Diagnostic Radiology Physics with MATLAB®: A Problem-Solving Approach

Cover
Half Title
Series Page
Title Page
Copyright Page
Dedication
Contents
SECTION I: General topics
	CHAPTER 1: The role of programming in healthcare
		1.1. WHAT PROGRAMMING CAN DO FOR YOU
		1.2. WHAT PROGRAMMING CAN DO FOR YOUR CLINIC: CHANGE THE NATURE OF ROUTINE WORK
		1.3. WHAT PROGRAMMING CAN DO FOR YOUR CLINIC: ENABLE RESEARCH AND INNOVATION
		1.4. WITH GREAT POWER COMES GREAT RESPONSIBILITY
		1.5. CONCLUSION
	CHAPTER 2: MATLAB fundamentals
		2.1. INTRODUCTION
		2.2. VARIABLES AND DATA TYPES
		2.3. ARRAYS AND MATRIX MANIPULATION
		2.4. MORE DATA TYPES
		2.5. CONDITIONAL OPERATORS AND LOGICAL INDEXING
		2.6. CONTROL FLOW
		2.7. USER-DEFINED FUNCTIONS
		2.8. DATA ANALYSIS
		2.9. VISUALIZATION
		2.10. HANDLING BIG DATA SETS
		2.11. CLASSES
		2.12. IMPROVING CODE PERFORMANCE
		2.13. EXERCISE—BASIC IMAGE PROCESSING
		2.14. CONCLUSION
	CHAPTER 3: Data sources in medical imaging
		3.1. INTRODUCTION
		3.2. THE DICOM STANDARD AND FILE FORMAT
		3.3. OTHER DATA SOURCES
		3.4. CONCLUSION
	CHAPTER 4: Importing, manipulating and displaying DICOM data in MATLAB
		4.1. INTRODUCTION
		4.2. IMPORTING IMAGE DATA
		4.3. WRITING AND ANONYMIZING DICOM DATA
		4.4. VISUALIZATION
		4.5. CONCLUSION
	CHAPTER 5: Creating automated workfows using MATLAB
		5.1. INTRODUCTION
		5.2. MANUAL CALCULATION OF SNR
		5.3. AUTOMATING THE SNR CALCULATION USING MATLAB
		5.4. CONCLUSION
	CHAPTER 6: Integration with other programming languages and environments
		6.1. INTRODUCTION
		6.2. WHEN TO USE OTHER PROGRAMMING LANGUAGES AND ENVIRONMENTS
		6.3. SYSTEM COMMANDS
		6.4. INTEGRATING WITH JAVA
		6.5. INTEGRATING WITH PYTHON
		6.6. INTEGRATING WITH THE .NET FRAMEWORK
		6.7. CONCLUSION
	CHAPTER 7: Good programming practices
		7.1. WHAT MAKES A GOOD PROGRAM
		7.2. GOOD PRACTICES
		7.3. CONCLUSION
	CHAPTER 8: Sharing software
		8.1. POTENTIAL OF CROWD-SOURCING
		8.2. SHARE CODE USING MATLAB FILE EXCHANGE
		8.3. SHARE CODE USING OTHER SOURCE-CODE HOSTING SITES
		8.4. CHOOSING THE OPTIMAL APPROACH: GUI OR NOT?
		8.5. BUILDING AN APP IN MATLAB
		8.6. CREATING EXECUTABLES WITH THE MATLAB COMPILER
		8.7. LICENSES
		8.8. CONCLUSION
	CHAPTER 9: Regulatory considerations when deploying your software in a clinical environment
		9.1. MEDICAL DEVICE REGULATIONS
		9.2. HEALTH INFORMATION PRIVACY
SECTION II: Problem-solving: examples from the trenches
	CHAPTER 10: Applying good software development processes in practice
		10.1. INTRODUCTION
		10.2. THE TRENCH IN QUESTION: RADIOCHROMIC FILM DOSIMETRY
		10.3. AN IN-HOUSE SOFTWARE VALIDATION CHECKLIST
		10.4. BEFORE WRITING THE CODE
		10.5. WHILE WRITING THE CODE
		10.6. AFTER WRITING THE CODE
		10.7. SUMMARY OF VALIDATION PROCESS AND OUTCOMES
		10.8. REGARDING CERTIFICATION
		10.9. CONCLUSION
	CHAPTER 11: Automating quality control tests and evaluating ATCM in computed tomography
		11.1. INTRODUCTION
		11.2. ANALYZING CT PHANTOM IMAGES
		11.3. APPLICATIONS IN CONSTANCY TESTS
		11.4. APPLICATIONS IN AUTOMATIC TUBE CURRENT MODULATION
		11.5. CONCLUSIONS
	CHAPTER 12: Parsing and analyzing Radiation Dose Structured Reports
		12.1. INTRODUCTION
		12.2. STRUCTURE OF RDSR OBJECTS
		12.3. PARSING RDSR OBJECTS
		12.4. ANALYZING PARSED RDSR DATA
		12.5. CONCLUSIONS
	CHAPTER 13: Methods of determining patient size surrogates using CT images
		13.1. INTRODUCTION
		13.2. STRUCTURE OF THE CODE
		13.3. CALCULATING SIZE METRICS FROM CT AXIAL IMAGES
		13.4. CALCULATING THE SIZE-SPECIFIC DOSE ESIMATE
		13.5. CONCLUSION
	CHAPTER 14: Reconstructing the geometry of x-ray interventions
		14.1. INTRODUCTION
		14.2. ELEMENTARY VECTOR ALGEBRA
		14.3. RECONSTRUCTING THE PATIENT-BEAM ALIGNMENT
		14.4. RECONSTRUCTING THE SOURCE-TO-SURFACE DISTANCE
		14.5. CALCULATING THE INCIDENT AIR KERMA
		14.6. CONCLUSION
	CHAPTER 15: Mammography and breast tomosynthesis simulation using Perlin noise
		15.1. INTRODUCTION
		15.2. GENERATING THE NOISE
		15.3. FRACTAL NOISE
		15.4. PRE-GENERATION
		15.5. THE FINAL TISSUE MODEL
		15.6. CONCLUSION: GENERATING BREAST TISSUE
	CHAPTER 16: xrTk: a MATLAB toolkit for x-ray physics calculations
		16.1. INTRODUCTION
		16.2. OPTIMIZING IMAGE QUALITY
		16.3. DISCUSSION
		16.4. CONCLUSIONS
	CHAPTER 17: Automating daily QC for an MRI scanner
		17.1. INTRODUCTION
		17.2. AUTOMATIC ANALYSIS OF QUALITY CONTROL IMAGES
		17.3. THE MAIN FUNCTION
		17.4. CONCLUSION
	CHAPTER 18: Image processing at scale by containerizing’ MATLAB
		18.1. INTRODUCTION
		18.2. IMPROVED DICOM SUPPORT BY MATLAB-JAVA INTEGRATION
		18.3. RUNNING MATLAB IN A CONTAINER
		18.4. EXAMPLE PROBLEM FOR CONTAINERIZATION
		18.5. XNAT: ORCHESTRATING THE IMAGE ANALYSIS OF LARGE PATIENT COHORTS
		18.6. CONCLUSION
	CHAPTER 19: Estimation of arterial wall movements
		19.1. THE LONGITUDINAL MOVEMENT OF THE ARTERIAL WALL
		19.2. BLOCK MATCHING
		19.3. ARTERIAL WALL MOVEMENT MEASUREMENTS
		19.4. CONCLUDING REMARKS
	CHAPTER 20: Importation and visualization of ultrasound data
		20.1. INTRODUCTION TO ULTRASOUND DATA
		20.2. STRUCTURE OF A DATA FILE
		20.3. READ DATA INTO MATLAB
		20.4. GENERATING AND VISUALIZING B-MODE IMAGES
		20.5. CONCLUSION
Index