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Description: Source data and code related to Jensen et al., Nat Comms, 2024 (https://www.nature.com/articles/s41467-024-46275-y, DOI: https://doi.org/10.1038/s41467-024-46275-y). For HCP users, this code should be sufficient to replicate figures, analyses and results presented in the manuscript and supplementary information. Non-HCP users first need to apply for access to the restricted and unrestricted HCP data (https://humanconnectome.org/). Intermediate analysis outputs will be shared with registered HCP users upon request whenever possible. We also include binary masks for all regions of interests included in the study and importantly, for the parcellation of the hypothalamus into seven nuclei that was developed in our study based on resting-state functional connectivity. Abstract: The hypothalamus is part of the hypothalamic-pituitary-adrenal axis which activates stress responses through release of cortisol. It is a small but heterogeneous structure comprising multiple nuclei. In vivo human neuroimaging has rarely succeeded in recording signals from individual hypothalamus nuclei. Here we use human resting-state fMRI (n=498) with high spatial resolution to examine relationships between the functional connectivity of specific hypothalamic nuclei and a dimensional marker of prolonged stress. First, we demonstrate that we can parcellate the human hypothalamus into seven nuclei in vivo. Using the functional connectivity between these nuclei and other subcortical structures including the amygdala, we significantly predict stress scores out-of-sample. Predictions use 0.0015% of all possible brain edges, are specific to stress, and improve when using nucleus-specific compared to whole-hypothalamus connectivity. Thus, stress relates to connectivity changes in precise and functionally meaningful subcortical networks, which may be exploited in future studies using interventions in stress disorders.