fMRI data acquisition and analysis for task-free, anesthetized rats
2 Universiteit Antwerpen = University of Antwerp
3 Douglas Mental Health University Institute [Montréal]
4 McGill University = Université McGill [Montréal, Canada]
5 UNC-Chapel Hill - Université de Caroline du Nord à Chapel Hill = University of North Carolina [Chapel Hill]
6 RadboudUMC - Radboud University Medical Center [Nijmegen]
7 PRC - Physiologie de la reproduction et des comportements [Nouzilly]
8 King‘s College London
9 IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia [Genova]
10 UEF - University of Eastern Finland = Itä-Suomen Yliopisto = Östra Finlands universitet
11 FAU - Friedrich-Alexander Universität Erlangen-Nürnberg = University of Erlangen-Nuremberg
12 CHUV - Centre Hospitalier Universitaire Vaudois = Lausanne University Hospital [Lausanne]
13 FORTH - Foundation for Research and Technology - Hellas
14 Bruker BioSpin MRI GmbH [Ettlingen, Germany]
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Résumé
Templates for the acquisition of large datasets such as the Human Connectome Project guide the neuroimaging community to reproducible data acquisition and scientific rigor. By contrast, small animal neuroimaging often relies on laboratory-specific protocols, which limit cross-study comparisons. The establishment of broadly validated protocols may facilitate the acquisition of large datasets, which are essential for uncovering potentially small effects often seen in functional MRI (fMRI) studies. Here, we outline a procedure for the acquisition of fMRI datasets in rats and describe animal handling, MRI sequence parameters, data conversion, preprocessing, quality control and data analysis. The procedure is designed to be generalizable across laboratories, has been validated by using datasets across 20 research centers with different scanners and field strengths ranging from 4.7 to 17.2 T and can be used in studies in which it is useful to compare functional connectivity measures across an extensive range of datasets. The MRI procedure requires 1 h per rat to complete and can be carried out by users with limited expertise in rat handling, MRI and data processing.