Brain Structure and Function

, Volume 221, Issue 2, pp 753–814 | Cite as

The connectome of the basal ganglia

  • Oliver Schmitt
  • Peter Eipert
  • Richard Kettlitz
  • Felix Leßmann
  • Andreas Wree
Original Article


The basal ganglia of the laboratory rat consist of a few core regions that are specifically interconnected by efferents and afferents of the central nervous system. In nearly 800 reports of tract-tracing investigations the connectivity of the basal ganglia is documented. The readout of connectivity data and the collation of all the connections of these reports in a database allows to generate a connectome. The collation, curation and analysis of such a huge amount of connectivity data is a great challenge and has not been performed before (Bohland et al. PloS One 4:e7200, 2009) in large connectomics projects based on meta-analysis of tract-tracing studies. Here, the basal ganglia connectome of the rat has been generated and analyzed using the consistent cross-platform and generic framework neuroVIISAS. Several advances of this connectome meta-study have been made: the collation of laterality data, the network-analysis of connectivity strengths and the assignment of regions to a hierarchically organized terminology. The basal ganglia connectome offers differences in contralateral connectivity of motoric regions in contrast to other regions. A modularity analysis of the weighted and directed connectome produced a specific grouping of regions. This result indicates a correlation of structural and functional subsystems. As a new finding, significant reciprocal connections of specific network motifs in this connectome were detected. All three principal basal ganglia pathways (direct, indirect, hyperdirect) could be determined in the connectome. By identifying these pathways it was found that there exist many further equivalent pathways possessing the same length and mean connectivity weight as the principal pathways. Based on the connectome data it is unknown why an excitation pattern may prefer principal rather than other equivalent pathways. In addition to these new findings the local graph-theoretical features of regions of the connectome have been determined. By performing graph theoretical analyses it turns out that beside the caudate putamen further regions like the mesencephalic reticular formation, amygdaloid complex and ventral tegmental area are important nodes in the basal ganglia connectome. The connectome data of this meta-study of tract-tracing reports of the basal ganglia are available for further network studies, the integration into neocortical connectomes and further extensive investigations of the basal ganglia dynamics in population simulations.


Connectome Connectomics Basal ganglia Caudate putamen Striatum Substantia nigra Neuroontology Digital atlasing Tract tracing Multiscale Network analysis Graph analysis 



All (all inputs and outputs)


Average degree


Accumbens nucleus


Amygdaloid complex


Lateral agranular prefrontal cortex


Medial agranular prefrontal cortex




Average weight


Betweenness centrality


Basal ganglia






Closeness centrality


Chain pattern of a motif


Centrolateral thalamic nucleus


Central medial thalamic nucleus


Central nervous system


Caudate putamen




Direct input from contralateral


Direct input from ipsilateral


Direct input from ipsi- and contralateral


Direct neighbor network


Direct output to contralateral


Direct output to ipsilateral


Direct output to ipsi- and contralateral


Dorsal raphe nucleus


Eigenvector centrality


Entorhinal cortex






In (input to a region; used in tables)


Symmetric input connection to a central node of a motif


Indirect neighbor network




Lateral globus pallidus


Lateral habenular nucleus


Mediodorsal thalamic nucleus lateral part


Mediodorsal thalamic nucleus medial part


Metric multidimensional scaling


Medial globus pallidus


Mesencephalic reticular formation


Out (Output of region; used in tables only)


Symmetric output connection from a central node of a motif


Paracentral thalamic nucleus


Principal component analysis


Parafascicular thalamic nucleus


Piriform cortex


Path length


Page rank centrality


Number of articles


Radiality of the input


Radiality of the output






Subtree input from contralateral


Subtree input from ipsilateral


Subtree input from ipsi- and contralateral


Subgraph centrality


Substantia nigra compact part


Substantia nigra reticular part


Subtree output to contralateral


Subtree output to ipsilateral


Subtree output to ipsi- and contralateral


Length of shortest path


Spiny neurons of the CPu


Subthalamic nucleus


Ventro anterior thalamic nucleus


Ventrolateral thalamic nucleus


Ventromedial thalamic nucleus


Ventral tegmental area A10



The authors thank Klaus-Peter Schmitz (Department of Biomedical Engineering, University of Rostock) for the support of the neuroVIISAS project. We thank Frauke Winzer, Susanne Lehmann, Antje Schümann, Jennifer Meinhardt, Ann-Christin Klünker for their faithful work on extending the database and mappings. All work was supported by the Faculty of Mathematics and Natural Sciences and of the Faculty of Medicine of the University of Rostock.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Oliver Schmitt
    • 1
  • Peter Eipert
    • 1
  • Richard Kettlitz
    • 1
  • Felix Leßmann
    • 1
  • Andreas Wree
    • 1
  1. 1.Department of AnatomyUniversity of RostockRostockGermany

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