fMRI protocol optimization for simultaneously studying small subcortical and cortical areas at 7 ​T

Steven Miletic, Pierre-Louis Bazin, Nikolaus Weiskopf, Wietske van der Zwaag, Birte U. Forstmann, Robert Trampel

Abstract: Highlights • Single and multi echo EPI protocols were compared for studying subcortex and cortex. • Both protocols had high spatial resolution, short echo times and whole-brain coverage. • The results show marginal differences in BOLD-sensitivity across the brain. Abstract Most fundamental cognitive processes rely on brain networks that include both cortical and subcortical structures. Studying such networks using functional magnetic resonance imaging (fMRI) requires a data acquisition protocol that provides blood-oxygenation-level dependent (BOLD) sensitivity across the entire brain. However, when using standard single echo, echo planar imaging protocols, researchers face a tradeoff between BOLD-sensitivity in cortex and in subcortical areas. Multi echo protocols avoid this tradeoff and can be used to optimize BOLD-sensitivity across the entire brain, at the cost of an increased repetition time. Here, we empirically compare the BOLD-sensitivity of a single echo protocol to a multi echo protocol. Both protocols were designed to meet the specific requirements for studying small, iron rich subcortical structures (including a relatively high spatial resolution and short echo times), while retaining coverage and BOLD-sensitivity in cortical areas. The results indicate that both sequences lead to similar BOLD-sensitivity across the brain at 7 ​T.