["Topics in Cognitive Science, EarlyView. ", "\nAbstract\nReliably identifying relevant brain areas implicated by the simulated activity from cognitive models is still an unsolved problem for cognitive modeling, particularly when matching model output with human electroencephalography (EEG) data. We propose a new method involving postprocessing of ACT‐R module activity and clustered EEG component activity, and performing generalized least squares analysis to find matching patterns between predicted and observed data, thereby inferring neural substrates of distinct cognitive processes. This approach holds several advantages over other methods by controlling for autocorrelation and unequal variances. To exemplify its application, we used a cognitive model and EEG data from a mental spatial transformation study to show how this method finds areas involved in representational and transformational spatial processing. Parietal areas involved with spatial activity were identified, in line with prior studies on spatial cognition. In addition, previously established associations between ACT‐R and brain areas were confirmed. Finally, we discuss limitations and possibilities of the approach."]