Strategies for motion- and respiration-robust estimation of fMRI intrinsic neural timescales

Abstract

Abstract Intrinsic neural timescales (INT) reflect the time window of neural integration within a brain region and can be measured via resting-state fMRI (rs-fMRI). Despite the potential relevance of INT to cognition, brain organization, and neuropsychiatric illness, the influences of physiological artifacts on rs-fMRI INT have not been systematically considered. Two artifacts, head motion and respiration, pose serious issues in rs-fMRI studies. Here, we described their impact on INT estimation and tested the ability of two denoising strategies for mitigating these artifacts, high-motion frame censoring and global signal regression (GSR). We used a subset of the HCP Young Adult dataset with runs annotated for breathing patterns (Lynch et al., 2020) and at least one “clean” (reference) run that had minimal head motion and no respiration artifacts; other runs from the same participants (n = 46) were labeled as “non-clean.” We found that non-clean runs exhibited brain-wide increases in INT compared to their respective clean runs and that the magnitude of error in INT between non-clean and clean runs correlated with the amount of head motion. Importantly, effect sizes were comparable to INT effects reported in the clinical literature. GSR and high-motion frame censoring improved the similarity between INT maps from non-clean runs and their respective clean run. Using a pseudo-random frame-censoring approach, we uncovered a relationship between the amount of censored frames and both the mean INT and mean error, suggesting that frame censoring itself biases INT estimation. A group-level correction procedure reduced this bias and improved similarity between non-clean runs and their respective clean run. Based on our findings, we offer recommendations for rs-fMRI INT studies, which include implementing GSR and high-motion frame censoring with Lomb-Scargle interpolation of censored data, and performing group-level correction of the bias introduced by frame censoring.