An In-depth Exploration of the Interplay between fMRI Methods and Theory in Cognitive Neuroscience

Functional magnetic resonance imaging (fMRI) has been a cornerstone of cognitive neuroscience since its invention in the 1990s. The methods that we use for fMRI data analysis allow us to test different theories of the brain, thus different analyses can lead us to different conclusions about how the brain produces cognition. There has been a centuries-long debate about the nature of neural processing, with some theories arguing for functional specialization or localization (e.g., face and scene processing) while other theories suggest that cognition is implemented in distributed representations across many neurons and brain regions. Importantly, these theories have received support via different types of analyses; therefore, having students implement hands-on data analysis to explore the results of different fMRI analyses can allow them to take a firsthand approach to thinking about highly influential theories in cognitive neuroscience. Moreover, these explorations allow students to see that there are not clearcut "right" or "wrong" answers in cognitive neuroscience, rather we effectively instantiate assumptions within our analytical approaches that can lead us to different conclusions. Here, I provide Python code that uses freely available software and data to teach students how to analyze fMRI data using traditional activation analysis and machine-learning-based multivariate pattern analysis (MVPA). Altogether, these resources help teach students about the paramount importance of methodology in shaping our theories of the brain, and I believe they will be helpful for introductory undergraduate courses, graduate-level courses, and as a first analysis for people working in labs that use fMRI.