Confirmation of resting-state BOLD fluctuations in the human brainstem and spinal cord after identification and removal of physiological noise

Abstract

Purpose: Resting-state functional MRI (rs-fMRI) has been used to investigate networks within the cortex, but its use in the brainstem (BS) and spinal cord (SC) has been limited. This region presents challenges for fMRI, partly because of sources of physiological noise. This study aims to quantify noise contributions to rs-fMRI, and to obtain evidence of resting-state blood oxygenation level–dependent (BOLD) fluctuations. Methods: Resting-state-fMRI data were obtained from the BS/SC in 16 participants, at 3 Tesla, with T2-weighted single-shot fast spin-echo imaging. The peripheral pulse, respiration, and expired CO2 were recorded continuously. Physiological noise was modeled from these recordings, movement parameters, and white matter regions. Model fits were then subtracted from the data. BOLD contributions were then investigated through connectivity. Results: Bulk motion was the largest contributor to the signal variance (19% of the total), followed by cardiac-related motion (14%), nonspecific signal variations detected in white matter (10%), respiratory-related motion (2.6%), and end-tidal CO2 variations (0.7%). After noise was removed, significant left-right connectivity was detected in the SC dorsal horns and ventral horns. Conclusions: Resting-state BOLD fluctuations are demonstrated in the SC, as are the dominant noise contributions. These findings are an essential step toward establishing rs-fMRI in the BS/SC. Magn Reson Med 78:2149–2156, 2017. © 2017 International Society for Magnetic Resonance in Medicine.