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<title>FMRIB Software Library</title>

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<span id="openzim-page-title" class="mw-page-title-main"><span class="mw-page-title-main">FMRIB Software Library</span></span>

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</style><table class="infobox vevent"><tbody><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Programmer" title="Programmer">Developer(s)</a></th><td class="infobox-data"><a rel="nofollow" class="external text" href="http://www.ndcn.ox.ac.uk/divisions/fmrib/fmrib-analysis-group">FMRIB Analysis Group</a></td></tr><tr style="display: none;"><td colspan="2" class="infobox-full-data"></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_release_life_cycle" title="Software release life cycle">Stable release</a></th><td class="infobox-data"><div style="margin:0px;">6.0.1

/ 11 March 2019<span style="display:none"> (<span class="bday dtstart published updated">2019-03-11</span>)</span></div></td></tr><tr style="display:none"><td colspan="2">

</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Written in</th><td class="infobox-data">C++, TCL</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Operating_system" title="Operating system">Operating system</a></th><td class="infobox-data"><a href="Linux" title="Linux">Linux</a>, <a href="MacOS" title="MacOS">macOS</a></td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Available in</th><td class="infobox-data">English</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_categories#Categorization_approaches" title="Software categories">Type</a></th><td class="infobox-data">Scientific visualization and image computing</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;"><a href="Software_license" title="Software license">License</a></th><td class="infobox-data">Custom, non-commercial</td></tr><tr><th scope="row" class="infobox-label" style="white-space: nowrap;">Website</th><td class="infobox-data"><span class="url"><a rel="nofollow" class="external text" href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL">fsl<wbr>.fmrib<wbr>.ox<wbr>.ac<wbr>.uk<wbr>/fsl<wbr>/fslwiki<wbr>/FSL</a></span></td></tr></tbody></table>

<p>The <b>FMRIB Software Library</b>, abbreviated <b>FSL</b>, is a software library containing image analysis and statistical tools for <a href="Functional_magnetic_resonance_imaging" title="Functional magnetic resonance imaging">functional</a>, <a href="MRI" class="mw-redirect" title="MRI">structural</a> and <a href="Diffusion_MRI" class="mw-redirect" title="Diffusion MRI">diffusion</a> MRI brain imaging data.

</p><p>FSL is available as both precompiled binaries and source code for Apple and PC (<a href="Linux" title="Linux">Linux</a>) computers. It is freely available for non-commercial use.

</p>

<div class="mw-heading mw-heading2"><h2 id="FSL_Functionality">FSL Functionality</h2></div>

<th colspan="2" style="text-align:left; padding-left:2em">Functional MRI

</th></tr>

<tr>

<td>FABBER

</td>

<td>FABBER is a <a href="Bayesian_inference" title="Bayesian inference">Bayesian</a> model fitting tool intended for use in task modelling of ASL data.

</td></tr>

<td>FEAT

</td>

<td>Model-based FMRI analysis with straightforward but powerful GUI: data preprocessing (including slice timing correction, MCFLIRT motion correction and PRELUDE+FUGUE EPI unwarping); FILM <a href="General_linear_model" title="General linear model">GLM</a> timeseries analysis with prewhitening; registration to structural and/or standard space images; and fully generalised mixed-effects group analysis using advanced <a href="Bayesian_inference" title="Bayesian inference">Bayesian</a> techniques.

</td></tr>

<td>MELODIC

</td>

<td>Model-free FMRI analysis using Probabilistic <a href="Independent_component_analysis" title="Independent component analysis">Independent Component Analysis</a> (PICA). MELODIC automatically estimates the number of interesting noise and signal sources in the data and because of the associated "noise model", is able to assign significances ("p-values") to the output spatial maps.

</td></tr>

<td>FLOBS

</td>

<td>Generation of optimal HRF basis functions and Bayesian activation estimation.

</td></tr>

<td>SMM

</td>

<td>Spatial mixture modelling – alternative hypothesis testing using histogram mixture modelling with spatial regularisation of the voxel classification into activation and non-activation.

</td></tr>

<tr>

<th colspan="2" style="text-align:left; padding-left:2em">Structural MRI

</th></tr>

<td>BET /

<p>BET2

</p>

</td>

<td>Brain Extraction Tool – segments brain from non-brain in structural and functional data, and models skull and scalp surfaces.<sup id="cite_ref-1" class="reference"><a href="#cite_note-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup>

</td></tr>

<td>SUSAN

</td>

<td>Nonlinear noise reduction.

</td></tr>

<td>FAST

</td>

<td>FMRIB's Automated Segmentation Tool – brain segmentation (into different tissue types) and bias field correction.

</td></tr>

<td>FLIRT

</td>

<td>FMRIB's Linear Image Registration Tool – linear inter- and intra-modal registration.<sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup>

</td></tr>

<td>FUGUE

</td>

<td>Unwarps geometric distortion in EPI images using B<sub>0</sub> field maps.

</td></tr>

<td>SIENA

</td>

<td>Structural brain change analysis, for estimating brain atrophy.

</td></tr>

<tr>

<th colspan="2" style="text-align:left; padding-left:2em">Diffusion MRI

</th></tr>

<td>FDT

</td>

<td>FMRIB's Diffusion Toolbox – tools for low-level diffusion parameter reconstruction and probabilistic tractography.

</td></tr>

<td>TBSS

</td>

<td>Tract-Based Spatial Statistics (part of FMRIB's Diffusion Toolbox) – voxelwise analysis of multi-subject diffusion data.<sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup>

</td></tr>

<tr>

<th colspan="2" style="text-align:left; padding-left:2em">Other tools

</th></tr>

<td>Inference

</td>

<td>Various inference/thresholding tools, including: Randomise (permutation-based inference tool for nonparametric statistical thresholding), cluster (cluster-based thresholding using GRF theory for inference), FDR (false discovery rate inference) and Glm (a GUI for creating model design matrices).

</td></tr>

<td>FSLeyes

</td>

<td>Interactive display tool for 3D and 4D data.

</td></tr>

<td>AVWUTILS

</td>

<td>Misc utils for converting and processing images.

</td></tr></tbody></table>

<div class="mw-heading mw-heading2"><h2 id="History_and_development">History and development</h2></div>

<p>FSL is written mainly by members of the FMRIB (Functional Magnetic Resonance Imaging of the Brain) Analysis Group, Oxford

University, UK. The first release of FSL was in 2000; there has been

approximately one major new release each year to date. The FMRIB

Analysis Group is primarily funded by the <a href="Wellcome_Trust" title="Wellcome Trust">Wellcome Trust</a> and the UK <a href="EPSRC" class="mw-redirect" title="EPSRC">EPSRC</a> and

<a href="Medical_Research_Council_(UK)" class="mw-redirect" title="Medical Research Council (UK)">MRC</a> Research Councils.

</p>

<li><a href="FreeSurfer" title="FreeSurfer">FreeSurfer</a></li>

<li><a href="Computational_anatomy_toolbox" title="Computational anatomy toolbox">Computational anatomy toolbox</a></li>

<li><a href="Neuroimaging" title="Neuroimaging">Neuroimaging</a></li></ul>

<div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2></div>

<ul><li><a rel="nofollow" class="external text" href="http://www.fmrib.ox.ac.uk/fsl">FSL website</a></li>

<li><a rel="nofollow" class="external text" href="https://www.ndcn.ox.ac.uk/divisions/fmrib/fmrib-analysis-group">FMRIB Analysis Group</a></li></ul>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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<li id="cite_note-1"><span class="mw-cite-backlink"><b><a href="#cite_ref-1">^</a></b></span> <span class="reference-text">S.M. Smith. <a rel="nofollow" class="external text" href="https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.10062">Fast robust automated brain extraction</a>. Human Brain Mapping, 17(3):143-155, November 2002.</span>

</li>

<li id="cite_note-2"><span class="mw-cite-backlink"><b><a href="#cite_ref-2">^</a></b></span> <span class="reference-text">Jenkinson, M., Bannister, P., Brady, J. M. and Smith, S. M. <a rel="nofollow" class="external text" href="https://web.archive.org/web/20180905175923/https://pdfs.semanticscholar.org/291c/9d66cf886ed27d89dc03d42a4612b66ab007.pdf">Improved Optimisation for the Robust and Accurate Linear Registration and Motion Correction of Brain Images</a>. NeuroImage, 17(2), 825-841, 2002.</span>

</li>

<li id="cite_note-3"><span class="mw-cite-backlink"><b><a href="#cite_ref-3">^</a></b></span> <span class="reference-text">S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens. <a rel="nofollow" class="external text" href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.459.2769&rep=rep1&type=pdf">Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data</a>. NeuroImage, 31:1487-1505, 2006.</span>

</li>

</ol></div></div>

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</style><div id="Image_processing_software87" style="font-size:114%;margin:0 4em"><a href="Image_processing" class="mw-redirect" title="Image processing">Image processing</a> software</div></th></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Free_software" title="Free software">Free</a></th><td class="navbox-list-with-group navbox-list navbox-odd hlist" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="3D_Slicer" title="3D Slicer">3D Slicer</a></li>

<li><a href="CellCognition" title="CellCognition">CellCognition</a></li>

<li><a href="CellProfiler" title="CellProfiler">CellProfiler</a></li>

<li><a href="Endrov" title="Endrov">Endrov</a></li>

<li><a href="FreeSurfer" title="FreeSurfer">FreeSurfer</a></li>

<li><a href="GemIdent" title="GemIdent">GemIdent</a></li>

<li><a href="GNU_Octave" title="GNU Octave">GNU Octave</a></li>

<li><a href="Ilastik" title="Ilastik">ilastik</a></li>

<li><a href="ImageJ" title="ImageJ">ImageJ</a></li>

<li><a href="InVesalius" title="InVesalius">InVesalius</a></li>

<li><a href="KNIME" title="KNIME">KNIME</a></li>

<li><a href="Mango_(software)" title="Mango (software)">Mango</a></li>

<li><a href="OpenCV" title="OpenCV">OpenCV</a></li>

<li><a href="OsiriX" title="OsiriX">OsiriX</a></li>

<li><a href="VIGRA" title="VIGRA">VIGRA</a></li>

</div></td></tr><tr><th scope="row" class="navbox-group" style="width:1%"><a href="Proprietary_software" title="Proprietary software">Proprietary</a></th><td class="navbox-list-with-group navbox-list navbox-even hlist" style="width:100%;padding:0"><div style="padding:0 0.25em">

<ul><li><a href="Amira_(software)" title="Amira (software)">Amira</a></li>

<li><a href="Analyze_(imaging_software)" title="Analyze (imaging software)">Analyze</a></li>

<li><a href="Aphelion_(software)" title="Aphelion (software)">Aphelion</a></li>

<li><a href="Avizo_(software)" title="Avizo (software)">Avizo</a></li>

<li><a href="Bitplane" title="Bitplane">Bitplane</a></li>

<ul><li><a href="Wolfram_Mathematica" class="mw-redirect" title="Wolfram Mathematica">Mathematica</a></li>

<li><a href="MATLAB" title="MATLAB">MATLAB</a></li>

<li><a href="Materialise_Mimics" title="Materialise Mimics">Mimics</a></li>

<li><a href="MountainsMap" title="MountainsMap">MountainsMap</a></li>

<li><a href="Tomviz" title="Tomviz">Tomviz</a></li>

<li><a href="Visage_SDK" title="Visage SDK">Visage SDK</a></li></ul>

</div></td></tr></tbody></table></div></div><div><div class="zim-footer">

This article is issued from <a class="external text" title="Last edited on 2024-10-15" href="https://en.wikipedia.org/wiki/?title=FMRIB_Software_Library&oldid=1251313937">Wikipedia</a>. The text is available under <a class="external text" href="https://creativecommons.org/licenses/by-sa/4.0/deed.en">Creative Commons Attribution-Share Alike 4.0</a> unless otherwise noted. Additional terms may apply for the media files.

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