The brainstem is a fundamental component of the central nervous system, yet it is typically excluded from in vivo human brain mapping efforts, precluding a complete understanding of how the brainstem influences cortical function. In this study, we used high-resolution 7-Tesla functional magnetic resonance imaging to derive a functional connectome encompassing cortex and 58 brainstem nuclei spanning the midbrain, pons and medulla. We identified a compact set of integrative hubs in the brainstem with widespread connectivity with cerebral cortex. Patterns of connectivity between brainstem and cerebral cortex manifest as neurophysiological oscillatory rhythms, patterns of cognitive functional specialization and the unimodal–transmodal functional hierarchy. This persistent alignment between cortical functional topographies and brainstem nuclei is shaped by the spatial arrangement of multiple neurotransmitter receptors and transporters. We replicated all findings using 3-Tesla data from the same participants. Collectively, this work demonstrates that multiple organizational features of cortical activity can be traced back to the brainstem.

脑干是中枢神经系统的基本组成部分，但它通常被排除在体内人脑映射工作之外，从而无法完全了解脑干如何影响皮层功能。在这项研究中，我们使用高分辨率 7-Tesla 功能磁共振成像得出一个功能性连接组，包括皮层和跨越中脑、脑桥和延髓的 58 个脑干核。我们在脑干中确定了一组紧凑的整合枢纽，与大脑皮层有广泛的连接。脑干和大脑皮层之间的连接模式表现为神经生理学振荡节律、认知功能专业化模式和单峰-跨模态功能层次结构。皮质功能拓扑图和脑干核之间的这种持续排列是由多个神经递质受体和转运蛋白的空间排列形成的。我们使用来自相同参与者的 3-Tesla 数据复制了所有发现。总的来说，这项工作表明，皮层活动的多个组织特征可以追溯到脑干。