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FMRIB Software Library v6.0
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 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, FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST
Using GPUs: Linux GPU requirements