Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)
- Autores
- Namias, Rafael; Donnelly Kehoe, Patricio Andres; D'amato, Juan Pablo; Nagel, J.
- Año de publicación
- 2015
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- 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.
Fil: Namias, Rafael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y Sistemas; Argentina. Universidad Nacional de Rosario; Argentina
Fil: Donnelly Kehoe, Patricio Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y Sistemas; Argentina. Universidad Nacional de Rosario; Argentina
Fil: D'amato, Juan Pablo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados; Argentina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Nagel, J.. Instituto Gamma; Argentina - Materia
-
Skullstripping
Magnetic Resonance Imaging
Neuroscience - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/15241
Ver los metadatos del registro completo
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Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET)Namias, RafaelDonnelly Kehoe, Patricio AndresD'amato, Juan PabloNagel, J.SkullstrippingMagnetic Resonance ImagingNeurosciencehttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1https://purl.org/becyt/ford/2.6https://purl.org/becyt/ford/2The 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.Fil: Namias, Rafael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y Sistemas; Argentina. Universidad Nacional de Rosario; ArgentinaFil: Donnelly Kehoe, Patricio Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y Sistemas; Argentina. Universidad Nacional de Rosario; ArgentinaFil: D'amato, Juan Pablo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados; Argentina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nagel, J.. Instituto Gamma; ArgentinaSpie2015info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/15241Namias, Rafael; Donnelly Kehoe, Patricio Andres; D'amato, Juan Pablo; Nagel, J.; Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET); Spie; Spie; 9681; -1-2015; 1-110277-786Xenginfo:eu-repo/semantics/altIdentifier/doi/10.1117/12.2207834info:eu-repo/semantics/altIdentifier/url/http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2479338info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:44:14Zoai:ri.conicet.gov.ar:11336/15241instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:44:15.229CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
title |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
spellingShingle |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) Namias, Rafael Skullstripping Magnetic Resonance Imaging Neuroscience |
title_short |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
title_full |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
title_fullStr |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
title_full_unstemmed |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
title_sort |
Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET) |
dc.creator.none.fl_str_mv |
Namias, Rafael Donnelly Kehoe, Patricio Andres D'amato, Juan Pablo Nagel, J. |
author |
Namias, Rafael |
author_facet |
Namias, Rafael Donnelly Kehoe, Patricio Andres D'amato, Juan Pablo Nagel, J. |
author_role |
author |
author2 |
Donnelly Kehoe, Patricio Andres D'amato, Juan Pablo Nagel, J. |
author2_role |
author author author |
dc.subject.none.fl_str_mv |
Skullstripping Magnetic Resonance Imaging Neuroscience |
topic |
Skullstripping Magnetic Resonance Imaging Neuroscience |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1 https://purl.org/becyt/ford/2.6 https://purl.org/becyt/ford/2 |
dc.description.none.fl_txt_mv |
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. Fil: Namias, Rafael. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y Sistemas; Argentina. Universidad Nacional de Rosario; Argentina Fil: Donnelly Kehoe, Patricio Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y Sistemas; Argentina. Universidad Nacional de Rosario; Argentina Fil: D'amato, Juan Pablo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados; Argentina; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Nagel, J.. Instituto Gamma; Argentina |
description |
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. |
publishDate |
2015 |
dc.date.none.fl_str_mv |
2015 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/15241 Namias, Rafael; Donnelly Kehoe, Patricio Andres; D'amato, Juan Pablo; Nagel, J.; Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET); Spie; Spie; 9681; -1-2015; 1-11 0277-786X |
url |
http://hdl.handle.net/11336/15241 |
identifier_str_mv |
Namias, Rafael; Donnelly Kehoe, Patricio Andres; D'amato, Juan Pablo; Nagel, J.; Fast, accurate, robust and Open Source Brain Extraction Tool (OSBET); Spie; Spie; 9681; -1-2015; 1-11 0277-786X |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/doi/10.1117/12.2207834 info:eu-repo/semantics/altIdentifier/url/http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2479338 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
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application/pdf application/pdf |
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Spie |
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CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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