Magnetic Resonance (MR) imaging-based motion and deformation tracking techniques combined with finite element (FE) analysis are a powerful method for soft tissue constitutive model parameter identification. However, deriving deformation data fromMR images is complex and generally requires validation. In this paper a validation method is presented based on a silicone gel phantom containing contrasting spherical markers. Tracking of thesemarkers provides a direct measure of deformation. Validation of in vivo medical imaging techniques is often challenging due to the lack of appropriate reference data and the validation method may lack an appropriate reference. This paper evaluates a validation method using simulated MR image data. This provided an appropriate reference and allowed different error sources to be studied independently and allowed evaluation of the method for various signal-to-noise ratios (SNRs). The geometric bias error was between 0–5.560× 10−3 voxels while the noisy magnitude MR image simulations demonstrated errors under 0.1161 voxels (SNR: 5–35).