FSL - The FMRIB Software Library

Release 1.3, June 2001

FMRIB Image Analysis Group, Oxford University

INTRODUCTION - LIST OF TOOLS - LICENSING - CONTRIBUTORS - DOWNLOADING AND RUNNING - WHAT'S NEW

INTRODUCTION TO FSL

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.

LIST OF TOOLS IN FSL

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

LICENSING

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.

CONTRIBUTORS

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.

DOWNLOADING, INSTALLING AND RUNNING FSL

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

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.

Compiling the source distribution

You will require:

GNU make (this should be named gmake to make sure that FSL uses this rather than any other "make" in your path)
GNU install (this should be named ginstall to make sure that FSL uses this rather than any other "install" in your path)
GCC C/C++ compiler (You need gcc-2.95.2 or higher; however, note that gcc-2.96 is broken and will not compile FSL properly.)

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

convert and display from the ImageMagick package with added TIFF support (place convert and display in fsl/bin)
gnuplot (place gnuplot in fsl/bin)
Tcl and Tk and Tix (configure all three with configure --prefix=$FSLDIR before installing and compile Tix with make CC='cc -fwritable-strings').

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

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

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.

WHAT'S NEW IN THIS RELEASE

Release 1.3, June 2001:

New: MELODIC - ICA-based model-free analysis of FMRI (and other 4D) data.
New: FAST - Brain segmentation (into different tissue types) and bias field correction.
New: FUGUE - Unwarps geometric distortion in EPI images using B₀ field maps.
New: SIENA - Structural brain change analysis, for estimating brain atrophy.
FEAT 4.03: new features include F-tests and improved organisation of GLM-setup GUI.
FLIRT: new features include image masking/weighting, different output interpolations, and allowing 2D registration.

Release 1.2a, May 2001 (not an FSL release but the version bundled with MEDx 3.40):

FEAT 4.02: new features include F-tests and improved organisation of GLM-setup GUI.

Release 1.2, December 2000:

All GUIs can now run standalone - i.e., nothing in FSL needs MEDx in order to run.
FSL now includes MCFLIRT motion correction, which is more accurate, and faster, than the other tested MC methods. FEAT uses MCFLIRT only.
FILM (the GLM method inside FEAT) now uses general least-squares, prewhitening the data before the final fitting. This gives more efficient activation estimation than the other methods tested, particularly for dense single-event experiments. It includes autocorrelation correction, using smoothing of autocorrelation coefficients and nonlinear spatial filtering to achieve robust estimation.
A new GUI "fsl" which calls the other main FSL tools.
The "model-free ANOVA" method has been renamed "IRVA" (Inter-Repetition Variance Analysis) to avoid later confusion with ICA truly model-free analysis (to be released shortly).

Release 1.1, August 2000:

FEAT (FMRI analysis) will now use FLIRT (registration) to automatically register your FMRI data to a high-resolution structural and/or standard image for you, without having to use the FLIRT GUI separately.
FEAT can now run group statistics (fixed-effects and random-effects) across groups of FEAT directories, either in a single long FEAT run (consisting of multiple first-level analyses followed by group-stats) or on previously created FEAT directories.
You can now explicitly demand that certain EVs in FEAT be orthogonalised with respect to other EVs in the design matrix.
There is a bug fix in FLIRT; previously (when using FLIRT in MEDx), Talairach co-ordinates were incorrect when using certain standard images.
FSL now works with both the latest MEDx release (3.30) and the previous version (3.20).

Release 1.0 (beta), June 2000. First ever release, containing:

BET
SUSAN
FLIRT
FEAT
IRVA (then referred to as "Model-free ANOVA")