Mapping cardiac and respiratory pulsations simultaneously with functional connectivity in the rat brain using zero echo time fMRI

Vascular pulsations are increasingly recognized as key contributors to cerebral perfusion and brain clearance mechanisms, with alterations linked to aging and neurodegenerative diseases. However, capturing fast physiological dynamics in preclinical models remains technically challenging due to high cardiac frequencies and small brain size. Here, we investigated the feasibility of zero echo time (ZTE) functional MRI (fMRI) to capture cardiac- and respiration-related pulsations across multiple temporal scales in the rat brain under isoflurane anesthesia. We used retrospective binning to assess cardiac- and respiration-related pulsations. Cardiovascular state was modulated with medetomidine, and functional connectivity analyses were performed to evaluate slower neural dynamics. ZTE fMRI robustly detected physiological pulsations across the brain, achieving effective temporal resolution of 8 ms, with the strongest signals observed in large arteries, consistent with an inflow‑based contrast mechanism. Cardiac pulsation amplitudes increased significantly under combined medetomidine-isoflurane anesthesia, whereas respiration‑related pulsations remained stable. Functional connectivity decreased under combined anesthesia, confirming ZTE fMRI sensitivity to slower neural dynamics. ZTE fMRI enables simultaneous assessment of cerebrovascular pulsatility and functional connectivity, providing a powerful tool for studying physiological brain dynamics in vivo.