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Neuroimage. 2012 Feb 1;59(3):2362-73. doi: 10.1016/j.neuroimage.2011.09.012. Epub 2011 Sep 16.

BEaST: brain extraction based on nonlocal segmentation technique.

Collaborators (1166)

Saradha A, Abdi H, Abdulkadir A, Acharya D, Achuthan A, Adluru N, Aghajanian J, Agrusti A, Agyemang A, Ahdidan J, Ahmad D, Ahmed S, Aisen P, Akhondi-Asl A, Aksu Y, Alberca R, Alcauter S, Alexander D, Alin A, Almeida F, Alvarez-Linera J, Amlien I, Anand S, Anderson D, Ang A, Angersbach S, Ansarian R, Aoyama E, Appannah A, Arfanakis K, Armor T, Arrighi M, Arumughababu SV, Arunagiri V, Ashe-McNalley C, Ashford W, Le Page A, Avants B, Aviv R, Awasthi S, Ayache N, Ayan-Oshodi M, Ayhan M, Sumana BV, Babic T, Baek Y, Bagepally B, Baird G, Baker J, Baker S, Bakker A, Barbash S, Bard J, Barker W, Bartlett J, Baruchin A, Battaglini I, Bauer C, Bayley P, Beck I, Becker J, Becker JA, Beckett L, Bednar M, Bedner A, Beg MF, Bekris L, Belaroussi B, Belloch V, Belmokhtar N, Ben Ahmed O, Bender JD, Benois-Pineau J, Bhaskar U, Bienkowska K, Biffi A, Bigler E, Bilgic B, Bishop C, Bittner D, Black S, Bloss C, Bocti C, Bohorquez A, Bokde A, Boone J, Boppana M, Borrie M, Bourgeat P, Bouttout H, Bowes M, Bowman D, Bowman G, Bracard S, Braskie M, Braunewell K, Breitner J, Bresell A, Brewer J, Brickhouse M, Brickman A, Britschgi M, Broadbent S, Brogren J, Brunton S, Buchsbaum M, Buckley C, Buerger K, Bunce D, Burnham S, Burns J, Burton D, Burzykowski T, Butler T, Cabeza R, Caffery T, Cairns N, Callhoff J, Calvini P, Carbotti A, Carle A, Carmasin J, Carmichael O, Carvalho J, Casabianca J, Casanova R, Casey A, Cash D, Cataldo R, Cedarbaum J, Cella M, Celsis P, Chakravarty M, Chang I, Chao L, Charil A, Chang CW, Chemali Z, Chen K, Chen S, Chen R, Chen Q, Chen JT, Chen G, Chen J, Chen W, Cheng WC, Cheng X, Cherkas Y, Chertkow H, Cheung V, Cheung C, Chiang G, Chiao P, Chibane MB, Chida N, Chin S, Ching C, Chisholm J, Cho C, Cho Y, Choe J, Choubey S, Chowbina S, Christensen AL, Ciocia G, Clark D, Clark C, Clarkson M, Clerc S, Clunie D, Coen M, Coimbra A, Compton D, Coppola G, Coubard O, Coulin S, Cover KS, Crane P, Crans G, Croop R, Crowther D, Crum W, Cui Y, Curry C, Cutter G, Da L, Daliri MR, Damato VD, Darby E, Darkner S, Davatzikos C, DavidPrakash B, Davidson C, Davis M, de Bruijne M, De Meyer G, De Nunzio G, DeCarli C, Dechairo B, DeDuck K, Dehghan H, Delfino M, Della Rosa PA, Dellavedova L, Delpassand E, Delrieu J, DeOrchis V, Dépy Carron D, Desjardins B, deToledo-Morrell L, Devanand D, Devanarayan V, Devier D, Devous M, Dgetluck N, Di J, Di X, Diaz-Arrastia R, Dickerson B, Dickie DA, Dill V, Ding X, Dinov I, Dobosh B, Dobson H, Dodge H, Dolman A, Dolmo BC, Donohue M, Dore V, Dorflinger E, Dowling M, Dragicevic N, Dubal D, Duchesne S, Duff K, Dukart J, Durazzo T, Dutta J, DWors R, Earl N, Edula G, Elcoroaristizabal X, Emahazion T, Endres C, Epstein N, Ereshefsky L, Eskildsen S, Espinosa A, Esposito M, Ewers M, Falcone G, Fan Y, Fan J, Fan L, Farahibozorg S, Farb N, Fardo D, Farias S, Farnum M, Farrer L, Fatke B, Faux N, Feldman H, Feldman S, Feldman B, Félix Z, Fennema-Notestine C, Fernandes M, Fernandez E, Ferreira MJ, Ferrer E, Fetterman B, Figurski M, Fillit H, Finch S, Fiot JB, Flenniken D, Fletcher E, Flores C, Longmire CF, Focke N, Forman M, Forsythe A, Fox S, Fox-Bosetti S, Foxhall S, Franko E, Freeman R, Friedrich CM, Friesenhahn M, Frisoni G, Fritzsche K, Fujimoto Y, Fujiwara K, Fullerton T, Gaffour Y, Galvin B, Gamst A, Gao S, Garg G, Gaser C, Gastineau E, Gattaz W, Gaubert M, Gauthier S, Gavett B, Ge T, Gemme G, Geraci J, Gholipour F, Ghosh D, Ghosh S, Gieschke R, Gill R, Gillespie W, Gitelman D, Gkontra X, Gleason C, Glymour MM, Godbey M, Gold B, Goldberg T, Goldman J, Gonzalez-Beltran A, Goodro R, Gore C, Gorriz JM, Goto M, Grachev I, Gradkowski W, Grandey E, Grasela T, Gray K, Greenberg B, Greicius M, Grill J, Gross A, Gross A, Grydeland H, Guignot I, Guo Q, Guo LH, Guo H, Gupta V, Guyot J, Habeck C, Habte F, Haight T, Hajaj C, Hajiesmaeili M, Hajjar I, Hammarstrom P, Hampel H, Han D, Han J, Han Z, Hanna Y, Hao Y, Hardy P, Harvey D, Hasan MK, Hayashi T, Haynes JD, He H, He Y, Head D, Heckemann R, Heegaard N, Heidebrink J, Hellyer P, Helwig M, Henderson D, Herholz K, Herskovits AZ, Hess C, Hildenbrand M, Ming AY, Hobart J, Hochstetler H, Hofer S, Hoffman J, Holder D, Hollingworth P, Holmes R, Hong Q, Honigberg L, Hope T, Hoppin J, Hot P, Hou Y, Hsieh H, Hsu A, Hu X, Hu M, Hu W, Hua WY, Huang S, Huang F, Huang Z, Huang CJ, Huang CC, Huang J, Hubbard R, Huentelman M, Huppertz HJ, Hurko O, Hurt S, Hutchins J, Hwang S, Hyun J, Ifeachor E, Iglesias M, Ikari Y, Ikonomidou V, Iman A, Imani F, Immermann F, Inlow M, Inoue L, Insel P, Irizarry M, Ishibashi T, Ishii K, Ismail S, Ito K, Iturria-Medina Y, Iwatsubo T, Jacks A, Jacobson M, Jacqmin P, Jaffe C, Jagust W, Janousova E, Jara H, Jasperse B, Jedynak B, Jefferson A, Jennings JR, Jenq J, Jessen W, Jia F, Jiang T, Jiao Y, Jing H, Johnson K, Johnson S, Johnson DK, Johnson J, Jones G, Jones M, Jones R, Joshi S, Jouvent E, Juengling F, Julin P, Junjie Z, Kabilan M, Kadish B, Kairui Z, Kam HJ, Kamboh MI, Kamer A, Kanakaraj S, Kanchev V, Kaneko T, Kaneta T, Kang H, Kang JH, Kang J, Karageorgiou E, Karantzoulis S, Karlawish J, Katz E, Kaushik SS, Kauwe J, Kawakami H, Kawashima S, Kaye E, Kazemi S, Ke H, Kelleher T, Kennedy R, Keogh B, Kerchner G, Kerr D, Keshava N, Khalil I, Khalil A, Khondker Z, Kihara T, Killeen N, Killiany R, Kim D, Kim H, Kim S, Kim JH, Kim A, Kim JH, Kimberg D, Kimura T, King R, Kirby J, Kirsch W, Klimas M, Kline R, Kling M, Klopfenstein E, Koen J, Koikkalainen J, Kokomoor A, Kong X, Koppel J, Korolev I, Kotran N, Kowalczyk A, Krahnke T, Krams M, Kuceyeski A, Kuhl D, Kumar V, Roy PK, Kuo J, Labrish C, Lai S, Lakatos A, Lalonde F, Lam OK, Lampron A, Landau S, Lane R, Lane B, Langbaum J, Langford D, Lanius V, Latella M, Leahy R, an Lee J, Lee D, Lee N, Lee S, Lee D, Lee G, Lefkimmiatis S, Lemaitre H, Lenfant P, Lenz R, Leong J, Leoutsakos JM, Leung YY, Levey A, Li R, Li X, Li W, Li X, Li M, Li L, Li J, Li G, Li Q, Li Y, Li J, Li J, Li Y, Li S, Liang K, Liang K, Liang P, Liang L, Liao W, Liaquat S, Liberman G, Lin L, Lin AL, Lin F, Liu T, Liu D, Liu L, Liu H, Liu S, Liu T, Liu X, Liu S, Liu L, Liu W, Liu G, Liu T, Liu Y, Liu C, Lo R, Lobanov V, Lockhart A, Loewenstein D, Logovinsky V, Long M, Long Z, Long X, Looi J, Lu H, Lu PH, Lucena N, Lukas C, Lukic A, Luo L, Luo X, Luo X, Lynch J, Ma SM, Mackin S, Mada M, Madabhushi A, Maglio S, Mahanta MS, Maikusa N, Maldjian J, Mandal I, Manjon J, Mantri N, Manzour A, Marchewka A, Marcus D, Margolin R, Marrett S, Marshall G, Gonzalez AM, Torteya AM, Mather M, Mathis C, Mattei P, Matthews D, McArdle J, McCarroll S, McEvoy L, McGeown W, McGinnis S, McGonigle J, McIntyre J, McLaren D, McQuail J, Meadowcroft M, Meda S, Melie-Garcia L, Melrose R, Mendelson A, Mendez M, Menendez E, Meng M, Meredith J, Metti A, Meyer C, Mez J, Mickael G, Miftahof R, Mikula M, Miller M, Millikin C, Nintun M, Mirza M, Mistridis P, Mitchell M, Mitsis E, Mon A, Moore D, Morabito FC, Birgani PM, Moratal D, Morimoto B, Mormino E, Morris J, Mortamet B, Moscato P, Mueller K, Mueller S, Mukherjee S, Mulder E, Mungas D, Munir K, Murayama S, Murphy M, Myers A, Sairam N, Nagata K, Nair A, Nativio R, Nazarparvar B, Nazeri A, Nejad L, Nekooei S, Nettiksimmons J, Neu S, Ng YB, Nguyen N, Nichols T, Nicodemus K, Niecko T, Nielsen C, Nishio T, Nordstrom M, Noshad S, Notomi K, Novak N, Nutakki GC, O'Bryant S, Obisesan T, Oh J, Okonkwo O, Olde Rikkert M, Oliveira A, Oliveira J, Oliver R, Olmos S, Oltra J, Ortner M, Osadebey M, Ostrowitzki S, Overholser R, Anishiya P, Chitra PK, Pa J, Palanisamy P, Pan S, Pan Z, Pande Y, Pardo J, Pardoe H, Park SH, Park S, Park L, Park H, Park MH, Parker C, Patel Y, Patil A, Patil M, Pawlak M, Payoux P, Pearson J, Pell G, Peng Y, Pennec X, Pepin JL, Pereira F, Perneczky R, Petitti D, Petrella J, Peyrat JM, Ngoc PT, Phillips J, Phillips N, Pian WT, Pierson R, Piovezan M, Pipitone J, Pirraglia E, Planes X, Podhorski A, Pollari M, Pomara N, Pontecorvo M, Popov V, Poppenk J, Posner H, Potkin S, Potter G, Potter E, Poulin S, Prastawa M, Prince J, Priya A, Pruessner J, Qiu W, Qu A, Qualls CD, Quarg P, Quinlan J, Rabbia M, Rajagovindan R, Rajeesh R, Rallabandi VP, Ramadubramani V, Ramage A, Ramirez A, Randolph C, Rao A, Rao H, Rao D, Raubertas R, Ray D, Razak H, Reed B, Reid A, Reilhac A, Reiner P, Reinsberger C, Restrepo L, Retico A, Rhatigan L, Rhinn H, Rhoades E, Ribbens A, Richard E, Richards J, Richter M, Riddle W, Ridgway G, Ries M, Ringman J, Rischall M, Rizk-Jackson A, Rizzi M, Robieson W, Rodriguez L, Rodriguez-Vieitez E, Rogalski E, Rogers E, Balderrama JR, Rokicki J, Romero K, Rorden C, Rosand J, Rosen O, Rosenberg P, Roubini E, Rousseau F, Rowe C, Rubin D, Rubright J, Rucinski M, Ruiz A, Rulseh A, Rusinek H, Ryan L, Saad A, Sabuncu M, Sahuquillo J, Said Y, Saito N, Sakata M, Salama M, Salazar D, Salter H, Saman S, Sanchez L, Sanders E, Sankar T, Santhamma S, Sarnel H, Sasaki T, Sasaya T, Sato H, Sattlecker M, Saumier D, Savio A, Saykin A, Scanlon B, Scharre D, Schegerin M, Schmand B, Schmansky N, Schmidt-Wilcke T, Schramm H, Schuerch M, Schwartz C, Schwartz E, Schwarz A, Schwarz J, Selnes P, Sembritzki K, Senjem M, Sevigny J, Sfikas G, Sghedoni R, Shah SK, Shahbaba B, Shams S, Shankle W, Shattuck D, Shaw L, Sheela J, Shen J, Shen Q, Shen W, Shen Q, Shera D, Sherman J, Sherva R, Shi J, Shokouhi S, Shukla V, Shulman J, Sideris K, Siegel R, Silveira M, Silverman D, Sim I, Simak A, Simmons A, Simoes R, Simmons A, Simoes R, Simon A, Simon M, Simpson I, Singh N, Singh SP, Sinha N, Siuciak J, Sjögren N, Skinner J, Smith M, Smith C, Smyth T, Snow S, Snyder P, Soares H, Soldan A, Soldea O, Solomon A, Solomon P, Som S, Song Z, Song S, Sosova I, Soydemir M, Spampinato MV, Speier W, Sperling R, Spiegel R, Spies L, Springate B, Staff R, Steffener J, Stern Y, Stokman H, Straw J, Stricker N, Stühler E, Styren S, Subramanian V, Suen S, Sugishita M, Sukkar R, Sun Y, Sun J, Sun Y, Sun Y, Sundell K, Suzuki A, Svetnik V, Swan M, Symons S, Szigeti K, Szoeke C, Sørensen L, Genish T, Takahasi T, Takeuchi T, Tanaka R, Tanchi C, Tancredi D, Tang Q, Tarnow E, Tartaglia MC, Tarver E, Tassy D, Tauber C, Taylor-Reinwald L, Teipel S, Teng E, Terriza F, Thambisetty M, Thames A, Thatavarti RS, Thiele F, Thomas R, Thomas B, Thomas C, Thompson W, Thompson P, Thornton-Wells T, Thorvaldsson V, Thurfjell L, Tokuda T, Toledo JB, Tölli T, Toma A, Tomita N, Toro R, Torrealdea P, Tosto G, Tosun D, Tousian M, Toussaint P, Toyoshiba H, Tractenberg RE, Triggs T, Trittschuh E, Trojanowski J, Trotta G, Huu TT, Truran D, Tsanas A, Tsang C, Tufail A, Tung J, Turken A, Ueda Y, Uematsu D, Ullrich L, Venkataraju KU, Umar N, Ungar L, Uzunbas G, Van de Nes J, van der Brug M, van der Lijn F, Van Hecke W, Van Horn J, Van Leemput K, Van Train K, Varkuti B, Vasanawala M, Veeraraghavan H, Vemuri P, Verma M, Videbaek C, Vidoni E, Villanueva-Meyer J, Vinyes G, Visser PJ, Vitek M, Vogel S, Voineskos A, Vos S, Vounou M, Wade S, Walsh A, Wan H, Wang T, Wang YM, Wang W, Wang A, Wang S, Wang L, Wang L, Wang Y, Wang LS, Wang L, Wang A, Wang Y, Wang X, Wang Z, Wang T, Ward M, Ward A, Watanabe T, Watson D, Webb D, Wefel J, Weiner M, Westlye LT, Wheland D, Whitcher B, White B, Whitlow C, Wilhelmsen K, Wilmot B, Wilson L, Wimsatt M, Wingo T, Wirth M, Wishart H, Wiste H, Wolf H, Wolke I, Wolz R, Wong K, Woo J, Woo E, Woods L, Worth A, Wu Y, Wu L, Wu E, Wyman B, Xiao G, Xie S, Xu J, Xu G, Xu S, Xu S, Xu Y, Xu YZ, Yamada T, Yamashita F, Yan P, Yan Y, Yang G, Yang W, Yang E, Yang HD, Yang J, Yang CY, Yang Z, Yang E, Yassa M, Yavorsky C, Ye BS, Ye L, Ye J, Yee L, Ying S, Yokoyama T, Young S, Young J, Younhyun J, Yu D, Yu S, Yu CQ, Yu P, Yu D, Yuan Y, Yuan G, Yuan K, Yuen B, Yushkevich P, Zaborszky L, Zagorodnov V, Zagorski M, Zahodne L, Zarei M, Zawadzki R, Zeitzer J, Zelinski E, Zeskind B, Zhan S, Zhang J, Zhang L, Zhang Z, Zhang L, Zhang Z, Zhang D, Zhang H, Zhang X, Zhang T, Zhang P, Zhao J, Zhao Q, Zhao P, Zhen X, Zhijun Y, Zhou L, Zhou B, Zhou Y, Zhou S, Zhu H, Zhu W, Zhu W, Zhu X, Ziegler G, Zilka S, Zisserman A, Zito G, Zu C, Zulfigar A.

Author information

  • 1McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, Canada. se@hst.aau.dk

Abstract

Brain extraction is an important step in the analysis of brain images. The variability in brain morphology and the difference in intensity characteristics due to imaging sequences make the development of a general purpose brain extraction algorithm challenging. To address this issue, we propose a new robust method (BEaST) dedicated to produce consistent and accurate brain extraction. This method is based on nonlocal segmentation embedded in a multi-resolution framework. A library of 80 priors is semi-automatically constructed from the NIH-sponsored MRI study of normal brain development, the International Consortium for Brain Mapping, and the Alzheimer's Disease Neuroimaging Initiative databases. In testing, a mean Dice similarity coefficient of 0.9834±0.0053 was obtained when performing leave-one-out cross validation selecting only 20 priors from the library. Validation using the online Segmentation Validation Engine resulted in a top ranking position with a mean Dice coefficient of 0.9781±0.0047. Robustness of BEaST is demonstrated on all baseline ADNI data, resulting in a very low failure rate. The segmentation accuracy of the method is better than two widely used publicly available methods and recent state-of-the-art hybrid approaches. BEaST provides results comparable to a recent label fusion approach, while being 40 times faster and requiring a much smaller library of priors.

Copyright © 2011 Elsevier Inc. All rights reserved.

PMID:
21945694
[PubMed - indexed for MEDLINE]
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