A method for performing pharmacokinetic analysis in magnetic resonance (MR) images includes administering a dose of contrast agent (CA) into a subject. A sequence of medical images is acquired of the subject at set temporal intervals. The time-based behavior of concentrations of CA is described within the subject for each voxel of each medical image of the sequence of medical images based on a reference voxel using a compartmental model for pharmacokinetic analysis that is based on a set of compartmental model parameters. The compartmental model is solved for each of the compartmental model parameters. The solution for the compartmental model parameters is used to estimate one or more parameters of physiological significance.