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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. •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.

Resting state-fMRI (rs-fMRI) in mice allows studying mechanisms underlying functional connectivity (FC) as well as alterations of FC occurring in murine models of neurological diseases. Mouse fMRI experiments are typically carried out under anesthesia to minimize animal movement and potential distress during examination. Yet, anesthesia inevitably affects FC patterns. Such effects have to be understood for proper interpretation of data. We have compared the influence of four commonly used anesthetics on rs-fMRI. Rs-fMRI data acquired under isoflurane, propofol, and urethane presented similar patterns when accounting for anesthesia depth. FC maps displayed bilateral correlation with respect to cortical seeds, but no significant inter-hemispheric striatal connectivity. In contrast, for medetomidine, we detected bilateral striatal but compromised inter-hemispheric cortical connectivity. The spatiotemporal patterns of the rs-fMRI signal have been rationalized considering anesthesia depth and pharmacodynamic properties of the anesthetics. Our results bridge the results from different studies from the burgeoning field of mouse rs-fMRI and offer a framework for understanding the influences of anesthetics on FC patterns. Utilizing this information, we suggest the combined use of medetomidine and isoflurane representing the two proposed classes of anesthetics; the combination of low doses of the two anesthetics retained strong correlations both within cortical and subcortical structures, without the potential seizure-inducing effects of medetomidine, rendering this regimen an attractive anesthesia for rs-fMRI in mice. •Analysis of modulatory effects by four anesthetics on mouse resting state-fMRI data.•Functional connectivity pattern relates to anesthetic depth and pharmacodynamics.•Functional connectivity patterns allow categorization of anesthetics in two classes.•Medetomidine/isoflurane combination retains cortical and subcortical connectivity.