χ-sepnet: Deep Neural Network for Magnetic Susceptibility Source Separation

Abstract

Magnetic susceptibility source separation (χ-separation), an advanced quantitative susceptibility mapping (QSM) method, enables the separate estimation of paramagnetic and diamagnetic susceptibility source distributions in the brain. Similar to QSM, it requires solving the ill-conditioned problem of dipole inversion, suffering from so-called streaking artifacts. Additionally, the method utilizes reversible transverse relaxation ($R_2^{\prime }{=R}_2^{*}-R_2$) to complement frequency shift information for estimating susceptibility source concentrations, requiring time-consuming data acquisition for $R_2$ (e.g., multi-echo spin-echo) in addition to multi-echo GRE data for $R_2^{*}$. To address these challenges, we develop a new deep learning network, χ-sepnet, and propose two deep learning-based susceptibility source separation pipelines, χ-sepnet-$R_2^{\prime }$ for inputs with multi-echo GRE and multi-echo spin-echo (or turbo spin-echo) and χ-sepnet-$R_2^{*}$ for input with multi-echo GRE only. The neural network is trained using multiple head orientation data that provide streaking artifact-free labels, generating high-quality χ-separation maps. The evaluation of the pipelines encompasses both qualitative and quantitative assessments in healthy subjects, and visual inspection of lesion characteristics in multiple sclerosis patients. The susceptibility source-separated maps of the proposed pipelines delineate detailed brain structures with substantially reduced artifacts compared to those from the conventional regularization-based reconstruction methods. In quantitative analysis, χ-sepnet-$R_2^{\prime }$ achieves the best outcomes followed by χ-sepnet-$R_2^{*}$, outperforming the conventional methods. When the lesions of multiple sclerosis patients are classified into subtypes, most lesions are identified as the same subtype in the maps from χ-sepnet-$R_2^{\prime }$ and χ-sepnet-$R_2^{*}$ (paramagnetic susceptibility: 99.6% and diamagnetic susceptibility: 98.4%; both out of 250 lesions). The χ-sepnet-$R_2^{*}$ pipeline, which only requires multi-echo GRE data, has demonstrated its potential to offer broad clinical and scientific applications, although further evaluations for various diseases and pathological conditions are necessary.