A magnetic resonance imaging (MRI) system, method and/or computer readable medium is configured to effect MR imaging with reduced ghosting artifacts by operations including determining spatially varying signal magnitude differences associated with first and second parts of a reference MR data, and reconstructing a diagnostic image based upon a first and a second parts of main scan data and the determined spatially varying signal magnitude differences. The first parts of the reference data and main scan data is acquired using a first readout gradient, and the second parts of the reference data and main scan data is acquired using a second readout gradient that is different from the first readout gradient.