Deep Learning-Based Desikan-Killiany Parcellation of the Brain Using Diffusion MRI

TL;DR

This paper introduces a deep learning framework for direct brain parcellation using only diffusion MRI data, eliminating the need for anatomical MRI and registration, thus improving accuracy and robustness in neuroimaging analyses.

Contribution

It presents a novel hierarchical two-stage deep learning model for Desikan-Killiany parcellation directly from diffusion MRI, outperforming existing methods and demonstrating strong generalization.

Findings

Achieves higher Dice scores than state-of-the-art models.

Demonstrates robustness across different datasets and protocols.

Provides a registration-free, reliable brain segmentation method.

Abstract

Accurate brain parcellation in diffusion MRI (dMRI) space is essential for advanced neuroimaging analyses. However, most existing approaches rely on anatomical MRI for segmentation and inter-modality registration, a process that can introduce errors and limit the versatility of the technique. In this study, we present a novel deep learning-based framework for direct parcellation based on the Desikan-Killiany (DK) atlas using only diffusion MRI data. Our method utilizes a hierarchical, two-stage segmentation network: the first stage performs coarse parcellation into broad brain regions, and the second stage refines the segmentation to delineate more detailed subregions within each coarse category. We conduct an extensive ablation study to evaluate various diffusion-derived parameter maps, identifying an optimal combination of fractional anisotropy, trace, sphericity, and maximum eigenvalue that enhances parellation accuracy. When evaluated on the Human Connectome Project and Consortium for Neuropsychiatric Phenomics datasets, our approach achieves superior Dice Similarity Coefficients compared to existing state-of-the-art models. Additionally, our method demonstrates robust generalization across different image resolutions and acquisition protocols, producing more homogeneous parcellations as measured by the relative standard deviation within regions. This work represents a significant advancement in dMRI-based brain segmentation, providing a precise, reliable, and registration-free solution that is critical for improved structural connectivity and microstructural analyses in both research and clinical applications. The implementation of our method is publicly available on github.com/xmindflow/DKParcellationdMRI.