Contributors Pablo abbona MD Neda jahanshad Department of Radiological Sciences Medical Imaging Informatics UCLA David Geffen school of medicine UCLA Biomedical Engineering IDI Denise aberle, mD Hooshang Kangaroo, MD Medical Imaging Informatics Medical Imaging Informatics Department of Radiological Sciences UCLA David Geffen School of medicine CLA David Geffen School of Medicine Corey Arnold, PhD Kambiz Motamedi. MD Medical Imaging Informatics Department of Radiological Sciences Department of Information Studies UCLA David Geffen School of medicine University of California, Los Angeles Lawrence Bassett, MD Craig Morioka, PhD epartment of Radiological Scie ences Department of Radiology UCLA David Geffen School of medicine Veteran's Administration Wadsworth Kathleen brown mD Nagesh Ragavendra, MD epartment of Radiological Sciences Department of Radiological Sciences UCLA David Geffen School of medicine UCLA David Geffen School of medicine Matthew Brown PhD James Sayre, PhD Thoracic Imaging Laboratory Departments of Biostatistics epartment of Radiological Sciences Radiological Sciences UCLA David Geffen School of medicine UCLA David Geffen School of medicine Suzie el-saden MD Leanne Seeger, MD Department of Radiology Department of Radiological Sciences Veteran's Administration Wadswort UCLA David Geffen School of medicine Los Angeles, California Ana Gomez. MD lya Shpitser, PhD Department of Radiological Sciences School of public health CLA David Geffen School of Medicine William Hsu, PhD Emily Watt, MLIS Medical Imaging Informatics Medical Imaging Informatics UCLA David Geffen School of medicine UCLA Biomedical Engineering IDP Juan Eugenio iglesias, MSc Medical Imaging Informatics
xv Contributors Pablo Abbona, MD Neda Jahanshad, BS Department of Radiological Sciences Medical Imaging Informatics UCLA David Geffen School of Medicine UCLA Biomedical Engineering IDP Denise Aberle, MD Hooshang Kangarloo, MD Medical Imaging Informatics & Medical Imaging Informatics Department of Radiological Sciences UCLA David Geffen School of Medicine UCLA David Geffen School of Medicine Corey Arnold, PhD Kambiz Motamedi, MD Medical Imaging Informatics & Department of Radiological Sciences Department of Information Studies UCLA David Geffen School of Medicine University of California, Los Angeles Lawrence Bassett, MD Craig Morioka, PhD Department of Radiological Sciences Department of Radiology UCLA David Geffen School of Medicine Veteran’s Administration Wadsworth Los Angeles, California Kathleen Brown, MD Nagesh Ragavendra, MD Department of Radiological Sciences Department of Radiological Sciences UCLA David Geffen School of Medicine UCLA David Geffen School of Medicine Matthew Brown, PhD James Sayre, PhD Thoracic Imaging Laboratory & Departments of Biostatistics & Department of Radiological Sciences Radiological Sciences UCLA David Geffen School of Medicine UCLA David Geffen School of Medicine Suzie El-Saden, MD Leanne Seeger, MD Department of Radiology Department of Radiological Sciences Veteran’s Administration Wadsworth UCLA David Geffen School of Medicine Los Angeles, California Ana Gomez, MD Ilya Shpitser, PhD Department of Radiological Sciences School of Public Health UCLA David Geffen School of Medicine Harvard University William Hsu, PhD Emily Watt, MLIS Medical Imaging Informatics Medical Imaging Informatics UCLA David Geffen School of Medicine UCLA Biomedical Engineering IDP Juan Eugenio Iglesias, MSc Medical Imaging Informatics UCLA Biomedical Engineering IDP
Table of contents FOREWORD..........................VI PREFACE CONTRIBUTORS TABLE OF CONTENTS PART I PERFORMING THE IMAGING EXAM CHAPTER 1: INTRODUCTION What is Medical Imaging Informatics? The Process of Care and the role of Imaging 13345 Medical Imaging Informatics: From Theory to Application Choosing a Protocol: The role of Medical Imaging Informatics Cost Consideratio A Historic Perspective and Moving Forward PACS: Capturing Images Electronically... Teleradiology: Standardizing Data and Communications Integrating Patient Data 10 Understanding Images: Todays Challenge References CHAPTER 2: A PRIMER ON IMAGING ANATOMY AND PHYSIOlOGY15 A Review of Basic Imaging Modalities. Projectional Imaging Core Physical Concepts maging Computed Tomography Additional CT Applications Magnetic Resonance Core Physical Concepts Imaging 37 Additional MR Imaging Sequences Ultrasound Imaging An Introduction to Imaging-based Anatomy Physiology Respiratory System The Larynx and Trachea The Lungs and Airways…. The Pleura, Chest Wall, and Respiratory Muscles Pulmonary Ventilation: Inspiration and Expiration.... ∴51 Pressure Relationships during Inspiration and Expiration actors Influencing Airflow Measures of Lung Function Basic Respiratory Imaging
xvii Table of Contents FOREWORD...................................................................................................VII PREFACE........................................................................................................XI CONTRIBUTORS..............................................................................................XV TABLE OF CONTENTS ..................................................................................... XVII PART I PERFORMING THE IMAGING EXAM ........................................................... 1 CHAPTER 1: INTRODUCTION .............................................................................. 3 What is Medical Imaging Informatics? .................................................................3 The Process of Care and the Role of Imaging ........................................................ 4 Medical Imaging Informatics: From Theory to Application ................................... 5 Improving the Use of Imaging......................................................................................... 5 Choosing a Protocol: The Role of Medical Imaging Informatics...................................... 6 Cost Considerations ........................................................................................................ 8 A Historic Perspective and Moving Forward ......................................................... 9 PACS: Capturing Images Electronically............................................................................ 9 Teleradiology: Standardizing Data and Communications ............................................. 10 Integrating Patient Data................................................................................................ 10 Understanding Images: Today’s Challenge ................................................................... 11 References.........................................................................................................12 CHAPTER 2: A PRIMER ON IMAGING ANATOMY AND PHYSIOLOGY ........................... 15 A Review of Basic Imaging Modalities ................................................................15 Projectional Imaging............................................................................................ 15 Core Physical Concepts ................................................................................................. 15 Imaging ......................................................................................................................... 17 Computed Tomography....................................................................................... 23 Imaging ......................................................................................................................... 23 Additional CT Applications ............................................................................................ 33 Magnetic Resonance ........................................................................................... 34 Core Physical Concepts ................................................................................................. 34 Imaging ......................................................................................................................... 37 Additional MR Imaging Sequences................................................................................ 40 Ultrasound Imaging ............................................................................................. 43 An Introduction to Imaging-based Anatomy & Physiology .................................45 Respiratory System.............................................................................................. 46 The Larynx and Trachea ................................................................................................ 46 The Lungs and Airways.................................................................................................. 47 The Pleura, Chest Wall, and Respiratory Muscles......................................................... 50 Pulmonary Ventilation: Inspiration and Expiration....................................................... 51 Pressure Relationships during Inspiration and Expiration ............................................ 51 Factors Influencing Airflow ........................................................................................... 52 Measures of Lung Function........................................................................................... 53 Basic Respiratory Imaging ............................................................................................. 54
XVIll Table of Contents Imaging Analysis of Pulmonary Pathophysiology... The brain Cerebral Hemispheres. Cerebral White Matter Basal nuclei Brainstem Cerebral vascular Anatomy. Breast Anatomy and Imaging Breast Imaging Breast Cancer and other Findings Musculoskeletal System Imaging of the Musculoskeletal System Cardiac System Basic Cardiac and Vascular Imaging 66176789 Basic Imaging of the Urinary System.. Urinary Medical Problems………. Upper Gastrointestinal (Gl) System 4 References 86 PART II INTEGRATING IMAGING INTO THE PATIENT RECORD CHAPTER 3: INFORMATION SYSTEMS ARCHITECTURES.......m.....93 The electronic medical record EMR Information Systems 94 Hospital Information Systems Picture Archive and Communication Systems... Data Standards for Communication and Representation DICOM(Digital Imaging and Communication in Medicine) The Dicom model 99 Health Level 7(HL7) 103 Messaging Protocol Reference Implementation Model(RIM) Clinical Document Architecture(CDA)... 105 Logical Observation Identifier Names and Codes(LOINC) Distributed Information Systems Peer-to-peer Architectures First Generation P2P: Centralized Searching Second Generation P2P: Simple Decentralized Searching(Query Flooding Second Generation P2P: Distributed Hash Tables 112 Third Generation P2P P2P Healthcare Applications rid Computing 16 Globus toolkit 118
xviii Table of Contents Imaging Analysis of Pulmonary Pathophysiology.......................................................... 56 The Brain ............................................................................................................. 58 Cerebral Hemispheres................................................................................................... 59 Cerebral White Matter.................................................................................................. 62 Basal Nuclei................................................................................................................... 62 Brainstem...................................................................................................................... 63 Meninges ...................................................................................................................... 63 Cerebral Vascular Anatomy........................................................................................... 64 Breast Anatomy and Imaging .............................................................................. 65 Breast Imaging .............................................................................................................. 66 Breast Cancer and other Findings ................................................................................. 69 Musculoskeletal System ...................................................................................... 71 Imaging of the Musculoskeletal System........................................................................ 72 Cardiac System .................................................................................................... 76 Cardiac Medical Problems............................................................................................. 77 Basic Cardiac and Vascular Imaging .............................................................................. 78 Urinary System .................................................................................................... 79 Basic Imaging of the Urinary System............................................................................. 80 Urinary Medical Problems ............................................................................................ 81 Upper Gastrointestinal (GI) System..................................................................... 84 References......................................................................................................... 86 PART II INTEGRATING IMAGING INTO THE PATIENT RECORD ...................................91 CHAPTER 3: INFORMATION SYSTEMS & ARCHITECTURES.........................................93 The Electronic Medical Record ........................................................................... 93 EMR Information Systems ................................................................................... 94 Hospital Information Systems....................................................................................... 95 Picture Archive and Communication Systems............................................................... 96 Data Standards for Communication and Representation.................................... 98 DICOM (Digital Imaging and Communication in Medicine)................................. 98 The DICOM Model ........................................................................................................ 99 DICOM Extensions....................................................................................................... 102 Health Level 7 (HL7)........................................................................................... 103 Messaging Protocol..................................................................................................... 103 Reference Implementation Model (RIM).................................................................... 104 Clinical Document Architecture (CDA) ........................................................................ 105 Logical Observation Identifier Names and Codes (LOINC) ................................ 107 Distributed Information Systems ..................................................................... 108 Peer-to-peer Architectures................................................................................ 108 First Generation P2P: Centralized Searching............................................................... 109 Second Generation P2P: Simple Decentralized Searching (Query Flooding) .............. 110 Second Generation P2P: Distributed Hash Tables ...................................................... 112 Third Generation P2P.................................................................................................. 113 P2P Healthcare Applications ....................................................................................... 115 Grid Computing ................................................................................................. 116 Globus Toolkit ............................................................................................................. 118 Condor ........................................................................................................................ 119
Table of Contents Grid Computing Healthcare Applications Cloud Computing: Beyond the Grid Discussion and Applications 122 Teleradiology, Telemedicine, and Telehealth 123 Integrating Medical Data Access Collaborative Clinical Research: Example Image Repositories 129 131 CHAPTER 4: MEDICAL DATA VISUALIZATION: TOWARD INTEGRATED CLINICAL WORKSTATIONS Navigating Clinical Data Elements of the display.... Visual Metaphors: Emphasizing Different Relationships 149 Multidimensional Relationships Causal Relationships Navigating Images Combining Information: Integrating the Medical Data... 161 Defining Context Defining the User… Defining the Task: Incorporating Workflow 164 Combining Graphical Metaphors Creating Integrated Displays…… 166 Interacting with Data 70 Imaging Workflow Workstation 174 Discussion and Applications 177 TimeLine: Problem-centric Visualization Data Reorganization. Visualization Dictionary.. Patient-centric visualization 8 PART III DOCUMENTING IMAGING FINDINGS CHAPTER 5: CHARACTERIZING IMAGING DATA 197 What is a pixel? Representing Space, Time, and energy 198 Mathematical Representations of Pixel Values. Physical Correspondence to the Real World 201 Compiling Scientific-quality Imaging Databases.. Improving Pixel Characterization. ∴203 Pre-acquisition: Standardizing Imaging Protocols Post-acquisition: Pixel Value Calibration and Mapping 204 Dealing with Image Noise Characterizing Noise Reduc
Table of Contents xix CHAPTER 4: MEDICAL DATA VISUALIZATION: TOWARD INTEGRATED CLINICAL Grid Computing Healthcare Applications.................................................................... 120 Cloud Computing: Beyond the Grid ............................................................................ 122 Discussion and Applications............................................................................. 122 Teleradiology, Telemedicine, and Telehealth.................................................... 123 Integrating Medical Data Access ....................................................................... 126 Collaborative Clinical Research: Example Image Repositories .......................... 129 References....................................................................................................... 131 WORKSTATIONS........................................................................................139 Navigating Clinical Data ................................................................................... 139 Elements of the Display..................................................................................... 140 Visual Metaphors: Emphasizing Different Relationships................................... 149 Temporal Representations.......................................................................................... 149 Spatial Representations .............................................................................................. 152 Multidimensional Relationships.................................................................................. 155 Causal Relationships ................................................................................................... 156 Navigating Images....................................................................................................... 157 Combining Information: Integrating the Medical Data ..................................... 161 Defining Context................................................................................................ 161 Defining the User ........................................................................................................ 162 Defining the Task: Incorporating Workflow ................................................................ 164 Combining Graphical Metaphors....................................................................... 166 Creating Integrated Displays....................................................................................... 166 Interacting with Data .................................................................................................. 170 Imaging Workflow & Workstations ................................................................... 174 Discussion and Applications............................................................................. 177 TimeLine: Problem-centric Visualization ........................................................... 178 Data Reorganization.................................................................................................... 179 Visualization Dictionary............................................................................................... 180 Patient-centric Visualization.............................................................................. 182 References....................................................................................................... 184 PART III DOCUMENTING IMAGING FINDINGS.....................................................195 CHAPTER 5: CHARACTERIZING IMAGING DATA....................................................197 What is a Pixel? ............................................................................................... 197 Representing Space, Time, and Energy ............................................................. 198 Mathematical Representations of Pixel Values........................................................... 199 Physical Correspondence to the Real World............................................................... 201 Compiling Scientific-quality Imaging Databases ............................................... 202 Improving Pixel Characterization....................................................................... 203 Pre-acquisition: Standardizing Imaging Protocols....................................................... 204 Post-acquisition: Pixel Value Calibration and Mapping............................................... 204 Dealing with Image Noise.................................................................................. 209 Characterizing Noise ................................................................................................... 210 Noise Reduction.......................................................................................................... 214
Table of Contents Registration: Improving Pixel Positional Characterization 218 218 Preprocessing User Interaction 223 Comparison of Methods. 223 Imaging Features 224 Appearance-based Image Features. Shape-based Image Features 27 Aggregating Features: Dimensionality Reduction Imaging Atlases and Group-wise Image Analysis The Need for Atlases 233 Creating Atlases sing Atlases 235 Discussion 239 Towards Medical Image analysis Mathematical Foundations Image Modeling 242 Linking Images to Additional Knowledge 242 References CHAPTER 6: NATURAL LANGUAGE PROCESSING OF MEDICAL REPORTS 257 An Introduction to medical nlp……257 Assessment of Application Requirements Overview of the medical Nlp Problem Medical NLP System Components Tasks 262 Identifying Document Structure: Structural Analysis Section Boundary Detection and Classification.... ∴263 Defining Word Sequences Named Entity Recognition and De- identification .273 Concept Coding: Ontological Mapping 276 The MetaMap Approach Data Mining and Lookup-Table Caches Phrasal Chunking 278 Context Modeling Classifier Design 28 Generation of Training Samples Linear Sequence Optimization...... Parsing: Relation Extraction and Constituency Parsing 285 Compositionality in Language Discussion 289 References
xx Table of Contents CHAPTER 6: NATURAL LANGUAGE PROCESSING OF MEDICAL REPORTS .................................................................................................257 An Introduction to Medical NLP ....................................................................... 257 Assessment of Application Requirements......................................................... 260 Overview of the Medical NLP Problem.............................................................. 261 Medical NLP System Components & Tasks ....................................................... 262 Identifying Document Structure: Structural Analysis ........................................ 262 Section Boundary Detection and Classification........................................................... 263 Sentence Boundary Detection .................................................................................... 264 Tokenization................................................................................................................ 265 Defining Word Sequences........................................................................................... 268 Named Entity Recognition and De-identification.............................................. 273 Concept Coding: Ontological Mapping.............................................................. 276 The MetaMap Approach ............................................................................................. 277 Data Mining and Lookup-Table Caches....................................................................... 278 Phrasal Chunking ............................................................................................... 278 Context Modeling ....................................................................................................... 280 Classifier Design .......................................................................................................... 282 Generation of Training Samples.................................................................................. 283 Linear Sequence Optimization .................................................................................... 285 Parsing: Relation Extraction and Constituency Parsing..................................... 285 Compositionality in Language ..................................................................................... 286 Discussion........................................................................................................ 289 References....................................................................................................... 290 Registration: Improving Pixel Positional Characterization ................................ 218 Transformations.......................................................................................................... 218 Similarity Metrics ........................................................................................................ 221 Preprocessing.............................................................................................................. 222 User Interaction .......................................................................................................... 223 Comparison of Methods ............................................................................................. 223 Imaging Features ............................................................................................... 224 Appearance-based Image Features............................................................................. 224 Shape-based Image Features ...................................................................................... 227 Feature Selection ........................................................................................................ 229 Aggregating Features: Dimensionality Reduction....................................................... 230 Imaging Atlases and Group-wise Image Analysis .............................................. 232 The Need for Atlases................................................................................................... 233 Creating Atlases .......................................................................................................... 233 Using Atlases............................................................................................................... 235 Morphometry ............................................................................................................. 237 Discussion........................................................................................................ 239 Towards Medical Image Analysis....................................................................... 240 Mathematical Foundations......................................................................................... 240 Image Modeling .......................................................................................................... 242 Linking Images to Additional Knowledge .................................................................... 242 References....................................................................................................... 244