Magnetic resonance imaging (MRI) using three-dimensional velocity encoding phase contrast methods offers the opportunity to quantify time-resolved 3D flow patterns in vivo. This technique can have a breakthrough impact on the evaluation, risk stratification and surgical planning in hemodynamic-related pathologies, e.g., cardiac valve diseases, arterial stenos or insufficiency, dilation, dissection or coartaction. Nevertheless, the limited time and space resolution of 4D MRI data restricts the accuracy of derivative calculations, which are necessary for the estimation of some very important characteristics such as vorticity and shear stress in the blood flow. In this paper we introduce a new accuracy measure for the shear stress and calculate the possible discrepancy with the use of a new software tool which automatically segment the vessels and provides the information along the center line, between two selected cross-sections and in the vicinity of the selected points. Results are provided both as maximum and time-averaged values in aorta, pulmonary artery, left and right ventricles and valves. The cavitation phenomena, revealed in artificial mitral heart valves, cause interest in such studies for the real valves, especially for the patients suffering from different cardio-vascular diseases. To estimate possible cavitation inception the vorticity and pressure drop in mitral valve were estimated.