Neuroimaging studies have identified a subgroup of patients with a Disorder of Consciousness (DOC) who, while being behaviorally non-responsive, are nevertheless able to follow commands by modulating their brain activity in motor imagery (MI) tasks. These techniques have even allowed for binary communication in a small number of DOC patients. However, the majority of patients who can follow commands are unable to use their responses to communicate. A similar dissociation between present command following (CF) and absent communication abilities has been reported in overt behavioral assessments. However, the neural correlates of this dissociation in both overt and covert modalities are unknown. Here, we used functional magnetic resonance imaging (fMRI) to explore the neural mechanisms underlying CF and selection of responses for binary communication using either executed or imagined movements. Fifteen healthy participants executed or imagined two different types of arm movements that were either pre-determined by the experimenters (CF) or decided by them (action selection, AS). Action selection involved greater activity in high-level associative areas in frontal and parietal regions than CF. Additionally, motor execution (ME), as compared to MI, activated contralateral motor cortex, while the opposite contrast revealed activation in the ipsilateral sensorimotor cortex and the left inferior frontal gyrus. Importantly, there was no interaction between the task (CF/AS) and modality (MI/ME). Our results suggest that the neural processes involved in following a motor command or selecting between two motor actions are not dependent on how the response is expressed (via ME/MI). They also suggest a potential neural basis for the distinction in cognitive abilities seen in DOC patients.