An open database of resting-state fMRI in awake rats

Abstract

Rodent models are essential to translational research in health and disease. Investigation in rodent brain function and organization at the systems level using resting-state functional magnetic resonance imaging (rsfMRI) has become increasingly popular. Due to this rapid progress, publicly shared rodent rsfMRI databases can be of particular interest and importance to the scientific community, as inspired by human neuroscience and psychiatric research that are substantially facilitated by open human neuroimaging datasets. However, such databases in rats are still rare. In this paper, we share an open rsfMRI database acquired in 90 rats with a well-established awake imaging paradigm that avoids anesthesia interference. Both raw and preprocessed data are made publicly available. Procedures in data preprocessing to remove artefacts induced by the scanner, head motion and non-neural physiological noise are described in details. We also showcase inter-regional functional connectivity and functional networks obtained from the database.

An isotropic EPI database and analytical pipelines for rat brain resting-state fMRI

“…Resting-state functional magnetic resonance imaging (fMRI) provides a non-invasive means to measure brain-wide functional connectivity (FC) without assigned tasks or stimuli ( Biswal, 2012 ). This translational approach has drastically expanded the scope of neuroimaging research in both humans ( Menon, 2011 ; Sadaghiani and Wirsich, 2020 ; Smith et al, 2013 ) and animals ( Chuang and Nasrallah, 2017 ; Coletta et al, 2020 ; Grandjean et al, 2020 ; Liska et al, 2015 ; Liu et al, 2020 ; Ma and Zhang, 2018 ; Pais-Roldan et al, 2018 ; Pan et al, 2015 ; Schwarz et al, 2009 ) by advancing our knowledge about the topologies and dynamics of functional brain networks ( He et al, 2018 ; Keilholz et al, 2016 ; Ma and Zhang, 2018 ; Sobczak et al, 2021 ). Several pioneering efforts have been made in the human fMRI community to minimize data variability arising from diverse implementation of data acquisition ( Casey et al, 2018 ; Van Essen et al, 2012 ; Yan et al, 2013 ), pre-processing ( Adhikari et al, 2019 ; Alfaro-Almagro et al, 2018 ; Benhajali et al, 2020 ; Esteban et al, 2019 ), and post-processing methodologies ( Smith et al, 2013 ; Wyman et al, 2013 ).…”

“…As a result, several databases and processing pipelines have been disseminated ( Casey et al, 2018 ; Glasser et al, 2016 ; Howell et al, 2019 ; Mueller et al, 2005 ; Sudlow et al, 2015 ; Van Essen et al, 2013 ; Yan et al, 2013 ), making significant contributions to data standardization and reproducibility. Similarly, several key initiatives have been led by researchers in the rodent fMRI community to develop and share databases ( Grandjean et al, 2020 ; Liu et al, 2020 ). Despite these efforts, progress has been hampered by challenges in the acquisition and analysis of rodent resting-state fMRI data using echo planar imaging (EPI).…”

“…In humans, EPI data is commonly acquired with isotropic spatial resolution and whole-brain coverage ( Smith et al, 2013 ; Van Essen et al, 2012 ). In rodents, however, EPI is predominantly acquired with anisotropic resolution ( Aedo-Jury et al, 2020 ; Albaugh et al, 2016 ; Broadwater et al, 2018 ; Hsu et al, 2016 ; Liang et al, 2018 ; Liu et al, 2020 ; Lu et al, 2012 ; Mandino et al, 2019; Pan et al, 2018 ; Tsai et al, 2020 ; Van Den Berge et al, 2017 ). This setting is inherited from the traditional coronal slicing used to view rodent brains in histological sections ( Paxinos and Watson, 2014 ; Paxinos et al, 2015 ).…”

Editorial: APPNING: Animal Population Imaging

“…The animal imaging community has also growing requirements for multicenter studies, for example to allow the comparison of academic results as in brain connectivity studies (Grandjean et al, 2020 ) or to characterize the effects of drugs (Bruns et al, 2015 ). To share preclinical imaging data and data analysis pipelines, only few tools are available that take into account the specificities of animal studies (Liu et al, 2020 ; Messinger et al, 2020 ), and few studies aim at standardization of acquisition and post-processing techniques.…”

Emerging imaging methods to study whole-brain function in rodent models

“…In this context, fMRI represents a valuable tool for addressing the growing need to formally identify common brain circuits between rodents and humans to determine the scope and limits of rodent translational models [ 62 , 63 ]. One caveat is that rodent fMRI is usually carried out in the anesthetized state to minimize head-motion during scanning, and only a handful of labs are acquiring fMRI data in awake animals [ 15 , 64 , 65 ]. The choice of anesthetic introduces confounds in fMRI measurements and is certainly a limitation for translating findings to humans [ 38 , 39 ].…”