1. A method for estimating a phase of a magnetic resonance signal using a magnetic resonance imaging (MRI) system, the steps of the method comprising: a) determining with a computer system at least two echo time spacings that define a duration of time between pairs of echo times, the at least two echo time spacings being determined by optimizing phase ambiguity functions that are associated with the at least two echo time spacings; b) acquiring data by directing a radio frequency (RF) system and a gradient system of the MRI system to perform a pulse sequence that includes forming echoes at a plurality of echo times that are spaced apart in time using the determined at least two echo time spacings; and c) estimating with a data processing server of the MRI system a phase value at each voxel location in an image matrix using the acquired data and the determined at least two echo time spacings.