DOI: 10.5281/zenodo.5565306
title: Functional MRI data from isoflurane-anesthetized macaques, marmosets, and rats

description: This dataset contains unprocessed task-free <strong>functional MRI (fMRI)</strong> data acquired in three different mammalian species: <strong>long-tailed macaques</strong> (<em>Macaca fascicularis</em>), <strong>common marmosets</strong> (<em>Callithrix jacchus</em>), and <strong>rats</strong> (<em>Rattus Norvegicus</em>, Wistar strain). The data were obtained during <strong>isoflurane anesthesia</strong>, 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. <strong>Related paper</strong> This dataset supplements the following preprint: Sirmpilatze N, Mylius J, Ortiz-Rios M, Baudewig J, Paasonen J, Golkowski D, Ranft A, Ilg R, Gröhn O, Boretius S. 2021. <em>Spatial signatures of anesthesia-induced burst-suppression differ between primates and rodents.</em> bioRxiv. doi:10.1101/2021.10.15.464515 <strong>Data structure</strong> The main data files are organized into four zipped folders - <em><strong>Macaque.zip, Marmoset.zip, Rat1.zip, Rat2.zip</strong></em> - 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. <em><strong>sub-01</strong>, <strong>sub-02</strong>,</em> etc.), as well as a tab-separated text file, <strong><em>participants.tsv</em></strong>, with some essential information about the subjects (e.g. age, weight, sex). Each subject-specific folder contains subfolders named <em><strong>func</strong> </em>and <strong><em>anat</em></strong>, storing fMRI and structural MRI data respectively. The (f)MRI data are provided in NIfTI format (suffixed with <strong><em>.nii.gz</em></strong>). Each NIfTI file is accompanied by a <strong><em>.json sidecar</em></strong> holding metadata. The <em><strong>func</strong></em> subfolders also include tab-separated text files named as <strong><em>{sub-id}_scans.tsv</em></strong> (e.g. <em><strong>sub-01_scans.tsv</strong></em>). These files provide additional information on the fMRI runs within the <em><strong>func</strong></em> subfolder, such as the isoflurane concentration during the acquisition of the fMRI run, duration of the run, etc. The column names in <em><strong>participants.tsv</strong></em> and <em><strong>{sub-id}_scans.tsv</strong></em> files are explained in accompanying <em><strong>participants.json </strong></em>and <em><strong>{sub-id}_scans.json</strong></em> files. <strong>BIDS-formatted datasets</strong> The basic characteristics of the datasets are given below. More details can be found in the preprint. <em><strong>Macaque</strong></em> <strong>Institution:<em> </em></strong>German Primate Center (Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung), Göttingen, Germany <strong>MR system:</strong> Siemens MAGNETOM Prisma 3T <strong>Anatomical MRI scan:</strong> T1-weighted (MPRAGE), 1 per subject <strong>fMRI scan:</strong> GE-EPI, 1 or 2 runs per subject, run duration 600 - 1200 s <strong>Subjects:</strong> 13 <em>Macaca fascicularis</em> <strong>Age range:</strong> 6.8 - 19.8 years <strong>Weight range:</strong> 3.6 - 8.1 kg <strong>Sex:</strong> all females <strong>Ethics oversight:</strong> Lower Saxony State Office for Consumer Protection and Food Safety, Hannover, Germany (approval number 33.19-42502-04-16/2278) <em><strong>Marmoset</strong></em> <strong>Institution:<em> </em></strong>German Primate Center (Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung), Göttingen, Germany <strong>MR system:</strong> Bruker BioSpec 9.4 T, equpped with B-GA 20S gradient <strong>Anatomical MRI scan:</strong> Proton density-weighted (PDw) with magnetization transfer (MT) pulse , 1 per subject <strong>fMRI scan:</strong> GE-EPI, 1 run per subject, run duration 600 s <strong>Subjects:</strong> 20 <em>Callithrix jacchus</em> <strong>Age range:</strong> 1.9 - 14.2 years <strong>Weight range:</strong> 337 - 517 g <strong>Sex:</strong> 10 females <strong>Ethics oversight:</strong> Lower Saxony State Office for Consumer Protection and Food Safety, Hannover, Germany (approval number 33.19-42502-04-17/2496) <em><strong>Rat1</strong></em> <strong>Institution:<em> </em></strong>German Primate Center (Deutsches Primatenzentrum GmbH - Leibniz-Institut für Primatenforschung), Göttingen, Germany <strong>MR system:</strong> Bruker BioSpec 9.4 T, equpped with B-GA 12S2 gradient <strong>Anatomical MRI scan:</strong> T2-weighted (TurboRARE) , 1 per subject <strong>fMRI scan:</strong> GE-EPI, 6 runs per subject (except for sub-10: 4 runs), run duration 720 s <strong>Subjects:</strong> 11 <em>Rattus norvegicus</em>, Wistar strain <strong>Weight range:</strong> 350 - 450 g <strong>Sex:</strong> all females <strong>Ethics oversight:</strong> Lower Saxony State Office for Consumer Protection and Food Safety, Hannover, Germany (approval number 33.19-42502-04-15/2042) <em><strong>Rat2</strong></em> <strong>Institution:<em> </em></strong>A.I.V. Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland <strong>MR system:</strong> Bruker PharmaScan 7 T <strong>Anatomical MRI scan:</strong> NOT provided <strong>fMRI scan:</strong> GE-EPI, 6 runs per subject (except for sub-10: 4 runs), run duration 720 s <strong>Subjects:</strong> 6 <em>Rattus norvegicus</em>, Wistar strain <strong>Weight range:</strong> 265 - 350 g <strong>Sex:</strong> all males <strong>Ethics oversight:</strong> Animal Ethics Committee of the Provincial Government of Southern Finland <strong>Example data</strong> 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 <strong><em>.json sidecars</em></strong>. A preview of these example scans is provided by <em><strong>0_preview.pdf.</strong></em>