Mesopontine-tegmental nuclei such as the pedunculotegmental, oral-pontine-reticular and paramedian-raphe nuclei modulate arousal and motor functions. Dysfunction of these nuclei is implicated in the pathogenesis of disorders of consciousness, sleep disorders, and neurodegenerative diseases. However, a stereotaxic probabilistic atlas of these nuclei in humans does not exist. We used segmentation of 1.1 mm-isotropic 7 Tesla diffusion-fractional-anisotropy and T2-weighted images to generate and validate an in vivo probabilistic neuroimaging structural atlas of these nuclei in MNI space. We constructed this atlas to aid the localization of these nuclei in conventional images in future research and clinical studies of arousal and motor functions.