Disclosed is a method and system for steady state free precession based magnetic resonance thermometry that measures changes in temperature on a pixel by pixel basis. The method comprises generating an RF pulse sequence used to find the proton resonance frequency shift, which is proportional to temperature change, processing the resultant MRI data to measure the proton frequency shift, and converting the measured proton frequency shift into change in temperature data. Further disclosed is a method for identifying and compensating for temperature drifts due to core heating of the gradient magnet.