An isotropic EPI database and analytical pipelines for rat brain resting-state fMRI.
An isotropic EPI database and analytical pipelines for rat brain resting-state fMRI.
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DOI：
10.1016/j.neuroimage.2021.118541
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发表时间：
2021-11
期刊：
影响因子：
5.7
通讯作者：
Shih YI
中科院分区：
文献类型：
--
作者：
Lee SH;Broadwater MA;Ban W;Wang TW;Kim HJ;Dumas JS;Vetreno RP;Herman MA;Morrow AL;Besheer J;Kash TL;Boettiger CA;Robinson DL;Crews FT;Shih YI
静息态功能磁共振成像（fMRI）通过增进我们对功能性大脑网络的拓扑、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。根据啮齿动物功能磁共振成像社区最近的关键举措，已经开发和共享了几个数据库，以提高在不同地点获取的数据的透明度、再现性和可解释性。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通常选择空间覆盖范围有限的各向异性回波平面成像 (EPI) 方案。具有各向异性分辨率和/或减少的大脑覆盖范围的成像具有显着的缺点，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 mm）、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。使用该协议，我们在 9.4 T MRI 系统上获得了 87 只健康大鼠的静息态 EPI fMRI 数据，这些大鼠在广泛使用的右美托咪定镇静状态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，并证明了其提高组级方法的准确性和简化 fMRI 数据预处理的能力。使用该数据库，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 k 均值聚类，以获得空间离散的功能感兴趣区域 (ROI)。使用基于欧几里得的层次聚类和基于模块化的分区，我们识别了大鼠大脑的拓扑组织。此外，已确定的群体级 FC 网络在不同菌株和性别中似乎都很强大。人类功能磁共振成像中常用的“三重网络”与大鼠大脑中的类似。通过这项工作，我们传播了原始和预处理的各向同性 EPI 数据、大鼠大脑 EPI 模板以及标准化大鼠大脑坐标中确定的功能 ROI 和网络。我们还公开我们的分析流程和脚本，希望促进大鼠大脑静息态功能磁共振成像研究的标准化。
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.
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影响因子：
3.5
作者：
Abraham A;Pedregosa F;Eickenberg M;Gervais P;Mueller A;Kossaifi J;Gramfort A;Thirion B;Varoquaux G
通讯作者：
Varoquaux G
DOI：
10.1093/cercor/bhaa305
发表时间：
2021-02-05
期刊：
Cerebral cortex (New York, N.Y. : 1991)
影响因子：
--
作者：
Belloy ME;Billings J;Abbas A;Kashyap A;Pan WJ;Hinz R;Vanreusel V;Van Audekerke J;Van der Linden A;Keilholz SD;Verhoye M;Keliris GA
通讯作者：
Keliris GA
影响因子：
3.4
作者：
Broadwater MA;Lee SH;Yu Y;Zhu H;Crews FT;Robinson DL;Shih YI
通讯作者：
Shih YI
影响因子：
5.7
作者：
Chen, NK;Dickey, CC;Panych, LP
通讯作者：
Panych, LP
影响因子：
7.7
作者：
Aedo-Jury, Felipe;Schwalm, Miriam;Stroh, Albrecht
通讯作者：
Stroh, Albrecht