A method for generating a magnetic resonance image of a moving subject comprises tracking the position and orientation of a target volume and modifying acquisition parameters for each line of k-space data using current position and orientation information. By approximating the target volume as a rigid object, the current position and orientation is translated into an offset vector and a rotation which are used to modify the acquisition of each k-space line individually. The offset along a slice direction is compensated for by changing the transmit frequency. The offset along the frequency-encoding direction is compensated for by changing the frequency of a reference demodulation signal. The offset along the phase direction is compensated for by changing the phase of a reference demodulation signal, or by adding a phase into the line of k-space data after acquisition. The rotation is applied directly to the logical axes to change the angles between the logical axes and the physical axes of a magnetic resonance imaging system.