An MRI system has two sets of gradient coils driven by two corresponding sets of gradient amplifiers. Logical gradient waveforms produced during a pulse sequence are rotated to produce corresponding physical gradient waveforms and these are distributed to drive both sets of coils simultaneously. Each distributed set of physical gradient waveforms is separately compensated for Eddy current errors, and a polarizing field Eddy current compensation signal is produced and used to modulate the RF reference frequency of the system transceiver.