Network- and Measure-Specific Mid-Term Reliability of Multi-Echo Resting-State Functional Magnetic Resonance Imaging on a Compact 3 Tesla Scanner

Abstract

Introduction Understanding mid-term test-retest reliability and within-subject variability is important for interpreting changes observed in longitudinal and intervention studies. The reliability of resting-state functional magnetic resonance imaging (rs-fMRI) is known to vary across measures and brain regions. However, how reliability differs across functional networks and connectivity-and amplitude-based measures, and whether multi-echo acquisition and processing modify these patterns, remain incompletely characterized. Methods Twenty-two healthy volunteers underwent two rs-fMRI sessions 15.7 ± 4.0 days apart on a Compact 3T scanner. Multi-echo, middle-echo, and independently acquired single-echo datasets were compared, with multi-echo independent component analysis additionally evaluated as a denoising approach. Functional connectivity (FC) and three amplitude-based measures were evaluated using the Schaefer 400 parcellation. Reliability was systematically assessed using intraclass correlation coefficient (ICC), within-subject standard deviation (wSD), and systematic bias at edge or regional, and network levels. Results Acquisition-dependent differences in reliability were generally modest. Multi-echo acquisition and processing increased functional connectivity strength and the magnitude of amplitude-based measures and improved inferior cortical coverage, but these enhancements did not consistently translate into substantially higher ICC or lower wSD. In contrast, reliability showed clear network-dependent differences. FC reliability varied markedly across network pairs and was not explained by connectivity strength alone; pairs involving the default mode and control networks generally showed more favorable profiles than several somatomotor and visual network pairs. Fractional amplitude of low-frequency fluctuations (fALFF) also showed network-dependent reliability, with the most favorable regional reproducibility observed in the default mode and control networks and lower reproducibility in the somatomotor and visual networks. Conclusion These findings provide practical mid-term reliability benchmarks for rs-fMRI on a Compact 3T scanner and show that measurement stability varies more clearly across measures and functional networks than across acquisition approaches. Key points Mid-term test-retest reliability varied more clearly across resting-state measures and functional networks than across acquisition and processing approaches. Multi-echo acquisition and processing enhanced functional connectivity strength, amplitude-based signal magnitude, and inferior cortical coverage but did not consistently improve reliability. Functional connectivity strength and fractional amplitude of low-frequency fluctuations showed distinct network-specific reliability profiles, with more favorable reproducibility in default mode and control networks than in several somatomotor and visual networks.