Skip to main content
Erschienen in: Journal of Digital Imaging 6/2014

01.12.2014

Automatic Cardiac Segmentation Using Semantic Information from Random Forests

verfasst von: Dwarikanath Mahapatra

Erschienen in: Journal of Imaging Informatics in Medicine | Ausgabe 6/2014

Einloggen, um Zugang zu erhalten

Abstract

We propose a fully automated method for segmenting the cardiac right ventricle (RV) from magnetic resonance (MR) images. Given a MR test image, it is first oversegmented into superpixels and each superpixel is analyzed to detect the presence of RV regions using random forest (RF) classifiers. The superpixels containing RV regions constitute the region of interest (ROI) which is used to segment the actual RV. Probability maps are generated for each ROI pixel using a second set of RF classifiers which give the probabilities of each pixel belonging to RV or background. The negative log-likelihood of these maps are used as penalty costs in a graph cut segmentation framework. Low-level features like intensity statistics, texture anisotropy and curvature asymmetry, and high level context features are used at different stages. Smoothness constraints are imposed based on semantic information (importance of each feature to the classification task) derived from the second set of learned RF classifiers. Experimental results show that compared to conventional method our algorithm achieves superior performance due to the inclusion of semantic knowledge and context information.
Literatur
1.
Zurück zum Zitat Allender S, Scarborough P, Peto V, Rayner M, Leal J, Luengo-Fernandez R, Gray A: European cardiovascular disease statistics, European Heart Network, 2008 Allender S, Scarborough P, Peto V, Rayner M, Leal J, Luengo-Fernandez R, Gray A: European cardiovascular disease statistics, European Heart Network, 2008
2.
Zurück zum Zitat Matthews JC, Dardas TF, Dorsch MP, Aaronson KD: Right sided heart failure: diagnosis and treatment strategies. Curr. Treat. Options Cardiovasc 10(4):329–341, 2008CrossRef Matthews JC, Dardas TF, Dorsch MP, Aaronson KD: Right sided heart failure: diagnosis and treatment strategies. Curr. Treat. Options Cardiovasc 10(4):329–341, 2008CrossRef
3.
Zurück zum Zitat Shors S, Fung C, Francois C, Finn P, Fieno D: Accurate quantification of right ventricular mass at MR imaging by using cine true fast imaging with steady state precession: study in dogs. Radiology 230(2):383–388, 2004PubMedCrossRef Shors S, Fung C, Francois C, Finn P, Fieno D: Accurate quantification of right ventricular mass at MR imaging by using cine true fast imaging with steady state precession: study in dogs. Radiology 230(2):383–388, 2004PubMedCrossRef
4.
Zurück zum Zitat Petitjean C, Dacher J-N: A review of segmentation methods in short axis cardiac mr images. Med. Imag. Anal. 15(2):169–184, 2011CrossRef Petitjean C, Dacher J-N: A review of segmentation methods in short axis cardiac mr images. Med. Imag. Anal. 15(2):169–184, 2011CrossRef
5.
Zurück zum Zitat Lapp RM, Lorenzo-Valdes M, Daniel Rueckert: 3d/4d cardiac segmentation using active appearance models, non-rigid registration, and the insight toolkit, in Proc. MICCAI, 2004, pp. 419–426 Lapp RM, Lorenzo-Valdes M, Daniel Rueckert: 3d/4d cardiac segmentation using active appearance models, non-rigid registration, and the insight toolkit, in Proc. MICCAI, 2004, pp. 419–426
6.
Zurück zum Zitat Zhuang X, Rhode KS, Razavi RS, Hawkes DJ, Ourselin S: A registration based propagation framework for automatic whole heart segmentation of cardiac MRI. IEEE Trans. Med. Imag. 29(9):1612–1625, 2010CrossRef Zhuang X, Rhode KS, Razavi RS, Hawkes DJ, Ourselin S: A registration based propagation framework for automatic whole heart segmentation of cardiac MRI. IEEE Trans. Med. Imag. 29(9):1612–1625, 2010CrossRef
7.
Zurück zum Zitat Lorenzo-Valdes M, Sanchez-Ortiz GI, Elkington AG, Mohiaddin RH, Rueckert D: Segmentation of 4d cardiac MR images using a probabilistic atlas and the EM algorithm. Med Image Anal. 8(3):255–265, 2004PubMedCrossRef Lorenzo-Valdes M, Sanchez-Ortiz GI, Elkington AG, Mohiaddin RH, Rueckert D: Segmentation of 4d cardiac MR images using a probabilistic atlas and the EM algorithm. Med Image Anal. 8(3):255–265, 2004PubMedCrossRef
8.
Zurück zum Zitat ElBaz MS, Fahmy AS: Active shape model with inter-profile modeling paradigm for cardiac right ventricle segmentation, in MICCAI, 2012, pp. 691–698 ElBaz MS, Fahmy AS: Active shape model with inter-profile modeling paradigm for cardiac right ventricle segmentation, in MICCAI, 2012, pp. 691–698
9.
Zurück zum Zitat Ou Y, Doshi J, Erus G, Davatzikos C: Multi-atlas segmentation of the right ventricle in cardiac mri, in Proc. MICCAI RV Segmentation Challenge, 2012 Ou Y, Doshi J, Erus G, Davatzikos C: Multi-atlas segmentation of the right ventricle in cardiac mri, in Proc. MICCAI RV Segmentation Challenge, 2012
10.
Zurück zum Zitat Zuluaga MA, Cardoso MJ, Ourselin S: Multi atlas fusion: Automatic right ventricle segmentation using multi-label fusion in cardiac mri, in Proc. MICCAI RV Segmentation Challenge, 2012 Zuluaga MA, Cardoso MJ, Ourselin S: Multi atlas fusion: Automatic right ventricle segmentation using multi-label fusion in cardiac mri, in Proc. MICCAI RV Segmentation Challenge, 2012
11.
Zurück zum Zitat Nambakhsh CMS, Rajchl M, Yuan J, Peters TM, Ben-Ayed I: Rapid automated 3d rv endocardium segmentation in mri via convex relaxation and distribution matching, in Proc. MICCAI RV Segmentation Challenge, 2012 Nambakhsh CMS, Rajchl M, Yuan J, Peters TM, Ben-Ayed I: Rapid automated 3d rv endocardium segmentation in mri via convex relaxation and distribution matching, in Proc. MICCAI RV Segmentation Challenge, 2012
12.
Zurück zum Zitat Grosgeorge D, Petitjean C, Ruan S, Caudron J, Dacher J: Right ventricle segmentation by graph cut with shape prior, in Proc. MICCAI RV Segmentation Challenge, 2012 Grosgeorge D, Petitjean C, Ruan S, Caudron J, Dacher J: Right ventricle segmentation by graph cut with shape prior, in Proc. MICCAI RV Segmentation Challenge, 2012
13.
Zurück zum Zitat Maier O, Jimenez-Carretero D, Santos A, Ledesma-Carbayo MJ: Right- ventricle segmentation with 4d region-merging graph cuts in mr, in Proc. MICCAI RV Segmentation Challenge, 2012 Maier O, Jimenez-Carretero D, Santos A, Ledesma-Carbayo MJ: Right- ventricle segmentation with 4d region-merging graph cuts in mr, in Proc. MICCAI RV Segmentation Challenge, 2012
14.
Zurück zum Zitat Paragios N: A variational approach for the segmentation of the left ventricle in cardiac image analysis. Intl. J. Comp. Vis. 50(3):345–362, 2002CrossRef Paragios N: A variational approach for the segmentation of the left ventricle in cardiac image analysis. Intl. J. Comp. Vis. 50(3):345–362, 2002CrossRef
15.
Zurück zum Zitat Lynch M, Ghita O, Whelan P: Left ventricle myocardium segmentation using a coupled level set with a-priori knowledge. Comput. Med. Imag. Graph. 30(4):255–262, 2006CrossRef Lynch M, Ghita O, Whelan P: Left ventricle myocardium segmentation using a coupled level set with a-priori knowledge. Comput. Med. Imag. Graph. 30(4):255–262, 2006CrossRef
16.
Zurück zum Zitat Lin X, Cowan B, Young A: Model based graph cut method for segmentation of the left ventricle, in In Proc: EMBC, 2005, pp. 3059–3062 Lin X, Cowan B, Young A: Model based graph cut method for segmentation of the left ventricle, in In Proc: EMBC, 2005, pp. 3059–3062
17.
Zurück zum Zitat Mahapatra D, Sun Y: Orientation histograms as shape priors for left ventricle segmentation using graph cuts, in In Proc: MICCAI, 2011, pp. 420–427 Mahapatra D, Sun Y: Orientation histograms as shape priors for left ventricle segmentation using graph cuts, in In Proc: MICCAI, 2011, pp. 420–427
18.
19.
Zurück zum Zitat Mahapatra D, Sun Y: Joint registration and segmentation of dynamic cardiac perfusion images using mrfs., in Proc. MICCAI, 2010, pp. 493–501 Mahapatra D, Sun Y: Joint registration and segmentation of dynamic cardiac perfusion images using mrfs., in Proc. MICCAI, 2010, pp. 493–501
20.
Zurück zum Zitat Mahapatra D, Sun Y: Integrating segmentation information for improved elastic registration of perfusion images using an mrf framework. IEEE Trans. Imag. Proc. 21(1):170–183, 2012CrossRef Mahapatra D, Sun Y: Integrating segmentation information for improved elastic registration of perfusion images using an mrf framework. IEEE Trans. Imag. Proc. 21(1):170–183, 2012CrossRef
21.
Zurück zum Zitat Mahapatra D: Cardiac LV and RV segmentation using mutual context information, in Proc. MICCAI-MLMI, 2012, pp. 201–208 Mahapatra D: Cardiac LV and RV segmentation using mutual context information, in Proc. MICCAI-MLMI, 2012, pp. 201–208
22.
Zurück zum Zitat Pluempitiwiriyawej C, Moura JMF, Wu YL, Ho C: STACS: new active contour scheme for cardiac MR image segmentation. IEEE Trans. Med. Imag. 24(5):593–603, 2005CrossRef Pluempitiwiriyawej C, Moura JMF, Wu YL, Ho C: STACS: new active contour scheme for cardiac MR image segmentation. IEEE Trans. Med. Imag. 24(5):593–603, 2005CrossRef
23.
Zurück zum Zitat Billet F, Sermeanst M, Delingette H, Ayache N: Cardiac motion recovery and boundary conditions estimation by coupling an electromechanical model and cine-MRI data, in Functional Imaging nad modeling of the heatt (FMIH), 2009, pp. 376–385 Billet F, Sermeanst M, Delingette H, Ayache N: Cardiac motion recovery and boundary conditions estimation by coupling an electromechanical model and cine-MRI data, in Functional Imaging nad modeling of the heatt (FMIH), 2009, pp. 376–385
24.
Zurück zum Zitat Lotjonen J, Kivisto S, Koikkalainen J, Smutek D, Lauerma K: Statistical shape model of atria, ventricles and epicardium from short- and long-axis mr images. Med Image Anal. 8(3):371–386, 2004PubMedCrossRef Lotjonen J, Kivisto S, Koikkalainen J, Smutek D, Lauerma K: Statistical shape model of atria, ventricles and epicardium from short- and long-axis mr images. Med Image Anal. 8(3):371–386, 2004PubMedCrossRef
25.
26.
Zurück zum Zitat Mahapatra D, Schueffler P, Tielbeek J, Makanyanga JC, Stoker J, Taylor SA, Vos FM, Buhmann JM: Automatic detection and segmentation of crohn’s disease tissues from abdominal mri. IEEE Trans. Med. Imaging 32(12):1232–1248, 2013CrossRef Mahapatra D, Schueffler P, Tielbeek J, Makanyanga JC, Stoker J, Taylor SA, Vos FM, Buhmann JM: Automatic detection and segmentation of crohn’s disease tissues from abdominal mri. IEEE Trans. Med. Imaging 32(12):1232–1248, 2013CrossRef
27.
Zurück zum Zitat Mahapatra D, Buhmann JM: Analyzing training information from random forests for improved image segmentation., In press IEEE Trans. Imag. Proc Mahapatra D, Buhmann JM: Analyzing training information from random forests for improved image segmentation., In press IEEE Trans. Imag. Proc
28.
Zurück zum Zitat Mahapatra D, Schüffler P, Tielbeek J, Vos FM, Buhmann JM: Crohn’s disease tissue segmentation from abdominal mri using semantic information and graph cuts, in Proc. IEEE ISBI, 2013, pp. 358–361 Mahapatra D, Schüffler P, Tielbeek J, Vos FM, Buhmann JM: Crohn’s disease tissue segmentation from abdominal mri using semantic information and graph cuts, in Proc. IEEE ISBI, 2013, pp. 358–361
29.
Zurück zum Zitat Berks M, Chen Z, Astley S, Taylor C: Detecting and classifying linear structures in mammograms using random forests, in IPMI, 2011, pp. 510–524 Berks M, Chen Z, Astley S, Taylor C: Detecting and classifying linear structures in mammograms using random forests, in IPMI, 2011, pp. 510–524
30.
Zurück zum Zitat Kelm BM, Mittal S, Zheng Y, et al: Detection, grading and classification of coronary stenoses in computed tomography angiography, in MICCAI, 2011, pp. 25–32 Kelm BM, Mittal S, Zheng Y, et al: Detection, grading and classification of coronary stenoses in computed tomography angiography, in MICCAI, 2011, pp. 25–32
31.
Zurück zum Zitat Mahapatra D, Schüffler PJ, Tielbeek J, Buhmann JM, Vos FM: A supervised learning based approach to detect crohn’s disease in abdominal mr volumes, in Proc. MICCAI workshop Computational and Clinical Applications in Abdominal Imaging (MICCAI-ABD), 2012, pp. 97–106 Mahapatra D, Schüffler PJ, Tielbeek J, Buhmann JM, Vos FM: A supervised learning based approach to detect crohn’s disease in abdominal mr volumes, in Proc. MICCAI workshop Computational and Clinical Applications in Abdominal Imaging (MICCAI-ABD), 2012, pp. 97–106
32.
Zurück zum Zitat Schffler PJ, Mahapatra D, Tielbeek JAW, Vos FM, Makanyanga J, Pends DA, Nio CY, Stoker J, Taylor SA, Buhmann JM: A model development pipeline for crohns disease severity assessment from magnetic resonance images, in In Proc: MICCAI-ABD, 2013, pp. 1–10 Schffler PJ, Mahapatra D, Tielbeek JAW, Vos FM, Makanyanga J, Pends DA, Nio CY, Stoker J, Taylor SA, Buhmann JM: A model development pipeline for crohns disease severity assessment from magnetic resonance images, in In Proc: MICCAI-ABD, 2013, pp. 1–10
33.
Zurück zum Zitat Mahapatra D, Schüffler P, Tielbeek J, Vos FM, Buhmann JM: Semi- supervised and active learning for automatic segmentation of crohn’s disease, in Proc. MICCAI, Part 2, 2013, pp. 214–221 Mahapatra D, Schüffler P, Tielbeek J, Vos FM, Buhmann JM: Semi- supervised and active learning for automatic segmentation of crohn’s disease, in Proc. MICCAI, Part 2, 2013, pp. 214–221
34.
Zurück zum Zitat Julesz B, Gilbert EN, Shepp LA, Frisch HL: Inability of humans to discriminate between visual textures that agree in second-order statistics-revisited. Perception 2(4):391–405, 1973PubMedCrossRef Julesz B, Gilbert EN, Shepp LA, Frisch HL: Inability of humans to discriminate between visual textures that agree in second-order statistics-revisited. Perception 2(4):391–405, 1973PubMedCrossRef
35.
Zurück zum Zitat Vos FM, Tielbeek FM, Naziroglu R, Li Z, Schüffler P, Mahapatra D, Alexander Wiebel, Lavini C, Buhmann J, Hege H, Stoker J, van Vliet L: Computational modeling for assessment of IBD: to be or not to be?, in Proc. IEEE EMBC, 2012, pp. 3974–3977 Vos FM, Tielbeek FM, Naziroglu R, Li Z, Schüffler P, Mahapatra D, Alexander Wiebel, Lavini C, Buhmann J, Hege H, Stoker J, van Vliet L: Computational modeling for assessment of IBD: to be or not to be?, in Proc. IEEE EMBC, 2012, pp. 3974–3977
36.
Zurück zum Zitat Mahapatra D, Saini MK, Sun Y: Illumination invariant tracking in office environments using neurobiology-saliency based particle filter, in IEEE ICME, 2008, pp. 953–956 Mahapatra D, Saini MK, Sun Y: Illumination invariant tracking in office environments using neurobiology-saliency based particle filter, in IEEE ICME, 2008, pp. 953–956
37.
Zurück zum Zitat Mahapatra D, Sun Y: Registration of dynamic renal mr images using neurobiological model of saliency, in Proc. ISBI, 2008, pp. 1119–1122 Mahapatra D, Sun Y: Registration of dynamic renal mr images using neurobiological model of saliency, in Proc. ISBI, 2008, pp. 1119–1122
38.
Zurück zum Zitat Mahapatra D, Sun Y: Nonrigid registration of dynamic renal MR images using a saliency based MRF model, in Proc. MICCAI, 2008, pp. 771–779 Mahapatra D, Sun Y: Nonrigid registration of dynamic renal MR images using a saliency based MRF model, in Proc. MICCAI, 2008, pp. 771–779
39.
Zurück zum Zitat Petrou M, Kovalev VA, Reichenbach JR: Three-dimensional nonlinear invisible boundary detection. IEEE Trans. Imag. Proc 15(10):3020–3032, 2006CrossRef Petrou M, Kovalev VA, Reichenbach JR: Three-dimensional nonlinear invisible boundary detection. IEEE Trans. Imag. Proc 15(10):3020–3032, 2006CrossRef
40.
Zurück zum Zitat De Valois RL, Albrecht DG, Thorell LG: Spatial-frequency selectivity of cells in macaque visual cortex. Vis. Res. 22(5):545–559, 1982PubMedCrossRef De Valois RL, Albrecht DG, Thorell LG: Spatial-frequency selectivity of cells in macaque visual cortex. Vis. Res. 22(5):545–559, 1982PubMedCrossRef
41.
Zurück zum Zitat Tu Z, Bai X: Auto-context and its application to high-level vision tasks and 3d brain image segmentation. IEEE Trans. Patt. Anal. Mach. Intell. 32(10):1744–1757, 2010CrossRef Tu Z, Bai X: Auto-context and its application to high-level vision tasks and 3d brain image segmentation. IEEE Trans. Patt. Anal. Mach. Intell. 32(10):1744–1757, 2010CrossRef
42.
Zurück zum Zitat Li W, Liao S, Feng Q, Chen W, Shen D: Learning image context for segmentation of prostate in ct-guided radiotherapy, in MICCAI, 2011, pp. 570–578 Li W, Liao S, Feng Q, Chen W, Shen D: Learning image context for segmentation of prostate in ct-guided radiotherapy, in MICCAI, 2011, pp. 570–578
43.
Zurück zum Zitat Mahapatra D, Buhmann JM: Prostate mri segmentation using learned semantic knowledge and graph cuts. In press IEEE Trans. Biomed. Engg 61(3):756–764, 2014CrossRef Mahapatra D, Buhmann JM: Prostate mri segmentation using learned semantic knowledge and graph cuts. In press IEEE Trans. Biomed. Engg 61(3):756–764, 2014CrossRef
44.
Zurück zum Zitat Criminsi A, Shotton J, Bucciarelli S: Decision forests with long range spatial context for organ localization, in MICCAI workshop on Probabilistic Models for Medical Image Analysis (MICCAI-PMMIA), 2009 Criminsi A, Shotton J, Bucciarelli S: Decision forests with long range spatial context for organ localization, in MICCAI workshop on Probabilistic Models for Medical Image Analysis (MICCAI-PMMIA), 2009
45.
Zurück zum Zitat Zheng Y, Barbu A, Beorgescu B, Scheuering M, Comaniciu D: Four chamber heart modeling and automatic segmentation for 3D cardiac CT volumes using marginal space learning and steerable features. IEEE Trans. Med. Imag. 27(11):1668–1681, 2008CrossRef Zheng Y, Barbu A, Beorgescu B, Scheuering M, Comaniciu D: Four chamber heart modeling and automatic segmentation for 3D cardiac CT volumes using marginal space learning and steerable features. IEEE Trans. Med. Imag. 27(11):1668–1681, 2008CrossRef
46.
Zurück zum Zitat Sled JG, Zijdenbos AP, Evans AC: A nonparametric method for automatic correction of intensity nonuniformity in mri data. IEEE Trans. Med. Imag. 17(1):87–97, 1998CrossRef Sled JG, Zijdenbos AP, Evans AC: A nonparametric method for automatic correction of intensity nonuniformity in mri data. IEEE Trans. Med. Imag. 17(1):87–97, 1998CrossRef
47.
Zurück zum Zitat Nyl LG, Udupa JK: On standardizing the mr image intensity scale. Magnetic resonance in medicine 42(6):1072–1081, 1999CrossRef Nyl LG, Udupa JK: On standardizing the mr image intensity scale. Magnetic resonance in medicine 42(6):1072–1081, 1999CrossRef
48.
Zurück zum Zitat Achanta R, Shaji A, Smith K, Lucchi A, Fua P, Ssstrunk S: Slic superpixels compared to state-of-the-art superpixel methods. IEEE Trans. Patt. Anal. Mach. Intell. 34(11):2274–2282, 2012CrossRef Achanta R, Shaji A, Smith K, Lucchi A, Fua P, Ssstrunk S: Slic superpixels compared to state-of-the-art superpixel methods. IEEE Trans. Patt. Anal. Mach. Intell. 34(11):2274–2282, 2012CrossRef
49.
Zurück zum Zitat Boykov Y, Veksler O: Fast approximate energy minimization via graph cuts. IEEE Trans. Pattern Anal. Mach. Intell. 23:1222–1239, 2001CrossRef Boykov Y, Veksler O: Fast approximate energy minimization via graph cuts. IEEE Trans. Pattern Anal. Mach. Intell. 23:1222–1239, 2001CrossRef
Metadaten
Titel
Automatic Cardiac Segmentation Using Semantic Information from Random Forests
verfasst von
Dwarikanath Mahapatra
Publikationsdatum
01.12.2014
Verlag
Springer US
Erschienen in
Journal of Imaging Informatics in Medicine / Ausgabe 6/2014
Print ISSN: 2948-2925
Elektronische ISSN: 2948-2933
DOI
https://doi.org/10.1007/s10278-014-9705-0

Weitere Artikel der Ausgabe 6/2014

Journal of Digital Imaging 6/2014 Zur Ausgabe

Update Radiologie

Bestellen Sie unseren Fach-Newsletter und bleiben Sie gut informiert.