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Motor impairments caused by stroke significantly affect daily activities and reduce quality of life, highlighting the need for effective rehabilitation strategies. This study presents a novel approach to classifying motor tasks using EEG data from acute stroke patients, focusing on left-hand motor imagery, right-hand motor imagery, and rest states. By using advanced source localization techniques, such as Minimum Norm Estimation (MNE), dipole fitting, and beamforming, integrated with a customized Residual Convolutional Neural Network (ResNetCNN) architecture, we achieved superior spatial pattern recognition in EEG data. Our approach yielded classification accuracies of 91.03% with dipole fitting, 89.07% with MNE, and 87.17% with beamforming, markedly surpassing the 55.57% to 72.21% range of traditional sensor domain methods. These results highlight the efficacy of transitioning from sensor to source domain in capturing precise brain activity. The enhanced accuracy and reliability of our method hold significant potential for advancing brain–computer interfaces (BCIs) in neurorehabilitation. This study emphasizes the importance of using advanced EEG classification techniques to provide clinicians with precise tools for developing individualized therapy plans, potentially leading to substantial improvements in motor function recovery and overall patient outcomes. Future work will focus on integrating these techniques into practical BCI systems and assessing their long-term impact on stroke rehabilitation.