Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation

Abstract Although several methods have been developed to automatically delineate subcortical gray matter structures from MR images, the accuracy of these algorithms has not been comprehensively examined. Most of earlier studies focused primarily on the hippocampus. Here, we assessed the accuracy of...

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Autores principales:	Gabor Perlaki, Reka Horvath, Szilvia Anett Nagy, Peter Bogner, Tamas Doczi, Jozsef Janszky, Gergely Orsi
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3adac2795686420a8e0d899b14a1ce02
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spelling	oai:doaj.org-article:3adac2795686420a8e0d899b14a1ce022021-12-02T16:06:33ZComparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation10.1038/s41598-017-02584-52045-2322https://doaj.org/article/3adac2795686420a8e0d899b14a1ce022017-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02584-5https://doaj.org/toc/2045-2322Abstract Although several methods have been developed to automatically delineate subcortical gray matter structures from MR images, the accuracy of these algorithms has not been comprehensively examined. Most of earlier studies focused primarily on the hippocampus. Here, we assessed the accuracy of two widely used non-commercial programs (FSL-FIRST and Freesurfer) for segmenting the caudate and putamen. T1-weighted 1 mm3 isotropic resolution MR images were acquired for thirty healthy subjects (15 females). Caudate nucleus and putamen were segmented manually by two independent observers and automatically by FIRST and Freesurfer (v4.5 and v5.3). Utilizing manual labels as reference standard the following measures were studied: Dice coefficient (D), percentage volume difference (PVD), absolute volume difference as well as intraclass correlation coefficient (ICC) for consistency and absolute agreement. For putamen segmentation, FIRST achieved higher D, lower PVD and higher ICC for absolute agreement with manual tracing than either version of Freesurfer. Freesurfer overestimated the putamen, while FIRST was not statistically different from manual tracing. The ICC for consistency with manual tracing was similar between the two methods. For caudate segmentation, FIRST and Freesurfer performed more similarly. In conclusion, Freesurfer and FIRST are not equivalent when comparing to manual tracing. FIRST was superior for putaminal segmentation.Gabor PerlakiReka HorvathSzilvia Anett NagyPeter BognerTamas DocziJozsef JanszkyGergely OrsiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gabor Perlaki Reka Horvath Szilvia Anett Nagy Peter Bogner Tamas Doczi Jozsef Janszky Gergely Orsi Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation
description	Abstract Although several methods have been developed to automatically delineate subcortical gray matter structures from MR images, the accuracy of these algorithms has not been comprehensively examined. Most of earlier studies focused primarily on the hippocampus. Here, we assessed the accuracy of two widely used non-commercial programs (FSL-FIRST and Freesurfer) for segmenting the caudate and putamen. T1-weighted 1 mm3 isotropic resolution MR images were acquired for thirty healthy subjects (15 females). Caudate nucleus and putamen were segmented manually by two independent observers and automatically by FIRST and Freesurfer (v4.5 and v5.3). Utilizing manual labels as reference standard the following measures were studied: Dice coefficient (D), percentage volume difference (PVD), absolute volume difference as well as intraclass correlation coefficient (ICC) for consistency and absolute agreement. For putamen segmentation, FIRST achieved higher D, lower PVD and higher ICC for absolute agreement with manual tracing than either version of Freesurfer. Freesurfer overestimated the putamen, while FIRST was not statistically different from manual tracing. The ICC for consistency with manual tracing was similar between the two methods. For caudate segmentation, FIRST and Freesurfer performed more similarly. In conclusion, Freesurfer and FIRST are not equivalent when comparing to manual tracing. FIRST was superior for putaminal segmentation.
format	article
author	Gabor Perlaki Reka Horvath Szilvia Anett Nagy Peter Bogner Tamas Doczi Jozsef Janszky Gergely Orsi
author_facet	Gabor Perlaki Reka Horvath Szilvia Anett Nagy Peter Bogner Tamas Doczi Jozsef Janszky Gergely Orsi
author_sort	Gabor Perlaki
title	Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation
title_short	Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation
title_full	Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation
title_fullStr	Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation
title_full_unstemmed	Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation
title_sort	comparison of accuracy between fsl’s first and freesurfer for caudate nucleus and putamen segmentation
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/3adac2795686420a8e0d899b14a1ce02
work_keys_str_mv	AT gaborperlaki comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation AT rekahorvath comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation AT szilviaanettnagy comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation AT peterbogner comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation AT tamasdoczi comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation AT jozsefjanszky comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation AT gergelyorsi comparisonofaccuracybetweenfslsfirstandfreesurferforcaudatenucleusandputamensegmentation
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Comparison of accuracy between FSL’s FIRST and Freesurfer for caudate nucleus and putamen segmentation

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