Automatic macaque brain segmentation based on 7T MRI

Abstract

BackgroundIn monkey neuroimaging, particularly magnetic resonance imaging (MRI) studies, quick and accurate automatic macaque brain segmentation is essential. However, there are few processing and analysis tools dedicated to automatic brain tissue segmentation and labeling of the macaque brain on a subject-specific basis. As a result, currently most adopted methods are through direct implementation of existing tools that have been designed for human brain. However, the operation steps combining different functional modules of a variety of processing and analysis tool software are inevitably complicated, cumbersome, time-consuming and labor-intensive. New methodIn this study, we proposed a novel quick and accurate automatic macaque brain segmentation method based on multi-atlas registration and majority-vote algorithm. First, the single-atlas method based on S-HAMMER is used to register each template image of the reference atlas set (including brain tissue labeled images and brain anatomical structure labeled images) to the preprocessed image to be segmented. Thus, we obtain the corresponding deformation field and spatially transform the labeled image, and then get multiple segmentation results by local weighted voting method, which perform label fusion to obtain the final labeled images of brain structures segmentation result. ResultsBy collecting high SNR and high spatial resolution images of macaque brain images from our 7T human MRI scanner, we have constructed two brain templates for each individual macaque subject, and macaque brain tissues and brain anatomical structure by one-atlas method. However, segmentation result of single-atlas method is not much accurate in some brain tissue area. It takes about 2 h and need more manual correction for segmentation. Automatic segmentation of macaque brain structure based on multi-atlas method was reasonably successful, the accuracy of segmentation was greatly improved without manual correction. Also, the proposed method provided good tissue fitting to V1 with smooth and continuous boundary. The Dice similarity of multi-atlas method showing 3.24%, 4.24%, 2.55%, 2.85%, 3.05%, and 0.35% improvement in image slices of 63, 66, 70, 71, 99 and 100, respectively. The entire processing time for the construction of a single template map took ~40 min. ConclusionsThis study proposed a novel automatic segmentation method of individual macaque brain structure based on multi-atlas registration method, which is concise and reliable. It may offer a valuable tool to applications in the field of brain and neuroscience research using the macaque as an experimental animal model.