Noninvasive temperature measurement is feasible with MRI to monitor changes in thermal therapy. Phase shift based MR thermometry gives an estimate of the relative temperature variation between thermal and baseline images. This technique is limited, however, when applied on targets under inter-frame motion. Simple image registration and subtraction are not adequate to recover the temperature properly since the phase shift due to temperature changes is corrupted by an unwanted phase shift. In this work, the unwanted phase shift is predicted from the raw registered phase shift map itself. To estimate the unwanted phase shift, a thin plate smoothing spline is fitted to the values outside the heated region. The spline value in the heated area serves as an estimate for the offset. The estimation result is applied to correct errors in the temperature maps of an ex-vivo experiment.