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The rhythm of electroencephalogram (EEG) depends on the neuroanatomical-based parameters such as white matter (WM) connectivity. However, the impacts of these parameters on the specific characteristics of EEG have not been clearly understood. Previous studies demonstrated that, these parameters contribute the inter-subject differences of EEG during performance of specific task such as motor imagery (MI). Though researchers have worked on this phenomenon, the idea is yet to be understood in terms of the mechanism that underlies such differences. Here, to tackle this issue, we began our investigations by first examining the structural features related to scalp EEG characteristics, which are event-related desynchronizations (ERDs), during MI using diffusion MRI. Twenty-four right-handed subjects were recruited to accomplish MI tasks and MRI scans. Based on the high spatial resolution of the structural and diffusion images, the motor-related WM links, such as basal ganglia (BG)-primary somatosensory cortex (SM1) pathway and supplementary motor area (SMA)-SM1 connection, were reconstructed by using probabilistic white matter tractography. Subsequently, the relationships of WM characteristics with EEG signals were investigated. These analyses demonstrated that WM pathway characteristics, including the connectivity strength and the positional characteristics of WM connectivity on SM1 (defined by the gyrus-sulcus ratio of connectivity, GSR), have a significant impact on ERDs when doing MI. Interestingly, the high GSR of WM connections between SM1 and BG were linked to the better ERDs. These results therefore, indicated that the connectivity in the gyrus of SM1 interacted with MI network which played the critical role for the scalp EEG signal extraction of MI to a great extent. The study provided the coupling mechanism between structural and dynamic physiological features of human brain, which would also contribute to understanding individual differences of EEG in MI-brain computer interface.