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The second-order statistics of a time-domain signal are very often used in blind and semi-blind channel estimation. Considering that the received signal in MIMO-OFDM systems might be corrupted in the time-domain due to some adverse factors such as frequency offset and large peak-to-average power ratio (PAPR), an IFFT processor is required in the receiver to achieve a good-quality time-domain signal. This additional IFFT incurs extra computational complexity and probably a long time delay as well in real-time communication systems. In this paper, we propose a new algorithm for the computation of the time-domain correlation matrix directly from the received frequency- domain signal. The proposed frequency-domain correlation matrix estimation method is then used to develop a new semi-blind MIMO-OFDM channel estimation approach. A number of computer simulation based experiments are conducted, confirming the effectiveness of the proposed method.