Revisiting the role of structural connectivity-based parcellation in thalamic nuclei segmentation: Benchmarking against recent state-of-the-art methods

by Daniel H. Nguyen, Debottama Das, Ali Bilgin, Dianne Patterson, Matthew Hook, Chris Butson, Alberto Cacciola, Vinod Kumar Jangir, Manojkumar Saranathan

Leveraging diffusion tractography, connectivity-based parcellation (CBP) is one of the oldest methods for thalamic nuclei segmentation. The goal of this work was to reassess CBP using higher spatial resolution diffusion MRI data and reconstruction algorithms, and to compare it with recent state-of-the-art methods for thalamic nuclei segmentation. Furthermore, these methods were systematically evaluated against three histological atlases and one functional MRI–based atlas to examine their relative anatomical similarities and differences. High resolution diffusion and T1-weighted MRI data from 67 healthy individuals in the Human Connectome Project Young Adult database were analyzed. CBP was performed using probabilistic tractography with cortical targets derived from combining labels of the Human Connectome Project Multi-Modal Parcellation 1.0 atlas into 8, 11, and 23 regions. Results were compared against three recent methods: orientation distribution function clustering (ODF), track density imaging (TDI), and structural MRI-based segmentation. Group level analyses were conducted in the Montreal Neurological Institute space, and Dice overlap coefficients were calculated using four atlases (three histological, one functional). CBP results using newer data and methods were still remarkably similar to the original CBP parcellation results. Across atlases, a consistent hierarchy was observed: HIPS-THOMAS performed best, followed by TDI, ODF, and CBP (Kendall’s W = 1.00, p = 0.007). Histological atlases showed strong mutual agreement (Pearson r = 0.71–0.85), whereas the Zhang atlas demonstrated lower concordance (Pearson r = 0.51–0.63). Despite methodological advances, CBP remains constrained in its ability to delineate thalamic nuclei with histological accuracy. By contrast, structural and diffusion microstructural approaches provided better nuclear localization. These findings highlight the need for hybrid workflows that integrate structural and diffusion-based information to enable more reliable thalamic segmentation for neuroscience research.