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Hello DCM experts, My apologies for reposting the following questions (just in case you missed it) regarding DCM analysis in SPM12. Thanks. ---------- Forwarded message --------- From: Martin Juneja <[log in to unmask]> Date: Thu, Mar 7, 2019 at 4:48 PM Subject: Defining covariates in DCM M.X matrix To: <[log in to unmask]> Dear DCM experts, I have two conditions for rsfMRI data: (1) pre and post treatment condition for treatment A for subject set 1 and (2) pre and post treatment condition for treatment B for subject set 2. I am interested in determining whether its treatment 'A' which improves effective connectivity within a network for set 1, or its treatment 'B' which improves effective connectivity within a network for set 2. I am following the step-by-step guide from here: https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_(PEB) Here, I have a question regarding defining M.X contrast file. I understand that if I define M.X as [1 1...;1 -1...], here first column represents mean connectivity over pre and post treatment conditions (for set 1 and then for set 2), and second column represents the difference between pre and post conditions. My question is how to define the covariates in column three (age), four (sex), five (amount of dose used) and six (time since stroke): *Q1:* Whether I mean center 'age', 'sex', 'amount of dose' and 'time since stroke' from overall sample i.e., from both conditions together, or calculate mean centered values separately for treatments A and B. *Q2:* For M.X matrix, should I use mean centered 'dose used' values only for post-treatment conditions and put 0's for pre-treatment condition, because there was no dose used during pre-treatment condition? Correct? *Q3:* For M.X matrix, should I use mean centered 'time since stroke' only for post-treatment condition and put 0's for pre-treatment condition? Or it will be same values for pre- and post-treatment condition because 'time since stroke' values are same for pre- and post conditions. *Q4: *If I want to compare connectivity for controls with post-treatment condition, then again should I mean center 'age' and 'sex' from overall sample or separately for controls and patients? Also, should I include 'time since stroke' and 'amount of dose' used also as covariates, which will of course be zeros for controls. Or there is no need to include 'time since stroke' and 'amount of dose' as covariates because I am comparing controls with patients. If so, I doubt then how to incorporate the variance as the 'amount of dose used' and 'time since stroke' values differ between treatments A and B. I would really appreciate any help.