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Refinements were made to a post-processing technique, termed the Thermal Stratification Analysis (TSA), that couples the mass fraction burned data to ignition timing predictions from the autoignition integral to calculate an apparent temperature distribution from an experimental HCCI data point. Specifically, the analysis is expanded to include all of the mass in the cylinder by fitting the unburned mass with an exponential function, characteristic of the wall-affected region. The analysis-derived temperature distributions are then validated in two ways. First, the output data from CFD simulations are processed with the Thermal Stratification Analysis and the calculated temperature distributions are compared to the known CFD distributions.