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, PCs (Linux and Windows) and Sun, 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 tool’s manual page (or the Analysis Group publications page), and also the FSL overview paper:
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
Next – see the list of tools in FSL.