Mount Sinai School of Medicine (Philips)

The dataset includes functional, diffusion, and structural data from 9 monkeys.

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 and Macaca fascicularis

Scan Procedures and Parameters

Animals were anesthetized with isoflurane (1.2%) and monitored for depth of anesthesia

Sample Description

• Sample size: 9
• Age distribution: 3.4-8.0 years
• Weight distribution: 4.70-7.42 kg
• Sex distribution: 8 male; 1 female

Click here for the full sample description (.csv)

Phenotypic Assessments

The monkeys went on to receive bilateral neurotoxic hippocampal lesions. The post-lesion data will be part of a future release, post-publication.

Scan Procedures and Parameters

Ethics approval: Icahn School of Medicine at Mount Sinai (ISMMS) IACUC

Animal care and housing: Animal care and housing: ISMMS is staffed with veterinarians with non-human primate expertise and a staff of skilled veterinary and husbandry technicians. Monkeys were housed singly (N=1) or in groups of 6 (N=8) indoors in standard primate caging, in housing rooms containing other monkeys. The single-housed monkey was the last in her group and had failed repeated attempts to find compatible cage mates from elsewhere in the colony. All monkeys received environmental enrichment consisting of toys and novel food items.

Any applicable training: All the males received cognitive tests in touch screen apparatus (object-in-place scene learning).

Scanning preparations

Anesthesia procedures: Anesthesia procedures: ketamine, buprenorphine prior to intubation and placement in stereotaxic frame; isoflurane maintenance anesthesia (to effect). For the resting-state fMRI scans, isoflurane levels were kept to a minimum to ensure the preservation of resting-state networks: mean isoflurane 1.2 %, range 1.0-1.6 %.

Time between anesthesia and scanning: Monkeys were placed in the scanner as soon as isoflurane anesthesia was initiated and stable. Resting-state fMRI was carried out at least 2 hours after ketamine administration, to reduce detrimental effects of ketamine on resting-state networks.

Head fixation: Monkeys were placed in an MRI-compatible stereotaxic frame (Crist).

Position in scanner and procedure used: Sphinx position feet first (recorded as head first supine in scanner; note that header info have been corrected to reflect anatomy). Fiducial marker placed on left side.

Contrast agent: none

During scanning

Physiological monitoring: pulse rate, SpO₂, end tidal CO₂, inspired/expired isoflurane, blood pressure

Additional procedures: Artificial ventilation was used to maintain end-tidal CO₂ in a normocapnic range wherever possible, to avoid effects of hypercapnia on the BOLD signal. Normothermia maintained by heated air blanket

Scan sequences

• Scanner type: Philips Achieva 3T
• Head coil: 4-channel phased array coil (Windmiller-Kolster Scientific), transmit through body coil
• Optimization of the magnetic field prior to data acquisition: None
• Resting-state:
  • Voxel resolution: 1.5 x 1.5 x 1.5 mm
  • TE: 19ms
  • TR: 2600ms
  • Volumes: 988
  • Gradient echo image included
• Diffusion-weighted:
• Voxel resolution: 1.0 x 1.0 x 1.0 mm
• TE: 107ms
• TR: 11000ms
• Slice gap: 1mm
• b-value: 1000s/mm²
• 120 directions (3 averages; reverse polarity images included
• Structural:
  • T1
  • Voxel resolution: 0.5 x 0.5 x 0.5 mm
  • TE: 6.93ms
  • TR: 1500ms
  • TI: 1100ms
  • Flip angle: 8° (3 averages)
  • dti.nii.gz contains the corrected diffusion data (topup and eddy) averaged across all 3 runs.
  • T2
  • Voxel resolution: 0.5 x 0.5 x 0.5 mm
  • TE: 366ms
  • TR: 2500ms
• Note: Not every monkey has all data files due to some issues with scanner overheating. Any data that was adversely affected by this heating has not been included.

Publications

• Froudist-Walsh et al. (2018) The Rhesus Monkey Hippocampus Critically Contributes to Scene Memory Retrieval, But Not New Learning. J Neurosci 38: 7800-7808 doi: 10.1523/JNEUROSCI.0832-18.2018
• Froudist-Walsh et al. (2018) Macro-connectomics and microstructure predict dynamic plasticity patterns in the non-human primate brain. eLife in press

Personnel

• Paula L. Croxson¹
• Lazar Fleysher ²
• Sean Froudist-Walsh ¹

¹Department of Neuroscience, Mount Sinai School of Medicine, New York, NY
²Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY

Acknowledgements

We thank Lazar Fleysher, Rafael O’Halloran, Prantik Kundu, Junqian Xu, Ronald Primm, Ignacio Medel, Pedro Hernandez, Carlos Rodriguez, Crystal Johnson, and Zahi Fayad for their support.

Funding

This data repository was supported by the Icahn School of Medicine at Mount Sinai.

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.