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UNIVERSIDAD POLITÉCNICA DE MADRID Marta Luna Serrano UNIVERSIDAD POLITÉCNICA DE MADRID ESCUELA TÉCNICA SUPERIOR DE INGENIEROS DE TELECOMUNICACIÓN Automated detection and classification of brain injury lesions on structural magnetic resonance imaging TESIS DOCTORAL Marta Luna Serrano Ingeniero de Telecomunicación Madrid, 2016 Departamento de Tecnología Fotónica y Bioingeniería Grupo de Bioingeniería y Telemedicina E.T.S.I. de Telecomunicación UNIVERSIDAD POLITÉCNICA DE MADRID Automated detection and classification of brain injury lesions on structural magnetic resonance imaging TESIS DOCTORAL Autor: Marta Luna Serrano Directores: Enrique J. Gómez Aguilera José María Tormos Muñoz Madrid, Febrero 2016 Tribunal formado por el Magnífico y Excelentísimo Sr. Rector de la Universidad Politécnica de Madrid. Presidente: Dª. Mª Elena Hernando Pérez Doctora Ingeniera de Telecomunicación Profesora Titular de Universidad Universidad Politécnica de Madrid Vocales: D. César Cáceres Taladriz Doctor Ingeniero de Telecomunicación Profesor Contratado Doctor Universidad Rey Juan Carlos D. Pablo Lamata de la Orden Doctor Ingeniero de Telecomunicación Sir Henry Dale Fellow & Lecturer King’s College of London D. Alberto García Molina Doctor en Neurociencias Neuropsicólogo adjunto Hospital de Neurorehabilitación Institut Guttmann Secretaria: Dª. Patricia Sánchez González Doctora Ingeniera de Telecomunicación Profesora Ayudante Doctor Universidad Politécnica de Madrid Suplentes: Dña. Laura Roa Romero Doctora en Ciencias Físicas Catedrática de Universidad Universidad de Sevilla D. Javier Resina Tosina Doctor Ingeniero de Telecomunicación Profesor Titular de Universidad Universidad de Sevilla Realizado el acto de defensa y lectura de la Tesis el día 5 de febrero de 2016 en Madrid. A mi constelación favorita: Cassiopea (Luis, Antonia, Consuelo, Raquel y Sergio), por mantener mi camino siempre iluminado, incluso en esas noches oscuras. <”Tened paciencia y tendréis ciencia” – Baltasar Gracián> ACKNOWLEDGMENTS CONTENT SUMMARY - ENGLISH ............................................................................................................................... 1 SUMMARY - SPANISH ............................................................................................................................... 3 I INTRODUCTION ............................................................................................................................ 5 I.1. CONTEXT ........................................................................................................................................ 7 I.1.1. Acquired brain injury and cognitive functions .................................................................... 7 I.1.1.1 Acquired brain injury ..................................................................................................................... 7 I.1.1.2 Cognitive functions ...................................................................................................................... 10 I.1.2. Neuroplasticity and Neurorehabilitation.......................................................................... 13 I.1.2.1 Neuroplasticity ............................................................................................................................ 13 I.1.2.2 Neurorehabilitation ..................................................................................................................... 14 I.1.3. Medical imaging on brain injury ...................................................................................... 16 I.1.4. Neuroimaging in neurorehabilitation............................................................................... 21 I.2. PROBLEM STATEMENT AND JUSTIFICATION OF THE RESEARCH .................................................................. 22 I.3. THESIS OUTLINE ............................................................................................................................. 28 II RESEARCH HYPOTHESES AND OBJECTIVES ...............................................................................29 II.1. RESEARCH HYPOTHESES .................................................................................................................. 31 II.1.1. General hypothesis ........................................................................................................... 31 II.1.2. On the feature extraction of medical imaging studies ..................................................... 31 II.1.3. On the automatic lesion detection in brain injury patients .............................................. 31 II.1.4. On the quality evaluation of lesion identification ............................................................ 31 II.2. OBJECTIVES .................................................................................................................................. 32 II.2.1. General objective ............................................................................................................. 32 II.2.2. Specific objectives ............................................................................................................ 32 III STATE OF THE ART ...................................................................................................................33 III.1. INTRODUCTION ......................................................................................................................... 35 III.2. LESION IDENTIFICATION ALGORITHMS ............................................................................................ 36 III.2.1. State of the Art ................................................................................................................. 36 III.2.2. Proposed Methodology .................................................................................................... 39 III.2.2.1 Pre-processing ........................................................................................................................... 40 III.2.2.1.1 Introduction ....................................................................................................................... 40 III.2.2.1.2 Skull – stripping.................................................................................................................. 41 III.2.2.1.3 Intensity Normalization ..................................................................................................... 42 III.2.2.1.4 Spatial Normalization......................................................................................................... 43 III.2.2.1.5 Analysis and Conclusions ................................................................................................... 44 III.2.2.2 Singular Points Identification ..................................................................................................... 46 III.2.2.2.1 Introduction ....................................................................................................................... 46 III.2.2.2.2 Singular Point Location: Types of Features and Detectors ................................................ 48 III.2.2.2.3 Orientation Assignment ..................................................................................................... 57 III.2.2.2.4 Singular Point Descriptor ................................................................................................... 58 III.2.2.2.5 Analysis and Conclusions ................................................................................................... 64 III.2.2.3 Registration ............................................................................................................................... 65 III.2.2.3.1 Introduction ....................................................................................................................... 65 III.2.2.3.2 Registration on Neuroimaging ........................................................................................... 67 III.2.2.3.3 Landmark-Based Registration Algorithms on Brain ........................................................... 70 III.2.2.3.4 Analysis and Conclusions ................................................................................................... 74 III.2.2.4 Brain Lesion Detection ............................................................................................................... 76 III.3. NEUROIMAGING SOFTWARE TOOLS .............................................................................................. 78 III.4. NEUROIMAGING DATABASES ....................................................................................................... 82 IV MATERIALS AND METHODS .....................................................................................................85 IV.1. MATERIALS .............................................................................................................................. 87 IV.1.1. Introduction ...................................................................................................................... 87 IV.1.2. Medical Imaging Studies .................................................................................................. 87 IV.1.3. Brain atlases ..................................................................................................................... 87 IV.1.4. Development Tools ........................................................................................................... 88 IV.2. METHODS ...............................................................................................................................
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