The capacity to categorize using the concepts same and different plays a central role in cognition. However, in any given circumstance, it can be difficult to tell whether a person or animal is performing same and different categorization using structured relational rules from propositional logic or perceptual change detection processes. Discrete, logical behavior can often be produced from continuous perceptual spaces, and continuous behavior can arise from systems relying on structured logical rules. Model-based neuroimaging, when used in conjunction with advances in task development, can aid in understanding how people accomplish same and different categorization. We review recent publications employing the model-based neuroimaging paradigm to isolate latent brain processes associated with use of structured, logical rules and continuous perceptual processes.