Rodent Automated Bold Improvement of EPI Sequences (RABIES): A standardized image processing and data quality platform for rodent fMRI

ABSTRACT Functional magnetic resonance imaging (fMRI) in rodents holds great potential for advancing our understanding of brain networks. Unlike the human fMRI community, there remains no standardized resource in rodents for image processing, analysis and quality control, posing significant reproducibility limitations. Our software platform, Rodent Automated Bold Improvement of EPI Sequences (RABIES), is a novel pipeline designed to address these limitations for preprocessing, quality control, and confound correction, along with best practices for reproducibility and transparency. We demonstrate the robustness of the preprocessing workflow by validating performance across multiple acquisition sites and both mouse and rat data. Building upon a thorough investigation into data quality metrics across acquisition sites, we introduce guidelines for the quality control of network analysis and offer recommendations for addressing issues. Taken together, the RABIES software will allow the emerging community to adopt reproducible practices and foster progress in translational neuroscience.