FSL - The FMRIB Software Library (beta release, June 2000)
| | FSL - The FMRIB Software Library (beta release, June 2000) |
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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.
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.
| Tool | Description | V | CLI | GUI |
|---|---|---|---|---|
| BET | Brain Extraction Tool - automatically segments brain from non-brain. | 1.1 |  |
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| FLIRT | FMRIB's Linear Image Registration Tool - automatic accurate robust linear (affine) inter- and intra-modal registration | |
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| 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 model-free analysis |
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| SUSAN | nonlinear (doesn't blur edges) noise reduction for 3D images | |
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| Model-Free ANOVA | tool for running an FMRI analysis without specifying a waveform (also available from inside FEAT) |
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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) | |
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| Segmentation and bias field correction, using Markov random fields to add neighourhood information to the segmentation | |
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| McFLIRT | FMRI motion correction | |
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| FMRI group analysis tool | |
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| Exploratory Data Analysis Techniques | |
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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 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.
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.
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:
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).