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= 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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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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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
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 * [[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]] -~