A three-dimensional projection reconstruction pulse sequence acquires two half echoes in a steady state free precession (SSFP) scan. A method for combining the two echoes to suppress either fat or water in the reconstructed image is described and includes shifting the phase of one echo and combining them in a regridding process used to transform the radial data to a Cartesian grid prior to image reconstruction. Images having either fat or water substantially suppressed are then produced by applying a phase difference mask to images reconstructed from the regridded data. These images are then further processed using information of the phase differences between the two half echoes. In this manner, more consistent and accurate suppression is achieved.