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Proceedings Paper

Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)
Author(s): R. Namias; P. Donnelly Kehoe; J. P. D'Amato; J. Nagel
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Paper 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.

Paper Details

Date Published: 22 December 2015
PDF: 10 pages
Proc. SPIE 9681, 11th International Symposium on Medical Information Processing and Analysis, 96810X (22 December 2015); doi: 10.1117/12.2207834
Show Author Affiliations
R. Namias, CIFASIS-CONICET (Argentina)
P. Donnelly Kehoe, Univ. Nacional de Rosario (Argentina)
J. P. D'Amato, Univ. Nacional del Centro (Argentina)
J. Nagel, Instituto Gamma (Argentina)


Published in SPIE Proceedings Vol. 9681:
11th International Symposium on Medical Information Processing and Analysis
Eduardo Romero; Natasha Lepore; Juan D. García-Arteaga; Jorge Brieva, Editor(s)

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