Dear Abraham,
To my knowledge you can create the DCM models with areas obtained from different contrasts. This can be useful to investigate interactions between conditions. I recommend clearly written paper by Klaas et.al.:
K.E. Stephan, W.D. Penny, R. Moran, H.E. Den Ouden, J. Daunizeau, and K.J. Friston. Ten simple rules for dynamic causal modelling. NeuroImage, 49(4):3099-3109, 2010.
Regards
Branislava
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