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In this paper we consider channel estimation for MIMO-OFDM systems, specifically when null carriers are placed at the border of the spectrum in order to limit interference with neighboring spectrums. Indeed, the presence of these null carriers leads to degradation on the transform domain channel estimation (TD-CE) because of a "border effect" phenomenon. Truncated singular value decomposition (TSVD) based method allows to improve the accuracy of the TD-CE by significantly reducing each "border effect". However, its application to MIMO systems may cause problem due to its high complexity. We propose in this paper, a solution based on the power profile of the transfer matrix in order to considerably reduce the complexity. The efficiency of the proposed solution is demonstrated within 3GPP system context.