A system and method for tracking temperature changes in tissue and bone is disclosed. In one aspect, the temperature changes are tracked simultaneously with high spatial encoding and temporal efficiency. The method is robust in terms of B0 and chemical shift off-resonance, as well as insensitive to eddy currents for accurate temperature mapping. Zero TE (ZTE) based MR thermometry is utilized herein to extract temperature changes from proton density and T1 weighted images. Additionally, T1 signal contamination is corrected for by calibrating T1 and B0 by using a variable flip angle method to achieve temperature mapping in bone, aqueous and adipose tissue simultaneously.