We present a novel method for tracking myocardial motion in 2D ultrasound sequences based on non-rigid registration using an anatomical free-form deformation (AFFD) model where the basis functions are locally oriented along the radial and circumferential direction of the left ventricle (LV). This formulation allows us to model the LV motion more naturally compared to previously proposed FFD's defined on a regular Cartesian grid (CFFD). In this paper we compare the performance of the AFFD against the CFFD model in an in-vivo setting. Short-axis images were acquired in five open-chest sheep using sonomicrometry as ground-truth deformation estimates. We demonstrated that regional end-systolic strain values assessed with the AFFD model are comparable with CFFD, while also displaying a statistically lower drift at the end of the cardiac cycle and a better agreement with a manual end-systolic reference. Furthermore, tracking using AFFD was visually more appealing to clinical experts.