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Thank you so much for the reply, I am not so much looking for connectivity as I am for doing the mean response. What I want to do is compare the mean response from the pre to the mean response in the post. My main concern is how to do this analysis using the FSL GUI. I have looked through some of the tutorials but I have found that the links for some of them are dead links now. thank you very much, Jaret This email is in response to this email: Hi Jaret, An empty model will not give you any results. What type of resting state analysis do you want to run? If it is a seed-based analysis then you need to extract the timeseries from the seed ROI and feed that in. Alternative analyses that don’t use feat at all include an ICA + dual regression analysis, or using FSL nets to look at connectivity between pairs of nodes. I think you need to familiarise yourself a little with different options for resting state analysis (which are typically quite different from the first-level feat approach) and decide which approach is most applicable to your data/hypotheses. Best wishes, Janine