Macaca mulatta and Macaca fascicularis anatomical and functional MRI data

The ION dataset includes anatomical, field map, and fMRI data from 8 monkeys: 4 Macaca mulatta and 4 Macaca fascicularis. The data is provided both as a directory structure compressed as all_the_data.zip, and as individual files. The correspondence between the directory structure and the individual files is contained in the file tree.json. The bash command source unflatten.sh can be used to convert the individual files into the original directory structure. Scanner Specifications Siemens Tim Trio 3T whole-body scanner with or without head-only gradient insert (Siemens AC88) 8-channel phased-array transceiver coils Optimization of the magnetic field prior to data acquisition: Manual shimming Sample Description Sample size: 8 Age distribution: 3.80-5.99 years Weight distribution: 5.0-10.2 kg Sex distribution: 7 male, 1 female Click here for the full sample description (.csv download) Scan Procedures and Parameters Ethics approval: All experimental procedures for nonhuman primate research were approved by the Institutional Animal Care and Use Committee in the Institute of Neuroscience and by the Biomedical Research Ethics Committee, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and conformed to National Institutes of Health guidelines for the humane care and use of laboratory animals. Animal care and housing: Animals were housed in single cage Any applicable training: none Scanning preparations Anesthesia procedures: Anesthesia of the animals was inducted with an intramuscular injection of a cocktail of dexmedetomidine (18 - 30 µg/kg) and midazolam (0.2 - 0.3 mg/kg), supplemented with atropine sulfate (0.05 mg/kg). After intubation, anesthesia was maintained using the lowest possible concentration of isoflurane gas via a MRI-compatible ventilator. Time between anesthesia and scanning: Scanning lasted about 1.5 hours after induction. Head fixation: Custom-built MRI-compatible stereotaxic frame Position in scanner and procedure used: Sphinx position Contrast agent: none During scanning Physiological monitoring: Physiological parameters including blood oxygenation, ECG, rectal temperature, respiration rate and end-tidal CO2 were monitored. Oxygen saturation was kept over 95%. Additional procedures: Animals were ventilated by a MRI-compatible ventilator. Body temperature was kept constant using hot water blanket. Scan sequences Resting-state: Gradient-echo EPI TR: 2000ms TE: 29ms Flip angle: 77° Field of view: 96 x 96 mm In plane resolution: 1.5 x 1.5 mm Slices number: 32 Slice thickness: 2.5mm GRAPPA factor: 2 Measurements: 200 Slice direction: Coronal slice Structural: T1 MPRAGE Sequence Voxel resolution: 0.5 x 0.5 x 0.5 mm TE: 3.12ms TR: 2500ms TI: 1100ms Flip angle: 9° Slice direction: 44 sagittal slices Number of averages: 2 Additional: Field map: a pair of gradient echo images TE1: 4.22ms TE2: 6.68ms Orientation and resolution: same as resting-state images Intended for EPI distortion correction Publications Lv, Q., Yang, L., Li, G., Wang, Z., Shen, Z., Yu, W., Jiang, Q., Hou, B., Pu, J., Hu, H., & Wang, Z. (2016). Large-Scale Persistent Network Reconfiguration Induced by Ketamine in Anesthetized Monkeys: Relevance to Mood Disorders. Biological Psychiatry, 79(9), 765–775. https://doi.org/10.1016/j.biopsych.2015.02.028 Personnel Zheng Wang1 1Institute of Neuroscience, Key Laboratory of Primate Neurobiology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China Acknowledgements The authors thank Drs. Lawrence Wald, Ravi Menon, John Gore, Franz Schmitt, Renate Jerecic, Thomas Benner, Kecheng Liu, Ignacio Vallines, and Hui Liu for their generous help and contribution to the construction of our custom-tuned gradient-insert (AC88) 3T MRI facility for nonhuman primate subjects. Funding Hundred Talent Program of Chinese Academy of Sciences (Technology) (Zheng Wang) Chinese 973 Program (2011CBA00400) The “Strategic Priority Research Program (B) of the Chinese Academy of Sciences (XDB02030004) The Outstanding Youth Grant (Hailan Hu) Detailed information can be found at http://fcon_1000.projects.nitrc.org/indi/PRIME/ion.html. Citation Wang, Z. (2019). Macaca mulatta and Macaca fascicularis anatomical and functional MRI data [Data set]. Zenodo. https://doi.org/10.5281/ZENODO.3402112. Milham, M. P., Ai, L., Koo, B., Xu, T., Amiez, C., Balezeau, F., … Schroeder, C. E. (2018). An Open Resource for Non-human Primate Imaging. Neuron, 100(1), 61–74.e2. https://doi.org/10.1016/j.neuron.2018.08.039.

ION数据集包含8只非人灵长类的解剖影像、场图与功能磁共振成像（fMRI）数据，其中4只为恒河猴（Macaca mulatta），4只为食蟹猴（Macaca fascicularis）。该数据集以两种形式提供：一是打包为all_the_data.zip的目录结构，二是独立单个文件。目录结构与单个文件的对应关系详见tree.json文件，可通过bash命令`source unflatten.sh`将单个文件还原为原始目录结构。

扫描仪规格：采用西门子Tim Trio 3T全身扫描仪，可搭配或不搭配头部专用梯度线圈插件（Siemens AC88），配备8通道相控阵收发线圈。数据采集前的磁场优化采用手动匀场方式。

样本说明：样本总量为8只，年龄分布为3.80~5.99岁，体重分布为5.0~10.2 kg，性别分布为7雄1雌。完整样本说明可点击此处下载（.csv格式）。

扫描流程与参数
伦理审批：所有非人灵长类动物研究的实验流程均获得中国科学院上海生命科学研究院神经科学研究所实验动物伦理审查委员会与生物医学研究伦理委员会批准，符合美国国立卫生研究院（NIH）实验动物人道饲养与使用指南。
动物饲养与安置：实验动物采用单笼饲养。
相关训练：无相关训练。
扫描前准备：
麻醉流程：通过肌肉注射复合麻醉剂诱导麻醉，药剂组分为右美托咪定（18~30 µg/kg）与咪达唑仑（0.2~0.3 mg/kg），并辅以硫酸阿托品（0.05 mg/kg）。气管插管后，通过MRI兼容呼吸机使用最低有效浓度的异氟烷维持麻醉。
麻醉至扫描的时间间隔：诱导麻醉后约1.5小时开始扫描。
头部固定：采用定制MRI兼容立体定位框架。
扫描体位与操作流程：采用斯芬克斯体位（Sphinx position）。
对比剂使用：未使用对比剂。
扫描过程中生理监测：监测包括血氧饱和度、心电图、直肠温度、呼吸频率与呼气末二氧化碳分压在内的多项生理参数，维持血氧饱和度高于95%。
额外操作：通过MRI兼容呼吸机维持动物通气，使用热水毯维持体温恒定。
扫描序列：
1. 静息态扫描：采用梯度回波平面成像（Gradient-echo EPI）序列，参数如下：重复时间（TR）=2000ms，回波时间（TE）=29ms，翻转角=77°，视野（FOV）=96×96 mm，平面分辨率=1.5×1.5 mm，扫描层数=32，层厚=2.5 mm，广义自动校准部分并行采集（GRAPPA）因子=2，测量次数=200，扫描层方向为冠状位。
2. 结构像扫描：采用T1加权磁化准备快速梯度回波（MPRAGE）序列，体素分辨率=0.5×0.5×0.5 mm，TE=3.12ms，TR=2500ms，反转时间（TI）=1100ms，翻转角=9°，扫描层方向为44层矢状位，平均采集次数=2。
3. 场图扫描：采用一对梯度回波图像，TE1=4.22ms，TE2=6.68ms，方位与分辨率与静息态图像一致，用于EPI图像畸变校正。

相关发表文献：
Lv, Q., Yang, L., Li, G., Wang, Z., Shen, Z., Yu, W., Jiang, Q., Hou, B., Pu, J., Hu, H., & Wang, Z. (2016). 氯胺酮麻醉猴的大规模持续网络重构：与心境障碍的关联. 《生物精神病学》, 79(9), 765–775. https://doi.org/10.1016/j.biopsych.2015.02.028

研究人员：郑王（Zheng Wang）¹ ¹中国科学院上海生命科学研究院神经科学研究所，灵长类神经生物学重点实验室，中国上海。

致谢：作者感谢Lawrence Wald博士、Ravi Menon博士、John Gore博士、Franz Schmitt博士、Renate Jerecic博士、Thomas Benner博士、刘克成博士、Ignacio Vallines博士与刘辉博士，感谢他们为非人灵长类动物专用的定制梯度插件（AC88）3T MRI扫描设备的搭建提供的慷慨帮助与贡献。

资助信息：中国科学院百人计划（技术类）（郑王）；中国973计划（2011CBA00400）；中国科学院战略性先导科技专项（B类）（XDB02030004）；优秀青年基金（胡海岚）。

详细信息可访问：http://fcon_1000.projects.nitrc.org/indi/PRIME/ion.html。
引用格式：
1. Wang, Z. (2019). 恒河猴与食蟹猴解剖与功能磁共振成像数据集 [数据集]. Zenodo. https://doi.org/10.5281/ZENODO.3402112.
2. Milham, M. P., Ai, L., Koo, B., Xu, T., Amiez, C., Balezeau, F., … Schroeder, C. E. (2018). 非人灵长类成像开放资源. 《神经元》, 100(1), 61–74.e2. https://doi.org/10.1016/j.neuron.2018.08.039.