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BACKGROUND: The aim of this study was to determine whether computer-aided training (CAT) of motor tasks would increase muscle activity and change its spatial distribution in a patient with a bilateral upper-limb congenital transverse deficiency. We believe that our study makes a significant contribution to the literature because it demonstrates the usefulness of CAT in promoting the neuromuscular adaptation in people with congenital limb deficiencies and altered body image. CASE PRESENTATION: The patient with bilateral upper-limb congenital transverse deficiency and the healthy control subject performed 12 weeks of the CAT. The subject's task was to imagine reaching and grasping a book with the hand. Subjects were provided a visual animation of that movement and sensory feedback to facilitate the mental engagement to accomplish the task. High-density electromyography (HD-EMG; 64-electrode) were collected from the trapezius muscle during a shrug isometric contraction before and after 4, 8, 12 weeks of the training. After training, we observed in our patient changes in the spatial distribution of the activation, and the increased average intensity of the EMG maps and maximal force. CONCLUSIONS: These results, although from only one patient, suggest that mental training supported by computer-generated visual and sensory stimuli leads to beneficial changes in muscle strength and activity. The increased muscle activation and changed spatial distribution of the EMG activity after mental training may indicate the training-induced functional plasticity of the motor activation strategy within the trapezius muscle in individual with bilateral upper-limb congenital transverse deficiency. Marked changes in spatial distribution during the submaximal contraction in the patient after training could be associated with changes of the neural drive to the muscle, which corresponds with specific (unfamiliar for patient) motor task. These findings are relevant to neuromuscular functional rehabilitation in patients with a bilateral upper-limb congenital transverse deficiency especially before and after upper limb transplantation and to development of the EMG based prostheses.