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.