Netherlands Institute for Neuroscience

Amsterdam, The Netherlands

The dataset includes structural and resting state data from 2 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

Sample Description

• Sample size: 2
• Age distribution: 5-6 years
• Weight distribution: 7.5-10.5 kg
• Sex distribution: Both male

Click here for the full sample description (.csv)

Phenotypic Assessments

Scan Procedures and Parameters

Ethics approval: All experiments were approved by the Institutional Animal Care and Use Committee of the Royal Netherlands Academy of Arts and Sciences.

Animal care and housing: Netherlands Institute for Neuroscience. Social housing, mostly in pairs. Dedicated NHP housing facility and technicians/caretakers. Cage enrichment.

Any applicable training: Animals were gradually accustomed to the scanning environment by training them in a dedicated Mock scanner fitted with a speaker system to emulate scanner noise.

Scanning preparations

Anesthesia procedures: Medetomidine 0.08 ml/kg (concentration 1 mg/ml) and Ketamine 0.07 ml/kg (concentration 100 mg/ml) is given intramuscular. If the procedure is still ongoing after ~60 minutes, another dose of 0.07 ml/kg Ketamine is given.

Time between anesthesia and scanning: ~15 minutes

Head fixation: Implanted custom-made PEI/PEEK head holder. Fixed to the skulls with ceramic screws (Thomas Recording) and acrylic cement (Palacos R+G).

Position in scanner and procedure used:

• Anesthetised: Stereotactic device (Kopf 1430)
• Awake: Sphinx position in primate chair

Contrast agent: None

During scanning

Physiological monitoring:

• Anesthetised: heart rate and respiration monitored
• Awake: none

Additional procedures:

• Anesthetised: hot water bottle to maintain body temperature
• Awake: none

Scan sequences

• Scanner type: Philips Ingenia 3T
• Head coil: Custom-made 8 channel phased array receive coil (KU Leuven) with a custom 16 channel pre-amplifier (MRcoils).
• Optimization of the magnetic field prior to data acquisition: n/a
• Resting-state:
  • TE: 20ms
  • TR: 2500ms
  • Bandwidth/pixel (Hz/px): 1113
  • Sequence: GE-EPI (MS-FFE)
  • Parallel acquisition: SENSE (2x in AP direction)
  • Phase encoding direction: AP
  • Fat suppression: yes
  • Slice orientation: T
  • Slice acquisition order: SI
  • Reconstructed resolution (RO x PE x SL): 1.25 x 1.25 x 1.25 mm
  • Reconstructed image matrix (RO x PE x SL): 68 x 70 x 44 px
  • Number of Volumes: 230
  • Number of initial volumes discarded by scanner: 2
  • Acquisition time (m:s): 9:45
  • Flip angle: 77.2°
• Structural:
  • T1
  • TE: 6ms
  • TR: 13ms
  • TI: 900ms
  • Flip angle: 8°
  • Bandwidth/pixel (Hz/px): 113
  • Sequence: 3D-FFE, multishot TFE (150 TFE shots)
  • Parallel acquisition: no
  • Slice orientation: T
  • Phase encoding direction: AP
  • Reconstructed resolution (RO x PE x SL): 0.6 x 0.6 x 0.6 mm
  • Reconstructed image dimensions (RO x PE x SL): 224 x 224 x 100
  • Acquisition time (m:s): 8:42
  • T2
  • Reconstructed resolution (RO x PE x SL): 0.6 x 0.6 x 0.6 mm
  • TE: 80ms
  • TR: 4477ms
• Additional:
  • B0

Personnel

• P. Christiaan Klink^1,2
• Pieter R. Roelfsema^1,2,3

¹Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands²Psychiatry Department, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
³Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands

Acknowledgements

We thank Kor Brandsma and Anneke Ditewig for help with animal training and surgical procedures, and Jonathan Williford for help with animal training, data collection, and analysis.

Funding

Netherlands Organisation for Scientific Research (NWO):

• Brain and Cognition grant 433-09-208 [PRR]
• ALW grant 823-02-010 [PRR]
• VENI grant 451-13-023 [PCK]

European Union:

• Seventh Framework Program (project 269921 "BrainScaleS")[PRR]
• Marie Curie action "ABC" grant agreement 7202070 "Human Brain Project" [PRR]
• ERC grant agreement 339490 "Cortic_al_gorithms"

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.