This study describes a high-resolution in-vivo magnetic resonance imaging atlas of the human hypothalamic region.

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 data release were included in this study.
This template was used to delineate hypothalamic (n=13) and extrahypothalamic (n=12) gray and white matter structures.

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

Files of the hypothalamic region 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:
MDA_990HCP_atlas_labels_0.25mm.nii.gz
MDA_990HCP_atlas_labels_0.5mm.nii.gz
-an archive of binary images of each structure separately:
MDA_990HCP_isolated_nuclei_0.25mm_resolution.zip
-an archive of the three example clinical datasets containing the three labels delineating the volume of tissue activated (VTA) 
of the two DBS patients (example 1 Alzheimer patient with forniceal DBS; example 2 patient receiving DBS for morbid obesity) and
the label delineating the metastasis of example 3. These labels are provided in MNI152b space for two reasons:
1) to allow for visualization of the label in relation to the hypothalamic atlas
2) to protect patient confidentiality  
example_labels_MNI152_template_space.zip

A set of the final hypothalamic region atlas segmentation is also provided aligned to the MNI152 2009b template:
-the full volume segmentation in 0.25 and 0.5 millimeter isotropic resolution:
MNI152b_atlas_labels_0.25mm.nii.gz
MNI152b_atlas_labels_0.5mm.nii.gz
-an archive of binary images of each structure separately:
MNI152b_isolated_nuclei_0.25mm_resolution.zip
MNI152b_isolated_nuclei_0.5mm_resolution.zip


Tables that describe the average structure volumes in the subjects used to generate the MDAs:
Average_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, Robert Gramer, Alexandre Boutet, Andres M. Lozano

Affiliations:
Division of Neurosurgery, Depatment of Surgery, Toronto Western Hospital, University of Toronto, Canada.