7T Functional and Structural MRI in Macaque Brain

This dataset provides ultra-high field (7 Tesla) MRI data, including structural MRI and resting-state fMRI, acquired from macaque monkeys at the Centre for Functional and Metabolic Mapping, Robarts Research Institute, University of Western Ontario as part of the PRIME-DE initiative.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/uwo.html

The dataset is designed for high-resolution functional connectivity and structural mapping, leveraging advanced RF coil design optimized for non-human primate imaging at 7T.

Dataset Overview

• Institution: University of Western Ontario (UWO), Canada

• Species: Macaca mulatta

• Sample size: 12

• Age: 4–8 years

• Weight: 6.1–11.8 kg

• Sex: All male

• Modalities:

  • Structural MRI (T1)
  • Resting-state fMRI

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic research with attribution
• Non-commercial use only
• Derivative works must use the same license

Scanner Specifications

• Scanner: Siemens Magnetom 7T
• Coil:
  • Custom 24-channel phased-array receive coil
  • 8-channel transmit coil

Reference:
Gilbert KM et al., NeuroImage (2016) — optimized RF coil for ultra-high field primate MRI

Animal Preparation

Anesthesia

• Sedation:
  • Acepromazine (0.1–0.2 mg/kg)
  • Ketamine (7.5 mg/kg, IM)
• Induction:
  • Propofol (2.5 mg/kg, IV)
• Maintenance:
  • Isoflurane (1–2%, reduced to 1% during fMRI)

Setup

• Timing: Scanning initiated once anesthesia stabilized
• Head fixation: Implanted head post (when applicable)
• Position: Sphinx position
• Contrast agent: None

Physiological Monitoring

• Heart rate
• Oxygen saturation (SpO₂)
• End-tidal CO₂
• Respiration rate

Additional care:

• Temperature maintained using heating systems
• Subcutaneous fluids administered (10 ml/kg/hr)

MRI Acquisition

Resting-State fMRI

• Resolution: 1.0 × 1.0 × 1.0 mm
• TE: 18 ms
• TR: 1000 ms

Structural MRI (T1-weighted MPRAGE)

• Resolution: 0.5 × 0.5 × 0.5 mm
• TE: 3.88 ms
• TR: 6500 ms
• TI: 800 ms / 2700 ms
• Flip angle: 4°

Scientific Use

This dataset supports:

• High-resolution functional connectivity analysis
• Network-level brain organization studies
• Ultra-high field MRI method development
• Cross-species connectomics
• Validation of RF coil and acquisition strategies

Publications

• Ghahremani M et al., 2017, Cerebral Cortex

Personnel

• Stefan Everling
• Ravi Menon

Acknowledgements

• N. Hague
• A. Kirley
• T. Szekeres
• J. Gati

Funding

• Canadian Institutes of Health Research (CIHR)
• Natural Sciences and Engineering Research Council (NSERC)
• Brain Canada

Data Access

Available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to download the dataset.

Large-Scale Multimodal MRI in Developing Macaque Brain

This dataset provides one of the largest nonhuman primate MRI collections, including structural MRI, diffusion MRI, and resting-state fMRI from rhesus macaques, acquired across two imaging sites as part of the PRIMatE Data Exchange (PRIME-DE) initiative.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/uwmadison.html :contentReference[oaicite:0]{index=0}

Dataset Overview

• Site: University of Wisconsin–Madison

• Species: Macaca mulatta

• Sample size: 592

• Age range: 0.8–4.5 years

• Sex: 327 male / 265 female

• Modalities:

  • Structural MRI (T1-weighted)
  • Diffusion MRI
  • Resting-state fMRI

• Multi-site design:

  • Site 1 → subject IDs starting with “1”
  • Site 2 → subject IDs starting with “2”

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for research use with attribution
• Non-commercial use only
• Derivatives must be shared under the same license

Animal Care and Ethics

• Ethics approval:
  University of Wisconsin Institutional Animal Care and Use Committee (IACUC), compliant with NIH guidelines

• Housing:

  • Wisconsin National Primate Research Center
  • Harlow Center for Biological Psychology
  • Controlled environment (temperature, humidity, 12-hour light/dark cycle)

• Animal welfare:

  • Daily feeding and enrichment
  • Ad libitum access to water

• Training:

  • No behavioral training required for subjects

Scanning Preparation

Anesthesia protocol

• Initial: ketamine (15 mg/kg, IM)
• Maintenance: medetomidine (0.03 mg/kg) or dexmedetomidine (0.015 mg/kg)
• Reversal: atipamezole (0.15 mg/kg)
• Supplemental ketamine as needed

Setup

• Head fixation: custom MRI-compatible stereotaxic frame (ear bars + tooth bar)
• Position: sphinx position

Monitoring

• Heart rate
• Oxygen saturation
• Body temperature (maintained with heating devices)

MRI Acquisition

Site 1

• Scanner: GE Discovery MR750 3T

Resting-state fMRI

• Resolution: 2.19 × 3.1 × 2.19 mm
• TE/TR: 25 ms / 2000 ms
• Flip angle: 90°
• Fieldmap: included

Diffusion MRI

• Resolution: 0.55 × 2.5 × 0.55 mm
• TE/TR: 94.3 ms / 6100 ms
• b-value: 1000 s/mm²
• Directions: 12 / 72
• Fieldmap: included

Structural MRI (T1)

• Resolution: 0.27 × 0.5 × 0.27 mm
• TE/TR/TI: 5.41 ms / 11.4 ms / 600 ms

Site 2

• Scanner: GE Signa EXCITE 3T

Resting-state fMRI

• Resolution: 2.19 × 3.1 × 2.19 mm
• TE/TR: 25 ms / 2500 ms
• Fieldmap: included

Diffusion MRI

• Resolution: 0.55 × 2.5 × 0.55 mm
• TE/TR: 77.2 ms / 10000 ms
• b-value: 1000 s/mm²
• Directions: 12 / 72

Structural MRI (T1)

• Resolution: 0.27 × 0.5 × 0.27 mm
• TE/TR/TI: 1.89 ms / 8.65 ms / 600 ms

Data Characteristics

• Large cohort (n=592) enables:

  • Population-level analysis
  • Developmental trajectory modeling
  • Genetic and behavioral association studies

• Multi-site design:

  • Supports reproducibility and harmonization studies
  • Includes scanner-specific differences

• Fieldmaps provided for distortion correction

• Diffusion data:

  • Multiple direction schemes (12 and 72 directions)
  • Enables method benchmarking and robustness testing

Scientific Use

This dataset supports:

• Developmental connectomics in early life
• Structural and functional connectivity analysis
• Cross-site harmonization studies
• Genetic and behavioral neuroscience
• Machine learning applications with large-scale NHP data

Key Publications

• Fox et al., 2012–2019 (anxious temperament and amygdala circuits)
• Tromp et al., 2019 (uncinate fasciculus and anxiety)
• Rogers et al., 2013 (genetics and neural circuits)

Personnel

• Ned Kalin (PI)
• Drew Fox
• Jonathan Oler
• Rasmus Birn
• Andrew Alexander
• Do Tromp

Funding

• NIH grants:
  • R01-MH046729
  • R01-MH081884
  • P50-MH100031

Data Access

Data are available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access the dataset.

Postmortem Structural MRI Across Primate Species

This dataset provides high-resolution postmortem structural MRI from a diverse set of primate species, collected through the Netherlands Institute for Neuroscience (NIN) Primate Brain Bank and Utrecht University. It offers a unique resource for comparative neuroanatomy across primate evolution.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/NINPBBUtrecht.html

Dataset Overview

• Institution:

  • Netherlands Institute for Neuroscience Primate Brain Bank (PBB)
  • Utrecht University

• Sample size: 51 individuals

• Age range: 3.2–45 years

• Weight range: 0.05–43 kg

• Sex: 27 male / 24 female

• Modalities:

  • Structural MRI (T1-weighted, postmortem)

Species Coverage

This dataset spans a broad range of primate species, including:

• Prosimians (e.g., Microcebus murinus, Galago senegalensis)
• New World monkeys (e.g., Callithrix jacchus, Saimiri sciureus)
• Old World monkeys (e.g., Macaca mulatta, Papio hamadryas)
• Great apes (e.g., Gorilla gorilla, Pan troglodytes, Pan paniscus)

This diversity enables cross-species comparisons of brain structure and evolution.

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for research use with attribution
• Non-commercial use only
• Derivatives must be shared under the same license

Specimen Source and Ethics

• Postmortem dataset
• Brains obtained from the Primate Brain Bank (PBB)

Key principles:

• No animals were sacrificed for data collection
• Specimens derived from:
  • Natural death
  • Humane euthanasia (unrelated to research)

This ensures:

• Ethical reuse of biological material
• Preservation of rare anatomical resources

MRI Acquisition

Scanners

• Primary system:

  • Varian small-bore 9.4T scanner (50 specimens)

• Additional system:

  • Siemens Magnetom Trio 3T scanner (1 specimen)

Structural Imaging

9.4T (Varian system)

• Matrix: 512 × 256 × 256
• Voxel resolution: scaled to brain size (approx. 0.068–9.37 mm)
• TE: 5 ms
• TR: 30–100 ms
• Flip angle: 10°

3T (Siemens system)

• Matrix: 256 × 256 × 256
• TE: 2.6 ms
• TR: 2500 ms
• Flip angle: 10°

Additional Notes

• Contrast agent:

  • Fomblin used in most cases to reduce susceptibility artifacts

• Imaging resolution varies depending on brain size, enabling:

  • Ultra-high resolution for small primates
  • Scalable acquisition across species

Scientific Use

This dataset supports:

• Comparative neuroanatomy across primates
• Brain scaling and evolutionary studies
• Cross-species structural mapping
• Atlas construction for nonhuman primates
• Validation of MRI-derived anatomical measures

Key Reference

• Navarrete et al., 2018
  Primate brain anatomy: New volumetric MRI measurements
  Brain, Behavior and Evolution

Personnel

• Ana F. Navarrete
• Erwin L. A. Blezer
• Orlin S. Todorov
• Patrik Lindenfors
• Kevin N. Laland
• Simon M. Reader

Funding

• John Templeton Foundation
• Canada Foundation for Innovation
• Anna-Greta och Holger Crafoords Stiftelse

Acknowledgements

Thanks to the NIN Primate Brain Bank and collaborators for providing access to preserved primate brain specimens.

Data Access

Data are available via the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.

7T Multimodal MRI in Macaque Brain

This dataset provides high-field (7 Tesla) multimodal MRI data, including structural MRI, diffusion MRI, and resting-state fMRI, collected from macaque monkeys at the University of Minnesota as part of the PRIME-DE initiative.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/uminn.html

The dataset is notable for its 7T acquisition, enabling high spatial resolution and improved signal-to-noise for studying brain structure and connectivity.

Dataset Overview

• Institution: University of Minnesota

• Species: Macaca mulatta

• Sample size: 2

• Age: >10 years

• Sex: Both female

• Modalities:

  • Structural MRI (T1, T2)
  • Diffusion MRI
  • Resting-state fMRI

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic research with attribution
• Non-commercial use only
• Derivative works must use the same license

Scanner Specifications

• Scanner: Siemens 7T
• Head coil: 4-channel clamshell coil

Reference:

• Adriany et al., ISMRM 2010 — 21-channel transceiver array for NHP imaging at 7T

Animal Preparation

Anesthesia

• Isoflurane (2.5%)
• Continuous monitoring of anesthesia depth

Setup

• Time before scanning: ~30 minutes post-anesthesia
• Head fixation: Fixed to the coil
• Position: Sphinx position
• Contrast agent: None

Physiological Monitoring

• Physiological signals monitored during scanning

MRI Acquisition

Resting-State fMRI

• Resolution: 1.4 × 1.4 × 1.4 mm
• TE: 24 ms
• TR: 1000 ms
• Field of view: 140 mm
• Includes gradient-echo reference images

Diffusion MRI

• Resolution: 1.4 × 1.4 × 1.4 mm
• TE: 115 ms
• TR: 6400 ms
• b-values: 800 and 1600 s/mm²
• Slice gap: 1.4 mm

Structural MRI

T1-weighted

• Resolution: 0.3 × 0.3 × 0.3 mm
• TE: 3.65 ms
• TR: 2500 ms
• TI: 1100 ms
• Flip angle: 7°

T2-weighted

• Resolution: 0.3 × 0.3 × 0.3 mm
• TE: 307 ms
• TR: 3000 ms

Scientific Use

This dataset supports:

• High-resolution structural mapping at ultra-high field
• Diffusion-based connectivity analysis
• Functional connectivity studies
• Method development for 7T MRI
• Cross-field comparisons (3T vs 7T)

Personnel

• Essa Yacoub
• Noam Harel

Acknowledgements

• Gregor Adriany
• Lynn Utecht

Funding

Supported by:

• R01-NS081118
• R01-NS085188
• P41-EB015894
• P30-NS076408
• University of Minnesota Udall Center (P50NS098573)

Data Access

Available via PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) for access.

Multimodal MRI in Aging Macaque Brain

This dataset provides structural MRI, diffusion MRI, and resting-state fMRI from macaque brains, collected at the University of California, Davis and the California National Primate Research Center (CNPRC) as part of the PRIMatE Data Exchange (PRIME-DE) initiative.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/ucdavis.html

The dataset is particularly valuable for studying aging-related brain changes, connectivity, and microstructure in nonhuman primates.

Dataset Overview

• Institution:

  • University of California, Davis
  • California National Primate Research Center (CNPRC)

• Species: Macaca mulatta

• Sample size: 19

• Age range: 18.5–22.5 years (aged cohort)

• Weight: 7.28–14.95 kg

• Sex: All female

• Modalities:

  • Structural MRI (T1, T2)
  • Diffusion MRI
  • Resting-state fMRI

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic use with attribution
• Non-commercial use only
• Derivative works must follow the same license

Scanner Specifications

• Scanner: Siemens Skyra 3T
• Coil: 4-channel clamshell coil

Animal Care and Ethics

• Ethics approval: UC Davis IACUC

• Housing:

  • Pair-housed (majority) or single-housed when necessary
  • Indoor primate housing with environmental enrichment
  • Veterinary staff support and behavioral care

Scanning Preparation

Anesthesia

• Pre-medication:

  • Ketamine
  • Dexmedetomidine
  • Buprenorphine

• Maintenance:

  • Isoflurane (1–2%)

Setup

• Head fixation: MRI-compatible stereotaxic frame (Kopf)
• Position: Sphinx position (head first)
• Contrast agent: None

Physiological Monitoring

• Pulse rate
• Oxygen saturation (SpO₂)
• End-tidal CO₂
• Blood pressure
• Inspired/expired isoflurane

Additional:

• Artificial ventilation to maintain normocapnia
• Temperature maintained with heated air blanket

MRI Acquisition

Resting-State fMRI

• Resolution: 1.4 × 1.4 × 1.4 mm
• TE: 24 ms
• TR: 1600 ms
• Field of view: 140 mm
• Includes gradient-echo reference images

Diffusion MRI

• Resolution: 1.4 × 1.4 × 1.4 mm
• TE: 115 ms
• TR: 6400 ms
• b-values: 800 and 1600 s/mm²
• Slice gap: 1.4 mm

Structural MRI

T1-weighted

• Resolution: 0.3 × 0.3 × 0.3 mm
• TE: 3.65 ms
• TR: 2500 ms
• TI: 1100 ms
• Flip angle: 7°

T2-weighted

• Resolution: 0.3 × 0.3 × 0.3 mm
• TE: 307 ms
• TR: 3000 ms

Scientific Use

This dataset supports:

• Aging-related changes in brain structure and connectivity
• Diffusion-based microstructural analysis
• Functional connectivity and network organization
• Cross-species comparisons of aging trajectories
• Multimodal integration of structure and function

Personnel

• Mark G. Baxter, PhD
• Paula L. Croxson, DPhil
• John H. Morrison, PhD

Acknowledgements

• Mary Roberts
• Deborah Kent
• Lisa Novik
• Michael Buonocore (deceased)

Funding

• National Institute on Aging (NIA)
  • Grant: P01-AG016765

Data Access

Data are available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.

Structural and Resting-State MRI in Macaque Brain

This dataset provides structural MRI and resting-state fMRI from a large cohort of macaque monkeys, collected at the Stem Cell and Brain Research Institute (SBRI), Lyon as part of the PRIMatE Data Exchange (PRIME-DE) initiative. :contentReference[oaicite:0]{index=0}

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/sbri.html

The dataset is particularly valuable for studies of brain function, cognition, and neurodegenerative models in nonhuman primates.

Dataset Overview

• Institution: Stem Cell and Brain Research Institute (SBRI), Lyon

• Species:

  • Macaca mulatta (n = 16)
  • Macaca fascicularis (n = 6)

• Sample size: 22

• Age range: 3.6–14 years

• Weight: 2.4–11.4 kg

• Sex: 9 male, 13 female

• Modalities:

  • Structural MRI (T1, T2)
  • Resting-state fMRI

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic use with attribution
• Non-commercial use only
• Derivatives must follow the same license

Animal Care and Ethics

• Ethics approval:
  Approved under multiple European and French regulatory frameworks (1986, 2010 directives) and local ethics committee CELYNE (C2EA #42)

• Housing:
  Animals housed in social enclosures (at least in pairs)

Scanning Preparation

Anesthesia protocols

Two protocols were used:

1. Short scans (structural):

   • Zoletil (15 mg/kg) after atropine premedication

2. Long scans (fMRI):

   • Ketamine (7 mg/kg) + xylazine (0.5 mg/kg)
   • Maintained with isoflurane (~1%)
   • Mechanical ventilation applied

• Timing:
  Resting-state fMRI acquired ≥1 hour after anesthesia induction

Setup

• Head fixation: MRI-compatible stereotaxic frame (Kopf)
• Position: Stereotaxic (head horizontal)

Physiological Monitoring

• Heart rate
• Oxygen saturation (PO₂)
• Ventilation parameters and CO₂ (during isoflurane)

MRI Acquisition

Scanner systems

• Siemens Sonata 1.5T
• Siemens Prisma 3T

Coils

• 1.5T: 10 cm ring coil
• 3T: Siemens L11 and L7 ring coils

Imaging Modalities

Resting-State fMRI

• Resolution: 1.7 × 1.7 × 1.7 mm
• TR: 1700 ms
• TE: 30 ms
• Runs: 5 runs × 12 minutes

Structural MRI

1.5T acquisitions (majority)

• T1 (MPRAGE):
  • 0.6 × 0.6 × 0.6 mm (n = 16)
  • 0.6 × 0.6 × 1 mm (n = 3)
  • TR: 2.16 s
  • TE: 2.89 s

3T acquisitions

• T1 (MPRAGE):

  • 0.5 × 0.5 × 0.5 mm
  • TR: 3 s
  • TE: 3.62 s

• T2 (SPACE):

  • 0.5 × 0.5 × 0.5 mm
  • TR: 3 s
  • TE: 366 ms

Scientific Use

This dataset supports:

• Functional connectivity analysis
• Studies of cognitive control and decision-making
• Investigation of dopaminergic system alterations
• Longitudinal and disease-model research (e.g., Parkinson’s models)
• Cross-species comparison of brain networks

Publications

Representative works include:

• Wilson et al., PLoS Biology (2016)
• Stoll et al., Nature Communications (2016)
• Vezoli et al., NeuroImage (2014)
• Khamassi et al., Progress in Brain Research (2013)

Personnel

• Emmanuel Procyk
• Charles R.E. Wilson
• Céline Amiez

Acknowledgements

• CERMEP Lyon imaging center
• Primage platform
• Animal facility staff and technical support teams

Funding

• Agence Nationale de la Recherche (ANR)
• Fondation Neurodis
• LabEx CORTEX (ANR-11-LABX-0042)
• Fondation de France
• Human Frontier Science Program
• Fondation pour la Recherche Médicale

Data Access

Data are available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.

Structural and Functional MRI in Macaque Brain

This dataset provides anatomical MRI and functional MRI (fMRI) from macaque brains, collected at Rockefeller University as part of the PRIMatE Data Exchange (PRIME-DE) initiative.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/rockefeller.html

The dataset supports studies of brain organization, functional networks, and cross-species neuroscience.

Dataset Overview

• Institution: Rockefeller University
• Species: Macaca mulatta
• Modalities:
  • Structural MRI
  • Functional MRI (resting-state and/or task-based depending on sessions)

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for research use with attribution
• Non-commercial use only
• Derivatives must be shared under the same license

Scanner Specifications

• Scanner: 3 Tesla MRI system
• Coil: Custom or site-specific primate coil configuration

Animal Care and Ethics

• All procedures were approved by the appropriate Institutional Animal Care and Use Committee (IACUC)

• Conducted in accordance with NIH guidelines for animal research

• Housing and care:

  • Managed by trained veterinary and husbandry staff
  • Environmental enrichment provided

Scanning Preparation

Anesthesia

• Typically includes sedation (e.g., ketamine-based protocols)
• Maintenance with inhaled anesthetics (e.g., isoflurane)

Setup

• Head fixation: MRI-compatible stereotaxic frame
• Position: Sphinx or standard primate positioning
• Contrast agent: Not typically used

Physiological Monitoring

• Heart rate
• Respiration
• Oxygen saturation
• Body temperature

Monitoring ensures stable physiological conditions during scanning.

MRI Acquisition

Structural MRI

• High-resolution anatomical imaging
• Typically includes T1-weighted scans

Functional MRI

• Resting-state and/or task-based fMRI
• Gradient-echo EPI sequences
• Parameters optimized for macaque brain imaging

Scientific Use

This dataset supports:

• Functional connectivity analysis
• Network organization studies in primates
• Cross-species comparisons (human vs. macaque)
• Validation of neuroimaging methods
• Studies of cognition and brain systems

Personnel

• Researchers and staff at Rockefeller University contributing to primate neuroimaging

Funding

Supported by institutional and NIH-related funding sources for primate neuroscience research.

Data Access

Data are available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.

Anatomical and Resting-State fMRI in Macaque Brain

This dataset provides structural MRI and resting-state fMRI from nonhuman primates, acquired at the University of Rochester Medical Center / Del Monte Institute for Neuroscience as part of the PRIMatE Data Exchange (PRIME-DE) initiative.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/rochester.html

The dataset supports investigations of functional connectivity and brain organization in macaque models.

Dataset Overview

• Institution:
  University of Rochester Medical Center
  Del Monte Institute for Neuroscience

• Species: Macaca fascicularis

• Sample size: 3

• Age: 3 years

• Weight: 3.1–4.2 kg

• Sex: 2 male, 1 female

• Modalities:

  • Structural MRI (T1-weighted)
  • Resting-state fMRI

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic use with attribution
• Non-commercial use only
• Derivative works must follow the same license

Animal Care and Ethics

• Ethics approval:
  University Committee on Animal Resources (UCAR), University of Rochester

• Guidelines:
  Conducted in accordance with NIH guidelines for humane animal research

• Housing:
  Single-cage housing

Scanning Preparation

Anesthesia

• Isoflurane gas: 1–1.25%
• Administered immediately prior to scanning
• Scan duration: ~1–2 hours

Setup

• Head fixation: Stereotaxic apparatus
• Position: Sphinx position

Physiological Monitoring

• Respiratory rate
• End-tidal CO₂ (ETCO₂)

Animals were mechanically ventilated using an MRI-compatible ventilator.

MRI Acquisition

Scanner and hardware

• Scanner: Siemens Prisma 3T (horizontal bore)
• Head coil: Custom-built

Imaging Modalities

Structural MRI (T1-weighted)

• Resolution: 0.5 × 0.5 mm
• TE: 4.4 ms
• TR: 1880 ms
• TI: 1020 ms
• Flip angle: 10°

Resting-State fMRI

• Resolution: 1.5 × 1.5 mm
• TE: 32 ms
• TR: 2730 ms
• Flip angle: 70°

Scientific Use

This dataset enables:

• Functional connectivity analysis in macaques
• Network modeling of resting-state brain activity
• Validation of cross-species connectomic methods
• Development of causal modeling approaches (e.g., Granger causality)

Investigators

• Julie L. Fudge, MD
• Edmund Kwok, PhD
• Keshov K. Sharma, PhD

Personnel

• Keshov K. Sharma, PhD
• Anas Z. Abidin, PhD

Acknowledgements

• Jianhui Zhong, PhD
• Arun Venkataraman, MD-PhD
• Axel Wismueller, MD-PhD

Funding

Supported by:

• URMC Center for Advanced Brain Imaging and Neurophysiology

Project:

• Large-scale Granger causality modeling of resting-state data in the macaque (2018–2021)

Data Access

Data are available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.

Anatomical, Diffusion, and Resting-State fMRI in Macaque Brain

This dataset provides structural MRI, high-angular resolution diffusion MRI, and resting-state fMRI from macaque brains, acquired at the Princeton Neuroscience & Psychology (NA&P) Lab as part of the PRIMatE Data Exchange (PRIME-DE) initiative. :contentReference[oaicite:0]{index=0}

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/princeton.html

The dataset is designed for connectomics, tractography, and multimodal integration in nonhuman primates.

Dataset Overview

• Institution: Princeton University (NA&P Lab)

• Species: Macaca mulatta

• Sample size: 2

• Age: 3 years

• Weight: 4.7–5.5 kg

• Sex: Male (2)

• Modalities:

  • Structural MRI (T1, T2)
  • Diffusion MRI (multi-shell, high-direction)
  • Resting-state fMRI

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic use with attribution
• Non-commercial use only
• Derivatives must be shared under the same license

Scanner Specifications

• Scanner: Siemens Prisma VE11C 3T
• Coil: Siemens Loop Coil (11 cm)
• Stereotaxic system: Kopf 1430M

Animal Care and Ethics

• Ethics approval: Princeton University IACUC

• Housing:

  • Pair-housed animals
  • Environmental enrichment (toys, foraging devices, enrichment space)

Scanning Preparation

Anesthesia

• Structural & diffusion sessions:

  • Ketamine (10 mg/kg IM) + isoflurane (2.5–3.0%)

• Resting-state session:

  • Ketamine (10 mg/kg IM) + xylazine (0.5 mg/kg IM)
  • Maintained with additional ketamine

Setup

• Head fixation: MRI-compatible stereotaxic frame (Kopf 1430M)
• Position: Sphinx position
• Contrast agent: None

Physiological Monitoring

• ECG, pulse, respiration
• Body temperature (fiber optic probe)
• SpO₂ and end-tidal CO₂ (diffusion sessions)

Additional:

• Artificial ventilation (diffusion sessions)
• Temperature maintained with heated blanket system

MRI Acquisition

Structural MRI (Session 1)

T1-weighted (MPRAGE)

• Resolution: 0.5 × 0.5 × 0.5 mm
• TE: 2.32 ms
• TR: 2700 ms
• TI: 850 ms
• Flip angle: 9°
• Multiple averages and scans

T2-weighted (SPACE)

• Resolution: 0.5 × 0.5 × 0.5 mm
• TE: 398 ms
• TR: 3500 ms

Diffusion MRI

Session 2 (2-shell)

• Resolution: 1 × 1 × 1 mm
• TE/TR: 83 ms / 7200 ms
• Directions:
  • 50 @ b = 1250 s/mm²
  • 100 @ b = 2500 s/mm²
• b0 images: 14
• Total scans: 10 (half reversed phase encoding)

Session 3 (3-shell)

• Resolution: 1 × 1 × 1 mm
• TE/TR: 83 ms / 8000 ms
• Directions:
  • 91 @ b = 850
  • 90 @ b = 1650
  • 90 @ b = 2500 s/mm²
• b0 images: 18
• Total scans: 4 (half reversed phase encoding)

Resting-State fMRI (Session 4)

• Resolution: 1.65 × 1.65 × 1.65 mm
• TE: 26.2 ms
• TR: 1975 ms
• Slices: 32
• Flip angle: 70°
• Measurements: 456
• Scans: 4 (half reversed phase encoding)

Experimental Notes

• Each session includes its own T1 scan
• Diffusion and fMRI datasets include:
  • Separate folders
  • Corresponding bvec/bval files
  • Reversed phase-encoding acquisitions
• Physiological recordings are included for fMRI
• Specialized EPI sequences via University of Minnesota C2P agreement

Scientific Use

This dataset supports:

• High-resolution tractography and connectome mapping
• Multi-shell diffusion modeling (e.g., HARDI, multi-compartment models)
• Functional connectivity and network dynamics
• Cross-modal integration (structure–function relationships)
• Method development for preprocessing and artifact correction

Personnel

• Mark Pinsk
• Sabine Kastner

Funding

• NIMH 1P50MH109429
• NIMH R01MH064043
• NEI R01EY017699

Data Access

Data are available through the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.

Resting-State and Structural MRI in Macaque Brain

This dataset provides resting-state fMRI and high-resolution structural MRI from macaques, collected at the Oregon National Primate Research Center (ONPRC) and Oregon Health & Science University (OHSU). It is designed to support studies of functional connectivity and brain organization in nonhuman primates.

• Source: https://fcon_1000.projects.nitrc.org/indi/PRIME/ohsu.html

Dataset Overview

• Institution:

  • Oregon National Primate Research Center (ONPRC)
  • Oregon Health & Science University (OHSU)

• Species: Macaca mulatta

• Sample size: 2

• Age: 5 years

• Weight: 7.3–8.5 kg

• Sex: Male (2)

• Modalities:

  • Resting-state fMRI
  • Structural MRI (T1, T2)

Usage Agreement

This dataset is shared under:

Creative Commons Attribution-NonCommercial-ShareAlike (CC BY-NC-SA)

• Free for academic research use with attribution
• Non-commercial use only
• Derivatives must be shared under the same license

Animal Care and Ethics

• Ethics approval:
  Oregon National Primate Research Center Institutional Animal Care and Use Committee

• Guidelines:
  Conducted in accordance with NIH guidelines for animal research

• Housing:

  • Indoor pair housing with age-matched partners
  • Temporary separation for fasting prior to scans
  • Reunited after recovery

Scanning Preparation

Anesthesia protocol

• Initial sedation: Ketamine (10 mg/kg, IM)
• Maintenance: Isoflurane (1–1.5%)
• Blood sampling for iron monitoring
• Temperature measured pre/post scan

Timing

• ~20 minutes from sedation to scanner placement
• fMRI acquisition begins ≥45 minutes after ketamine

Setup

• Head fixation: Foam padding and wedges
• Position: Dorsal recumbency (supine), head centered in coil
• Contrast agent: Ferumoxytol (8 mg/kg, IV)

Physiological Monitoring

Continuous monitoring during scanning:

• Oxygen saturation (SpO₂)
• Respiration
• End-tidal CO₂ (ETCO₂)
• Pulse and blood pressure

Additional support:

• Temperature regulation via water mat
• IV saline to maintain catheter patency

MRI Acquisition

Scanner and hardware

• Scanner: Siemens Tim Trio 3T
• Coil: 15-channel knee coil

Imaging Modalities

Resting-State fMRI

• Resolution: 1.5 × 1.5 × 1.5 mm
• TR: 2070 ms
• TE: 25 ms
• Flip angle: 90°

Structural MRI

T1-weighted (MPRAGE)

• Resolution: 0.5 × 0.5 × 0.5 mm
• TE: 3.33 ms
• TR: 2600 ms
• TI: 900 ms
• Flip angle: 8°

T2-weighted

• Resolution: 0.5 × 0.5 × 0.5 mm
• TE: 407 ms
• TR: 3200 ms

Scientific Use

This dataset supports:

• Functional connectivity analyses in macaques
• Cross-species comparisons of brain networks
• Investigation of neurovascular effects using contrast-enhanced fMRI
• Development of preprocessing and analysis pipelines for NHP imaging

Personnel

• Elinor L. Sullivan
• Julian Ramirez
• Eric Feczko
• Jennifer Bagley
• Eric Earl
• Oscar Miranda-Domingue
• Damien Fair

Funding

• NIH R01 MH107508
• P51 OD011092 (ONPRC support)

Acknowledgements

Support from the Advanced Imaging Research Center technical staff is acknowledged.

Data Access

Data are available via the PRIME-DE / INDI platform.
Users must register with the 1000 Functional Connectomes Project (NITRC) to access and download the dataset.