Left ventricular segmentation from MRI datasets with edge modelling conditional random fields
Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium...
Ausführliche Beschreibung
Autor*in: |
Dreijer, Janto F [verfasserIn] |
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Englisch |
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2013 |
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Anmerkung: |
© Dreijer et al.; licensee BioMed Central Ltd. 2013 |
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Übergeordnetes Werk: |
Enthalten in: BMC medical imaging - London : BioMed Central, 2001, 13(2013), 1 vom: 31. Juli |
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Übergeordnetes Werk: |
volume:13 ; year:2013 ; number:1 ; day:31 ; month:07 |
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DOI / URN: |
10.1186/1471-2342-13-24 |
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SPR027474666 |
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520 | |a Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. | ||
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10.1186/1471-2342-13-24 doi (DE-627)SPR027474666 (SPR)1471-2342-13-24-e DE-627 ger DE-627 rakwb eng Dreijer, Janto F verfasserin aut Left ventricular segmentation from MRI datasets with edge modelling conditional random fields 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Dreijer et al.; licensee BioMed Central Ltd. 2013 Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. Ground Truth (dpeaa)DE-He213 Video Sequence (dpeaa)DE-He213 Papillary Muscle (dpeaa)DE-He213 Markov Random Fields (dpeaa)DE-He213 Conditional Random Field (dpeaa)DE-He213 Herbst, Ben M aut du Preez, Johan A aut Enthalten in BMC medical imaging London : BioMed Central, 2001 13(2013), 1 vom: 31. Juli (DE-627)33679911X (DE-600)2061975-3 1471-2342 nnns volume:13 year:2013 number:1 day:31 month:07 https://dx.doi.org/10.1186/1471-2342-13-24 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2013 1 31 07 |
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10.1186/1471-2342-13-24 doi (DE-627)SPR027474666 (SPR)1471-2342-13-24-e DE-627 ger DE-627 rakwb eng Dreijer, Janto F verfasserin aut Left ventricular segmentation from MRI datasets with edge modelling conditional random fields 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Dreijer et al.; licensee BioMed Central Ltd. 2013 Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. Ground Truth (dpeaa)DE-He213 Video Sequence (dpeaa)DE-He213 Papillary Muscle (dpeaa)DE-He213 Markov Random Fields (dpeaa)DE-He213 Conditional Random Field (dpeaa)DE-He213 Herbst, Ben M aut du Preez, Johan A aut Enthalten in BMC medical imaging London : BioMed Central, 2001 13(2013), 1 vom: 31. Juli (DE-627)33679911X (DE-600)2061975-3 1471-2342 nnns volume:13 year:2013 number:1 day:31 month:07 https://dx.doi.org/10.1186/1471-2342-13-24 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2013 1 31 07 |
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10.1186/1471-2342-13-24 doi (DE-627)SPR027474666 (SPR)1471-2342-13-24-e DE-627 ger DE-627 rakwb eng Dreijer, Janto F verfasserin aut Left ventricular segmentation from MRI datasets with edge modelling conditional random fields 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Dreijer et al.; licensee BioMed Central Ltd. 2013 Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. Ground Truth (dpeaa)DE-He213 Video Sequence (dpeaa)DE-He213 Papillary Muscle (dpeaa)DE-He213 Markov Random Fields (dpeaa)DE-He213 Conditional Random Field (dpeaa)DE-He213 Herbst, Ben M aut du Preez, Johan A aut Enthalten in BMC medical imaging London : BioMed Central, 2001 13(2013), 1 vom: 31. Juli (DE-627)33679911X (DE-600)2061975-3 1471-2342 nnns volume:13 year:2013 number:1 day:31 month:07 https://dx.doi.org/10.1186/1471-2342-13-24 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2013 1 31 07 |
allfieldsGer |
10.1186/1471-2342-13-24 doi (DE-627)SPR027474666 (SPR)1471-2342-13-24-e DE-627 ger DE-627 rakwb eng Dreijer, Janto F verfasserin aut Left ventricular segmentation from MRI datasets with edge modelling conditional random fields 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Dreijer et al.; licensee BioMed Central Ltd. 2013 Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. Ground Truth (dpeaa)DE-He213 Video Sequence (dpeaa)DE-He213 Papillary Muscle (dpeaa)DE-He213 Markov Random Fields (dpeaa)DE-He213 Conditional Random Field (dpeaa)DE-He213 Herbst, Ben M aut du Preez, Johan A aut Enthalten in BMC medical imaging London : BioMed Central, 2001 13(2013), 1 vom: 31. Juli (DE-627)33679911X (DE-600)2061975-3 1471-2342 nnns volume:13 year:2013 number:1 day:31 month:07 https://dx.doi.org/10.1186/1471-2342-13-24 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2013 1 31 07 |
allfieldsSound |
10.1186/1471-2342-13-24 doi (DE-627)SPR027474666 (SPR)1471-2342-13-24-e DE-627 ger DE-627 rakwb eng Dreijer, Janto F verfasserin aut Left ventricular segmentation from MRI datasets with edge modelling conditional random fields 2013 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Dreijer et al.; licensee BioMed Central Ltd. 2013 Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. Ground Truth (dpeaa)DE-He213 Video Sequence (dpeaa)DE-He213 Papillary Muscle (dpeaa)DE-He213 Markov Random Fields (dpeaa)DE-He213 Conditional Random Field (dpeaa)DE-He213 Herbst, Ben M aut du Preez, Johan A aut Enthalten in BMC medical imaging London : BioMed Central, 2001 13(2013), 1 vom: 31. Juli (DE-627)33679911X (DE-600)2061975-3 1471-2342 nnns volume:13 year:2013 number:1 day:31 month:07 https://dx.doi.org/10.1186/1471-2342-13-24 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2013 1 31 07 |
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Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. 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Left ventricular segmentation from MRI datasets with edge modelling conditional random fields |
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Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. © Dreijer et al.; licensee BioMed Central Ltd. 2013 |
abstractGer |
Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. © Dreijer et al.; licensee BioMed Central Ltd. 2013 |
abstract_unstemmed |
Background This paper considers automatic segmentation of the left cardiac ventricle in short axis magnetic resonance images. Various aspects, such as the presence of papillary muscles near the endocardium border, makes simple threshold based segmentation difficult. Methods The endo- and epicardium are modelled as two series of radii which are inter-related using features describing shape and motion. Image features are derived from edge information from human annotated images. The features are combined within a discriminatively trained Conditional Random Field (CRF). Loopy belief propagation is used to infer segmentations when an unsegmented video sequence is given. Powell’s method is applied to find CRF parameters by minimizing the difference between ground truth annotations and the inferred contours. We also describe how the endocardium centre points are calculated from a single human-provided centre point in the first frame, through minimization of frame alignment error. Results We present and analyse the results of segmentation. The algorithm exhibits robustness against inclusion of the papillary muscles by integrating shape and motion information. Possible future improvements are identified. Conclusions The presented model integrates shape and motion information to segment the inner and outer contours in the presence of papillary muscles. On the Sunnybrook dataset we find an average Dice metric of 0.91±0.02 and 0.93±0.02 for the inner and outer segmentations, respectively. Particularly problematic are patients with hypertrophy where the blood pool disappears from view at end-systole. © Dreijer et al.; licensee BioMed Central Ltd. 2013 |
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score |
7.3989134 |