Automated brain extraction and associated 3D inspection layers for the Rhesus macaque MRI datasets

Abstract

As we know, the rhesus macaque as a non-human primate is quite similar to human being in genetics. And it has become an essential animal model anatomy and physiology in many modern medicine research such as the cardiovascular and cerebrovascular diseases in recent years. This paper describes a pipeline from the raw rhesus macaque brain MRI data to intuitive 3D inspection its layers. Brain extraction is an initial step for subsequent analyses, but most of the existing methods so far are designed for human brain, which doesn't work well with the rhesus macaque. Firstly, we propose a reliable and efficient method to extract the brain from MRI datasets based on dividing the brain into blocks. Then, we design a trapezoid opacity transfer function based on CUDA-based real-time volume ray-casting, which is dedicated for the volume rendering to make the inspection more intuitive. Besides, the inspection of different tissues benefits understanding the volumetric datasets, so we also design layer filter for the segmented rhesus macaque brain datasets, which facilitates inspection of interior in ROI by an intuitive bimanual interaction via a Leap Motion sensor. Our experiments prove the usability and efficiency of the proposed methods.