Image processing
The QSM images were reconstructed from GRE data using the SEPIA (SuscEptibility mapping PIpeline tool for phAse images) toolbox [The magnitude image, in the same space as the QSM image, was used for registration and was obtained by summing the squares of magnitude images among different TEs. 3D T1, T2, and magnitude images were skull-stripped using BET in FSL. By using citatlaskit (Summarized steps of the pipeline for image preprocessing. The phase images were unwrapped, and the background field was removed with the regularisation-enabled SHARP filtering method. Magnetic susceptibility was quantitatively calculated using MEDI and quantitative susceptibility map (QSM) images were generated. T1, T2, and magnitude images were skull-stripped. By using Advanced Normalization Tool (ANTs), SyN multimodal warping was performed using joint T1 and T2 cost function to transform the high-resolution probabilistic subcortical brain nuclei atlas in CIT168 space to individual space. Eventually, the QSM value of each subcortical nuclei was extracted from each manually refined region of interest (ROI) based on the subcortical nuclei atlas