Fig. 1: QSM processing and IDP analyses.

a, QSM processing pipeline for UK Biobank swMRI data. Blue arrows indicate the main processing steps. Step 1, channel combination using MCPC-3D-S. Step 2, phase unwrapping using a Laplacian-based algorithm. Step 3, background field removal using V-SHARP. Step 4, dipole inversion using iLSQR. Black arrows indicate the brain mask evolution, and orange arrows indicate the brain mask applied at each step. Briefly, the brain mask provided by UK Biobank (Mask1, pink) was first used for the channel combination step. To exclude unreliable voxels in the vicinity of sinus cavities, the mask was subsequently refined using a ‘phase reliability’ map (PR, black box; Mask2, yellow). After background field removal, the output mask from V-SHARP was further refined using the phase reliability map, with the resulting mask (Mask3, green) used for dipole inversion. Full details about the pipeline are provided in Methods. b, QSM atlas generated by averaging χ maps (non-linearly registered to MNI space) from 35,273 individuals; ppb, parts per billion. c, Association between QSM WMH IDP and WMH volume IDP (r = –0.446). d, Example association between T2* left accumbens IDP and median field gradient measured in the left accumbens before (r = –0.506) and after (r = 0.0612) deconfounding based on a physical model (details in Supplementary Information, section 2); n = 35,273 individuals were used to compute Pearson correlation r values shown in c and d.