Dear Tammar

> We would like to ask your opinion on two matters, please:
> 1. We have 3 conditions in our study (Experimental, Control, Baseline). Our DCM includes only Experimental & Control conditions.
We compared two analyses:
> i. DCM using F contrast that includes all three conditions.
> ii. DCM using F contrast that includes only two conditions (without Baseline) We found a difference in the explained variance.
> It seems weird because the Baseline condition is not defined in the intrinsic conditions in both DCMs.
> What is the reason? Which F contrast is recommended?

The F-contrast tells SPM which effects to regress out of the time series during VOI extraction. Are there unmodelled rest periods or inter-trial intervals in addition to the Baseline condition? If so, I recommend you keep baseline in the F-contrast (i.e., don't regress it out). If there are no rest periods - so the entire time series is Experimental, Control or Baseline, then I don't think it really matters either way. Use whichever gives you nicer results. (My personal preference is to only regress out factors like breathing, head motion, session means.)

> 2. Is there any preventive to include many between-regions modulatory connections?
> We did not find so, but we want to make sure it is doesn't come at the expense of something else.

Use as many parameters as you think might be necessary to explain your data. Then assess whether you could have used a simpler model, by using Bayesian model reduction to switch off particular parameters.

Best
Peter