This study describes a high-resolution in-vivo magnetic resonance imaging atlas of the human hypothalamus. We employed a minimum deformation averaging (MDA) pipeline to produce a normalized (MNI152b), high-resolution template from multimodal (T1w and T2w) magnetic resonance imaging (MRI) datasets. 990 subjects derived from the HCP1200 date release were included in this study. This template was used to delineate hypothalamic (n=13) and extrahypothalamic (n=12) gray and white matter structures. Files (in bold) of the hypothalamus atlas segmentation (tables (.csv) and images (nifti format)): -a table with the structure name, abbreviation and label number: Volumes_names-labels.csv -the full volume segmentation in 0.25 and 0.5 millimeter isotropic resolution: atlas_labels_0.25mm.nii.gz atlas_labels_0.5mm.nii.gz -an archive of binary images of each structure separately: isolated_nuclei_0.25mm_resolution.zip The high-contrast, high-resolution MDA template images in 0.25 and 0.5 millimeter isotropic resolution: MDA_990HCP_t1_MNI152b_0.25.nii.gz MDA_990HCP_t1_MNI152b_0.5.nii.gz MDA_990HCP_t2_MNI152b_0.25.nii.gz MDA_990HCP_t2_MNI152b_0.5.nii.gz Tables that describe the average structure volumes in the subjects used to generate the MDAs: Average_left_right_hemispheric_hypothalamic_volumes_by_Sex.csv Average_left_right_hemispheric_hypothalamic_volumes.csv Estimated_volumes_of_hypothalamus_proper_its_divisions_and_nuclei.csv Authors: Clemens Neudorfer, Jürgen Germann, Gavin J.B. Elias, Alexandre Boutet, Robert Gramer, Andres M. Lozano Affiliations: Division of Neurosurgery, Depatment of Surgery, Toronto Western Hospital, University of Toronto, Canada.