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研究生: 李駿賢
Chun-Hsien Lee
論文名稱: 以圓柱採樣訓練深度神經網絡改進頭頸部電腦斷層掃描的骨骼偵測和分割
Cylindrical Sampling for Deep Neural Network Training to Improve Bone Detection and Segmentation in Head and Neck Computed Tomography Datasets
指導教授: 黃輝揚
Hui-Yang Huang
口試委員:
學位類別: 碩士
Master
系所名稱: 生醫理工學院 - 生醫科學與工程學系
Department of Biomedical Sciences and Engineering
論文出版年: 2022
畢業學年度: 110
語文別: 英文
論文頁數: 68
中文關鍵詞: 電腦斷層血管造影語義分割下顎骨自動分割脊椎自動分割
外文關鍵詞: Computed Tomography Angiography, Automatic Mandible Segmentation, Automatic Vertebra Segmentation
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  • 減骨圖像處理技術常用於斷層掃描血管造影 (CTA) 以協助臨床診斷,近年來深度學習技術的蓬勃發展,通過採用由圖形處理器 (GPU) 實現的深度卷積神經網絡模型可以進一步改進減骨 CTA。監督式學習已被證明是有效訓練人工智能分析醫學圖像的方法,其中標記數據集的品質在模型收斂速度中扮演至關重要的作用。然而,大多數現有方法在標記醫學圖像方面的一個主要弱點是需要領域專家知識。此外,標記“大數據”所需的極高時間成本使得三維 (3D) 醫學數據標記成為一項極具挑戰性的任務。由於合格的專家人數有限和 3D 數據註釋動脈和靜脈血管的困難度高。標記 CTA 血管在現實環境下難以實現。相比之下,標記CTA骨骼是一種更可行的方法。在這項研究中,我們提出了一種圓柱採樣策略,以幫助非專家標記下頜骨和脊柱以進行電腦斷層掃描 (CT)的標記與機器學習訓練。它利用了相對於身體縱軸的準解剖對稱性。這種圓柱採樣方法允許生成帶有泛解剖地標的 2D 採樣掃描,這些解剖地標是透過沿縱軸有較佳的解剖結構連續性旋轉不同角度中得出的。本研究包含 20 個電腦斷層掃描血管造影數據集, 使用我們提議的圓柱採樣掃描方法以手動或自動標記C1、C2脊柱骨和下頜骨,並記錄和比較每個骨骼的標記時間。在圖像標記過程之後,我們使用以 FPN-ResNeXt 為主幹的深度學習語義分割Unet模型,將所提出的圓柱掃描與傳統(橫向、矢狀和冠狀)掃描做機器學習收斂性的比較分析。隨機選擇15個CTA數據(75%)作為訓練集,其餘5個(25%)作為測試集,實驗分別用 1、5、10 和 15 個CTA數據訓練模型,每個實驗分別重複5次。總體而言,該神經網絡模型在圓柱、橫向、矢狀和冠狀掃描中分別未能收斂 1 (5%)、12 (60%)、1 (5%) 和 5 (25%) 次。圓柱採樣方法在 C1、C2 和下頜骨分割中分別產生了 91.3%、92.8% 和 93.8% 的最高測試 F1 分數。用於標記下頜骨的時間分別為,每個圓柱採樣的CTA數據約需要 90 分鐘而每個橫向採樣的CTA數據則約需要190分鐘。實驗結果顯示,我們所提出的電腦斷層掃描圓柱採樣方法不僅減少了標記所需時間並且可以訓練出更準確的骨骼分割深度學習神經網絡模型。


    Bone-subtraction is an image processing technique that is often used in clinical settings to enhance computed tomography angiography (CTA) interpretation. With the newly developed deep learning technology, bone-subtraction CTA can potentially be further improved by adopting deep convolutional neural network (CNN) models implemented with advanced graphic processing units (GPU). Supervised learning has been proven to be an effective approach to creating artificial intelligence for medical image analysis, where the quality of labeled datasets plays the essential role in the speed of model convergence. However, a major drawback of most existing approaches in labeling medical images is that domain expert knowledge is required. Further, the extremely high time cost for labeling “big data” has made three dimensional (3D) medical data labeling a challenging task. Labeling vessels in CTA is difficult to achieve in practice due to shortage of qualified experts and the intrinsic difficulty in annotating arterial and venous vessels in 3D data. In contrast, labeling bones is a more feasible approach. In this study, we propose a cylindrical sampling strategy to assist non-experts in labeling mandible and spine for computed tomography (CT) scans. It takes advantage of the quasi-anatomical symmetry in respective to the body’s longitudinal axis. This cylindrical sampling approach allows generating 2D resampled scans with pan anatomical landmarks which are derived from the continuum of anatomical structures by rotating different angles along the longitudinal axis. Twenty computed tomography angiography datasets were included in this study. C1, C2 spinal bones, and mandibles were manually or automatically labeled by using the proposed cylindrical resampling scans. The labeling time for each bone was recorded and compared. After the image labeling process, we also conducted an experiment in comparing the convergency of the proposed cylindrical scans with traditional (transverse, sagittal, and coronal) scans using a deep learning semantic segmentation Unet model with an FPN-ResNeXt backbone. Fifteen subjects (75%) were randomly selected as the training set, and the remaining 5 subjects (25%) were used as the test set. The model was trained with 1, 5, 10, and 15 subjects respectively. The experiment was repeated for 5 times. In total, the model failed to converge 1 (5%), 12 (60%), 1 (5%), and 5 (25%) times for cylindrical, transverse, sagittal, and coronal scans respectively. The cylindrical approach generated the highest test F1-scores of 91.3%, 92.8%, and 93.8% in C1, C2, and mandible segmentation respectively. The time used in labeling cylindrical and transverse mandible scans was 90 and 190 minutes per subject respectively. The experimental results show that the proposed cylindrical sampling method for head and neck CTA not only reduces the labeling time but also achieves better segmentation of bones.

    中文摘要 i Abstract ii Table of contents v List of Tables vii List of Figures viii Chapter 1 Introduction 1 Chapter 2 Literature Review 5 2.1 Sematic Segmentation 5 2.2 Metal Artifact Reduction 6 2.3 Computer-Aided Diagnosis (CAD) 7 2.4 Application of Anatomical Structure Segmentation 8 2.4.1 Mandible Segmentation 8 2.4.2 Spine Segmentation 9 2.5 The Convergence of Deep Learning 9 Chapter 3 Data Preprocessing and Annotation 11 3.1 Head and Neck Computed Tomography Angiography 11 3.2 Data Sampling Methods 12 3.2.1 The Conventional Sampling in Computed Tomography 13 3.2.2 Cylindrical Sampling 14 3.3 Mandible and Spine Segmentation Labeling 17 3.3.1 Mandible Segmentation Labeling 17 3.3.2 Spine Segmentation Labeling 19 3.4 3D Reconstruction Strategy and Mask Augmentation 19 Chapter 4 Software Implementation and Experimental Design 23 4.1 Software Implementation 23 4.2 Experimental Design 23 4.2.1 Mask R-CNN for Mandible Segmentation (Exp I.) 24 4.2.2 FPN-ResNeXt for segmentation of three different bones (Exp II.) 26 4.3 Statistical Analysis 28 Chapter 5 Results 30 Chapter 6 Discussion 42 6.1 Cases of Misjudgment in Experiments I and II 42 6.2 The Labeling Strategy of Spine 45 6.3 Model Training and Bone Mask Labeling Time Comparison 47 6.4 Bone Segmentation for Contrast Enhanced Images 48 6.5 Study Limitations 49 Chapter 7 Conclusion 50 References 51

    [1] Saxena A, Ng EYK, Lim ST. Imaging modalities to diagnose carotid artery stenosis: progress and prospect. Biomed Eng Online. 2019 May 28;18(1):66. doi: 10.1186/s12938-019-0685-7. PMID: 31138235; PMCID: PMC6537161.
    [2] Xu, G., Ma, M., Liu, X. & Hankey, G. J. Is there a stroke belt in China and
    why? Stroke 44, 1775–1783 (2013).
    [3] Markus HS, van der Worp HB, Rothwell PM. Posterior circulation ischaemic stroke and transient ischaemic attack: diagnosis, investigation, and secondary prevention. Lancet Neurol. 2013;12(10):989-998. doi:10.1016/S1474-4422(13)70211-4.
    [4] Stayman AN, Nogueira RG, Gupta R. A systematic review of stenting and angioplasty of symptomatic extracranial vertebral artery stenosis. Stroke. 2011;42(8):2212-2216. doi:10.1161/STROKEAHA.110.611459
    [5] Compter A, van der Worp HB, Schonewille WJ, et al. Stenting versus medical treatment in patients with symptomatic vertebral artery stenosis: a randomised open-label phase 2 trial. Lancet Neurol. 2015;14(6):606-614. doi:10.1016/S1474-4422(15)00017-4
    [6] Markus HS, Larsson SC, Kuker W, et al. Stenting for symptomatic vertebral artery stenosis: The Vertebral Artery Ischaemia Stenting Trial. Neurology. 2017;89(12):1229- 1236. doi:10.1212/WNL.0000000000004385.
    [7] Hilkewich, M. W. Written observations as a part of computed tomography
    angiography post processing by medical radiation technologists: a pilot
    project. J. Med Imaging Radiat. Sci. 45, 31–36 (2014).
    [8] Wen-Hsiang Cheng, Hui-Yang Huang. Using Deep Learning to Generate Bone Subtraction CT Angiography for Improving Vertebral Artery Segmentation
    [9] McBee, M. P. et al. Deep learning in radiology. Acad. Radio. 25, 1472–1480
    (2018).
    [10] Byrne, N.; Velasco Forte, M.; Tandon, A.; Valverde, I.; Hussain, T. A Systematic Review of Image Segmentation Methodology, Used in the Additive Manufacture of Patient-Specific 3D Printed Models of the Cardiovascular System. JRSM Cardiovasc. Dis. 2016, 5, 2048004016645467.
    [11] M. David Jenkins, T. A. Carr, M. I. Iglesias, T. Buggy and G. Morison, "A Deep Convolutional Neural Network for Semantic Pixel-Wise Segmentation of Road and Pavement Surface Cracks," 2018 26th European Signal Processing Conference (EUSIPCO), 2018, pp. 2120-2124, doi: 10.23919/EUSIPCO.2018.8553280.
    [12] Huang C, Davis L, Townshend J (2002) An assessment of support vector machines for land cover classification. Int J Remote Sens 23(4):725–749
    [13] Moon N, Bullitt E, Van Leemput K, Gerig G (2002) Automatic brain and tumor segmentation. Med Image Comput Comput Assist Interv MICCAI 2002:372–379
    [14] Qiu B, Guo J, Kraeima J, Glas HH, Borra RJH, Witjes MJH, van Ooijen PMA. Automatic segmentation of the mandible from computed tomography scans for 3D virtual surgical planning using the convolutional neural network. Phys Med Biol. 2019 Sep 5;64(17):175020. doi: 10.1088/1361-6560/ab2c95. PMID: 31239411.
    [15] Fritsch J, Kuehnl T, Geiger A (2013) A new performance measure and evaluation benchmark for road detection algorithms. In: International conference on intelligent transportation systems (ITSC)
    [16] Menze M, Geiger A (2015) Object scene flow for autonomous vehicles. In: Proceedings of the conference on computer vision and pattern recognition (CVPR
    [17] Cordts M, Omran M, Ramos S, Rehfeld T, Enzweiler M, Benenson R, Franke U, Roth S, Schiele B (2016) The cityscapes dataset for semantic urban scene understanding. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp 3213–3223
    [18] Nicolas Vandenbroucke, Ludovic Macaire, Jack-Gérard Postaire, Color image segmentation by pixel classification in an adapted hybrid color space. Application to soccer image analysis, Computer Vision and Image Understanding, Volume 90, Issue 2, 2003, Pages 190-216, ISSN 1077-3142, https://doi.org/10.1016/S1077-3142(03)00025-0.
    [19] Lowe DG (2004) Distinctive image features from scale-invariant keypoints. Int J Comput Vis 60(2):91–110
    [20] Zheng L, Li G, Bao Y (2010) Improvement of grayscale image 2D maximum entropy threshold segmentation method. In: 2010 international conference on logistics systems and intelligent management, vol 1. IEEE, pp 324–328
    [21] S. Na, L. Xumin and G. Yong, "Research on k-means Clustering Algorithm: An Improved k-means Clustering Algorithm," 2010 Third International Symposium on Intelligent Information Technology and Security Informatics, 2010, pp. 63-67, doi: 10.1109/IITSI.2010.74
    [22] Long J, Shelhamer E, Darrell T (2014) Fully convolutional networks for semantic segmentation. IEEE Trans Pattern Anal Mach Intell 79(10):1337–1342
    [23] Chen LC, Papandreou G, Kokkinos I, Murphy K, Yuille AL (2016b) Deeplab: semantic image segmentation with deep convolutional nets, atrous convolution, and fully connected crfs. arXiv preprint arXiv:1606.00915
    [24] Olaf Ronneberger, Philipp Fischer, Thomas Brox, U-Net: Convolutional Networks for Biomedical Image Segmentation. arXiv:1505.04597
    [25] Liang-Chieh Chen, Yukun Zhu, George Papandreou, Florian Schroff,
    Hartwig Adam. Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation. arXiv:1802.02611v3
    [26] Kaiming He, Georgia Gkioxari, Piotr Dollár, Ross Girshick. Mask R-CNN.
    arXiv:1703.06870v3
    [27] Lee MJ, Kim S, Lee SA, et al. Overcoming artifacts from me-tallic orthopedic implants at high-field-strength MR imaging and multidetector CT. RadioGraphics 2007;27(3):791–803.
    [28] Barmeir E, Dubowitz B, Roffman M. Computed tomogra-phy in the assessment and planning of complicated total hip replacement. Acta Orthop Scand 1982;53(4):597–604.
    [29] Kalender WA, Hebel R, Ebersberger J. Reduction of CT artifacts caused by metallic implants. Radiology 1987;164(2):576–577
    [30] Wellenberg RHH, Hakvoort ET, Slump CH, Boomsma MF, Maas M, Streekstra GJ. Metal artifact reduction techniques in musculoskeletal CT-imaging. Eur J Radiol. 2018 Oct;107:60-69. doi: 10.1016/j.ejrad.2018.08.010. Epub 2018 Aug 12. PMID: 30292274.
    [31] Kunio Doi, Computer-aided diagnosis in medical imaging: Historical review, current status and future potential, Computerized Medical Imaging and Graphics, Volume 31, Issues 4–5, 2007, Pages 198-211, ISSN 0895-6111,
    [32] de Dombal F T, Leaper D J, Staniland J R, McCann A P, Horrocks J C. Computer-aided Diagnosis of Acute Abdominal Pain Br Med J 1972; 2 :9 doi:10.1136/bmj.2.5804.9
    [33] Kunio Doi, Heber MacMahon, Shigehiko Katsuragawa, Robert M Nishikawa, Yulei Jiang, Computer-aided diagnosis in radiology: potential and pitfalls, European Journal of Radiology, Volume 31, Issue 2, 1999, Pages 97-109, ISSN 0720-048X,
    [34] Alex Krizhevsky, Ilya Sutskever, and Geoffrey E. Hinton. 2017. ImageNet
    classification with deep convolutional neural networks. Commun. ACM 60, 6 (June
    2017), 84–90. DOI:https://doi.org/10.1145/3065386
    [35] Kaiming He, Xiangyu Zhang, Shaoqing Ren, Jian Sun.Deep Residual Learning for Image Recognition. arXiv:1512.03385
    [36] O. Ronneberger, P. Fischer, T. Brox. U-net: Convolutional networks for biomedical image segmentation. International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Springer (2015), pp. 234-241, 10.1007/978-3-319-24574-4_28
    [37] Zhu, W.; Huang, Y.; Tang, H.; Qian, Z.; Du, N.; Fan, W.; Xie, X. AnatomyNet: Deep 3D Squeeze-and-excitation U-Nets for fast and fully automated whole-volume anatomical segmentation. arXiv 2018, arXiv:1808.05238.
    [38] Qiu B, Guo J, Kraeima J, Glas HH, Borra RJH, Witjes MJH, van Ooijen PMA. Automatic segmentation of the mandible from computed tomography scans for 3D virtual surgical planning using the convolutional neural network. Phys Med Biol. 2019 Sep 5;64(17):175020. doi: 10.1088/1361-6560/ab2c95. PMID: 31239411.
    [39] Sekuboyina, A., Kukačka, J., Kirschke, J.S., Menze, B.H., Valentinitsch, A. (2018). Attention-Driven Deep Learning for Pathological Spine Segmentation. In: Glocker, B., Yao, J., Vrtovec, T., Frangi, A., Zheng, G. (eds) Computational Methods and Clinical Applications in Musculoskeletal Imaging. MSKI 2017. Lecture Notes in Computer Science(), vol 10734. Springer, Cham. https://doi.org/10.1007/978-3-319-74113-0_10
    [40] Kadoury, S., Labelle, H., Paragios, N.: Spine segmentation in medical images using manifold embeddings and higher-order MRFs. IEEE Trans. Med. Imaging 32(7), 1227–1238 (2013)
    [41] Lootus, M., Kadir, T., Zisserman, A.: Automated radiological grading of spinal MRI. In: Yao, J., et al. (eds.) CSI 2014. LNCVB, vol. 20, pp. 119–130. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-14148-0_11
    [42] Glocker, B., Feulner, J., Criminisi, A., Haynor, D., Konukoglu, E.: Automatic localization and identification of vertebrae in arbitrary field-of-view CT scans. In: Ayache, N., et al. (eds.) Proceedings of 15th International Conference on Medical Image Computing and Computer-Assisted Intervention – MICCAI 2012. LNCS, vol. 7512, pp. 590–598. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33454-2_73
    [43] Chen, H., Shen, C., Qin, J., Ni, D., Shi, L., Cheng, J.C.Y., Heng, P.-A.: Automatic localization and identification of vertebrae in Spine CT via a joint learning model with deep neural networks. In: Navab, N., Hornegger, J., Wells, W.M., Frangi, A.F. (eds.) MICCAI 2015. LNCS, vol. 9349, pp. 515–522. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-24553-9_63
    [44] Adam: A Method for Stochastic Optimization. Diederik P. Kingma, Jimmy Ba. Published as a conference paper at the 3rd International Conference for Learning Representations, San Diego, 2015. arXiv:1412.6980 [cs.LG]
    [45] On the importance of initialization and momentum in deep learning. Ilya Sutskever, James Martens, George Dahl, Geoffrey Hinton. Proceedings of the 30th International Conference on Machine Learning, PMLR 28(3):1139-1147, 2013.
    [46] Adaptive Subgradient Methods for Online Learning and Stochastic Optimization. John Duchi, Elad Hazan, Yoram Singer. Journal of Machine Learning Research 12 (2011) 2121-2159
    [47] On Loss Functions for Deep Neural Networks in Classification. Katarzyna Janocha, Wojciech Marian Czarnecki. arXiv:1702.05659 [cs.LG]
    [48] Massimo Salvi, U. Rajendra Acharya, Filippo Molinari, Kristen M. Meiburger, The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis, Computers in Biology and Medicine, Volume 128, 2021, 104129, ISSN 0010-4825, https://doi.org/10.1016/j.compbiomed.2020.104129.
    [49] Yu, F. & Koltun, V. (2015). Multi-scale context aggregation by dilated convolutions, arXiv preprint arXiv:1511.07122 .
    [50] Zhao, H., Shi, J., Qi, X., Wang, X. & Jia, J. (2017). Pyramid scene parsing network, IEEE Conf. on Computer Vision and Pattern Recognition (CVPR), pp. 2881–2890.

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