In this paper, the Fourier transform based minimum mean square error (FT-based MMSE) method is used to calculate the regional cerebral blood volume (rCBV) in magnetic resonance (MR) perfusion imaging, and the method is improved to handle the existing noise in the imaging process. In the experiments with signal-to-noise ratio (SNR) of 50 dB, the rCBV values were compared with the results using MMSE method. The effects of different SNRs on the estimation of rCBV were analyzed. The experimental results showed that MMSE was a simple way to filter the measurement noise, and could calculate rCBV accurately. Compared with other existing methods, the present method is not sensitive to environment, and furthermore, it is suitable to deal with the perfusion images acquired from the environment with larger SNR.