Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)

R. Namias; P. Donnelly Kehoe; J. P. D'Amato; J. Nagel

doi:10.1117/12.2207834

22 December 2015 Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)

R. Namias, P. Donnelly Kehoe, J. P. D'Amato, J. Nagel

Author Affiliations +

Proceedings Volume 9681, 11th International Symposium on Medical Information Processing and Analysis; 96810X (2015) https://doi.org/10.1117/12.2207834
Event: 11th International Symposium on Medical Information Processing and Analysis (SIPAIM 2015), 2015, Cuenca, Ecuador

Abstract

The removal of non-brain regions in neuroimaging is a critical task to perform a favorable preprocessing. The skull-stripping depends on different factors including the noise level in the image, the anatomy of the subject being scanned and the acquisition sequence. For these and other reasons, an ideal brain extraction method should be fast, accurate, user friendly, open-source and knowledge based (to allow for the interaction with the algorithm in case the expected outcome is not being obtained), producing stable results and making it possible to automate the process for large datasets. There are already a large number of validated tools to perform this task but none of them meets the desired characteristics. In this paper we introduced an open source brain extraction tool (OSBET), composed of four steps using simple well-known operations such as: optimal thresholding, binary morphology, labeling and geometrical analysis that aims to assemble all the desired features. We present an experiment comparing OSBET with other six state-of-the-art techniques against a publicly available dataset consisting of 40 T₁-weighted 3D scans and their corresponding manually segmented images. OSBET gave both: a short duration with an excellent accuracy, getting the best Dice Coefficient metric. Further validation should be performed, for instance, in unhealthy population, to generalize its usage for clinical purposes.

Citation Download Citation

R. Namias, P. Donnelly Kehoe, J. P. D'Amato, and J. Nagel "Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)", Proc. SPIE 9681, 11th International Symposium on Medical Information Processing and Analysis, 96810X (22 December 2015); https://doi.org/10.1117/12.2207834

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KEYWORDS

Brain

Image segmentation

Scanning probe microscopy

Neuroimaging

Magnetic resonance imaging

Head

Skull

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