Abstract
Neural representation refers to the brain activity that stands in for one's cognitive experience, and in cognitive neuroscience, the principal method to studying neural representations is representational similarity analysis (RSA). The classic RSA (cRSA) approach examines the overall quality of representations across numerous items by assessing the correspondence between two representational similarity matrices (RSMs): one based on a theoretical model of stimulus similarity and the other based on similarity in measured neural data. However, because cRSA cannot model representation at the level of individual trials, it is fundamentally limited in its ability to assess subject-, stimulus-, and trial-level variances that all influence representation. Here, we formally introduce trial-level RSA (tRSA), an analytical framework that estimates the strength of neural representation for singular experimental trials and evaluates hypotheses using multi-level models. First, we verified the correspondence between tRSA and cRSA in quantifying the overall representation strength across all trials. Second, we compared the statistical inferences drawn from both approaches using simulated data that reflected a wide range of scenarios. Compared to cRSA, the multi-level framework of tRSA was both more theoretically appropriate and significantly sensitive to true effects. Third, using real fMRI datasets, we further demonstrated several issues with cRSA, to which tRSA was more robust. Finally, we presented some novel findings of neural representations that could only be assessed with tRSA and not cRSA. In summary, tRSA proves to be a robust and versatile analytical approach for cognitive neuroscience and beyond.