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Referenceless proton resonance frequency (PRF) shift thermometry provides a means to measure temperature changes during minimally invasive thermotherapy that is inherently robust to motion and tissue displacement. However, if the referenceless method is used to determine temperature changes during prostate ablation, phase gaps between water and fat in image regions used to determine the background phase can confound the phase estimation. We demonstrate an extension to referenceless thermometry which eliminates this problem by allowing background phase estimation in the presence of phase discontinuities between aqueous and fatty tissue. In this method, images are acquired with a multi-echo sequence and binary water and fat maps are generated from a Dixon reconstruction. For the background phase estimation, water and fat regions are treated separately and the phase offset between the two tissue types is determined. The method is demonstrated feasibile in phantoms and during in vivo thermal ablation of canine prostate.