Strong spatial distortion of the DW-ssEPI sequence prevents its utilization in radiotherapy planning and treatment adaptation. In this work, a 3D diffusion-prepared magnitude-stabilized bSSFP sequence was developed and validated at 1.5T. A phase navigator was acquired during the catalyzation stage of the bSSFP readout to estimate the spatial variation of the signal phase, and a locally low-rank constrained reconstruction was developed to resolve the phase variation. The sequence was validated on a diffusion phantom and healthy volunteers. It provided submillimeter geometric fidelity and acceptable ADC accuracy, which makes it a promising candidate for treatment planning and adaptation of the brain.