The right tool for the right question --- beyond the encoding versus decoding dichotomy

Abstract: There are two major questions that neuroimaging studies attempt to answer: First, how are sensory stimuli represented in the brain (which we term the stimulus-based setting)? And, second, how does the brain generate cognition (termed the response-based setting)? There has been a lively debate in the neuroimaging community whether encoding and decoding models can provide insights into these questions. In this commentary, we construct two simple and analytically tractable examples to demonstrate that while an encoding model analysis helps with the former, neither model is appropriate to satisfactorily answer the latter question. Consequently, we argue that if we want to understand how the brain generates cognition, we need to move beyond the encoding versus decoding dichotomy and instead discuss and develop tools that are specifically tailored to our endeavour.