A Novel Magnetic Field Gradient Based Thresholding Method to Improve Brain Masking for QSM

Motivation: Artefacts in QSM reconstructions can persist even after optimal noise-based masking methods are used, especially in EPI-QSM, due to challenging regions caused by large field gradients rather than noise. Goal(s): To reduce brain QSM artefacts using a novel, automated brain mask thresholding method. Approach: Regions with high magnitude of the field gradients (MFG) were removed from the brain mask used for background field removal and/or susceptibility calculation. Results: Thresholding the mask based on the MFG of the local field map was superior to thresholding the total field map. MFG-based thresholding reduced artifacts in 2D-EPI and 3D-GRE QSM compared to noise-based thresholding. Impact: Thresholding the brain mask based on the magnitude of local field gradients improves brain QSM quality by reducing streaking artefacts compared to state-of-the-art noise-based thresholding. This automated MFG-based masking method particularly improves rapid 2D-EPI-QSM as well as conventional 3D-GRE QSM.