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Hi, yes the varcope is computed from the residuals, using the formula: var(c' b)=c' pX AVA' pX' c sigsq where c' is the contrast vector b is the estimated effect size (beta or pe) pX is the pinv of the design matrix AVA' is the covariance/whitening sigsq is the estimate of the residuals Cheers, Steve. On Mon, 14 Jun 2004, SUBSCRIBE FSL Zhang, X wrote: > Dear FSL experts: > I thought GLM formular only yields one residual array > data-sum(pe*design matrix) = residual (number of volumes by 1 array) > how can we get a varcope for every contrast? could you tell me what > is the formula to get a varcope for a particular contrast? > Appreciate your help > > yours Xian > Stephen M. Smith DPhil Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve