Multi-Scale Functional Granularity in the Thalamus and Basal Ganglia

Poster No:


Submission Type:

Abstract Submission 


Vinod Kumar1, Christian Beckmann2, Erik van Oort2, Klaus Scheffler3, Wolfgang Grodd1


1Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, 2Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands, 3Max-Planck Institute for Biological Cybernetics, University of Tuebingen, Tuebingen, Germany


The thalamus (Th) and basal ganglia (BG) harbor numerous of closely connected cell groups extending from the basis of the telencephalon onto the mesencephalon and forming separate nuclei covering numerous functional and neuromodulatory units. The BG consists of spatially neighboured but segregated sub-structures, i.e., caudate (CD), putamen (PU) and globus pallidum (GP). Both, the Th and BG are integral components of different functional systems, and both anchors dynamically with diverse cortical areas via the several pathways to enable sensory, motor, cognitive and emotional processing. However, little is known about the functional distinction and diversity of these subcortical regions in humans. Therefore, we thought to examine whether high-resolution imaging coupled with a reliable, functional parcellation could assess a reproducible and more detailed functional anatomy of the Th and BG.


Data acquisition: Gradient-echo EPI was used to acquire the resting state fMRI (r-fMRI) data. TR: 1000 ms, TE: 22.2 ms, flip angle 45 deg, FOV: 208 x 208 mm (RO x PE), Matrix: 130 x 130 (RO x PE), slice thickness: 1.6 mm; 85 slices; 1.6 mm isotropic voxels, Multiband factor: 5, iPAT: 2, Partial Fourier (pF) sampling: 7/8, Echo spacing: 0.64 ms, Bandwidth: 1924 Hz/Px, 4 Runs, 900 frames per run, Duration/Run: 16:00 minutes [1].

Subjects: The data sample consisted of 62 young healthy subjects (22-36 years old; genetically unrelated). Each subject consisted of four resting state fMRI (r-fMRI) sessions, and all four sessions were used in the analysis.

Data Analysis: The data were preprocessed using HCP pipeline [2]. The instantaneous connectivity parcellation [3] was performed. Subsequently, a split half reproducibility analysis was performed to unravel the most robust and reproducible number of functionally similar parcels within the left and right Th, CD, PU and GP (s. Fig. 1).


The functional parcellation revealed fine-grained diffused patches, but the parcels varied in size, location and reliability scores between both hemispheres (s. Fig. 2). This variability of the left and right parcels seemingly reflects functional differences between both hemispheres. A split-half reproducibility analysis revealed that there no unique most reliable but instead a multi-scale functional organization exists.
The detailed overview on the split-half reliability scores are given below (s. Fig. 1).
a) Thalamus: A rigorous split half reproducibility analysis depicts a first well-defined peak with 4 and 6 parcels, which matches with gross delineation different thalamic nuclei groups [4], i.e., the anterior, posterior, medial and lateral group. As the dimensionality increases, a second reliable peak was found at 38 parcels, exceeding the total number of histologically defined nuclei [4], but seemingly delineates a more detailed function of specific nuclei.
b) Caudate: right CD peaks highly at 8, 10, 18, 36, left CD at 10, 13, and 35 parcels.
c) Putamen: Right PU peaks at 5, 14, 24, 27, 43, 44, and 45 parcels. The left PU 6, 16, 22, 46 and 47 parcels.
d) Pallidum: The right GP peaks at, 10, 17, 19, 27, 33, 48, and 49 parcels - the left GP at 8, 18, 28 and 35.
Supporting Image: OHBM1_1.png
Supporting Image: OHBM2.png


The group ICP analysis revealed a stable and robust functional parcellation of the thalamus and the basal ganglia with a rough bilateral symmetry. However, the parcels showed variability in size and location. A detailed comparison of split-half reproducibility analysis revealed that the Th and BG exhibit a multi-scale functional organizations at rest.

Imaging Methods:


Modeling and Analysis Methods:

Segmentation and Parcellation 2


Anatomy and Functional Systems
Subcortical Structures 1


Basal Ganglia

1|2Indicates the priority used for review

My abstract is being submitted as a Software Demonstration.


Please indicate below if your study was a "resting state" or "task-activation” study.

Resting state

Healthy subjects only or patients (note that patient studies may also involve healthy subjects):

Healthy subjects

Was any human subjects research approved by the relevant Institutional Review Board or ethics panel? NOTE: Any human subjects studies without IRB approval will be automatically rejected.

Not applicable

Was any animal research approved by the relevant IACUC or other animal research panel? NOTE: Any animal studies without IACUC approval will be automatically rejected.

Not applicable

Please indicate which methods were used in your research:

Functional MRI

For human MRI, what field strength scanner do you use?


Which processing packages did you use for your study?


Provide references using author date format

[1] D. C. Van Essen et al., „The Human Connectome Project: a data acquisition perspective“, NeuroImage, Bd. 62, Nr. 4, S. 2222–2231, Okt. 2012.
[2] M. F. Glasser et al.u, „The minimal preprocessing pipelines for the Human Connectome Project“, NeuroImage, Bd. 80, S. 105–124, Okt. 2013.
[3] E. S. B. van Oort et al.„ Functional parcellation using time courses of instantaneous connectivity“, NeuroImage, Bd. 170, S. 31–40, Apr. 2018.
[4] A. Morel, M. Magnin, and D. Jeanmonod, „Multiarchitectonic and stereotactic atlas of the human thalamus“, J. Comp. Neurol., Bd. 387, Nr. 4, S. 588–630, 1997.