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 Referencesxx 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