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Hi Dushyant,

The methods are spread across different papers. Try having a look into these that I'm pasting below, and also the references inside each:

• Beckmann CF, Jenkinson M, Smith SM. General multilevel linear modeling for group analysis in FMRI. Neuroimage. 2003 Oct;20(2):1052–63.
  
• Jenkinson M, Beckmann CF, Behrens TEJ, Woolrich MW, Smith SM. Fsl. Neuroimage. 2011 Sep 16;62:782–90.
  
• Jenkinson M, Beckmann CF, Behrens TEJ, Woolrich MW, Smith SM. Fsl. Neuroimage. 2011 Sep 16;62:782–90.
  
• Smith S, Jenkinson M, Beckmann CF, Miller K, Woolrich M. Meaningful design and contrast estimability in FMRI. Neuroimage. 2007 Jan 1;34(1):127–36.
  
• Smith S, Jenkinson M, Beckmann CF, Miller K, Woolrich M. Meaningful design and contrast estimability in FMRI. Neuroimage. 2007 Jan 1;34(1):127–36.
  
• Smith SM, Beckmann CF, Ramnani N, Woolrich MW, Bannister PR, Jenkinson M, et al. Variability in fMRI: a re-examination of inter-session differences. Hum Brain Mapp. 2005 Mar;24(3):248–57.
  
• Smith SM, Beckmann CF, Ramnani N, Woolrich MW, Bannister PR, Jenkinson M, et al. Variability in fMRI: a re-examination of inter-session differences. Hum Brain Mapp. 2005 Mar;24(3):248–57.
  
• Smith SM, Jenkinson M, Woolrich MW, Beckmann CF, Behrens TEJ, Johansen-Berg H, et al. Advances in functional and structural MR image analysis and implementation as FSL. Neuroimage. 2004 Jan;23(Suppl. 1):208–19.
  
• Smith SM, Jenkinson M, Woolrich MW, Beckmann CF, Behrens TEJ, Johansen-Berg H, et al. Advances in functional and structural MR image analysis and implementation as FSL. Neuroimage. 2004 Jan;23(Suppl. 1):208–19.
  
• Woolrich M, Ripley B, Brady J, Smith S. Nonparametric estimation of temporal autocorrelation in FMRI. Neuroimage. 2000 May;11(5):S610–S610.
  
• Woolrich MW, Behrens TEJ, Beckmann CF, Jenkinson M, Smith SM. Multilevel linear modelling for FMRI group analysis using Bayesian inference. Neuroimage. 2004 Apr;21(4):1732–47.
  
• Woolrich MW, Behrens TEJ, Smith SM. Constrained linear basis sets for HRF modelling using Variational Bayes. Neuroimage. 2004 Apr;21(4):1748–61.
  
• Woolrich MW, Jbabdi S, Patenaude B, Chappell M, Makni S, Behrens T, et al. Bayesian analysis of neuroimaging data in FSL. Neuroimage. Elsevier B.V.; 2009 Mar;45(1 Suppl):S173–86.
  
• Woolrich MW, Ripley BD, Brady M, Smith SM. Temporal autocorrelation in univariate linear modeling of FMRI data. Neuroimage. 2001 Dec;14(6):1370–86.

Also, have a look into the Technical Reports in the FMRIB website: http://www.fmrib.ox.ac.uk/analysis/techrep (it's down at the moment but should be back online this afternoon).