FSL - The FMRIB Software Library (beta release, June 2000)


CONTENTS


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.

Some of the tools in FSL can be run from the unix command line. This means that you can use them without any other packages installed on your computer. For example, BET brain extraction and FLIRT image registration can be used in this way.

Also, some of the FSL tools can be run as point-and-click X-Windows GUIs (graphical user interfaces). Some users will find this easier than from the unix command line.

Many of the FSL tools can be run in both ways. The GUIs can only, at present, be used as extensions of MEDx. MEDx is a GUI-driven commercial image analysis and display package, available from Sensor Systems. A future release of FSL will allow the running of the GUIs without MEDx.

For up-to-date information regarding FSL see the FSL home page or email fsl@fmrib.ox.ac.uk.

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LIST OF TOOLS IN FSL

Tools which can be run from the Unix command line are so marked under "CLI" (Command Line Interface), and tools which can be run as a GUI as an extension of MEDx are so marked under "GUI". There are also a number of scripts which extend the functionality of MEDx; for the full list of FSL MEDx extensions, see the FSL MEDx Menu Page.


ToolDescriptionVCLIGUI
BETBrain Extraction Tool - automatically segments brain from non-brain.1.1YY
FLIRTFMRIB's Linear Image Registration Tool - automatic accurate robust linear (affine) inter- and intra-modal registration YY
FEATFMRIB's Easy Analysis Tool - Advanced FMRI analysis with easy-to-use GUI, FILM (FMRIB's Improved Linear Model, the main program at the heart of FEAT) analysis and model-free analysis Y
SUSANnonlinear (doesn't blur edges) noise reduction for 3D images YY
Model-Free ANOVAtool for running an FMRI analysis without specifying a waveform (also available from inside FEAT) Y

In the future, we will be adding to FSL:
ToolDescriptionCLIGUI
EROSExtraction of Robust Orientation using Symmetry - robust detection of the mid-sagittal plane)YY
Segmentation and bias field correction, using Markov random fields to add neighourhood information to the segmentationYY
McFLIRTFMRI motion correctionYY
FMRI group analysis toolYY
Exploratory Data Analysis TechniquesYY

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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.

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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 model-free FMRI analysis 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; Alison Noble, Lecturer, Medical Vision Lab, Dept. Engineering Science; Brian Ripley, Professor of Applied Statistics, Dept. Statistics.

FMRIB is largely supported by the Medical Research Council, UK. Financial support is also gratefully received from EPSRC and GlaxoWellcome.

FSL uses the following third party freeware, for which we are very grateful: Newmat, Cephes, Gnuplot, Sphere tesselation, ImageMagick and gifmerge.

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DOWNLOADING, INSTALLING AND RUNNING FSL

Downloading

FSL is available as a single package. As well as the uncompiled FSL 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.

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.

Compiling the uncompiled distribution

You will require:

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

Running

To run the FSL tools from the command line, you can find the tools in fsl/bin. All programs use Analyze 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).

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Steve Smith
FMRIB Analysis Group

Copyright © 2000, University of Oxford