Automated brain extraction of multisequence MRI using artificial neural networks.
artificial neural networks
brain extraction
deep learning
magnetic resonance imaging
neuroimaging
skull stripping
Journal
Human brain mapping
ISSN: 1097-0193
Titre abrégé: Hum Brain Mapp
Pays: United States
ID NLM: 9419065
Informations de publication
Date de publication:
01 12 2019
01 12 2019
Historique:
received:
10
12
2018
revised:
19
07
2019
accepted:
23
07
2019
pubmed:
14
8
2019
medline:
17
4
2020
entrez:
13
8
2019
Statut:
ppublish
Résumé
Brain extraction is a critical preprocessing step in the analysis of neuroimaging studies conducted with magnetic resonance imaging (MRI) and influences the accuracy of downstream analyses. The majority of brain extraction algorithms are, however, optimized for processing healthy brains and thus frequently fail in the presence of pathologically altered brain or when applied to heterogeneous MRI datasets. Here we introduce a new, rigorously validated algorithm (termed HD-BET) relying on artificial neural networks that aim to overcome these limitations. We demonstrate that HD-BET outperforms six popular, publicly available brain extraction algorithms in several large-scale neuroimaging datasets, including one from a prospective multicentric trial in neuro-oncology, yielding state-of-the-art performance with median improvements of +1.16 to +2.50 points for the Dice coefficient and -0.66 to -2.51 mm for the Hausdorff distance. Importantly, the HD-BET algorithm, which shows robust performance in the presence of pathology or treatment-induced tissue alterations, is applicable to a broad range of MRI sequence types and is not influenced by variations in MRI hardware and acquisition parameters encountered in both research and clinical practice. For broader accessibility, the HD-BET prediction algorithm is made freely available (www.neuroAI-HD.org) and may become an essential component for robust, automated, high-throughput processing of MRI neuroimaging data.
Identifiants
pubmed: 31403237
doi: 10.1002/hbm.24750
pmc: PMC6865732
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4952-4964Subventions
Organisme : Else Kröner-Fresenius Foundation
Pays : International
Organisme : Medical Faculty Heidelberg Postdoc-Program
Pays : International
Informations de copyright
© 2019 The Authors. Human Brain Mapping published by Wiley Periodicals, Inc.
Références
Neuroimage. 2010 Jul 1;51(3):1047-56
pubmed: 20226258
Eur J Radiol Open. 2018 Jan 28;5:20-23
pubmed: 29719853
Neurology. 2015 Feb 24;84(8):784-93
pubmed: 25632085
Nat Rev Neurol. 2010 Feb;6(2):67-77
pubmed: 20139996
IEEE Trans Med Imaging. 2001 Jan;20(1):45-57
pubmed: 11293691
Neuroimage. 2006 Feb 1;29(3):838-52
pubmed: 16269250
IEEE Trans Med Imaging. 2011 Sep;30(9):1617-34
pubmed: 21880566
Neuroimage. 2012 Jul 16;61(4):1484-94
pubmed: 22484407
Hum Brain Mapp. 2019 Dec 1;40(17):4952-4964
pubmed: 31403237
PLoS One. 2014 Dec 16;9(12):e115551
pubmed: 25514672
Neuroimage. 2017 Feb 1;146:132-147
pubmed: 27864083
Neuroimage. 2000 Sep;12(3):340-56
pubmed: 10944416
Hum Brain Mapp. 2006 Feb;27(2):99-113
pubmed: 15986433
Lancet Oncol. 2019 May;20(5):728-740
pubmed: 30952559
Neuroimage. 2018 Apr 15;170:482-494
pubmed: 28807870
Neuroimage. 2012 Feb 1;59(3):2362-73
pubmed: 21945694
Hum Brain Mapp. 2018 Nov;39(11):4241-4257
pubmed: 29972616
J Digit Imaging. 2016 Jun;29(3):365-79
pubmed: 26628083
IEEE Trans Med Imaging. 2017 Nov;36(11):2319-2330
pubmed: 28678704
Med Image Anal. 2010 Jun;14(3):360-72
pubmed: 20303318
Med Image Anal. 2001 Jun;5(2):143-56
pubmed: 11516708
Hum Brain Mapp. 2002 Nov;17(3):143-55
pubmed: 12391568
Neuroinformatics. 2021 Jan;19(1):127-140
pubmed: 32578020
Gigascience. 2016 Oct 25;5(1):45
pubmed: 27782853
Neuroimage. 1999 Feb;9(2):179-94
pubmed: 9931268
Neuroimage. 2016 Apr 1;129:460-469
pubmed: 26808333
Comput Biomed Res. 1996 Jun;29(3):162-73
pubmed: 8812068
IEEE Trans Med Imaging. 2015 Oct;34(10):1993-2024
pubmed: 25494501
N Engl J Med. 2017 Nov 16;377(20):1954-1963
pubmed: 29141164
IEEE Trans Pattern Anal Mach Intell. 2015 Nov;37(11):2153-63
pubmed: 26440258
Neuroimage. 2009 Oct 15;48(1):63-72
pubmed: 19573611
J Neurosci Methods. 2010 May 15;188(2):316-25
pubmed: 20230858
Med Image Anal. 2002 Jun;6(2):129-42
pubmed: 12045000
J Neuroimaging. 2006 Apr;16(2):146-53
pubmed: 16629737
Neuroimage. 2008 Feb 1;39(3):1064-80
pubmed: 18037310
Neuroimage. 2010 May 15;51(1):214-20
pubmed: 20123029
Neuroimage. 2006 Jul 1;31(3):1116-28
pubmed: 16545965
J Comput Assist Tomogr. 1993 Jul-Aug;17(4):536-46
pubmed: 8331222
Neuroimage. 2018 Aug 1;176:431-445
pubmed: 29730494
Neuroimage. 2001 May;13(5):856-76
pubmed: 11304082