Faculdade de Engenharia da Universidade do Porto Computational Analysis of Magnetic Resonance Images of the Upper Airways: Algorithms and Applications Jessica Condesso Delmoral February 2015 ii Computational Analysis of Magnetic Resonance Images of the Upper Airways: Algorithms and Applications Jessica Condesso Delmoral Monograph of Preparation for Dissertation on Integrated Master in Bioengineering – Branch of Biomedical Engineering Faculty of Engineering of the University of Porto Supervisor: Prof. Doutor João Manuel R. S. Tavares Prof. Auxiliar do Departamento de Engenharia Mecânica e Gestão Industrial Faculdade de Engenharia da Universidade do Porto Co-Supervisor: Dra. Sandra Rua Ventura Escola Superior de Tecnologia da Saúde do Porto February 2015 iii iv Abstract This monograph report falls within the issues addressed in Computer Vision, specifically under the field of three-dimensional (3D) Reconstruction of anatomically relevant structures in medical images. The tasks of imaging and quantification of the tongue’s anatomy is of great relevance on applications of further study and analysis of the incomplete knowledge of the anatomic and physiological mechanisms that govern it, the physiology included in the tasks of breathing, swallowing and speech production, and finally its application to surgical planning, post-operative rehabilitation and the study of new adaptations acquired upon possible changes in function of pathological origin, such as in the presence of tongue cancer, surgical intervention or aging. The sparse knowledge of these mechanisms represents a prominent gap in the established anatomy of the human body. However, advances under the Computer Vision field over the years, have allowed the development of new tools of analysis that can be applied to medical images of the human body. Accordingly, this can fulfill the gap on the understanding of the human tongue functionality, using the improvement of areas of image reconstruction and segmentation. For the study of soft tissues, the state of the art technic for visualization is Magnetic Resonance imaging (MRI), since it provides the best image contrast of soft tissues such as the muscular tissue of the tongue. The state of the art technics of image processing and computer vision applied in the study of the human tongue are described in this report as well as the different stages of this analysis in order to obtain the best quality on analysis and reconstruction that include various technics of image registration using Mutual Information similarity measure, and segmentation though supervised and semi-supervised seed growing, landmark-based procedures, among others. v Contents ABSTRACT ..................................................................................................................... V CONTENTS ................................................................................................................... VI LIST OF FIGURES ......................................................................................................... VIII LIST OF TABLES ............................................................................................................ IX NOMENCLATURE .......................................................................................................... X - INTRODUCTION .......................................................................................... 1 1.1. MOTIVATION ............................................................................................................ 2 1.2. OBJECTIVES ............................................................................................................... 2 1.3. REPORT ORGANIZATION .............................................................................................. 3 HUMAN UPPER AIRWAY ANATOMY .............................................................. 5 2.1. ANATOMY OF THE TONGUE .......................................................................................... 6 2.2. NEUROPHYSIOLOGICAL CONTROL OF THE TONGUE ......................................................... 12 2.3. SPEECH PRODUCTION, RESPIRATION AND DEGLUTITION ................................................. 13 2.4. FINAL CONSIDERATIONS ............................................................................................ 16 - MAGNETIC RESONANCE IMAGING IN THE CONTEXT OF UPPER AIRWAY STRUCTURAL COMPONENTS .............................................................................................. 19 3.1. INTRODUCTION ........................................................................................................ 19 3.2. BASIC PRINCIPLES IN MAGNETIC RESONANCE IMAGING .................................................. 20 3.3. RELAXATION TIMES .................................................................................................. 21 3.4. K-SPACE ................................................................................................................. 22 3.5. CONTRAST AND TISSUE SIGNAL IN RM ......................................................................... 22 3.5.1. TR, TE and Pulse Sequences ............................................................................. 23 3.6. LIMITATIONS AND DETERMINANT CONSIDERATIONS ....................................................... 23 - STATE OF THE ART .................................................................................... 25 4.1 INTRODUCTION ............................................................................................................ 25 4.2 STATE OF THE ART ........................................................................................................ 25 4.3 MRI 3D VOLUMES IMAGE SEGMENTATION TECHNICS ......................................................... 27 4.3.1. DICOM Standard Overview and Volumetric Data ........................................... 27 4.3.2. Slice-to-Volume Registration ........................................................................... 29 vi 4.3.3. Super Resolution Volumes ............................................................................... 30 4.3.4. Segmentation .................................................................................................. 30 4.4 3D RECONSTRUCTION .................................................................................................. 32 – FINAL CONCLUSIONS AND FUTURE PERSPECTIVES .................................... 33 5.1. FINAL CONCLUSIONS ................................................................................................ 33 5.2. FUTURE PERSPECTIVES .............................................................................................. 33 REFERENCES ................................................................................................................ 35 vii List of Figures Figure 2.1 - MR Midsagittal image (slice) indicating the vocal tract’s structures. From Rua Ventura et al. (2011). ............................................................... 5 Figure 2.2 - Side view of the skull. The styloid process is just posterior to the mandible........................................................................................... 6 Figure 2.3 - Tongue’s attachments and neighboring structures in a sagittal anatomical view. From Gray (1918). .......................................................... 7 Figure 2.4 - Extrinsic muscle of the tongue. Styloglossus visible at center top (in red). From Gray1019 modified by Uwe Gille. ................................................ 9 Figure 2.5 - Muscles of the tongue, from Takemoto (2001). GG genioglossus, T transversus, V verticalis, HG hyoglossus, IL inferior longitudinalis, S superior longitudinalis, PG palatoglossus, SG Styloglossus. ......................................... 11 Figure 2.6 - Tongue contour extracted from midsagittal images, during production of vocalic sounds present in Portuguese language. From (Ventura et al., 2008). ..... 14 Figure 2.7 - Abd-El-Malek (1955) illustration of the preparatory stage of mastication. ...................................................................................... 15 Figure 2.8 - Abd-El-Malek (1955) illustration of the throwing stage of mastication. ..................................................................................................... 15 Figure 2.9 - Abd-El-Malek (1955) illustration of the guarding stage of mastication. ..................................................................................................... 15 Figure 2.10 - Abd-El-Malek (1955) illustration of the initial stage of deglutition. 16 Figure 3.1 - Spin orientation of atoms within tissues under no external field (a), and under a horizontal external field (b). Adapted from (Rinck, 2001). ..................... 20 Figure 3.2 - Representation of equilibrium magnetization vector B0, and the modulated magnetic RF field, at Larmor frequency, which forms a spiral magnetic field, oriented in the z axis. Consequent spin precession phenomenon with angle θ of deflection is represented. Adapted from (Rinck, 2001). .................................. 20 viii List of Tables Table I - Muscles of tongue movement. From Seikel et al. (2009). ................. 10 ix Nomenclature 2D Two Dimensional 3D Three Dimensional CAD Computer-Aided Diagnosis DTI Diffusion Tensor Imaging GG Genioglossus muscle GTF Game-theoretic Framework MI Mutual Information MRI Magnetic Resonance Imaging NMCs neuromuscular compartments PET Positron Emission Tomography RF Radiofrequency RW Random Walker