Neuroimaging and in particular functional magnetic resonance imaging (fMRI) of olfactory function relies on the ability to model the time course of brain responses elicited by odor stimuli. In this study we compared two templates of olfactory brain activation by comparing levels of correlation in regions critical to olfactory processing with either a stimulation-based template or a perception-based template, derived from perception profiles acquired off-line during a simulated fMRI session. fMRI signal was more correlated with the perception-based template than with the stimulation-based template in all regions. This effect was not observed when comparing correlations obtained with the exact same templates shifted in time by 12 s. Therefore, the improvement due to the use of the perception-based template was not only caused by a difference of shape between the stimulation-based and the perception-based template but was specifically related to the olfactory stimulation performed. These results suggest that the perception-based template better represents brain activity in response to olfactory stimulation and might help improve data processing of fMRI studies investigating olfactory function.