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Article: Knowledge-Guided Robust MRI Brain Extraction for Diverse Large-Scale Neuroimaging Studies on Humans and Non-Human Primates

TitleKnowledge-Guided Robust MRI Brain Extraction for Diverse Large-Scale Neuroimaging Studies on Humans and Non-Human Primates
Authors
Issue Date2014
PublisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action
Citation
PLOS ONE, 2014, v. 9 n. 1, article no. e77810 How to Cite?
AbstractAccurate and robust brain extraction is a critical step in most neuroimaging analysis pipelines. In particular, for the large-scale multi-site neuroimaging studies involving a significant number of subjects with diverse age and diagnostic groups, accurate and robust extraction of the brain automatically and consistently is highly desirable. In this paper, we introduce population-specific probability maps to guide the brain extraction of diverse subject groups, including both healthy and diseased adult human populations, both developing and aging human populations, as well as non-human primates. Specifically, the proposed method combines an atlas-based approach, for coarse skull-stripping, with a deformable-surface-based approach that is guided by local intensity information and population-specific prior information learned from a set of real brain images for more localized refinement. Comprehensive quantitative evaluations were performed on the diverse large-scale populations of ADNI dataset with over 800 subjects (55 approximately 90 years of age, multi-site, various diagnosis groups), OASIS dataset with over 400 subjects (18 approximately 96 years of age, wide age range, various diagnosis groups), and NIH pediatrics dataset with 150 subjects (5 approximately 18 years of age, multi-site, wide age range as a complementary age group to the adult dataset). The results demonstrate that our method consistently yields the best overall results across almost the entire human life span, with only a single set of parameters. To demonstrate its capability to work on non-human primates, the proposed method is further evaluated using a rhesus macaque dataset with 20 subjects. Quantitative comparisons with popularly used state-of-the-art methods, including BET, Two-pass BET, BET-B, BSE, HWA, ROBEX and AFNI, demonstrate that the proposed method performs favorably with superior performance on all testing datasets, indicating its robustness and effectiveness.
Persistent Identifierhttp://hdl.handle.net/10722/204957
ISSN
2015 Impact Factor: 3.057
2015 SCImago Journal Rankings: 1.395
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_US
dc.contributor.authorNie, Jen_US
dc.contributor.authorYap, PTen_US
dc.contributor.authorLi, Gen_US
dc.contributor.authorShi, Fen_US
dc.contributor.authorGeng, Xen_US
dc.contributor.authorGuo, Len_US
dc.contributor.authorShen, Den_US
dc.date.accessioned2014-09-20T01:14:17Z-
dc.date.available2014-09-20T01:14:17Z-
dc.date.issued2014en_US
dc.identifier.citationPLOS ONE, 2014, v. 9 n. 1, article no. e77810en_US
dc.identifier.issn1932-6203-
dc.identifier.urihttp://hdl.handle.net/10722/204957-
dc.description.abstractAccurate and robust brain extraction is a critical step in most neuroimaging analysis pipelines. In particular, for the large-scale multi-site neuroimaging studies involving a significant number of subjects with diverse age and diagnostic groups, accurate and robust extraction of the brain automatically and consistently is highly desirable. In this paper, we introduce population-specific probability maps to guide the brain extraction of diverse subject groups, including both healthy and diseased adult human populations, both developing and aging human populations, as well as non-human primates. Specifically, the proposed method combines an atlas-based approach, for coarse skull-stripping, with a deformable-surface-based approach that is guided by local intensity information and population-specific prior information learned from a set of real brain images for more localized refinement. Comprehensive quantitative evaluations were performed on the diverse large-scale populations of ADNI dataset with over 800 subjects (55 approximately 90 years of age, multi-site, various diagnosis groups), OASIS dataset with over 400 subjects (18 approximately 96 years of age, wide age range, various diagnosis groups), and NIH pediatrics dataset with 150 subjects (5 approximately 18 years of age, multi-site, wide age range as a complementary age group to the adult dataset). The results demonstrate that our method consistently yields the best overall results across almost the entire human life span, with only a single set of parameters. To demonstrate its capability to work on non-human primates, the proposed method is further evaluated using a rhesus macaque dataset with 20 subjects. Quantitative comparisons with popularly used state-of-the-art methods, including BET, Two-pass BET, BET-B, BSE, HWA, ROBEX and AFNI, demonstrate that the proposed method performs favorably with superior performance on all testing datasets, indicating its robustness and effectiveness.en_US
dc.languageengen_US
dc.publisherPublic Library of Science. The Journal's web site is located at http://www.plosone.org/home.action-
dc.relation.ispartofPLOS ONEen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshBrain - ultrastructure-
dc.subject.meshBrain Mapping - methods - statistics and numerical data-
dc.subject.meshImage Processing, Computer-Assisted - statistics and numerical data-
dc.subject.meshNeuroimaging - statistics and numerical data-
dc.subject.meshSoftware-
dc.titleKnowledge-Guided Robust MRI Brain Extraction for Diverse Large-Scale Neuroimaging Studies on Humans and Non-Human Primatesen_US
dc.typeArticleen_US
dc.identifier.emailGeng, X: gengx@hku.hken_US
dc.identifier.authorityGeng, X=rp01678en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1371/journal.pone.0077810-
dc.identifier.pmid24489639-
dc.identifier.pmcidPMC3906014-
dc.identifier.hkuros239147en_US
dc.identifier.volume9-
dc.identifier.issue1-
dc.identifier.isiWOS:000330570000002-
dc.publisher.placeUnited States-

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