Atlas-Based Brain Extraction Is Robust Across RAT MRI Studies

Brain extraction is a ubiquitous initial step in MRI analysis pipelines. Although there are several solutions for human imaging, existing rodent imaging tools often perform poorly on new data with acquisition protocols and parameters that differ from the images with which the tools were developed. Here, we adapted antsBrainExtraction (from the popular ANTs neuroimaging toolbox), which implements atlasbased brain extraction of adult humans, for use with rat MRI data. The new tool, artsBrainExtraction, was evaluated on 190 images from three different scanners, utilising six imaging protocols that differ in contrast, resolution, and field-of-view. The tool produced highly accurate brain masks in 186 (98%) of the images and adequate masks in the other four. We present a reliable brain extraction tool for rodent images that is agnostic to the imaging protocol and can be extended to further image modalities and non-human populations.