Macaca mulatta structural and diffusion weighted MRI data

The AMU dataset includes structural and diffusion weighted MRI data from 4 Macaca mulatta monkeys.

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.

Sample Description

• Sample size: 4
• Age distribution: 7-8 years
• Weight distribution: 7.5-12.5 kgs
• Sex distribution: 3 male, 1 female

Click here for the full sample description (.csv download)

Scan Procedures and Parameters

Ethics approval: obtained at local Ethics Committee

Animal care and housing: At Institut de Neurosciences de La Timone

Any applicable training: N/A

Scanning preparations

Anesthesia procedures: Isoflurane

Time between anesthesia and scanning: None- anesthesia was performed and monitored during scanning.

Head fixation: Kopf frame and ear bars

Position in scanner and procedure used: Sphinx position. Fiducial marker placed on right side.

Contrast agent: None

During scanning

Physiological monitoring: Heart rate, respiration

Additional procedures: Ventilation

Scan sequences

• Scanner type: Siemens Prisma 3T
• Head coil: Body transmit array, 11cm loop receiving coil
• Optimization of the magnetic field prior to data acquisition: Automatic B0 shimming procedures from Siemens
•  
• Diffusion-weighted:
  • Diffusion SE-EPI sequence
  • Voxel resolution: 1 x 1 x 1 mm
  • TE: 87.6ms
  • TR: 7520ms
  • 64b1000
  • 6b300
  • 5b0
  • Two repetitions with reversed phase encoding direction
• Structural:
  • T1
    • MPRAGE sequence
    • Voxel resolution: 0.8 x 0.8 x 0.8 mm
    • TE: 2.04ms
    • TR: 2900ms
    • TI: 1000ms
  • T2
    • 3D SPACE sequence
    • Voxel resolution: 0.8 x 0.8 x 0.8mm
    • TE: 561ms
    • TR: 3200ms
  • QSM
    • 3D GRE sequence
    • Voxel resolution: 0.93 x 0.93 x 1mm
    • TE: 2.7-42ms
    • TR: 45ms

Personnel

• Thomas Brochier¹
• Pascal Belin¹
• Frédéric Chavanne¹
• Lionel Velly¹
• Clémentine Bodin¹
• Luc Renaud^1,2
• Marc Martin^1,2
• Laurence Boes^1,2
• Julien Sein¹
• Bruno Nazarian¹
• Jean-Luc Anton¹

¹Institut de Neurosciences de la Timone (INT), UMR7289 CNRS & Aix-Marseille Université, Marseille, France
²Centre d’Exploration Fonctionnelle et de Formation en Primatologie (CE2F-PRIM), UMS5737 CNRS & Aix-Marseille Université, Marseille, France

Acknowledgements

We gratefully acknowledge the support of French France-Life Imaging (FLI) and Infrastructures en Biologie Santé et Agronomie (IBISA)

Funding

Project PRIMAVOICE, PI Belin, French Agence Nationale de la Recherche

Detailed information can be found at http://fcon_1000.projects.nitrc.org/indi/PRIME/amu.html.

Citation

• Brochier, T., Belin, P., Chavanne, F., Velly, L., Bodin, C., Renaud, L., Martin, M., Boes, L., Sein, J., Nazarian, B., & Anton, J.-L. (2019). Macaca mulatta structural and diffusion weighted MRI data [Data set]. Zenodo. https://doi.org/10.5281/ZENODO.3402456.
• 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.