Functional MRI data from isoflurane-anesthetized macaques, marmosets, and rats

This dataset contains unprocessed task-free functional MRI (fMRI) data acquired in three different mammalian species: long-tailed macaques (Macaca fascicularis), common marmosets (Callithrix jacchus), and rats (Rattus Norvegicus, Wistar strain). The data were obtained during isoflurane anesthesia, with the animals intubated and mechanically ventilated. All experiments were carried out in accordance with the guidelines from  Directive 2010/63/EU of the European Parliament on the protection of animals used for scientific purposes.

Related paper

This dataset supplements the following manuscript:

Sirmpilatze N, Mylius J, Ortiz-Rios M, Baudewig J, Paasonen J, Golkowski D, Ranft A, Ilg R, Gröhn O, Boretius S. Spatial signatures of anesthesia-induced burst-suppression differ between primates and rodents. eLife 2022;11:e74813. DOI: https://doi.org/10.7554/eLife.74813

Data structure

The main data files are organized into four zipped folders - Macaque.zip, Marmoset.zip, Rat1.zip, Rat2.zip - each constituting a dataset formatted according to the Brain Imaging Data Structure specifications (BIDS v1.6.0).

Each BIDS-formatted dataset contains subfolders for individual subjects (e.g. sub-01, sub-02, etc.), as well as a tab-separated text file, participants.tsv, with some essential information about the subjects (e.g. age, weight, sex).

Each subject-specific folder contains subfolders named func and anat, storing fMRI and structural MRI data respectively. The (f)MRI data are provided in NIfTI format (suffixed with .nii.gz). Each NIfTI file is accompanied by a .json sidecar holding metadata.

The func subfolders also include tab-separated text files named as {sub-id}_scans.tsv (e.g. sub-01_scans.tsv). These files provide additional information on the fMRI runs within the func subfolder, such as the isoflurane concentration during the acquisition of the fMRI run, duration of the run, etc.

The column names in participants.tsv and {sub-id}_scans.tsv files are explained in accompanying participants.json and {sub-id}_scans.json files.

BIDS-formatted datasets

The basic characteristics of the datasets are given below. More details can be found in the preprint.

Macaque

Institution: German Primate Center (Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung), Göttingen, Germany

MR system: Siemens MAGNETOM Prisma 3T

Anatomical MRI scan: T1-weighted (MPRAGE), 1 per subject

fMRI scan: GE-EPI, 1 or 2 runs per subject, run duration 600 - 1200 s

Subjects: 13 Macaca fascicularis

Age range: 6.8 - 19.8 years

Weight range: 3.6 - 8.1 kg

Sex: all females

Ethics oversight: Lower Saxony State Office for Consumer Protection and Food Safety, Hannover, Germany (approval number 33.19-42502-04-16/2278)

Marmoset

Institution: German Primate Center (Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung), Göttingen, Germany

MR system: Bruker BioSpec 9.4 T, equpped with B-GA 20S gradient

Anatomical MRI scan: Proton density-weighted (PDw) with magnetization transfer (MT) pulse, 1 per subject

fMRI scan: GE-EPI, 1 run per subject, run duration 600 s (except for sub-21, containing 4 runs of 300 s duration each).

Subjects: 21 Callithrix jacchus

Age range: 1.9 - 14.2 years

Weight range: 337 - 517 g

Sex: 11 females

Ethics oversight: Lower Saxony State Office for Consumer Protection and Food Safety, Hannover, Germany (approval numbers 33.19-42502-04-17/2496 and 33.19-42502-04-17/2535)

Rat1

Institution: German Primate Center (Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung), Göttingen, Germany

MR system: Bruker BioSpec 9.4 T, equpped with B-GA 12S2 gradient

Anatomical MRI scan: T2-weighted (TurboRARE), 1 per subject

fMRI scan: GE-EPI, 6 runs per subject (except for sub-10: 4 runs), run duration 720  s

Subjects: 11 Rattus norvegicus, Wistar strain

Weight range: 350 - 450 g

Sex: all females

Ethics oversight: Lower Saxony State Office for Consumer Protection and Food Safety, Hannover, Germany (approval number 33.19-42502-04-15/2042)

Rat2

Institution: A.I.V. Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland

MR system: Bruker PharmaScan 7 T

Anatomical MRI scan: NOT provided

fMRI scan: GE-EPI, 6 runs per subject (except for sub-10: 4 runs), run duration 720  s

Subjects: 6 Rattus norvegicus, Wistar strain

Weight range: 265 - 350 g

Sex: all males

Ethics oversight: Animal Ethics Committee of the Provincial Government of Southern Finland

Example data

Before you commit to downloading the BIDS-formatted datasets, we encourage you to examine the example data that we provide in the root folder. These include one anatomical (stuctural MRI) and one functional (fMRI) scan from each of the four datasets (Rat2 contains functional scans only), with their respecitve .json sidecars. A preview of these example scans is provided by 0_preview.pdf.