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In this paper we investigate adaptive channel estimation for frequency domain equalization (FDE) in a single carrier (SC) multiple-input multiple-output (MIMO) system. Two types of channel estimation methods are proposed, assuming uncorrelated and correlated frequency bins. The FDE coefficients are computed using the channel estimates. It is shown that our proposed structures significantly outperform the adaptive FDE without channel estimation at high SNR. In particular, the proposed LMS-SCE FDE approaches the performance of FDE with perfect channel state information (CSI), and has a fast convergence speed and reasonably low complexity.