Peter is right; the hypothalamus is curiously missing from almost all commonly available atlases except for the Talairach daemon. We have the Keuken sub-cortical atlas available, but it is also missing the hypothalamus. I did a little research to find some others and found some good leads. You can look yourself at these, but this recent one was easy to get working with AFNI and integrated with whereami.
http://afni.nimh.nih.gov/pub/dist/atlases/Pauli_subcortical/subcortical_dist.tgz
Download and expand tgz file
tar xzvf subcortical_dist.tgz
@AfniEnv -set AFNI_SUPP_ATLAS_DIR `pwd`/subcortical_dist
[
www.nature.com]
[
osf.io]
[
www.sciencedirect.com]
[
www.braininteratlas.be]
The hypothalamus is labeled "HTH" in the linked atlas.
HTH,
Daniel