A method for generating a susceptibility (or T2*) weighted magnetic resonance (MR) image includes defining a pulse sequence having a plurality of gradient echoes and acquiring MR data for each of the plurality of gradient echoes. A weighting function is applied to image data for each gradient echo such as MR data (e.g., k-space data) or magnitude images associated with each gradient echo. A susceptibility weighted image is generated by combining the image data for each gradient echo based on at least the application of the weighting function.