A learning-based wrapper method to correct systematic errors in automatic image segmentation: consistently improved performance in hippocampus, cortex and brain segmentation.
We propose a simple but generally applicable approach to improving the accuracy of automatic image segmentation algorithms relative to manual segmentations. The approach is based on the hypothesis that a large fraction of the errors produced by automatic segmentation are systematic, i.e., occur consistently from subject to subject, and serves as a wrapper method around a given host segmentation method. The wrapper method attempts to learn the intensity, spatial and contextual patterns associated with systematic segmentation errors produced by the host method on training data for which manual segmentations are available. The method then attempts to correct such errors in segmentations produced by the host method on new images. One practical use of the proposed wrapper method is to adapt existing segmentation tools, without explicit modification, to imaging data and segmentation protocols that are different from those on which the tools were trained and tuned. An open-source implementation of the proposed wrapper method is provided, and can be applied to a wide range of image segmentation problems. The wrapper method is evaluated with four host brain MRI segmentation methods: hippocampus segmentation using FreeSurfer (Fischl et al., 2002); hippocampus segmentation using multi-atlas label fusion (Artaechevarria et al., 2009); brain extraction using BET (Smith, 2002); and brain tissue segmentation using FAST (Zhang et al., 2001). The wrapper method generates 72%, 14%, 29% and 21% fewer erroneously segmented voxels than the respective host segmentation methods. In the hippocampus segmentation experiment with multi-atlas label fusion as the host method, the average Dice overlap between reference segmentations and segmentations produced by the wrapper method is 0.908 for normal controls and 0.893 for patients with mild cognitive impairment. Average Dice overlaps of 0.964, 0.905 and 0.951 are obtained for brain extraction, white matter segmentation and gray matter segmentation, respectively.
Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA. hongzhiw@mail.med.upenn.edu
Hongzhi
H
Wang
Sandhitsu R
SR
Das
Jung Wook
JW
Suh
Murat
M
Altinay
John
J
Pluta
Caryne
C
Craige
Brian
B
Avants
Paul A
PA
Yushkevich
D000368:Aged; D000465:Algorithms; D000544:Alzheimer Disease / Q000473:pathology; D001185:Artificial Intelligence; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology* / Q000473:pathology; D002540:Cerebral Cortex / Q000033:anatomy & histology* / Q000473:pathology; D016208:Databases, Factual; D005260:Female; D006624:Hippocampus / Q000033:anatomy & histology* / Q000473:pathology; D006801:Humans; D007089:Image Enhancement / Q000379:methods; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008297:Male; D008875:Middle Aged; D012984:Software
IEEE Trans Med Imaging. 2004 Jul;23(7):903-21
15250643
Neuroimage. 2010 Oct 1;52(4):1355-66
20441794
IEEE Trans Med Imaging. 2006 Dec;25(12):1547-64
17167991
Neuroimage. 2010 Jul 15;51(4):1345-59
20230901
Neuroimage. 2011 Jan;54 Suppl 1:S218-26
20353827
Neuroimage. 2008 May 1;40(4):1655-71
18353687
Neuroimage. 2008 Dec;43(4):708-20
18761411
Neuroimage. 2008 Jul 1;41(3):735-46
18455931
J Neurosci Methods. 2009 Oct 15;183(2):255-66
19467263
Neuroimage. 2006 Oct 15;33(1):115-26
16860573
Neuroimage. 2007 May 15;36(1):38-47
17428687
IEEE Trans Med Imaging. 2006 Sep;25(9):1233-45
16967808
IEEE Trans Med Imaging. 2010 Oct;29(10):1714-29
20562040
AJNR Am J Neuroradiol. 1996 Jun-Jul;17(6):1091-8
8791921
Hippocampus. 2009 Jun;19(6):565-71
19437413
IEEE Trans Med Imaging. 2001 Jan;20(1):45-57
11293691
Neuroimage. 2009 Jul 1;46(3):726-38
19245840
Neuroimage. 2009 Jul 1;46(3):749-61
19236922
Psychiatry Res. 2010 Mar 30;181(3):219-25
20153146
Neuroimage. 2010 Apr 1;50(2):434-45
20005963
Neuroimage. 2009 Apr 15;45(3):855-66
19162198
Hum Brain Mapp. 2002 Nov;17(3):143-55
12391568
IEEE Trans Med Imaging. 2007 Apr;26(4):541-52
17427741
Epilepsia. 2009 Dec;50(12):2586-92
19682030
Neuroimage. 2005 Oct 1;27(4):979-90
15990339
Neuroimage. 2007 May 1;35(4):1516-30
17383900
Neuroimage. 2004;23 Suppl 1:S208-19
15501092
Neuroimage. 2008 Jan 1;39(1):238-47
17904870
IEEE Trans Med Imaging. 2009 Aug;28(8):1266-77
19228554
IEEE Trans Biomed Eng. 2009 Jul;56(7):1838-48
19336280
Philos Trans A Math Phys Eng Sci. 2008 Jul 13;366(1874):2361-75
18407896
IEEE Trans Med Imaging. 2010 Jan;29(1):30-43
19457748
Med Image Anal. 2002 Jun;6(2):129-42
12045000
Med Image Anal. 2008 Feb;12(1):26-41
17659998
Neuroimage. 2006 Aug 1;32(1):79-92
16697666
IEEE Trans Pattern Anal Mach Intell. 2010 Oct;32(10):1744-57
20724753
Neuron. 2002 Jan 31;33(3):341-55
11832223
Neuroimage. 2006 Jul 1;31(3):1116-28
16545965
Med Image Comput Comput Assist Interv. 2008;11(Pt 1):194-201
18979748
PLoS One. 2009;4(4):e5265
19370155
Med Image Anal. 2006 Oct;10(5):726-39
16919993
Neuroimage. 2004 Jul;22(3):1060-75
15219578