Superpixel-ComBat multi-site harmonization of unpaired T1W MRI data in Huntington’s disease

Abstract Background Pooling multi-site MRI data is essential for well-powered neuroimaging analyses, particularly in Huntington’s disease (HD), where large cohorts are needed to study disease-stage heterogeneity and subtle progressive neuroanatomical change. However, scanner-related variability hinders direct data pooling, confounding image-level methods such as voxel-based morphometry (VBM). Superpixel-ComBat (SP-ComBat), a voxel-level image-harmonization framework, effectively removes scanner effects but depends on traveling-subject data that are rarely available retrospectively. We extend SP-ComBat to unpaired multi-site T1-weighted MRI by introducing a pseudo-pairing framework that leverages demographically matched controls across scanners as surrogate traveling subjects. Methods Two pipelines were developed to estimate scanner effects under retrospective constraints: pipeline 1 used a small set of well-matched pseudo-pairs (n = 4) with bootstrap resampling to address scanners with limited sample sizes, while pipeline 2 used the recommended number of pseudo-pairs (n = 16) without resampling. Pseudo-pair images were parcellated into 3D-superpixels, and ComBat was applied within clusters to estimate scanner-specific adjustments for native-space harmonization. Pipeline performance was assessed in a representative multi-study dataset comprising six scanners from three HD cohorts (HD-YAS, HD-CSF, TRACK-HD; N = 144) and replicated in the full multi-study dataset (FMD; N = 548). Results Both pipelines improved image quality, aligned scanner-specific intensities, and preserved disease-related structural patterns. Pipeline 2 showed superior parameter re-estimation stability and was selected for the FMD. Harmonization eliminated systematic segmentation errors, enabled a single unified VBM pipeline across scanners, and increased sensitivity to HD-related voxel-wise atrophy. Conclusions SP-ComBat was effectively adapted for harmonization of unpaired multi-site structural MRI, reducing scanner bias while preserving biological variability and supporting unified VBM analyses across scanners.