EPI-RARE-fMRI-Awake pigeon

Functional magnetic resonance imaging (fMRI) in awake small animals like pigeons or birdsongs opens a new window into the neural fundaments of cognitive behavior. However, high-field fMRI in the avian brain is challenging due to strong local magnetic field inhomogeneities caused by air cavities in the skull. A spoiled gradient-echo fMRI sequence has already been used to map the auditory network in birdsong, but due to susceptibility artifacts, only 50% of the whole brain could be recorded. Since whole-brain fMRI coverage is vital to reveal whole-brain networks, a MRI sequence that is less susceptible to these artifacts was required. This was recently achieved in various bird species by using a rapid acquisition with a relaxation enhancement (RARE) sequence. Weak BOLD sensitivity, low temporal resolution, and heat caused by the long train of radiofrequency refocusing pulses are the main limits of RARE fMRI at high magnetic fields. To go beyond some of these limitations, we here describe the implementation of a two-segmented SE-EPI. The proposed sequence covers the whole brain of awake pigeons. In this study, we implemented a two-segmented SE-EPI sequence that improves the temporal resolution and sensitivity of BOLD fMRI compared to the traditional RARE sequence as a reference sequence for the avian brain. These improvements open new windows in avian research to go beyond the block-design experiments and investigate functional connectivity and higher-order cognitive abilities. This sequence may thus be relevant to those animal fMRI studies that suffer from susceptibility artifacts.