Newcastle University Medical School, Institute of Neuroscience, United Kingdom

The Newcastle University PRIME dataset includes anatomical and fMRI data from 14 research bred macaques (Macaca mulatta).

Usage Agreement

Creative Commons – Attribution-NonCommercial Share Alike (CC-BY-NC-SA)- Standard INDI data sharing policy. Prohibits use of the data for commercial purposes.

Species

Macaca mulatta

Scanner Specifications

• Vertical Bruker 4.7T primate dedicated scanner (see publications for details).
• Head coil: Single channel or 4-8 channel parallel imaging coils used.
• Optimization of the magnetic field prior to data acquisition: 2nd order shim, Bruker and custom scanning sequence optimisation.

Sample Description

• Sample size: 14
• Age distribution: 3.9-13.14 years
• Weight distribution: 7.2-18 kg
• Sex distribution: 12 male, 2 female

Click here for the full sample description (.csv)

Scan Procedures and Parameters

Ethics approval: All of the animal procedures performed were approved by the UK Home Office and comply with the Animal Scientific Procedures Act (1986) on the care and use of animals in research and with the European Directive on the protection of animals used in research (2010/63/EU). We support the Animal Research Reporting of In VivoExperiments (ARRIVE) principles on reporting animal research. All persons involved in this project were Home Office certified and the work was strictly regulated by the U.K. Home Office. Local Animal Welfare Review Body (AWERB) approval was obtained. The 3Rs principles compliance and assessment was conducted by National Centre for 3Rs (NC3Rs). Animal in Sciences Committee (UK) approval was obtained as part of the Home Office Project License approval.

Animal care and housing: All animals were housed and cared for in a group-housed colony, and animals performed behavioural training on various tasks for auditory and visual neuroscience.

Any applicable training: none prior to MRI scanning

Anesthesia procedures: All but two of the macaques (32099 and 32101) were scanned awake. See Data Sharing Table and Slater et al., J.Nsci. Meth. (2016) for details on the anaesthetised scanning. Anaesthetised scans were conducted during anaesthesia.

Head fixation: MRI compatible head-post or non-invasive head immobilisation.

Position in scanner and procedure used: Animals scanned upright and working on tasks or at rest.

Contrast agent: None

Physiological monitoring: Used eye tracking, video and audio monitoring during scanning.

Scan sequences

• Resting-state:
  • TE: 17ms
  • TR: 2600ms
  • Effective Echo Spacing: 0.63ms
  • Phase Encoding Direction: Encoded in columns (COL)
• Diffusion-weighted: to be submitted in future data sharing efforts
• Structural:
  • T1 structural, MDEFT sequence with parameters
  • TE: 6ms
  • TR: 750 ms
  • Inversion delay: 700ms
  • Number of slices: 22
  • In-plane field of view: 12.8 x 9.6cm² on a grid of 256 x 192 voxels
  • Voxel resolution: 0.5 x 0.5 x 2mm
  • Number of segments: 8

Publications related to this dataset

• Rinne T, Muers R, Salo E, Slater H & Petkov CI. (2017) Functional imaging of audio-visual selective attention in monkeys and humans: How do lapses in monkey performance affect cross-species correspondences? Cerebral Cortex, 27: 3471-84.
• Poirier C, Baumann S, Joly O, Hunter D, Balezeau F, Sun L, Rees A, Petkov CI, Thiele A, Griffiths TD. (2017) Auditory motion specific mechanisms in the monkey brain. PLoS Biology e2001379.
• Slater H, Milne AE, Wilson B, Muers RS, Balezeau F, Hunter D, Thiele A, Griffiths T & Petkov CI. (2016) Individually customizable non-invasive head immobilization system for non-human primates with an option for voluntary engagement. J. Nsci. Methods, 269, 46–60.
• Wilson, B., Kikuchi, Y., Sun, L., Hunter, D., Dick, F., Smith, K., Thiele, A., Griffiths, T., Marslen-Wilson, W.D., & Petkov C.I. (2015) Auditory sequence processing reveals evolutionarily conserved regions of frontal cortex in human and nonhuman primates. Nature Communications, 6: 8901 doi:10.1038/ncomms9901.
• Baumann S, Joly O, Rees A, Petkov CI, Sun L, Thiele A & Griffiths TD (2015) The topography of frequency and time representations in primate auditory cortices. eLife. ePub ahead of print.
• Schönwiesner, M., Dechent, P., Voit, D., Petkov, C. I., & Krumbholz, K. (2014) Parcellation of Human and Monkey Core Auditory Cortex with fMRI Pattern Classification and Objective Detection of Tonotopic Gradient Reversals. Cerebral Cortex, epub ahead of print (6/2014; doi: 10.1093/cercor/bhu124).
• Baumann S, Griffiths TD, Sun L, Petkov CI, Thiele A & Rees A (2011) Orthogonal representation of sound dimensions in the primate midbrain. Nature Neuroscience, 14(4): 423-5.

Personnel

• Jennifer Nacef & Christopher I. Petkov
• Fabien Balezeau & Timothy D. Griffiths
• Colline Poirier & Alexander Thiele
• Michael Ortiz & Michael Schmid
• MRI Support staff: David Hunter

Acknowledgements

We thank Fabien Balezeau and David Hunter for assistance with scanning. We also thank Melissa Bateson, PI on NC3Rs Grant application supporting this data collection (NC/K000802/1). Petkov lab acknowledges Ben Wilson, Ross Muers & Heather Slater for data collection and contributions.

Funding

• Wellcome Trust (WT091681MA received by TDG; WT092606AIA received by CIP and YK)
• National Centre for 3Rs: Project grant received by AT, CP and Melissa Bateson (NC/K000802/1). Pilot grant received by CIP and Heather Slater (NC/K000608/1)
• U.K. Biotechnology and Biological Sciences Research Council (BBSRC grant number BB/J009849/1 received by CIP and YK, joint with Quoc Vuong)
• National Institutes of Health intramural contract received by CIP and YK (M. Mishkin laboratory)

The funders had no role in study design, data collection and analysis.

Downloads

Click here to download the data. Users will first be prompted to log on to NITRC and will need to register with the 1000 Functional Connectomes Project website on NITRC to gain access to the PRIME-DE datasets.