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| ## page was renamed from Overview ## page was renamed from MyStartingPage = FSL = FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK. FSL runs on Apple and PCs (Linux and Windows (via a Virtual Machine)), and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces). |
---- = FMRIB Software Library = Created by the [[https://www.win.ox.ac.uk/research/copy_of_analysis-research/analysis-research|Analysis Group]], FMRIB, Oxford, UK. |
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| To quote the relevant references for FSL tools you should look in the individual tool's manual page (or the Analysis Group publications page), and also please reference the FSL overview papers: 1) M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-186, 2009. 2) S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004. |
{{{#!wiki caution Please note this is a legacy website, the current documentation is available [[https://fsl.fmrib.ox.ac.uk/fsl/docs/#/|here]] }}} |
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| The [[http://www.epsrc.ac.uk/|UK EPSRC]] is the largest provider of funding for the FMRIB Analysis Group, and for this we are extremely grateful. We are also very grateful for significant financial support from [[http://www.mrc.ac.uk/|UK MRC]], [[http://www.bbsrc.ac.uk/|UK BBSRC]], [[http://www.gsk.com/|GlaxoSmithKline CIC]] and [[http://www.pfizer.co.uk/|Pfizer UK]]. | ---- Registration for the [[https://open.win.ox.ac.uk/pages/fslcourse/website/index.html|2024 FSL Course]] is now open! /* '''All material for the [[https://open.win.ox.ac.uk/pages/fslcourse/website/index.html|FSL Course]] is available online, including full lecture recordings and practical overviews.''' */ |
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| What's in FSL: see the [[FslTools|list of tools]]. | ---- FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. It runs on macOS (Intel and M1/M2), Linux, and Windows via the Windows Subsystem for Linux, and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces). To quote the relevant references for FSL tools you should look in the individual tools' manual pages, and also please reference one or more of the FSL overview papers: {{{#!wiki references [[http://www.ncbi.nlm.nih.gov/pubmed/19059349|1.]] M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. !NeuroImage, 45:S173-86, 2009 [[http://www.ncbi.nlm.nih.gov/pubmed/15501092|2.]] S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. Neuro''''''Image, 23(S1):208-19, 2004 [[http://www.ncbi.nlm.nih.gov/pubmed/21979382|3.]] M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. !NeuroImage, 62:782-90, 2012 }}} ---- * [[FslInstallation|Download/Install]] and [[Licence|licence]] * [[FslOverview|Overview of FSL tools]] * ~-Functional MRI: [[FEAT]], [[MELODIC]], [[FABBER]], [[BASIL]], [[verbena|VERBENA]] -~ * ~-Structural MRI: [[BET]], [[FAST]], [[FIRST]], [[FLIRT]] & [[FNIRT]], [[FSLVBM]], [[SIENA|SIENA & SIENAX]], [[MIST]], [[BIANCA]], [[MSM]], [[fsl_anat]] -~ * ~-Diffusion MRI: [[FDT]], [[TBSS]], [[XTRACT]], [[eddy]], [[topup]], [[eddyqc]] -~ * ~-GLM / Stats: [[GLM|GLM general advice]], [[Randomise]], [[PALM]], [[Cluster]], [[FDR]], [[DualRegression|Dual Regression]], [[Mm]], [[FLOBS]] -~ * ~-Other: [[FSLeyes]], [[Fslutils]], [[Atlases]], [[Atlasquery]], [[SUSAN]], [[FUGUE]], [[MCFLIRT]], [[Miscvis]], [[POSSUM]], [[baycest|BayCEST]], [[ICA_PNM]], [[FSL-MRS]] -~ * ~-Using GPUs: [[GPU|Linux GPU requirements]]-~ * ~-[[WhatsNew|Version history and release notes]] -~ * ~-[[Support|Support: Email forum, FAQ, tutorials, commercial licensing]] -~ * ~-The [[https://open.win.ox.ac.uk/pages/fslcourse/website/index.html|FSL Course - including full lecture recordings, practicals and example data]] -~ * ~-[[Contributors]] -~ * ~-[[OtherSoftware|Related software & FSL plugins]] -~ |
FMRIB Software Library
Created by the Analysis Group, FMRIB, Oxford, UK.
Please note this is a legacy website, the current documentation is available here
Registration for the 2024 FSL Course is now open!
FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. It runs on macOS (Intel and M1/M2), Linux, and Windows via the Windows Subsystem for Linux, and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces). To quote the relevant references for FSL tools you should look in the individual tools' manual pages, and also please reference one or more of the FSL overview papers:
1. M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004
3. M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012
Structural MRI: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, MIST, BIANCA, MSM, fsl_anat
GLM / Stats: GLM general advice, Randomise, PALM, Cluster, FDR, Dual Regression, Mm, FLOBS
Other: FSLeyes, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST, ICA_PNM, FSL-MRS
Using GPUs: Linux GPU requirements
The FSL Course - including full lecture recordings, practicals and example data