Reducing Variability in Deep Gray Matter QSM Using Differential ROI Referencing: A Phantom and In Vivo Evaluation

Quantitative susceptibility mapping (QSM) measures the intrinsic magnetic susceptibility of tissues. Because susceptibility values are inherently relative rather than absolute, referencing to a region of interest (ROI) is commonly employed to mitigate intersubject and acquisition-related variability. To validate the feasibility and robustness of a differential ROI reference method in QSM using both digital phantom and in vivo data, particularly for deep gray matter susceptibility analysis. In the digital phantom study, susceptibility values in the caudate nucleus were assessed with and without differential referencing across various simulation conditions (slab widths, brain mask erosion levels, air susceptibility). In the in vivo study, susceptibility differences between 16 patients with Parkinson's disease (PD) and 16 controls were compared across multiple deep gray matter ROIs under variable acquisition parameters. A one-way ANOVA statistical test was used in the in vivo study with multiple-comparison correction via the Benjamini-Hochberg false discovery rate (FDR-BH), with significance set at p < 0.05. In this study, "accuracy" refers specifically to the phantom study where ground-truth susceptibility values are known. In vivo, where such ground truth is unavailable, "robustness" and "group-discrimination sensitivity" are used as surrogate indicators of accuracy. Robustness was evaluated by the consistency of susceptibility differences across varying acquisition parameters, whereas group-discrimination sensitivity was evaluated by the ability to detect disease-related group differences between PD patients and controls. In the digital phantom study, the proposed method demonstrated stable susceptibility estimates across all conditions, with minimal deviation from true values when referencing anatomically adjacent ROIs. In the in vivo study, referenced susceptibility values (e.g., substantia nigra minus putamen) yielded consistent and significant group differences across acquisition scenarios, whereas unreferenced values were more variable. The differential ROI reference method reduces susceptibility variability associated with acquisition and processing factors. This approach may offer a practical and pathology-resilient referencing alternative for deep brain analysis in neurodegenerative diseases.