Macaca mulatta structural and diffusion weighted MRI data

The AMU dataset includes structural and diffusion weighted MRI data from 4 Macaca mulatta monkeys.

The data is provided both as a directory structure compressed as all_the_data.zip, and as individual files. The correspondence between the directory structure and the individual files is contained in the file tree.json. The bash command source unflatten.sh can be used to convert the individual files into the original directory structure.

Sample Description

Sample size: 4

Age distribution: 7-8 years

Weight distribution: 7.5-12.5 kgs

Sex distribution: 3 male, 1 female

Click here for the full sample description (.csv download)

Scan Procedures and Parameters

Ethics approval: obtained at local Ethics Committee

Animal care and housing: At Institut de Neurosciences de La Timone

Any applicable training: N/A

Scanning preparations

Anesthesia procedures: Isoflurane

Time between anesthesia and scanning: None- anesthesia was performed and monitored during scanning.

Head fixation: Kopf frame and ear bars

Position in scanner and procedure used: Sphinx position. Fiducial marker placed on right side.

Contrast agent: None

During scanning

Physiological monitoring: Heart rate, respiration

Additional procedures: Ventilation

Scan sequences

Scanner type: Siemens Prisma 3T

Head coil: Body transmit array, 11cm loop receiving coil

Optimization of the magnetic field prior to data acquisition: Automatic B0 shimming procedures from Siemens

Diffusion-weighted:

Diffusion SE-EPI sequence

Voxel resolution: 1 x 1 x 1 mm

TE: 87.6ms

TR: 7520ms

64b1000

6b300

5b0

Two repetitions with reversed phase encoding direction

Structural:

T1

MPRAGE sequence

Voxel resolution: 0.8 x 0.8 x 0.8 mm

TE: 2.04ms

TR: 2900ms

TI: 1000ms

T2

3D SPACE sequence

Voxel resolution: 0.8 x 0.8 x 0.8mm

TE: 561ms

TR: 3200ms

QSM

3D GRE sequence

Voxel resolution: 0.93 x 0.93 x 1mm

TE: 2.7-42ms

TR: 45ms

Personnel

Thomas Brochier1

Pascal Belin1

Frédéric Chavanne1

Lionel Velly1

Clémentine Bodin1

Luc Renaud1,2

Marc Martin1,2

Laurence Boes1,2

Julien Sein1

Bruno Nazarian1

Jean-Luc Anton1

1Institut de Neurosciences de la Timone (INT), UMR7289 CNRS & Aix-Marseille Université, Marseille, France
2Centre d’Exploration Fonctionnelle et de Formation en Primatologie (CE2F-PRIM), UMS5737 CNRS & Aix-Marseille Université, Marseille, France

Acknowledgements

We gratefully acknowledge the support of French France-Life Imaging (FLI) and Infrastructures en Biologie Santé et Agronomie (IBISA)

Funding

Project PRIMAVOICE, PI Belin, French Agence Nationale de la Recherche

Detailed information can be found at http://fcon_1000.projects.nitrc.org/indi/PRIME/amu.html.

Citation

Brochier, T., Belin, P., Chavanne, F., Velly, L., Bodin, C., Renaud, L., Martin, M., Boes, L., Sein, J., Nazarian, B., & Anton, J.-L. (2019). Macaca mulatta structural and diffusion weighted MRI data [Data set]. Zenodo. https://doi.org/10.5281/ZENODO.3402456.

Milham, M. P., Ai, L., Koo, B., Xu, T., Amiez, C., Balezeau, F., … Schroeder, C. E. (2018). An Open Resource for Non-human Primate Imaging. Neuron, 100(1), 61–74.e2. https://doi.org/10.1016/j.neuron.2018.08.039.