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

Abstract

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.

Keywords

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

Abbreviations

A

All (all inputs and outputs)

AD

Average degree

Ac

Accumbens nucleus

AC

Amygdaloid complex

AGl

Lateral agranular prefrontal cortex

AGm

Medial agranular prefrontal cortex

Aut

Authoritativeness

AW

Average weight

BC

Betweenness centrality

BG

Basal ganglia

C

Circle

CC

Cluster-coefficient

CE

Closeness centrality

chain

Chain pattern of a motif

CL

Centrolateral thalamic nucleus

CM

Central medial thalamic nucleus

CNS

Central nervous system

CPu

Caudate putamen

DG

Degree

Dic

Direct input from contralateral

Dii

Direct input from ipsilateral

Dis

Direct input from ipsi- and contralateral

DNN

Direct neighbor network

Doc

Direct output to contralateral

Doi

Direct output to ipsilateral

Dos

Direct output to ipsi- and contralateral

DR

Dorsal raphe nucleus

EC

Eigenvector centrality

Ent

Entorhinal cortex

HIPP

Hippocampus

Hub

Hubness

I

In (input to a region; used in tables)

in

Symmetric input connection to a central node of a motif

INN

Indirect neighbor network

L

Laterality

LGP

Lateral globus pallidus

LHb

Lateral habenular nucleus

MDL

Mediodorsal thalamic nucleus lateral part

MDM

Mediodorsal thalamic nucleus medial part

MDS

Metric multidimensional scaling

MGP

Medial globus pallidus

MRF

Mesencephalic reticular formation

O

Out (Output of region; used in tables only)

out

Symmetric output connection from a central node of a motif

PC

Paracentral thalamic nucleus

PCA

Principal component analysis

PF

Parafascicular thalamic nucleus

Pir

Piriform cortex

PL

Path length

PRC

Page rank centrality

Pub

Number of articles

RADin

Radiality of the input

RADout

Radiality of the output

Rec

Reciprocal

Rel

Reliability

Sic

Subtree input from contralateral

Sii

Subtree input from ipsilateral

Sis

Subtree input from ipsi- and contralateral

SG

Subgraph centrality

SNC

Substantia nigra compact part

SNR

Substantia nigra reticular part

Soc

Subtree output to contralateral

Soi

Subtree output to ipsilateral

Sos

Subtree output to ipsi- and contralateral

SP

Length of shortest path

SPN

Spiny neurons of the CPu

STh

Subthalamic nucleus

VA

Ventro anterior thalamic nucleus

VL

Ventrolateral thalamic nucleus

VM

Ventromedial thalamic nucleus

VTA

Ventral tegmental area A10

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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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