Skip to main content
National MagLab logo

The MagLab is funded by the National Science Foundation and the State of Florida.

AMRIS FAIR Data: Standardizing Rat Brain Imaging Datasets

Published June 14, 2023

A variety of factors such as sex, strain, anesthesia, magnetic field strength, and breathing rate can affect the results of an fMRI scan. Image reprinted from original citation
A variety of factors such as sex, strain, anesthesia, magnetic field strength, and breathing rate can affect the results of an fMRI scan. Image reprinted from original citation

Datasets of rat brain imaging can be difficult to compare due to the different conditions used to collect them. The Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility participated in a multi-institution study to develop a standardized protocol for functional MRI rat brain datasets, work that will help data be reused effectively to yield new discoveries. 

What is the development?

The MagLab’s AMRIS facility, hosted at the University of Florida’s McKnight Brain Institute, participated in an international collaboration that aggregated and analyzed 65 rat brain fMRI (function magnetic resonance imaging) datasets from 45 institutions. The collaboration developed an optimized and standardized protocol to be used by researchers to store data from future rat brain imaging experiments.

Why is this important?

Rats are commonly used in pharmacological studies due to their similarities with humans in terms of drug metabolism, brain structure, and ability to learn complex tasks. However, combining and comparing datasets from different experiments has historically been made very difficult because brain imaging data is typically collected under a variety of different conditions (for example, different rat strains, anesthesia, or imaging instrumentation).

By conducting experiments with the standardized protocol created by this collaboration, researchers can ensure that their datasets are able to be reused effectively by others. This innovation will greatly increase the pool of available high-quality data, improving researchers’ ability to study rat brain connectivity and make new discoveries. The authors have openly shared all the data and the details of the protocol in open access databases to maximize their accessibility and value for the neuroscience community.

Who did the research?

Joanes Grandjean1,2, et al. (including more than 200 researchers in the collaboration)

1Donders Institute for Brain, Behaviour, and Cognition, Radboud University, Nijmegen, The Netherlands 2Department for Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands

Why did they need the MagLab?

The MagLab contributed a portion of the data in the MultiRat dataset that was used to develop the standardized protocol. The authors needed to ensure that their protocol would be valid across a wide range of different magnetic resonance imaging instruments, including those with both low and high magnetic field strength. The MagLab’s high magnetic field strength magnets were essential for this purpose.

Details for scientists


This research was funded by the following grants: G.S. Boebinger (NSF DMR-1644779)

For more information, contact David Butcher.

Tools They Used

Facility: AMRIS Facility (750 MHz/89 mm Bruker Avance III HD )

Citation: Grandjean, J. et al. A consensus protocol for functional connectivity analysis in the rat brain. Nat Neurosci 26, 673–681 (2023). (

Data Citation: MultiRat dataset (; StandardRat dataset (

Software Citation: RABIES: Rodent Automated Bold Improvement of EPI Sequences (

magnifying glass icon

Search Science Highlights

Search our library of Science Highlights to see notablr research from all of our facilities.

Last modified on 14 June 2023