The paper presents architecture and details of software implementation of a client-server system developed to investigate the hemodynamics in the brain in real-time mode. That is our own implementation of distributed registering, recording, an analysis of blood flow velocity (BFV), arterial blood pressure (BP). Input signals (BFV, BP) are treated as quasiperiodic stochastic processes. The analysis is performed by spectral methods of stochastic processes theory. FFT algorithm is in use to get spectra estimates. Modified Welch estimator is applied to evaluate consistent estimates of harmonics amplitudes. GUI is implemented in client software to display input signals and their estimates. The results of the software clinical testing in which course we studied the M-wave phenomenon are given.