A human subcortical connectome at 400 μm resolution

Maffei, C.; Gong, T.; Neudorfer, C.; Sung, D.; Mihir, D.; Gunalan, K.; Ghosh, S. S.; Augustinack, J. C.; Huang, S. Y.; Richardson, M.; Haber, S. N.; Yendiki, A.

doi:10.64898/2026.03.31.715699

bioRxiv · 10.64898/2026.03.31.715699

A human subcortical connectome at 400 μm resolution

Maffei, C.·Gong, T.·Neudorfer, C.·Sung, D.·Mihir, D.·Gunalan, K.·Ghosh, S. S.·Augustinack, J. C.·Huang, S. Y.·Richardson, M.·Haber, S. N.·Yendiki, A.

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Abstract

The fiber pathways of the human subcortex are of particular importance in clinical neuroscience, as they are targeted by neuromodulation therapies, such as deep brain stimulation (DBS) and lesion approaches, in various motor and psychiatric disorders. However, the complexity, size, and position of these pathways make them challenging to image non-invasively with diffusion MRI (dMRI). As a result, recent efforts in atlasing these pathways to guide neuromodulation have resorted to using synthetic data. Here we present the first extensive reconstruction of fiber pathways of the human subcortex with ultra-high-resolution dMRI. We leverage a unique, ex vivo dMRI dataset acquired by the BRAIN CONNECTS center for Large-scale Imaging of Neural Circuits (LINC) on the first-of-its-kind Connectome 2.0 scanner. Our contribution is two-fold. First, by showing the feasibility of reconstructing these pathways with non-invasive neuroimaging at the single subject level, we set the stage for future research into reconstructing them in vivo in individual patients. Second, we provide a high-definition atlas of basal-ganglia-thalamocortical circuits that is readily extensible via our publicly released data and annotations. As a first demonstration of its clinical validity, we align our atlas to "hotspots" from previous DBS studies and identify pathways associated with therapeutic or side effects.

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Maffei, C., Gong, T., Neudorfer, C., Sung, D., Mihir, D., Gunalan, K., Ghosh, S. S., Augustinack, J. C., Huang, S. Y., Richardson, M., Haber, S. N., Yendiki, A.. 2026-04-03. A human subcortical connectome at 400 μm resolution. https://doi.org/10.64898/2026.03.31.715699

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