Awake rodent fMRI: gradient-echo echo planar imaging versus compressed-sensing fast low angle shot

Abstract

Abstract Awake rodent fMRI is increasingly becoming a reliable neuroimaging technique to study neuronal activity at both the whole brain and high-resolution laminar scales. Prior studies have focused on developing acclimation protocols, experimental paradigms, and hardware to optimize outcomes. However, little effort has been made to address the impact of pulse sequence selection on detecting brain activation in awake fMRI experiments. In the current study, we compare gradient-echo echo planar imaging (GE-EPI) and compressed-sensing fast low angle shot (CS-FLASH) sequences with cerebral blood volume-weighted (CBVw) contrast enhancement to investigate their sensitivity to hemodynamic activity in the olfactory bulb of awake rodents. Compared to GE-EPI, CS-FLASH had comparable motion parameters but was more sensitive to large motions, often resulting in corruption of the image quality. The use of framewise displacement as a motion censoring technique may over censor the data, requiring alternative approaches, such as spatial correlation censoring. CS-FLASH images were qualitatively sharper than GE-EPI; however, the contrast-to-noise ratio for odor activation was consistently greater for GE-EPI compared to CS-FLASH that cannot be explained by olfactory adaptation alone. The activation maps of CS-FLASH to four different odors showed spatially unique patterns consistent with GE-EPI, but with lower z-scores or detection sensitivity. Activation maps were consistent with previously established histological findings. Additionally, odor-evoked laminar activation was greatest in the superficial layers that decreased with laminar depth, consistent with prior findings. We conclude that CS-FLASH produces sharper images with equivalent spatial activation maps to GE-EPI, albeit with lower statistical strength and CNR; and without being prohibited by motion-related image distortion.