A linked independent component analysis framework for characterizing site-effect patterns in multi-site structural and functional MRI.

Introduction: Large-scale multi-site magnetic resonance imaging (MRI) improves population coverage and statistical power, but scanner- and protocol-related variability can obscure biological effects. Most harmonization methods aim to reduce site-related variance for downstream analysis, whereas less attention has been paid to where site effects are spatially expressed, whether they are reproducible across site compositions, and which acquisition parameters contribute to them. Methods: We developed a modality-wise Linked Independent Component Analysis (LICA) framework to identify and interpret site-effect patterns in structural and resting-state functional MRI. Grey matter (GM) volume, amplitude of low-frequency fluctuation (ALFF), and regional homogeneity (ReHo) maps were analyzed separately. For each imaging measure, LICA decomposed voxel-wise maps into spatial components and subject-level loadings. Components were classified according to their associations with site labels and biological covariates, their spatial reproducibility was assessed using stepwise site-inclusion analyses, and their technical attribution was evaluated using cross-validated models based on site labels and recorded acquisition parameters. The framework was applied to ABIDE II GM maps from 913 participants across 18 sites and ALFF and ReHo maps from 795 participants across 16 sites. Results: LICA identified site-related components across all three imaging measures. Site effects were not limited to uniform global shifts, but formed modality-specific spatial patterns. GM volume showed a dominant and highly stable whole-brain site-effect pattern, together with site-specific and regional components. In contrast, ALFF and ReHo showed more heterogeneous functional patterns, including global, focal, and scattered configurations. Site labels explained the largest proportion of loading variance, whereas recorded acquisition parameters showed modality-dependent contributions: TR and TE were more prominent for structural site effects, while FA, voxel size, TR, and scanner model contributed more strongly to functional site effects. Discussion: The proposed framework provides a component-level diagnostic approach for multi-site MRI analysis. By mapping, stabilizing, and technically interpreting site-effect patterns, it complements conventional harmonization methods and may improve the transparency and reproducibility of multi-site structural and functional MRI studies.