| FSL - The FMRIB Software Library (Release 1.2, December 2000) | ![]() |
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.
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".
Tool | Description | V | CLI | GUI |
---|---|---|---|---|
BET | Brain Extraction Tool - automatically segments brain from non-brain. | 1.1 | ![]() | ![]() |
FLIRT | FMRIB's Linear Image Registration Tool - automatic accurate robust linear (affine) inter- and intra-modal registration | 2.2 | ![]() | ![]() |
FEAT | FMRIB'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 statistics | 4.0 | ![]() | |
SUSAN | nonlinear (doesn't blur edges) noise reduction for 3D images | ![]() | ![]() | |
IRVA | Inter-Repetition Variance Analysis - tool for running an FMRI analysis without specifying a waveform (also available from inside FEAT) | ![]() |
In the future, we will be adding to FSL:
Tool | Description | CLI | GUI |
---|---|---|---|
EROS | Extraction of Robust Orientation using Symmetry - robust detection of the mid-sagittal plane) | ![]() | ![]() |
ABSIIC | Segmentation and bias field correction, using Markov random fields to add neighourhood information to the segmentation | ![]() | ![]() |
MELODIC | ICA model-free FMRI analysis | ![]() | ![]() |
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), 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.
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.
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.
You will require:
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
Release 1.2, December 2000:
Release 1.1, August 2000: