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Transfer learning (TL) has been widely used in motor imagery (MI) based brain-computer interfaces (BCIs) to reduce the calibration effort for a new subject, and demonstrated promising performance. While a closed-loop MI-based BCI system, after electroencephalogram (EEG) signal acquisition and temporal filtering, includes spatial filtering, feature engineering, and classification blocks before sending out the control signal to an external device, previous approaches only considered TL in one or two such components. This paper proposes that TL could be considered in all three components (spatial filtering, feature engineering, and classification) of MI-based BCIs. Furthermore, it is also very important to specifically add a data alignment component before spatial filtering to make the data from different subjects more consistent, and hence to facilitate subsequential TL. Offline calibration experiments on two MI datasets verified our proposal. Especially, integrating data alignment and sophisticated TL approaches can significantly improve the classification performance, and hence greatly reduces the calibration effort.