Personalized Prediction of Differences in fMRI Connectivity Estimates Across Preprocessing Pipelines

Longitudinal functional MRI of the human brain is valuable for tracking changes in functional connectivity (FC) associated with disease progression or treatment response. Even so, measured FC values depend on preprocessing, and nuisance regression and temporal filtering affect individuals differently. We examined whether we could use earlier scans to predict how preprocessing would affect a later scan. In 69 ADNI (Alzheimer’s Disease Neuroimaging Initiative) participants scanned three times, we measured how nuisance regression and filtering, alone and in sequence, changed the measured FC. A ridge regression model combined these responses with baseline FC from the third scan to predict the effect of reversing the processing order. Just four coefficients were shared across 79,800 connections. In leave-one-participant-out testing, mean squared error was 0.012, compared with 0.017 for predicting the same average response for everyone. It outperformed the best of seven alternative predictions chosen for each participant (0.013; normalized gain 0.069, 95% bootstrap interval 0.006–0.134), with lower error in 44 of 69 participants. About half the benefit of using each person’s earlier responses, rather than the average across participants, came from which connections changed. This advantage persisted after accounting for acquisition variables. The ADNI-trained model reduced mean error in ten Midnight Scan Club participants without refitting. These results support using personal preprocessing history to predict changes in connectivity estimates on newly acquired scans.