Correlations between responses in visual cortex and perceptual performance help draw a functional link between neural activity and visually guided behavior. These correlations are commonly derived with ROC-based neural-behavioral covariances (referred to as choice or detect probability) using boxcar analysis windows. Although boxcar windows capture the covariation between neural activity and behavior during steady-state stimulus presentations, they are not optimized to capture these correlations during short time-varying visual inputs. In this study, we implemented a matched-filter technique, combined with cross-validation, to improve the estimation of ROC-based neural-behavioral covariance under short and dynamic stimulus conditions. We show that this approach maximizes the area under the ROC curve and converges to the true neural-behavioral covariance using a Poisson spiking model. We also demonstrate that the matched filter, combined with cross-validation, reveals the dynamics of the neural-behavioral covariations of individual MT neurons during the detection of a brief motion stimulus.