Patients with an atrial septal defect (ASD) have a left to right shunt with associated complications. Currently, various imaging modalities, including echocardiography and invasive cardiac catheterization, are utilized in the management of these patients. Cardiac magnetic resonance (CMR) imaging provides a novel and non-invasive approach for imaging patients with ASDs. A study of vortices generated within the right atrium (RA) during the diastolic phase of the cardiac cycle can provide useful information on the change in the magnitude of vorticity pre-and post-ASD closure. The motion estimation of blood applied to CMR is performed. In this study we present, a two dimensional (2D) visualization of in-vivo right atrial flow. This is constructed using flow velocities measured from the intensity shifts of turbulent blood flow regions in MRI. In particular, the flow vortices can be quantified and measured, against controls and patients with ASD, to extend medical knowledge of septal defects and their haemodynamic effects.