References

1. Mori S, Crain BJ, Chacko VP, van Zijl PCM. Three dimensional tracking of axonal projections in the brain by magnetic resonance imaging. Ann Neurol 1999; 45: 265-269
2. Tuch DS, Reese TG, Wiegell MR, Wedeen VJ. Diffusion MRI of complex neural architecture.Neuron. 2003 Dec 4;40(5):885-95
3. Diffusion-tensor MRI: theory, experimental design and data analysis - a technical review. Basser PJ, Jones DK. NMR Biomed. 2002 Nov-Dec;15(7-8):456-67. Review.
4. Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution.Tournier JD, Calamante F, Gadian DG, Connelly A.Neuroimage. 2004 Nov;23(3):1176-85.

If you plan on using FSL:
Characterization and propagation of uncertainty in diffusion-weighted MR imaging. Behrens TE, Woolrich MW, Jenkinson M, Johansen-Berg H, Nunes RG, Clare S, Matthews PM, Brady JM, Smith SM. Magn Reson Med. 2003 Nov;50(5):1077-88.
Probabilistic diffusion tractography with multiple fibre orientations: What can we gain? Behrens TE, Berg HJ, Jbabdi S, Rushworth MF, Woolrich MW. Neuroimage. 2007 Jan 1;34(1):144-55.