Dear FreeSurfer expert
I have calculated the residuals as y-x*beta as described in 
(Bernal-Rusiel et al., 2012).  What is the best method to calculate 
cohenD or any other map of effective size with lme?

   Can I calculate cohenD as
R=y-desingmatrix*Bhat
cohenD=gamma./(sqrt(sum(r.^2)/df2-1))

Reference

Bernal-Rusiel, J.L., et al., 2012. Statistical analysis of longitudinal 
neuroimage data with Linear Mixed Effects models. Neuroimage. 66C, 249-260.

Best regards

Knut Jørgen

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