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Khorshidi A. Tumor segmentation via enhanced area growth algorithm for lung CT images. BMC Med Imaging 2023; 23:189. [PMID: 37986046 PMCID: PMC10662793 DOI: 10.1186/s12880-023-01126-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Since lung tumors are in dynamic conditions, the study of tumor growth and its changes is of great importance in primary diagnosis. METHODS Enhanced area growth (EAG) algorithm is introduced to segment the lung tumor in 2D and 3D modes on 60 patients CT images from four different databases by MATLAB software. The contrast augmentation, color intensity and maximum primary tumor radius determination, thresholding, start and neighbor points' designation in an array, and then modifying the points in the braid on average are the early steps of the proposed algorithm. To determine the new tumor boundaries, the maximum distance from the color-intensity center point of the primary tumor to the modified points is appointed via considering a larger target region and new threshold. The tumor center is divided into different subsections and then all previous stages are repeated from new designated points to define diverse boundaries for the tumor. An interpolation between these boundaries creates a new tumor boundary. The intersections with the tumor boundaries are firmed for edge correction phase, after drawing diverse lines from the tumor center at relevant angles. Each of the new regions is annexed to the core region to achieve a segmented tumor surface by meeting certain conditions. RESULTS The multipoint-growth-starting-point grouping fashioned a desired consequence in the precise delineation of the tumor. The proposed algorithm enhanced tumor identification by more than 16% with a reasonable accuracy acceptance rate. At the same time, it largely assurances the independence of the last outcome from the starting point. By significance difference of p < 0.05, the dice coefficients were 0.80 ± 0.02 and 0.92 ± 0.03, respectively, for primary and enhanced algorithms. Lung area determination alongside automatic thresholding and also starting from several points along with edge improvement may reduce human errors in radiologists' interpretation of tumor areas and selection of the algorithm's starting point. CONCLUSIONS The proposed algorithm enhanced tumor detection by more than 18% with a sufficient acceptance ratio of accuracy. Since the enhanced algorithm is independent of matrix size and image thickness, it is very likely that it can be easily applied to other contiguous tumor images. TRIAL REGISTRATION PAZHOUHAN, PAZHOUHAN98000032. Registered 4 January 2021, http://pazhouhan.gerums.ac.ir/webreclist/view.action?webreclist_code=19300.
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Affiliation(s)
- Abdollah Khorshidi
- School of Paramedical, Gerash University of Medical Sciences, P.O. Box: 7441758666, Gerash, Iran.
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2
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Pawar SP, Talbar SN. LungSeg-Net: Lung field segmentation using generative adversarial network. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2020.102296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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3
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Soltani-Nabipour J, Khorshidi A, Noorian B. Lung tumor segmentation using improved region growing algorithm. NUCLEAR ENGINEERING AND TECHNOLOGY 2020. [DOI: 10.1016/j.net.2020.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Xia H, Sun W, Song S, Mou X. Md-Net: Multi-scale Dilated Convolution Network for CT Images Segmentation. Neural Process Lett 2020. [DOI: 10.1007/s11063-020-10230-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Chen G, Xiang D, Zhang B, Tian H, Yang X, Shi F, Zhu W, Tian B, Chen X. Automatic Pathological Lung Segmentation in Low-Dose CT Image Using Eigenspace Sparse Shape Composition. IEEE TRANSACTIONS ON MEDICAL IMAGING 2019; 38:1736-1749. [PMID: 30605097 DOI: 10.1109/tmi.2018.2890510] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The segmentation of lungs with severe pathology is a nontrivial problem in the clinical application. Due to complex structures, pathological changes, individual differences, and low image quality, accurate lung segmentation in clinical 3-D computed tomography (CT) images is still a challenging task. To overcome these problems, a novel dictionary-based approach is introduced to automatically segment pathological lungs in 3-D low-dose CT images. Sparse shape composition is integrated with the eigenvector space shape prior model, called eigenspace sparse shape composition, to reduce local shape reconstruction error caused by the weak and misleading appearance prior information. To initialize the shape model, a landmark recognition method based on discriminative appearance dictionary is introduced to handle lesions and local details. Furthermore, a new vertex search strategy based on the gradient vector flow field is also proposed to drive the shape deformation to the target boundary. The proposed algorithm is tested on 78 3-D low-dose CT images with lung tumors. Compared to the state-of-the-art methods, the proposed approach can robustly and accurately detect pathological lung surface.
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6
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Zhang W, Wang X, Zhang P, Chen J. Global optimal hybrid geometric active contour for automated lung segmentation on CT images. Comput Biol Med 2017; 91:168-180. [DOI: 10.1016/j.compbiomed.2017.10.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/03/2017] [Accepted: 10/07/2017] [Indexed: 11/27/2022]
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7
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Low-rank and sparse decomposition based shape model and probabilistic atlas for automatic pathological organ segmentation. Med Image Anal 2017; 38:30-49. [PMID: 28279915 DOI: 10.1016/j.media.2017.02.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/21/2022]
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8
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Automatic Approach for Lung Segmentation with Juxta-Pleural Nodules from Thoracic CT Based on Contour Tracing and Correction. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2016; 2016:2962047. [PMID: 27974907 PMCID: PMC5128731 DOI: 10.1155/2016/2962047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/24/2016] [Indexed: 11/18/2022]
Abstract
This paper presents a fully automatic framework for lung segmentation, in which juxta-pleural nodule problem is brought into strong focus. The proposed scheme consists of three phases: skin boundary detection, rough segmentation of lung contour, and pulmonary parenchyma refinement. Firstly, chest skin boundary is extracted through image aligning, morphology operation, and connective region analysis. Secondly, diagonal-based border tracing is implemented for lung contour segmentation, with maximum cost path algorithm used for separating the left and right lungs. Finally, by arc-based border smoothing and concave-based border correction, the refined pulmonary parenchyma is obtained. The proposed scheme is evaluated on 45 volumes of chest scans, with volume difference (VD) 11.15 ± 69.63 cm3, volume overlap error (VOE) 3.5057 ± 1.3719%, average surface distance (ASD) 0.7917 ± 0.2741 mm, root mean square distance (RMSD) 1.6957 ± 0.6568 mm, maximum symmetric absolute surface distance (MSD) 21.3430 ± 8.1743 mm, and average time-cost 2 seconds per image. The preliminary results on accuracy and complexity prove that our scheme is a promising tool for lung segmentation with juxta-pleural nodules.
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Mattonen SA, Tetar S, Palma DA, Louie AV, Senan S, Ward AD. Imaging texture analysis for automated prediction of lung cancer recurrence after stereotactic radiotherapy. J Med Imaging (Bellingham) 2015; 2:041010. [PMID: 26835492 DOI: 10.1117/1.jmi.2.4.041010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 10/06/2015] [Indexed: 12/25/2022] Open
Abstract
Benign radiation-induced lung injury (RILI) is not uncommon following stereotactic ablative radiotherapy (SABR) for lung cancer and can be difficult to differentiate from tumor recurrence on follow-up imaging. We previously showed the ability of computed tomography (CT) texture analysis to predict recurrence. The aim of this study was to evaluate and compare the accuracy of recurrence prediction using manual region-of-interest segmentation to that of a semiautomatic approach. We analyzed 22 patients treated for 24 lesions (11 recurrences, 13 RILI). Consolidative and ground-glass opacity (GGO) regions were manually delineated. The longest axial diameter of the consolidative region on each post-SABR CT image was measured. This line segment is routinely obtained as part of the clinical imaging workflow and was used as input to automatically delineate the consolidative region and subsequently derive a periconsolidative region to sample GGO tissue. Texture features were calculated, and at two to five months post-SABR, the entropy texture measure within the semiautomatic segmentations showed prediction accuracies [areas under the receiver operating characteristic curve (AUC): 0.70 to 0.73] similar to those of manual GGO segmentations (AUC: 0.64). After integration into the clinical workflow, this decision support system has the potential to support earlier salvage for patients with recurrence and fewer investigations of benign RILI.
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Affiliation(s)
- Sarah A Mattonen
- The University of Western Ontario , Department of Medical Biophysics, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Shyama Tetar
- VU University Medical Center , Department of Radiation Oncology, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - David A Palma
- The University of Western Ontario, Department of Medical Biophysics, 1151 Richmond Street, London, Ontario N6A 3K7, Canada; London Regional Cancer Program, Division of Radiation Oncology, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Alexander V Louie
- London Regional Cancer Program , Division of Radiation Oncology, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Suresh Senan
- VU University Medical Center , Department of Radiation Oncology, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Aaron D Ward
- The University of Western Ontario , Department of Medical Biophysics, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
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Automatic Classification of Normal and Cancer Lung CT Images Using Multiscale AM-FM Features. Int J Biomed Imaging 2015; 2015:230830. [PMID: 26451137 PMCID: PMC4587437 DOI: 10.1155/2015/230830] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/24/2015] [Accepted: 09/01/2015] [Indexed: 11/17/2022] Open
Abstract
Computer-aided diagnostic (CAD) systems provide fast and reliable diagnosis for medical images. In this paper, CAD system is proposed to analyze and automatically segment the lungs and classify each lung into normal or cancer. Using 70 different patients' lung CT dataset, Wiener filtering on the original CT images is applied firstly as a preprocessing step. Secondly, we combine histogram analysis with thresholding and morphological operations to segment the lung regions and extract each lung separately. Amplitude-Modulation Frequency-Modulation (AM-FM) method thirdly, has been used to extract features for ROIs. Then, the significant AM-FM features have been selected using Partial Least Squares Regression (PLSR) for classification step. Finally, K-nearest neighbour (KNN), support vector machine (SVM), naïve Bayes, and linear classifiers have been used with the selected AM-FM features. The performance of each classifier in terms of accuracy, sensitivity, and specificity is evaluated. The results indicate that our proposed CAD system succeeded to differentiate between normal and cancer lungs and achieved 95% accuracy in case of the linear classifier.
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Doel T, Gavaghan DJ, Grau V. Review of automatic pulmonary lobe segmentation methods from CT. Comput Med Imaging Graph 2015; 40:13-29. [PMID: 25467805 DOI: 10.1016/j.compmedimag.2014.10.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 10/11/2014] [Accepted: 10/15/2014] [Indexed: 11/17/2022]
Abstract
The computational detection of pulmonary lobes from CT images is a challenging segmentation problem with important respiratory health care applications, including surgical planning and regional image analysis. Several authors have proposed automated algorithms and we present a methodological review. These algorithms share a number of common stages and we consider each stage in turn, comparing the methods applied by each author and discussing their relative strengths. No standard method has yet emerged and none of the published methods have been demonstrated across a full range of clinical pathologies and imaging protocols. We discuss how improved methods could be developed by combining different approaches, and we use this to propose a workflow for the development of new algorithms.
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Affiliation(s)
- Tom Doel
- Department of Computer Science, University of Oxford, Oxford, UK.
| | - David J Gavaghan
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Vicente Grau
- Department of Engineering Science and Oxford e-Research Centre, University of Oxford, Oxford, UK
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12
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Shen S, Bui AAT, Cong J, Hsu W. An automated lung segmentation approach using bidirectional chain codes to improve nodule detection accuracy. Comput Biol Med 2014; 57:139-49. [PMID: 25557199 DOI: 10.1016/j.compbiomed.2014.12.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/06/2014] [Accepted: 12/10/2014] [Indexed: 11/18/2022]
Abstract
Computer-aided detection and diagnosis (CAD) has been widely investigated to improve radiologists׳ diagnostic accuracy in detecting and characterizing lung disease, as well as to assist with the processing of increasingly sizable volumes of imaging. Lung segmentation is a requisite preprocessing step for most CAD schemes. This paper proposes a parameter-free lung segmentation algorithm with the aim of improving lung nodule detection accuracy, focusing on juxtapleural nodules. A bidirectional chain coding method combined with a support vector machine (SVM) classifier is used to selectively smooth the lung border while minimizing the over-segmentation of adjacent regions. This automated method was tested on 233 computed tomography (CT) studies from the lung imaging database consortium (LIDC), representing 403 juxtapleural nodules. The approach obtained a 92.6% re-inclusion rate. Segmentation accuracy was further validated on 10 randomly selected CT series, finding a 0.3% average over-segmentation ratio and 2.4% under-segmentation rate when compared to manually segmented reference standards done by an expert.
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Affiliation(s)
- Shiwen Shen
- Department of Bioengineering, University of California, Los Angeles, CA, USA; Medical Imaging Informatics (MII) Group, Department of Radiological Sciences, University of California, Los Angeles, CA, USA.
| | - Alex A T Bui
- Medical Imaging Informatics (MII) Group, Department of Radiological Sciences, University of California, Los Angeles, CA, USA
| | - Jason Cong
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - William Hsu
- Medical Imaging Informatics (MII) Group, Department of Radiological Sciences, University of California, Los Angeles, CA, USA
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13
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Automatic segmentation of anatomical structures from CT scans of thorax for RTP. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2014; 2014:472890. [PMID: 25587349 PMCID: PMC4281476 DOI: 10.1155/2014/472890] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022]
Abstract
Modern radiotherapy techniques are vulnerable to delineation inaccuracies owing to the steep dose gradient around the target. In this aspect, accurate contouring comprises an indispensable part of optimal radiation treatment planning (RTP). We suggest a fully automated method to segment the lungs, trachea/main bronchi, and spinal canal accurately from computed tomography (CT) scans of patients with lung cancer to use for RTP. For this purpose, we developed a new algorithm for inclusion of excluded pathological areas into the segmented lungs and a modified version of the fuzzy segmentation by morphological reconstruction for spinal canal segmentation and implemented some image processing algorithms along with them. To assess the accuracy, we performed two comparisons between the automatically obtained results and the results obtained manually by an expert. The average volume overlap ratio values range between 94.30 ± 3.93% and 99.11 ± 0.26% on the two different datasets. We obtained the average symmetric surface distance values between the ranges of 0.28 ± 0.21 mm and 0.89 ± 0.32 mm by using the same datasets. Our method provides favorable results in the segmentation of CT scans of patients with lung cancer and can avoid heavy computational load and might offer expedited segmentation that can be used in RTP.
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14
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Mansoor A, Bagci U, Xu Z, Foster B, Olivier KN, Elinoff JM, Suffredini AF, Udupa JK, Mollura DJ. A generic approach to pathological lung segmentation. IEEE TRANSACTIONS ON MEDICAL IMAGING 2014; 33:2293-310. [PMID: 25020069 PMCID: PMC5542015 DOI: 10.1109/tmi.2014.2337057] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In this study, we propose a novel pathological lung segmentation method that takes into account neighbor prior constraints and a novel pathology recognition system. Our proposed framework has two stages; during stage one, we adapted the fuzzy connectedness (FC) image segmentation algorithm to perform initial lung parenchyma extraction. In parallel, we estimate the lung volume using rib-cage information without explicitly delineating lungs. This rudimentary, but intelligent lung volume estimation system allows comparison of volume differences between rib cage and FC based lung volume measurements. Significant volume difference indicates the presence of pathology, which invokes the second stage of the proposed framework for the refinement of segmented lung. In stage two, texture-based features are utilized to detect abnormal imaging patterns (consolidations, ground glass, interstitial thickening, tree-inbud, honeycombing, nodules, and micro-nodules) that might have been missed during the first stage of the algorithm. This refinement stage is further completed by a novel neighboring anatomy-guided segmentation approach to include abnormalities with weak textures, and pleura regions. We evaluated the accuracy and efficiency of the proposed method on more than 400 CT scans with the presence of a wide spectrum of abnormalities. To our best of knowledge, this is the first study to evaluate all abnormal imaging patterns in a single segmentation framework. The quantitative results show that our pathological lung segmentation method improves on current standards because of its high sensitivity and specificity and may have considerable potential to enhance the performance of routine clinical tasks.
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Xin Y, Song G, Cereda M, Kadlecek S, Hamedani H, Jiang Y, Rajaei J, Clapp J, Profka H, Meeder N, Wu J, Tustison NJ, Gee JC, Rizi RR. Semiautomatic segmentation of longitudinal computed tomography images in a rat model of lung injury by surfactant depletion. J Appl Physiol (1985) 2014; 118:377-85. [PMID: 25640150 DOI: 10.1152/japplphysiol.00627.2014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Quantitative analysis of computed tomography (CT) is essential to the study of acute lung injury. However, quantitative CT is made difficult by poor lung aeration, which complicates the critical step of image segmentation. To overcome this obstacle, this study sought to develop and validate a semiautomated, multilandmark, registration-based scheme for lung segmentation that is effective in conditions of poor aeration. Expiratory and inspiratory CT images were obtained in rats (n = 8) with surfactant depletion of incremental severity to mimic worsening aeration. Trained operators manually delineated the images to provide a comparative landmark. Semiautomatic segmentation originated from a single, previously segmented reference image obtained at healthy baseline. Deformable registration of the target images (after surfactant depletion) was performed using the symmetric diffeomorphic transformation model with B-spline regularization. Registration used multiple landmarks (i.e., rib cage, spine, and lung parenchyma) to minimize the effect of poor aeration. Then target images were automatically segmented by applying the calculated transformation function to the reference image contour. Semiautomatically and manually segmented contours proved to be highly similar in all aeration conditions, including those characterized by more severe surfactant depletion and expiration. The Dice similarity coefficient was over 0.9 in most conditions, confirming high agreement, irrespective of poor aeration. Furthermore, CT density-based measurements of gas volume, tissue mass, and lung aeration distribution were minimally affected by the method of segmentation. Moving forward, multilandmark registration has the potential to streamline quantitative CT analysis by enabling semiautomatic image segmentation of lungs with a broad range of injury severity.
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Affiliation(s)
- Yi Xin
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gang Song
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maurizio Cereda
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Stephen Kadlecek
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hooman Hamedani
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yunqing Jiang
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennia Rajaei
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Justin Clapp
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harrilla Profka
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Natalie Meeder
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jue Wu
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nicholas J Tustison
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, Virginia
| | - James C Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rahim R Rizi
- Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania
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Abstract
The diversity in appearance of diseased lung tissue makes automatic segmentation of lungs from CT with severe pathologies challenging. To overcome this challenge, we rely on contextual constraints from neighboring anatomies to detect and segment lung tissue across a variety of pathologies. We propose an algorithm that combines statistical learning with these anatomical constraints to seek a segmentation of the lung consistent with adjacent structures, such as the heart, liver, spleen, and ribs. We demonstrate that our algorithm reduces the number of failed detections and increases the accuracy of the segmentation on unseen test cases with severe pathologies.
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Gammon ST, Foje N, Brewer EM, Owers E, Downs CA, Budde MD, Leevy WM, Helms MN. Preclinical anatomical, molecular, and functional imaging of the lung with multiple modalities. Am J Physiol Lung Cell Mol Physiol 2014; 306:L897-914. [DOI: 10.1152/ajplung.00007.2014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In vivo imaging is an important tool for preclinical studies of lung function and disease. The widespread availability of multimodal animal imaging systems and the rapid rate of diagnostic contrast agent development have empowered researchers to noninvasively study lung function and pulmonary disorders. Investigators can identify, track, and quantify biological processes over time. In this review, we highlight the fundamental principles of bioluminescence, fluorescence, planar X-ray, X-ray computed tomography, magnetic resonance imaging, and nuclear imaging modalities (such as positron emission tomography and single photon emission computed tomography) that have been successfully employed for the study of lung function and pulmonary disorders in a preclinical setting. The major principles, benefits, and applications of each imaging modality and technology are reviewed. Limitations and the future prospective of multimodal imaging in pulmonary physiology are also discussed. In vivo imaging bridges molecular biological studies, drug design and discovery, and the imaging field with modern medical practice, and, as such, will continue to be a mainstay in biomedical research.
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Affiliation(s)
- Seth T. Gammon
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nathan Foje
- Department of Biological Sciences, Notre Dame Integrated Imaging Facility, Notre Dame, Indiana
| | - Elizabeth M. Brewer
- Department of Pediatrics Center for Cystic Fibrosis and Airways Disease Research, Emory University, Atlanta, Georgia
| | - Elizabeth Owers
- Department of Biological Sciences, Notre Dame Integrated Imaging Facility, Notre Dame, Indiana
| | - Charles A. Downs
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia; and
| | - Matthew D. Budde
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - W. Matthew Leevy
- Department of Biological Sciences, Notre Dame Integrated Imaging Facility, Notre Dame, Indiana
| | - My N. Helms
- Department of Pediatrics Center for Cystic Fibrosis and Airways Disease Research, Emory University, Atlanta, Georgia
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van Rikxoort EM, van Ginneken B. Automated segmentation of pulmonary structures in thoracic computed tomography scans: a review. Phys Med Biol 2014; 58:R187-220. [PMID: 23956328 DOI: 10.1088/0031-9155/58/17/r187] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Computed tomography (CT) is the modality of choice for imaging the lungs in vivo. Sub-millimeter isotropic images of the lungs can be obtained within seconds, allowing the detection of small lesions and detailed analysis of disease processes. The high resolution of thoracic CT and the high prevalence of lung diseases require a high degree of automation in the analysis pipeline. The automated segmentation of pulmonary structures in thoracic CT has been an important research topic for over a decade now. This systematic review provides an overview of current literature. We discuss segmentation methods for the lungs, the pulmonary vasculature, the airways, including airway tree construction and airway wall segmentation, the fissures, the lobes and the pulmonary segments. For each topic, the current state of the art is summarized, and topics for future research are identified.
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Affiliation(s)
- Eva M van Rikxoort
- Diagnostic Image Analysis Group, Department of Radiology, Radboud University Nijmegen Medical Centre, The Netherlands.
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Guo Y, Zhou C, Chan HP, Chughtai A, Wei J, Hadjiiski LM, Kazerooni EA. Automated iterative neutrosophic lung segmentation for image analysis in thoracic computed tomography. Med Phys 2013; 40:081912. [PMID: 23927326 PMCID: PMC3732305 DOI: 10.1118/1.4812679] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 06/09/2013] [Accepted: 06/12/2013] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Lung segmentation is a fundamental step in many image analysis applications for lung diseases and abnormalities in thoracic computed tomography (CT). The authors have previously developed a lung segmentation method based on expectation-maximization (EM) analysis and morphological operations (EMM) for our computer-aided detection (CAD) system for pulmonary embolism (PE) in CT pulmonary angiography (CTPA). However, due to the large variations in pathology that may be present in thoracic CT images, it is difficult to extract the lung regions accurately, especially when the lung parenchyma contains extensive lung diseases. The purpose of this study is to develop a new method that can provide accurate lung segmentation, including those affected by lung diseases. METHODS An iterative neutrosophic lung segmentation (INLS) method was developed to improve the EMM segmentation utilizing the anatomic features of the ribs and lungs. The initial lung regions (ILRs) were extracted using our previously developed EMM method, in which the ribs were extracted using 3D hierarchical EM segmentation and the ribcage was constructed using morphological operations. Based on the anatomic features of ribs and lungs, the initial EMM segmentation was refined using INLS to obtain the final lung regions. In the INLS method, the anatomic features were mapped into a neutrosophic domain, and the neutrosophic operation was performed iteratively to refine the ILRs. With IRB approval, 5 and 58 CTPA scans were collected retrospectively and used as training and test sets, of which 2 and 34 cases had lung diseases, respectively. The lung regions manually outlined by an experienced thoracic radiologist were used as reference standard for performance evaluation of the automated lung segmentation. The percentage overlap area (POA), the Hausdorff distance (Hdist), and the average distance (AvgDist) of the lung boundaries relative to the reference standard were used as performance metrics. RESULTS The proposed method achieved larger POAs and smaller distance errors than the EMM method. For the 58 test cases, the average POA, Hdist, and AvgDist were improved from 85.4±18.4%, 22.6±29.4 mm, and 3.5±5.4 mm using EMM to 91.2±6.7%, 16.0±11.3 mm, and 2.5±1.0 mm using INLS, respectively. The improvements were statistically significant (p<0.05). To evaluate the accuracy of the INLS method in the identification of the lung boundaries affected by lung diseases, the authors separately analyzed the performance of the proposed method on the cases with versus without the lung diseases. The results showed that the cases without lung diseases were segmented more accurately than the cases with lung diseases by both the EMM and the INLS methods, but the INLS method achieved better performance than the EMM method in both cases. CONCLUSIONS The new INLS method utilizing the anatomic features of the rib and lung significantly improved the accuracy of lung segmentation, especially for the cases affected by lung diseases. Improvement in lung segmentation will facilitate many image analysis tasks and CAD applications for lung diseases and abnormalities in thoracic CT, including automated PE detection.
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Affiliation(s)
- Yanhui Guo
- Department of Radiology, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Meng X, Qiang Y, Zhu S, Fuhrman C, Siegfried JM, Pu J. Illustration of the obstacles in computerized lung segmentation using examples. Med Phys 2012; 39:4984-91. [PMID: 22894423 DOI: 10.1118/1.4737023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Automated lung volume segmentation is often a preprocessing step in quantitative lung computed tomography (CT) image analysis. The objective of this study is to identify the obstacles in computerized lung volume segmentation and illustrate those explicitly using real examples. Awareness of these "difficult" cases may be helpful for the development of a robust and consistent lung segmentation algorithm. METHODS We collected a large diverse dataset consisting of 2768 chest CT examinations acquired on 2292 subjects from various sources. These examinations cover a wide range of diseases, including lung cancer, chronic obstructive pulmonary disease, human immunodeficiency virus, pulmonary embolism, pneumonia, asthma, and interstitial lung disease (ILD). The CT acquisition protocols, including dose, scanners, and reconstruction kernels, vary significantly. After the application of a "neutral" thresholding-based approach to the collected CT examinations in a batch manner, the failed cases were subjectively identified and classified into different subgroups. RESULTS Totally, 121 failed examinations are identified, corresponding to a failure ratio of 4.4%. These failed cases are summarized as 11 different subgroups, which is further classified into 3 broad categories: (1) failure caused by diseases, (2) failure caused by anatomy variability, and (3) failure caused by external factors. The failure percentages in these categories are 62.0%, 32.2%, and 5.8%, respectively. CONCLUSIONS The presence of specific lung diseases (e.g., pulmonary nodules, ILD, and pneumonia) is the primary issue in computerized lung segmentation. The segmentation failures caused by external factors and anatomy variety are relatively low but unavoidable in practice. It is desirable to develop robust schemes to handle these issues in a single pass when a large number of CT examinations need to be analyzed.
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Affiliation(s)
- Xin Meng
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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21
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Wang S, Summers RM. Machine learning and radiology. Med Image Anal 2012; 16:933-51. [PMID: 22465077 PMCID: PMC3372692 DOI: 10.1016/j.media.2012.02.005] [Citation(s) in RCA: 341] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 01/05/2012] [Accepted: 02/12/2012] [Indexed: 02/06/2023]
Abstract
In this paper, we give a short introduction to machine learning and survey its applications in radiology. We focused on six categories of applications in radiology: medical image segmentation, registration, computer aided detection and diagnosis, brain function or activity analysis and neurological disease diagnosis from fMR images, content-based image retrieval systems for CT or MRI images, and text analysis of radiology reports using natural language processing (NLP) and natural language understanding (NLU). This survey shows that machine learning plays a key role in many radiology applications. Machine learning identifies complex patterns automatically and helps radiologists make intelligent decisions on radiology data such as conventional radiographs, CT, MRI, and PET images and radiology reports. In many applications, the performance of machine learning-based automatic detection and diagnosis systems has shown to be comparable to that of a well-trained and experienced radiologist. Technology development in machine learning and radiology will benefit from each other in the long run. Key contributions and common characteristics of machine learning techniques in radiology are discussed. We also discuss the problem of translating machine learning applications to the radiology clinical setting, including advantages and potential barriers.
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Affiliation(s)
- Shijun Wang
- Imaging Biomarkers and Computer-Aided Diagnosis Laboratory, Radiology and Imaging Sciences, National Institutes of Health Clinical Center, Building 10 Room 1C224D MSC 1182, Bethesda, MD 20892-1182
| | - Ronald M. Summers
- Imaging Biomarkers and Computer-Aided Diagnosis Laboratory, Radiology and Imaging Sciences, National Institutes of Health Clinical Center, Building 10 Room 1C224D MSC 1182, Bethesda, MD 20892-1182
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22
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Sun S, Bauer C, Beichel R. Automated 3-D segmentation of lungs with lung cancer in CT data using a novel robust active shape model approach. IEEE TRANSACTIONS ON MEDICAL IMAGING 2012; 31:449-60. [PMID: 21997248 PMCID: PMC3657761 DOI: 10.1109/tmi.2011.2171357] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Segmentation of lungs with (large) lung cancer regions is a nontrivial problem. We present a new fully automated approach for segmentation of lungs with such high-density pathologies. Our method consists of two main processing steps. First, a novel robust active shape model (RASM) matching method is utilized to roughly segment the outline of the lungs. The initial position of the RASM is found by means of a rib cage detection method. Second, an optimal surface finding approach is utilized to further adapt the initial segmentation result to the lung. Left and right lungs are segmented individually. An evaluation on 30 data sets with 40 abnormal (lung cancer) and 20 normal left/right lungs resulted in an average Dice coefficient of 0.975±0.006 and a mean absolute surface distance error of 0.84±0.23 mm, respectively. Experiments on the same 30 data sets showed that our methods delivered statistically significant better segmentation results, compared to two commercially available lung segmentation approaches. In addition, our RASM approach is generally applicable and suitable for large shape models.
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Affiliation(s)
- Shanhui Sun
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA 52242 USA
| | - Christian Bauer
- Department of Electrical and Computer Engineering, The University of Iowa, Iowa City, IA 52242 USA
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Tustison NJ, Cook TS, Song G, Gee JC. Pulmonary kinematics from image data: a review. Acad Radiol 2011; 18:402-17. [PMID: 21377592 DOI: 10.1016/j.acra.2010.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 09/02/2010] [Accepted: 10/25/2010] [Indexed: 10/18/2022]
Abstract
The effects of certain lung pathologies include alterations in lung physiology negatively affecting pulmonary compliance. Current approaches to diagnosis and treatment assessment of lung disease commonly rely on pulmonary function testing. Such testing is limited to global measures of lung function, neglecting regional measurements, which are critical for early diagnosis and localization of disease. Increased accessibility to medical image acquisition strategies with high spatiotemporal resolution coupled with the development of sophisticated intensity-based and geometric registration techniques has resulted in the recent exploration of modeling pulmonary motion for calculating local measures of deformation. In this review, the authors provide a broad overview of such research efforts for the estimation of pulmonary deformation. This includes discussion of various techniques, current trends in validation approaches, and the public availability of software and data resources.
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Multi-stage learning for robust lung segmentation in challenging CT volumes. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2011; 14:667-74. [PMID: 22003757 DOI: 10.1007/978-3-642-23626-6_82] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Simple algorithms for segmenting healthy lung parenchyma in CT are unable to deal with high density tissue common in pulmonary diseases. To overcome this problem, we propose a multi-stage learning-based approach that combines anatomical information to predict an initialization of a statistical shape model of the lungs. The initialization first detects the carina of the trachea, and uses this to detect a set of automatically selected stable landmarks on regions near the lung (e.g., ribs, spine). These landmarks are used to align the shape model, which is then refined through boundary detection to obtain fine-grained segmentation. Robustness is obtained through hierarchical use of discriminative classifiers that are trained on a range of manually annotated data of diseased and healthy lungs. We demonstrate fast detection (35s per volume on average) and segmentation of 2 mm accuracy on challenging data.
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Pu J, Paik DS, Meng X, Roos JE, Rubin GD. Shape "break-and-repair" strategy and its application to automated medical image segmentation. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2011; 17:115-24. [PMID: 21071791 PMCID: PMC3099140 DOI: 10.1109/tvcg.2010.56] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In three-dimensional medical imaging, segmentation of specific anatomy structure is often a preprocessing step for computer-aided detection/diagnosis (CAD) purposes, and its performance has a significant impact on diagnosis of diseases as well as objective quantitative assessment of therapeutic efficacy. However, the existence of various diseases, image noise or artifacts, and individual anatomical variety generally impose a challenge for accurate segmentation of specific structures. To address these problems, a shape analysis strategy termed "break-and-repair" is presented in this study to facilitate automated medical image segmentation. Similar to surface approximation using a limited number of control points, the basic idea is to remove problematic regions and then estimate a smooth and complete surface shape by representing the remaining regions with high fidelity as an implicit function. The innovation of this shape analysis strategy is the capability of solving challenging medical image segmentation problems in a unified framework, regardless of the variability of anatomical structures in question. In our implementation, principal curvature analysis is used to identify and remove the problematic regions and radial basis function (RBF) based implicit surface fitting is used to achieve a closed (or complete) surface boundary. The feasibility and performance of this strategy are demonstrated by applying it to automated segmentation of two completely different anatomical structures depicted on CT examinations, namely human lungs and pulmonary nodules. Our quantitative experiments on a large number of clinical CT examinations collected from different sources demonstrate the accuracy, robustness, and generality of the shape "break-and-repair" strategy in medical image segmentation.
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Affiliation(s)
- Jiantao Pu
- Department of Radiology and Department of Bioengineering, University of Pittsburgh, 3362 Fifth Ave, Pittsburgh, PA 15213
| | - David S. Paik
- Department of Radiology, Stanford University, 300 Pasteur Dr., Stanford, CA 94305
| | - Xin Meng
- Department of Structural Biology, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA 15260
| | - Justus E. Roos
- Department of Radiology, Stanford University, 300 Pasteur Dr., Stanford, CA 94305
| | - Geoffrey D. Rubin
- Department of Radiology, Stanford University, 300 Pasteur Dr., Stanford, CA 94305
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Academic Radiology: A Decade of Change. Acad Radiol 2009. [DOI: 10.1016/j.acra.2009.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Wang J, Li F, Li Q. Automated segmentation of lungs with severe interstitial lung disease in CT. Med Phys 2009; 36:4592-9. [PMID: 19928090 PMCID: PMC2771715 DOI: 10.1118/1.3222872] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/12/2009] [Accepted: 08/13/2009] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Accurate segmentation of lungs with severe interstitial lung disease (ILD) in thoracic computed tomography (CT) is an important and difficult task in the development of computer-aided diagnosis (CAD) systems. Therefore, we developed in this study a texture analysis-based method for accurate segmentation of lungs with severe ILD in multidetector CT scans. METHODS Our database consisted of 76 CT scans, including 31 normal cases and 45 abnormal cases with moderate or severe ILD. The lungs in three selected slices for each CT scan were first manually delineated by a medical physicist, and then confirmed or revised by an expert chest radiologist, and they were used as the reference standard for lung segmentation. To segment the lungs, we first employed a CT value thresholding technique to obtain an initial lung estimate, including normal and mild ILD lung parenchyma. We then used texture-feature images derived from the co-occurrence matrix to further identify abnormal lung regions with severe ILD. Finally, we combined the identified abnormal lung regions with the initial lungs to generate the final lung segmentation result. The overlap rate, volume agreement, mean absolute distance (MAD), and maximum absolute distance (dmax) between the automatically segmented lungs and the reference lungs were employed to evaluate the performance of the segmentation method. RESULTS Our segmentation method achieved a mean overlap rate of 96.7%, a mean volume agreement of 98.5%, a mean MAD of 0.84 mm, and a mean dmax of 10.84 mm for all the cases in our database; a mean overlap rate of 97.7%, a mean volume agreement of 99.0%, a mean MAD of 0.66 mm, and a mean dmax of 9.59 mm for the 31 normal cases; and a mean overlap rate of 96.1%, a mean volume agreement of 98.1%, a mean MAD of 0.96 mm, and a mean dmax of 11.71 mm for the 45 abnormal cases with ILD. CONCLUSIONS Our lung segmentation method provided accurate segmentation results for abnormal CT scans with severe ILD and would be useful for developing CAD systems for quantification, detection, and diagnosis of ILD.
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Affiliation(s)
- Jiahui Wang
- Department of Radiology, Duke University, 2424 Erwin Road, Suite 302, Durham, North Carolina 27705, USA
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van Rikxoort EM, de Hoop B, Viergever MA, Prokop M, van Ginneken B. Automatic lung segmentation from thoracic computed tomography scans using a hybrid approach with error detection. Med Phys 2009; 36:2934-47. [DOI: 10.1118/1.3147146] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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