A meta-algorithm for brain extraction in MRI.

TitleA meta-algorithm for brain extraction in MRI.
Publication TypeJournal Article
Year of Publication2004
AuthorsRex, DE, Shattuck DW, Woods RP, Narr KL, Luders E, Rehm K, Stoltzner SE, Stolzner SE, Rottenberg DA, Toga AW
JournalNeuroImage
Volume23
Issue2
Pagination625-37
Date Published2004 Oct
ISSN1053-8119
KeywordsAdult, Algorithms, Artifacts, Artificial Intelligence, Brain, Cerebrospinal Fluid, False Negative Reactions, False Positive Reactions, Female, Humans, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Reference Values, Schizophrenia, Software
Abstract

Accurate identification of brain tissue and cerebrospinal fluid (CSF) in a whole-head MRI is a critical first step in many neuroimaging studies. Automating this procedure can eliminate intra- and interrater variance and greatly increase throughput for a labor-intensive step. Many available procedures perform differently across anatomy and under different acquisition protocols. We developed the Brain Extraction Meta-Algorithm (BEMA) to address these concerns. It executes many extraction algorithms and a registration procedure in parallel to combine the results in an intelligent fashion and obtain improved results over any of the individual algorithms. Using an atlas space, BEMA performs a voxelwise analysis of training data to determine the optimal Boolean combination of extraction algorithms to produce the most accurate result for a given voxel. This allows the provided extractors to be used differentially across anatomy, increasing both the accuracy and robustness of the procedure. We tested BEMA using modified forms of BrainSuite's Brain Surface Extractor (BSE), FSL's Brain Extraction Tool (BET), AFNI's 3dIntracranial, and FreeSurfer's MRI Watershed as well as FSL's FLIRT for the registration procedure. Training was performed on T1-weighted scans of 136 subjects from five separate data sets with different acquisition parameters on separate scanners. Testing was performed on 135 separate subjects from the same data sets. BEMA outperformed the individual algorithms, as well as interrater results from a subset of the scans, when compared for the mean Dice coefficient, a rating of the similarity of output masks to the manually defined gold standards.

DOI10.1111/j.1467-8624.2011.01677.x
Alternate JournalNeuroimage