An improved technique is described for acquiring MR image data such as needed for FSE-based Dixon imaging techniques. A gradient-induced echo shift is produced in the pulse sequences by a small gradient applied along the readout axis prior to a readout pulse. When necessary, another small pulse is applied along the readout axis, equal in area and opposite in polarity to the first, to compensate for the shifting effect. Similar pulses are applied for each acquisition window. While data with non-zero phase shifts between water and fat signals are collected as fractional echoes, no increase in echo spacing is necessary with the modified acquisition strategy. Images corresponding to different phase shifts are reconstructed using phase-sensitive partial Fourier reconstruction algorithms whenever necessary. These images are then used to separate different chemical species (such as water and fat) in the object to be imaged. Increased time efficiency is therefore achieved with the improved technique, with a significant reduction in degradation due to losses in slice coverage and increased image blurring and sensitivity to flow and motion due to T2-modulation along the echo train in conventional techniques.