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| = FMRIB Software Library v5.0 = | ---- = 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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| Created by the [[http://www.fmrib.ox.ac.uk/analysis|Analysis Group]], FMRIB, Oxford, UK. {{{#!wiki comment/dashed '''Announcing the [[http://fsl.fmrib.ox.ac.uk/fslcourse/current.html|2014 FSL Course]], 31 March - 4 April 2014, Oxford, UK''' |
{{{#!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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| FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both 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). 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: | ---- 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.''' */ ---- 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: |
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| [[http://www.ncbi.nlm.nih.gov/pubmed/21979382|1.]] M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. !NeuroImage, 62:782-90, 2012 | |
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| [[http://www.ncbi.nlm.nih.gov/pubmed/19059349|2.]] 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/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 |
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| [[http://www.ncbi.nlm.nih.gov/pubmed/15501092|3.]] 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/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 |
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| * [[FslInstallation|Download/Install]] and [[Licence|licence]] | |
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| * ~-Structural MRI: [[BET]], [[FAST]], [[FIRST]], [[FLIRT]] & [[FNIRT]], [[FSLVBM]], [[SIENA|SIENA & SIENAX]], [[fsl_anat]] -~ * ~-Diffusion MRI: [[FDT]], [[TBSS]], [[EDDY]], [[TOPUP]] -~ * ~-GLM / Stats: [[GLM|GLM general advice]], [[Randomise]], [[Cluster]], [[FDR]], [[DualRegression|Dual Regression]], [[Mm]], [[FLOBS]] -~ * ~-Other: [[http://fsl.fmrib.ox.ac.uk/fsl/fslview/|FSLView]], [[Fslutils]], [[Atlases]], [[Atlasquery]], [[SUSAN]], [[FUGUE]], [[MCFLIRT]], [[Miscvis]], [[POSSUM]], [[baycest|BayCEST]] -~ * [[WhatsNew|What's new in this release]] * [[Support|Support: Email forum, FAQ, tutorials]] * [[http://www.fmrib.ox.ac.uk/fslcourse|FSL Course: lecture slides, practicals and example data]] * [[Contributors]] * [[OtherSoftware|Related software & FSL plugins]] * [[FslInstallation|Download]], [[FslInstallation/Patches|patches]] and [[Licence|licence]] |
* ~-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