National Institute of Mental Health (Messinger)

The NIMH dataset includes anatomical, fMRI, and morphometric data from 3 rhesus monkeys, and the NIMH Macaque Template (NMT) package.

Usage Agreement

Custom Data Usage Agreement (DUA)- Users must complete a data usage agreement (DUA) prior to gaining access to the data. Contributors can customize the agreement as they see fit, including determining whether or not signatures from authorized institutional official are required prior to executing the DUA.

The DUA for this dataset will be released soon.

Species

Macaca mulatta

Scanner Specifications

• Resting state data was collected on a vertical 4.7T Bruker scanner. Anatomical scans for morphometric analysis and alignment of resting state data were collected on a horizontal 4.7T Bruker scanner.
• All head coils were custom-built. Subject 32160 was scanned with a 4 channel head coil, Subject 32161 with a Helmholtz volume coil, and Subject 32162 with a quadrature volume coil. Anatomical scans for morphometric analysis and alignment of resting state data were collected with a single loop volume coil.
• A PLACE scan was acquired during data collection to assess distortions arising from magnetic field inhomogeneity and the EPI data was PLACE corrected (Xiang and Ye, 2007) in all but one case (Subject 32161, Session1), where this procedure introduced a movement artifact.

Sample Description

• Sample size: 3
• Age distribution: 6-8 years (73-107 months)
• Weight distribution: 5.1-9.6 kg
• Sex distribution: 2 male/1 female

Click here for the full sample description (.csv)

Scan Procedures and Parameters

Ethics approval: National Institutes of Mental Health Animal Care and Use Committee

Animal care and housing: National Institutes of Health Guide for the Care and Use of Laboratory Animals, Central Animal Facility at the NIMH

Any applicable training: Monkeys were trained to perform a fixation task, with a central fixation spot and complex visual objects.

Anesthesia procedures: Subject 32162 was lightly sedated with Diazepan (0.56 mg/kg, i.m.) before the anatomical scan and rest scans 7-10. All subjects were anesthetized with isoflurane before anatomical scans used for alignment of resting state data and for morphometric analysis.

Time between anesthesia and scanning: Rest scans were collected 13-48 minutes after Diazepan was administered.

Head fixation: For resting state scans, animals were head fixed using a non-metallic head post affixed dorsally to the skull using ceramic screws and acrylic.

Position in scanner and procedure used: For resting state scans, monkeys were oriented vertically in a sitting position.

Contrast agent: MION was administered (14-18 mg/kg, i.v.) before most resting state scans (excepting Subject 32162, Session 1, rest scans 1 and 2).

Physiological monitoring: One eye was monitored visually and gaze direction was recorded for periods when the eye was open.

Additional procedures: N/A

Scan sequences

• Resting-state:
  • Voxel resolution: 1.5 x 1.5 x 1.5mm
  • In-plane matrix size: 64 x 34
  • Field of view: 96 x 48 x 60mm
  • Slice direction: sagittal (coronal for subject 32162)
  • TE: 12.8ms (20ms for scans without MION)
  • TR: 3000ms
  • Flip angle: 90°
• Structural:
  • T1 MDEFT Sequence
  • Voxel resolution: 0.5 x 0.5 x 1.5mm
  • In-plane matrix size: 192 x 96
  • Field of view: 96 x 48 x 69mm
  • Flip angle: 8°
  • Number of averages: 1
  • Separate anatomical scans were collected under isoflurane anesthesia at a resolution of 0.5×0.5×0.5 mm. Additional details are provided in Messinger_session_data.csv.

Downloads

The downloads consist of resting state, anatomical, and morphometric data from 3 subjects; three tables and a read_me files describing these data, and the NIMH Macaque Template (NMT) package.

Three tables describing the 3 subjects, 4 scan sessions, and 20 rest scans are included. Phenotypic Data describes the sex, age, weight, and species of each subject. Session Data describes those scanning parameters that remained fixed for an entire scan session (e.g. scan duration, TR, resolution) and the head coil used. Scan Data describes those things that changed across resting state scans, within a session. The read_me.txt file describes the naming scheme of the anatomical, resting state, and motion parameter files and what paper to reference when using this data.

The NMT package consists of the NIMH Macaque Template volume, segmentation masks, morphometric descriptions, surfaces, scripts for processing anatomical scans, and a read_me text file.

Publications

• Seidlitz, J., Sponheim, C., Glen, D., Frank, Q.Y., Saleem, K.S., Leopold, D.A., Ungerleider, L.G., & Messinger, A. (2017). A population MRI brain template and analysis tools for the macaque. NeuroImage.

Personnel

• Adam Messinger¹
• Benjamin Jung¹
• Jakob Seidlitz¹
• Leslie Ungerleider^1,2,3

¹Laboratory of Brain and Cognition, National Institute of Mental Health Bethesda, MD, USA
²Developmental Neurogenomics Unit, National Institute of Mental Health Bethesda, MD, USA
²Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom

Acknowledgements

The authors would like to acknowledge Benjamin Jung for compiling and aligning the data and putting it in BIDS format.

Funding

This work was funded by the Intramural Research Program of the NIMH (ZIC MH002899).

Downloads

The data for this site are password protected. Please complete the data usage agreement and submit to CMIDataUsage@childmind.org for access to the dataset.

Click here to download the encrypted 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.