Brain anatomy

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Basal ganglia

Data source:
Cite tractography:
Tractography of the illustrated fibers was created using the Autotrack function of DSI Studio software (https://dsi-studio.labsolver.org/) based on the averaged HCP-1065 young adult fiber templates (1 mm resolution) of the WU-Minn Consortium (Yeh FC. Population-based tract-to-region connectome of the human brain and its hierarchical topology. Nat Commun. 2022;13(1):4933. Published 2022 Aug 22. doi:10.1038/s41467-022-32595-4, https://brain.labsolver.org/hcp_template.html). A total of 3000-15000 tracts were generated for each pathway and were further filtered for false and unrelated fibers employing the default pathway recognition of the software based on the included tractography atlas (Yeh FC, Panesar S, Fernandes D, et al. Population-averaged atlas of the macroscale human structural connectome and its network topology. Neuroimage. 2018;178:57-68. doi:10.1016/j.neuroimage.2018.05.027).
Cite brain map regions:
Three dimensional models of cortical and subcortical brain regions were based on the maximum probability cytoarchitectonic maps from the Julich-Brain Atlas (v3.1) and the extended HCP-MMP atlas HCPex. Both atlases are provided in MNI ICBM 152 2009c Nonlinear Asymmetric space.
1. Julich-Brain Atlas, cytoarchitectonic maps (v3.1) DOI: 10.25493/KNSN-XB4, released 23.06.2024
https://search.kg.ebrains.eu/instances/f1fe19e8-99bd-44bc-9616-a52850680777
Amunts, K., Mohlberg, H., Bludau, S., Caspers, S., Lewis, L. B., Eickhoff, S. B., & Pieperhoff, P. (2023). Julich-Brain Atlas, cytoarchitectonic maps (v3.1) [Data set].
Amunts, K., Mohlberg, H., Bludau, S., & Zilles, K. (2020). Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture. Science, 369(6506), 988–992. DOI: 10.1126/science.abb4588
2. The extended Human Connectome Project multimodal parcellation atlas of the human cortex and subcortical areas (v1.1).
https://github.com/wayalan/HCPex
Huang CC, Rolls ET, Feng J, Lin CP. An extended Human Connectome Project multimodal parcellation atlas of the human cortex and subcortical areas. Brain Struct Funct. 2022 Apr;227(3):763-778. Epub 2021 Nov 17. doi: 10.1007/s00429-021-02421-6
Huang CC, Rolls ET, Hsu CH, Feng J, Lin CP. Extensive Cortical Connectivity of the Human Hippocampal Memory System: Beyond the "What" and "Where" Dual Stream Model. Cerebral Cortex. 2021 May 19;bhab113. doi: 10.1093/cercor/bhab113.
1. Basal ganglia
2. Cortico-Basal Ganglia-Thalamo-cortical loop pathway