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.
Highlights
Most fundamental cognitive processes rely on brain networks that include both cortical and subcortical structures (Forstmann et al, 2017)
BF01 1⁄4 2.50 Æ 0.58%, ‘anecdotal evidence’ for H0 BF01 1⁄4 62.43 Æ 0.83%, ‘very strong evidence’ for H0 BF01 1⁄4 155.72 Æ 0.88%, ‘decisive evidence’ for H0 still provides good blood-oxygenation-level dependent (BOLD)-sensitivity in cortical areas despite the low TE. When studying both cortical and subcortical structures using conventional single echo 2D echo-planar imaging (EPI) functional magnetic resonance imaging (fMRI) protocols, researchers are faced with a tradeoff between BOLD-sensitivity in the cortex and in the subcortex
We directly compared a multi echo protocol with a single echo protocol, both optimized for subcortex by using a relatively high spatial resolution combined with short echo times
Summary
Most fundamental cognitive processes rely on brain networks that include both cortical and subcortical structures (Forstmann et al, 2017). For a complete understanding of those brain networks, it is vital to study all components of the network simultaneously When studying such networks using functional magnetic resonance imaging (fMRI), cortical and subcortical structures put different and sometimes conflicting requirements on imaging protocols, causing researchers to face a tradeoff in BOLD-sensitivity between cortex and subcortex. An important factor underlying these conflicting requirements is the neurochemical composition of brain structures: Subcortical structures such as the STN, GPe, and GPi contain high concentrations of iron (Aquino et al, 2009; De Hollander et al, 2014; Deistung et al, 2013; Keuken et al, 2017, 2014), which leads to substantially shorter T2* relaxation times compared to cortical areas (Peters et al, 2007). Theory predicts that protocols using a short TE have suboptimal BOLD-sensitivity in cortical areas
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