Quantitative comparison of four brain extraction algorithms

In a companion paper (Rehm et al., 2004), we introduced Minneapolis Consensus Strip (MeStrip), a hybrid algorithm for brain/non-brain segmentation. In this paper, we compare the performance of MeStrip and three brain extraction algorithms (BEAs) in widespread use within the neuroimaging community-Statistical Parametric Mapping v.2 (SPM2), Brain Extraction Tool (BET), and Brain Surface Extractor (BSE)-to the gold standard of manually stripped T1-weighted MRI brain volumes. Our comparison was based on quantitative boundary and volume metrics, reproducibilily across repeat scans of a single subject, and assessments of performance consistency across datasets acquired on different scanners at different institutions. MeStrip, a hybrid method incorporating warping to a template, intensity thresholding, and edge detection, consistently outperformed SPM2, BET, and BSE, all of which rely on a single algorithmic strategy. (C) 2004 Elsevier Inc. All rights reserved.