Systems and methods for magnetic resonance fingerprinting (“MRF”) using highly differentiated trajectories that optimize differentiation between magnetic resonance signal patterns as a function of relaxation time(s) and static magnetic field homogeneity are described. Using the optimized acquisition parameters, MRF can be performed in the presence of inhomogeneous magnetic fields. Flip angle homogeneity can also be incorporated into the dictionary matching process to simultaneously estimate quantitative parameters of the subject and radio frequency coil transmission homogeneity profiles.