FSL - The FMRIB Software Library (Release 1.2, December 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.

FSL is completely self-contained. Most of the tools can be run either from the unix command line or as GUIs (graphical user interfaces).

Whilst the GUIs in FSL can be used standalone, you can also configure MEDx to access them, if you have it. (MEDx is a GUI-driven commercial image analysis and display package, available from Sensor Systems.) Also, at some point soon, MEDx will probably come with a version of FSL built in.

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 ticked under "CLI" (Command Line Interface) and tools which can be run as a GUI are ticked under "GUI".


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 registration2.2YY
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 HRF-model-free analysis, automatic registration to structural and/or standard space, and fixed- and random-effects group statistics4.0Y
SUSANnonlinear (doesn't blur edges) noise reduction for 3D images YY
IRVAInter-Repetition Variance Analysis - tool 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
ABSIICSegmentation and bias field correction, using Markov random fields to add neighourhood information to the segmentationYY
MELODICICA model-free FMRI analysisYY

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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 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), Nicola De Stefano (Neurometabolic Unit and NMR Center, University of Siena), 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: Newmat, Cephes, Gnuplot, Sphere tesselation, ImageMagick, Tcl/Tk/Tix 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 (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.

Compiling the uncompiled distribution

You will require:

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

Running

First, set environment variable FSLDIR to the top fsl directory name, e.g. /usr/local/fsl .

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 captilised (e.g. 'Bet'). The GUI called "fsl" is simply a pointer to the other main GUIs in FSL - you probably want to start with this.

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).

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

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WHAT'S NEW IN THIS RELEASE

Release 1.2, December 2000:


Release 1.1, August 2000:


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Steve Smith
FMRIB Analysis Group

Copyright © 2000, University of Oxford