Atherosclerotic plaques may rupture without warning and cause acute cardiovascular syndromes such as heart attack and stroke. Mechanical image analysis using MRI-based models with fluid-structure interactions (FSI) and MRI-determined material properties may improve the accuracy of plaque vulnerability assessment and rupture predictions. A plaque-phantom was set up to acquire plaque MR images under pressurized conditions. The 3D nonlinear modified Mooney-Rivlin (M-R) model was used to describe the material properties with parameters selected to fit the MRI data. The Navier-Stokes equations were used as the governing equations for the flow model. The fully-coupled FSI models were solved by ADINA. Our results indicate that doubling parameter values in the M-R model led to 12.5% decrease in structure maximum principal stress (Stress-P1) and 48% decrease in maximum principal strain (Strain-P1). Flow maximum shear stress (MSS) was almost unchanged. Results from a modified carotid plaque with 70% stenosis severity (by diameter) showed that Stress-P1 at the plaque throat from the wall-only model is 145% higher than that from the FSI model. MSS from a flow-only model is about 40% higher than that from the FSI model. This approach has the potential to develop non-invasive patient screening and diagnosis methods in clinical applications.