UW-Madison Rhesus MRI

The UW-Madison Rhesus MRI dataset includes anatomical, diffusion, and resting-state fMRI data from 592 macaque monkeys at two different sites. Subjects IDs start with "1" were acquired at site 1, subject IDs start with "2" were acquired at site 2.

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

Sample Description

• Sample size: 592
• Age distribution: 0.8-4.5 years
• Sex distribution: 327 male / 265 female

Click here for the full sample description (.csv)

Scan Procedures and Parameters

Ethics approval: Procedures were performed using protocols that were approved by the University of Wisconsin Institutional Animal Care and Use Committee in compliance with the Guide for the Care and Use of Laboratory Animals published by the US National Institutes of Health.

Animal care and housing: Monkeys were housed and cared for at the Wisconsin National Primate Research Center and the Harlow Center for Biological Psychology. Standard husbandry in a temperature- and humidity-controlled vivarium included a 12-h light/dark cycle, daily feeding sessions, ad libitum access to water, and daily enrichment.

Any applicable training: All study team members underwent extensive training to obtain proficiency in nonhuman primate handling, care, imaging, and anesthesia techniques. Animals did not undergo any training.

Scanning preparations

Anesthesia procedures: Monkeys were initially anesthetized using ketamine (15 mg/kg, IM), then given medetomidine (0.03 mg/kg, IM) or dexmedetomidine (0.015 mg/kg, IM). Additional doses of ketamine were administered as needed to maintain anesthesia. At the end of the procedure, atipamezole (0.15 mg/kg) was administered to reverse the medetomidine/dexmedetomidine.

Time between anesthesia and scanning: Scanning began approximately 30 minutes from first ketamine administration.

Head fixation: Monkeys were repositioned into a custom MRI compatible stereotaxic frame, which included ear bars and a tooth bar, that fit inside the MR coil.

Position in scanner and procedure used: Monkeys were scanned in the sphinx position with the nose pointing into the scanner.

During scanning

Physiological monitoring: Heart rate and oxygen saturation were monitored continuously and recorded at minimum every 15 minutes throughout the MR imaging procedure. Heated water bags, bottles, or pads and towels, blankets, and bubble wrap were used to maintain body temperature during imaging.

Scan sequences

Site 1:

• Scanner type: GE DISCOVERY_MR750 3.0T
• Head coil:
• Resting-state:
  • Voxel resolution: 2.1875 x 3.1 x 2.1875 mm
  • TE: 25ms
  • TR: 2000ms
  • Slice gap: 0.5mm
  • Flip angle: 90°
  • Effective echo spacing: 0.648ms
  • Phase encoding direction: k
  • Fieldmap included
• Diffusion-weighted:
  • Voxel resolution: 0.5469 x 2.5 x 0.5469 mm
  • TE: 94.3ms
  • TR: 6100ms
  • Flip angle: 90°
  • b-values: 1000s/mm²
  • Directions: 12 directions/72 directions
  • Effective echo spacing: 0.932ms
  • Phase encoding direction: k-
  • Fieldmap included
• Structural:
  • T1
  • Voxel resolution: 0.2734 x 0.5 x 0.2734 mm
  • TE: 5.412ms
  • TR: 11.4ms
  • TI: 600ms
  • Flip angle: 10°
  • Slice gap: 0.5mm

Site 2:

• Scanner type: GE Signa EXCITE 3.0T
• Head coil:
• Resting-state:
  • Voxel resolution: 2.1875 x 3.1 x 2.1875 mm
  • TE: 25ms
  • TR: 2500ms
  • Slice gap: 0.5mm
  • Flip angle: 90°
  • Effective echo spacing: 0.636ms
  • Phase encoding direction: k
  • Fieldmap included
• Diffusion-weighted:
  • Voxel resolution: 0.546875 x 2.5 x 0.546875 mm
  • TE: 77.2ms
  • TR: 10000ms
  • Flip angle: 90°
  • b-values: 1000s/mm²
  • Directions: 12 directions/72 directions
  • Effective echo spacing: 0.8ms
  • Phase encoding direction: k-
  • Fieldmap included
• Structural:
  • T1
  • Voxel resolution: 0.273438 x 0.5 x 0.273438 mm
  • TE: 1.888ms
  • TR: 8.648ms
  • TI: 600ms
  • Flip angle: 10°
  • Slice gap: 0.5mm

Publications

• Tromp DPM, Fox AS, Oler JA, Alexander AL, Kalin NH. The Relationship Between the Uncinate Fasciculus and Anxious Temperament Is Evolutionarily Conserved and Sexually Dimorphic. (2019) Biol Psychiatry. Dec 15;86(12):890-898.
• Fox AS, Oler JA, Birn RM, Shackman AJ, Alexander AL, Kalin NH. Functional Connectivity within the Primate Extended Amygdala Is Heritable and Associated with Early-Life Anxious Temperament. (2018) J Neurosci. Aug 29;38(35):7611-7621.
• Fox AS, Oler JA, Shackman AJ, Shelton SE, Raveendran M, McKay DR, Converse AK, Alexander A, Davidson RJ, Blangero J, Rogers J, Kalin NH. Intergenerational neural mediators of early-life anxious temperament. (2015) Proc Natl Acad Sci U S A. Jul 21;112(29):9118-22.
• Birn RM, Shackman AJ, Oler JA, Williams LE, McFarlin DR, Rogers GM, Shelton SE, Alexander AL, Pine DS, Slattery MJ, Davidson RJ, Fox AS, Kalin NH. (2014) Evolutionarily conserved prefrontal-amygdalar dysfunction in early-life anxiety. Mol Psychiatry. 19(8):915-22.
• Shackman AJ, Fox AS, Oler JA, Shelton SE, Davidson RJ, Kalin NH. (2013) Neural mechanisms underlying heterogeneity in the presentation of anxious temperament. (2013) Proc Natl Acad Sci U S A. 110(15):6145-50.
• Rogers J, Raveendran M, Fawcett GL, Fox AS, Shelton SE, Oler JA, Cheverud J, Muzny DM, Gibbs RA, Davidson RJ, Kalin NH. (2013) CRHR1 genotypes, neural circuits and the diathesis for anxiety and depression. Mol Psychiatry. 18(6):700-7.
• Fox AS, Oler JA, Shelton SE, Nanda SA, Davidson RJ, Roseboom PH, Kalin NH. (2012) Central amygdala nucleus (Ce) gene expression linked to increased trait-like Ce metabolism and anxious temperament in young primates. Proc Natl Acad Sci USA. 109(44):18108-13.
• Oler JA, Birn RM, Patriat R, Fox AS, Shelton SE, Burghy CA, Stodola DE, Essex MJ, Davidson RJ, Kalin NH. (2012) Evidence for coordinated functional activity within the extended amygdala of non-human and human primates. Neuroimage. 61(4):1059-66.
• Oler JA, Fox AS, Shelton SE, Rogers J, Dyer TD, Davidson RJ, Shelledy W, Oakes TR, Blangero J, Kalin NH. (2010) Amygdalar and hippocampal substrates of anxious temperament differ in their heritability. Nature. 466(7308):864-8.
• Roseboom PH, Nanda SA, Fox AS, Oler JA, Shackman AJ, Shelton SE, Davidson RJ, Kalin NH. (2013) Neuropeptide Y Receptor Gene Expression in the Primate Amygdala Predicts Anxious Temperament and Brain Metabolism. Biol Psychiatry. 76:850-857, 2015.

Personnel

• Ned Kalin, MD (Principal Investigator)
• Drew Fox, PhD
• Jonathan Oler, PhD
• Rasmus Birn, PhD
• Do Tromp, PhD
• Andy Alexander, PhD

Acknowledgements

We thank Steve Shelton, Helen Van Valkenberg, Marissa Riedel, and the personnel of the Harlow Center for Biological Psychology, the Wisconsin National Primate Research Center, the HealthEmotions Research Institute, and the Waisman Laboratory for Brain Imaging and Behavior.

Funding

This data repository was supported by the following grants: R01-MH046729, R01-MH081884, P50-MH100031

Usage notes

• Data was acquired at two different sites. Subjects IDs start with "1" were acquired at site 1, while subject IDs start with "2" were acquired at site 2.
• Computed fieldmaps are available for both sites. Site 1 also provides magnitude and phase images; however, it is recommended to use real and imaginary images instead of phase images because of the rounding issue caused by GE scanners.
• Diffusion weighted images were acquired with two different directions (12 directions and 72 directions).

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.