The measurement of the blood flow in the middle cerebral artery (MCA) using transcranial Doppler ultrasound (US) imaging is clinically relevant for the study of cerebral autoregulation. Especially in the aging population, impairement of the autoregulation may coincide or relate to loss of perfusion and consequently loss of brain function. The cerebral autoregulation can be assessed by relating the blood pressure to the blood flow in the brain. Doppler US is a widely used, non-invasive method to measure the blood flow in the MCA. However, Doppler flow imaging is known to produce results that are dependent of the operator. The angle of the probe insonation with respect to the centerline of the blood vessel is a well known factor for output variability. In patients also the skull must be traversed and the MCA must be detected, influencing the US signal intensity. In this contribution we report two studies. We describe first an in-vitro setup to study the Doppler flow in a situation where the ground truth is known. Secondly, we report on a study with healthy volunteers where the effects of small probe displacements on the flow velocity signals are investigated. For the latter purpose, a special probe holder was designed to control the experiment.