Resting-state functional magnetic resonance imaging (fMRI) has drastically expanded the scope of brain research by advancing our knowledge about the topologies, dynamics, and interspecies translatability of functional brain networks. Several databases have been developed and shared in accordance with recent key initiatives in the rodent fMRI community to enhance the transparency, reproducibility, and interpretability of data acquired at various sites. Despite these pioneering efforts, one notable challenge preventing efficient standardization in the field is the customary choice of anisotropic echo planar imaging (EPI) schemes with limited spatial coverage. Imaging with anisotropic resolution and/or reduced brain coverage has significant shortcomings including reduced registration accuracy and increased deviation in brain feature detection. Here we proposed a high-spatial-resolution (0.4 mm), isotropic, whole-brain EPI protocol for the rat brain using a horizontal slicing scheme that can maintain a functionally relevant repetition time (TR), avoid high gradient duty cycles, and offer unequivocal whole-brain coverage. Using this protocol, we acquired resting-state EPI fMRI data from 87 healthy rats under the widely used dexmedetomidine sedation supplemented with low-dose isoflurane on a 9.4 T MRI system. We developed an EPI template that closely approximates the Paxinos and Watson's rat brain coordinate system and demonstrated its ability to improve the accuracy of group-level approaches and streamline fMRI data pre-processing. Using this database, we employed a multi-scale dictionary-learning approach to identify reliable spatiotemporal features representing rat brain intrinsic activity. Subsequently, we performed k-means clustering on those features to obtain spatially discrete, functional regions of interest (ROIs). Using Euclidean-based hierarchical clustering and modularity-based partitioning, we identified the topological organizations of the rat brain. Additionally, the identified group-level FC network appeared robust across strains and sexes. The “triple-network” commonly adapted in human fMRI were resembled in the rat brain. Through this work, we disseminate raw and pre-processed isotropic EPI data, a rat brain EPI template, as well as identified functional ROIs and networks in standardized rat brain coordinates. We also make our analytical pipelines and scripts publicly available, with the hope of facilitating rat brain resting-state fMRI study standardization.

静息态功能磁共振成像 (fMRI) 通过推进我们对功能性大脑网络的拓扑结构、动力学和种间可翻译性的了解，极大地扩展了大脑研究的范围。根据啮齿动物 fMRI 社区最近的关键举措，已经开发和共享了几个数据库，以提高在各个站点获取的数据的透明度、可重复性和可解释性。尽管做出了这些开创性的努力，但阻碍该领域有效标准化的一个显着挑战是空间覆盖范围有限的各向异性回波平面成像 (EPI) 方案的习惯选择。具有各向异性分辨率和/或减少大脑覆盖率的成像具有显着缺点，包括配准精度降低和大脑特征检测偏差增加。在这里，我们提出了一种针对大鼠大脑的高空间分辨率（0.4 毫米）、各向同性、全脑 EPI 协议，使用水平切片方案可以保持功能相关的重复时间 (TR)，避免高梯度占空比，并提供明确的全脑覆盖。使用此协议，我们在 9.4 T MRI 系统上获得了 87 只健康大鼠的静息状态 EPI fMRI 数据，这些大鼠在广泛使用的 dexmedetomidine 镇静下辅以低剂量异氟醚。我们开发了一个 EPI 模板，该模板非常接近 Paxinos 和 Watson 的大鼠大脑坐标系，并展示了它提高组级方法准确性和简化 fMRI 数据预处理的能力。使用这个数据库，我们采用多尺度字典学习方法来识别代表大鼠大脑内在活动的可靠时空特征。随后，我们对这些特征进行了 k 均值聚类，以获得空间离散的感兴趣功能区域 (ROI)。使用基于欧几里德的层次聚类和基于模块化的分区，我们确定了大鼠大脑的拓扑组织。此外，已确定的组级 FC 网络在品系和性别之间表现出稳健性。通常适用于人类 fMRI 的“三重网络”与大鼠大脑相似。通过这项工作，我们传播原始和预处理的各向同性 EPI 数据、大鼠大脑 EPI 模板，以及在标准化大鼠大脑坐标中识别的功能 ROI 和网络。我们还公开了我们的分析管道和脚本，