction Tool - segments brain from non-brain in structural and functional data. | ![]() | ![]() | |
SUSAN | Nonlinear noise reduction. | ![]() | ![]() | |
FAST | FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction. | ![]() | ![]() | |
FLIRT | FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration. | ![]() | ![]() | |
FUGUE | Unwarps geometric distortion in EPI images using B0 field maps. | ![]() | ||
SIENA | Structural brain change analysis, for estimating brain atrophy. | ![]() | ||
Functional tools (note - BET, FLIRT and FUGUE are also used in functional analysis) | ||||
FEAT | FMRIB's Easy Analysis Tool - Advanced FMRI analysis with easy-to-use yet powerful GUI. Includes all necessary preprocesing, model-based and semi-model-free statistical analysis, automatic registration to structural and/or standard space, and fixed- and random-effects group statistics. | ![]() | ![]() | |
MCFLIRT | FMRI motion correction. | ![]() | ||
MELODIC | ICA-based model-free analysis of FMRI (and other 4D) data. | ![]() | ![]() | |
Miscellaneous tools. | ||||
AVWUTILS | Misc utils for converting and processing images. | ![]() | ||
SLICER | Simple (non-interactive) image display utilities | ![]() |
FSL is distributed as freeware under the GNU Public License. For detailed licensing information, please see the FSL LICENSE file, and also the GPL file.
The following people have contributed to the development of FSL: Peter Bannister, Christian Beckmann, Stuart Clare*, David Flitney, Peter Hansen, Mark Jenkinson, Didier Leibovici, Steve Smith, Mark Woolrich, Yongyue Zhang.
*Stuart is in the FMRIB physics group. The IRVA method was originally developed by Stuart at the MR Centre, Nottingham.
We are also grateful to the following people for very useful collaborations: Mike Brady (Professor of Information Engineering, Medical Vision Lab, Dept. Engineering Science, Oxford), Jacqueline Chen (MRS Lab, McConnell Brain Imaging Centre, MNI, Canada), Nicola De Stefano (Neurometabolic Unit and NMR Center, University of Siena, Italy), Jonathan Marchini (Dept. Statistics, Oxford), Paul Matthews (Director, FMRIB), Alison Noble (Reader, Medical Vision Lab, Dept. Engineering Science, Oxford), Brian Ripley (Professor of Applied Statistics, Dept. Statistics, Oxford) and the FMRIB Physics, Pain and Disease Groups.
FMRIB is largely supported by the Medical Research Council, UK. Financial support is also gratefully received from EPSRC and GlaxoWellcome.
FSL includes the following third party freeware, for which we are very
grateful:
Cephes,
Gifmerge.
Gnuplot,
ImageMagick,
Newmat,
Sphere tesselation and
Tcl/Tk/Tix.
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.
To unpack a distribution, you need gunzip and tar. Type
gunzip ???whatever???.tar.gz tar xvf ???whatever???.tar
If you want to run the GUIs as extensions of MEDx, then either the top level FSL directory (fsl) should be placed inside the top level MEDx directory, or you need to set an environment variable before running MEDx; set variable FSLDIR to the full path name of the top level FSL directory (fsl). You also need to install a few files into the standard MEDx distribution: see file fsl/etc/medx_customisation/README. Note that MEDx versions 3.4 (and higher) come bundled with FSL. If you integrate this release of FSL into MEDx (to take advantage of newer FSL features) then this will not interfere with the bundled FSL. The bundled FSL is accessed through the MEDx Toolbox whilst this version will appear on the main (small) MEDx window.
You will require:
First, set environment variable FSLDIR to the top fsl directory name, e.g. /usr/local/fsl . Next, include ${FSLDIR}/bin in your path.
To run the FSL tools from the command line, you can find the tools in fsl/bin. Where there is a choice between GUI and non-GUI version of a tool, the non-GUI version is fully lower case (e.g. 'bet'), whilst the GUI version is capitalised (e.g. 'Bet'). "fsl" is a simple GUI which will start up the main individual FSL GUI tools - you probably want to start with this.
All programs use Analyze (AVW) format files, as used by Analyze, MEDx, SPM etc.
Some of the tools are separately compiled for each image data type (8-bit unsigned, 16-bit signed, etc.) named e.g., bet_8UI, bet_16SI, etc. Note that there is a mechanism in place to choose which to call automatically; e.g., bet detects which data type is being processed, and then calls the appropriate binary name on the basis of the original program name (e.g. bet) and the data type (e.g. 16SI).
bash users: export FSLDIR=/usr/local/fsl; export PATH=$PATH:$FSLDIR/bin; $FSLDIR/bin/fsl
tcsh users: setenv FSLDIR /usr/local/fsl; setenv PATH ${PATH}:$FSLDIR/bin; $FSLDIR/bin/fsl
Release 1.3, June 2001:
Release 1.2a, May 2001 (not an FSL release but the version bundled with MEDx 3.40):
Release 1.2, December 2000:
Release 1.1, August 2000:
Release 1.0 (beta), June 2000. First ever release, containing: