Diff for "FSL" - FslWiki

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FMRIB Software Library v5.0 September 2012

Created by the Analysis Group, FMRIB, Oxford, UK.

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 the FSL overview papers:

1. M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012

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

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. NeuroImage, 23(S1):208-19, 2004

Overview of FSL tools
- Functional MRI: FEAT, MELODIC, FABBER, BASIL
- Structural MRI: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, fsl_anat
- Diffusion MRI: FDT, TBSS, EDDY, TOPUP
- Other tools: FSLView, Randomise, Dual Regression, FDR, Mm, Fslutils, Atlases, SUSAN, FUGUE, MCFLIRT, FLOBS, Miscvis, POSSUM
What's new in this release
Support: Email forum, FAQ, tutorials, courses, example data
Contributors
FSL plugins & other software
Download, patches and licence

-  ⇤ ← Revision 1 as of 12:55:49 03-08-2010 → 
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-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), 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).
+## page was renamed from Overview
## page was renamed from MyStartingPage
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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.
+~+ '''FMRIB Software Library &#160;v5.0 &#160;&#160;September 2012''' +~
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-The 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 UK MRC, UK BBSRC, GlaxoSmithKline CIC and Pfizer UK.
+Created by the [[http://www.fmrib.ox.ac.uk/analysis|Analysis Group]], FMRIB, Oxford, UK.
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-What's in FSL: see the list of tools.
+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 the FSL overview papers:
{{{#!wiki references
[[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

[[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/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
}}}

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 * [[FslOverview|Overview of FSL tools]] ~-
  * Functional MRI: [[FEAT]], [[MELODIC]], [[FABBER]], [[BASIL]]
  * Structural MRI: [[BET]], [[FAST]], [[FIRST]], [[FLIRT]] & [[FNIRT]], [[FSLVBM]], [[SIENA|SIENA & SIENAX]], [[fsl_anat]]
  * Diffusion MRI: [[FDT]], [[TBSS]], [[EDDY]], [[TOPUP]]
  * Other tools: [[http://www.fmrib.ox.ac.uk/fsl/fslview|FSLView]], [[Randomise]], [[DualRegression|Dual Regression]], [[FDR]], [[Mm]], [[Fslutils]], [[Atlases]], [[SUSAN]], [[FUGUE]], [[MCFLIRT]], [[FLOBS]], [[Miscvis]], [[POSSUM]]-~
 * [[WhatsNew|What's new in this release]]
 * [[Support|Support: Email forum, FAQ, tutorials, courses, example data]]
 * [[Contributors|Contributors]]
 * [[OtherSoftware|FSL plugins & other software]]
 * [[FslInstallation|Download]], [[FslInstallation/Patches|patches]] and [[Licence|licence]]