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Hi Jeremy, I would regress them out prior to running the gica (you can use unconfound for this) so that those confounds don't have a chance to affect the ICA results. However, I'm not entirely sure how possible it would be for the precise pattern of an RSN to be shaped by individual differences in a nuisance variable (e.g., head motion). It seems possible that such a difference could bias subsequent dual regression results in cases where you were examining a correlated factor (imagine a case where one group moved more than another group). I'm not sure if including subject-level nuisance regressor would completely mitigate that concern... See fsl_motion_outliers to remove spikes. Cheers, David On Dec 11, 2012, at 3:00 PM, Jeremy Elman wrote: > Hello all, > > I was wondering what the best way to account for subject specific nuisance factors is when running a dual regression analysis. Is it preferable to regress out motion parameters first and running the group ICA on this clean data, or to include these subject specific motion regressors after the first stage of DR? I guess my main question is whether doing one versus the other affects the group ICA in a significant way. > > I've also seen discussion that regressing out spikes may introduce some problems to the group ICA step. If I would like to regress out particular volumes due to motion or RF spikes, would this change the recommended process above? > > Thank you for your help! > Jeremy -------------------------------------------- David V. Smith, Ph.D. Postdoctoral Fellow, Delgado Lab Department of Psychology Rutgers University Newark, NJ 07102 --------------------------------------------