The present invention relates to a method for estimating perfusion indices (PI) in a mammal (200), e.g. a human. Data (DAT, DAT′) representative of a contrast agent concentration as a function of time of an injected contrast agent is obtained from a medical imaging system (100). Perfusion indices (PI) are found by applying a parametric model (PM) for capillary transit time distributions as a function of time, and a minorize-maximization (MM) type procedure, such as an expectation-maximization (EM) type procedure, with regularization. The minorize-maximization type procedure has an exact analytical expression for the variance of an observation error of the contrast agent (Cε) in a non-linear observation model for the contrast agent concentration used in the maximization step. Clinical tests performed for 7 patients show improved MTT mapping as compared to singular value decomposition (SVD), and reduced sensitivity to delay.