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Series in Medical Physics and Biomedical Engineering
Series Editors: Kwan-Hoong Ng, E. Russell Ritenour, and Slavik Tabakov

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e-Learning in Medical Physics and Engineering: Building Educational Modules with Moodle

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

Johan Helmenkamp, Robert Bujila, Gavin Poludniowski (Eds)

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Diagnostic Radiology Physics
with MATLAB®
A Problem-Solving Approach

Edited by
Johan Helmenkamp
Robert Bujila
Gavin Poludniowski
MATLAB® is a trademark of The MathWorks, Inc. and is used with permission. The MathWorks does not warrant the
accuracy of the text or exercises in this book. This book’s use or discussion of MATLAB® software or related products
does not constitute endorsement or sponsorship by The MathWorks of a particular pedagogical approach or particular
use of the MATLAB® software.

First edition published 2021

by CRC Press
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Contents

Section I General topics

Chapter 1  The role of programming in healthcare 3

J OHAN H ELMENKAMP AND R OBERT B UJILA and G AVIN P OLUDNIOWSKI
1.1 WHAT PROGRAMMING CAN DO FOR YOU 4
1.2 WHAT PROGRAMMING CAN DO FOR YOUR CLINIC: CHANGE
THE NATURE OF ROUTINE WORK 4
1.3 WHAT PROGRAMMING CAN DO FOR YOUR CLINIC: ENABLE
RESEARCH AND INNOVATION 5
1.4 WITH GREAT POWER COMES GREAT RESPONSIBILITY 6
1.5 CONCLUSION 6

Chapter 2  MATLAB fundamentals 7

J AVIER G AZZARRI and C INDY S OLOMON
2.1 INTRODUCTION 8
2.2 VARIABLES AND DATA TYPES 9
2.3 ARRAYS AND MATRIX MANIPULATION 10
2.4 MORE DATA TYPES 12
2.5 CONDITIONAL OPERATORS AND LOGICAL INDEXING 12
2.6 CONTROL FLOW 13
2.7 USER-DEFINED FUNCTIONS 16
2.8 DATA ANALYSIS 17
2.9 VISUALIZATION 18
2.10 HANDLING BIG DATA SETS 20
2.11 CLASSES 21
2.12 IMPROVING CODE PERFORMANCE 22
2.13 EXERCISE—BASIC IMAGE PROCESSING 23
2.14 CONCLUSION 25

Chapter 3  Data sources in medical imaging 27

J ONAS A NDERSSON AND J OSEF L UNDMAN , G AVIN P OLUDNIOWSKI and
R OBERT B UJILA
3.1 INTRODUCTION 28
3.2 THE DICOM STANDARD AND FILE FORMAT 30

vii
viii  Contents

3.3 OTHER DATA SOURCES 34

3.4 CONCLUSION 36

Chapter 4  Importing, manipulating and displaying DICOM data in

MATLAB 37
P IYUSH K HOPKAR , J OSEF L UNDMAN and V IJU R AVICHANDRAN
4.1 INTRODUCTION 38
4.2 IMPORTING IMAGE DATA 40
4.3 WRITING AND ANONYMIZING DICOM DATA 42
4.4 VISUALIZATION 45
4.5 CONCLUSION 52

Chapter 5  Creating automated workfows using MATLAB 53

J OHAN H ELMENKAMP and S VEN M ÅNSSON
5.1 INTRODUCTION 53
5.2 MANUAL CALCULATION OF SNR 55
5.3 AUTOMATING THE SNR CALCULATION USING MATLAB 56
5.4 CONCLUSION 63

Chapter 6  Integration with other programming languages and

environments 65
G AVIN P OLUDNIOWSKI and M ATT W HITAKER
6.1 INTRODUCTION 65
6.2 WHEN TO USE OTHER PROGRAMMING LANGUAGES AND
ENVIRONMENTS 66
6.3 SYSTEM COMMANDS 67
6.4 INTEGRATING WITH JAVA 69
6.5 INTEGRATING WITH PYTHON 71
6.6 INTEGRATING WITH THE .NET FRAMEWORK 74
6.7 CONCLUSION 77

Chapter 7  Good programming practices 79

YANLU WANG and P IYUSH K HOPKAR
7.1 WHAT MAKES A GOOD PROGRAM 79
7.2 GOOD PRACTICES 80
7.3 CONCLUSION 87

Chapter 8  Sharing software 89

YANLU WANG and P IYUSH K HOPKAR
8.1 POTENTIAL OF CROWD-SOURCING 90
8.2 SHARE CODE USING MATLAB FILE EXCHANGE 91
8.3 SHARE CODE USING OTHER SOURCE-CODE HOSTING SITES 91
 Contents  ix

8.4 CHOOSING THE OPTIMAL APPROACH: GUI OR NOT? 92

8.5 BUILDING AN APP IN MATLAB 93
8.6 CREATING EXECUTABLES WITH THE MATLAB COMPILER 98
8.7 LICENSES 101
8.8 CONCLUSION 103

Chapter 9  Regulatory considerations when deploying your software

in a clinical environment 105
P HILIP S. C OSGRIFF and J OHAN ÅTTING
9.1 MEDICAL DEVICE REGULATIONS 106
9.2 HEALTH INFORMATION PRIVACY 121

Section II Problem-solving: examples from the trenches

Chapter 10  Applying good software development processes

in practice 129
TANYA K AIRN
10.1 INTRODUCTION 130
10.2 THE TRENCH IN QUESTION: RADIOCHROMIC FILM
DOSIMETRY 131
10.3 AN IN-HOUSE SOFTWARE VALIDATION CHECKLIST 132
10.4 BEFORE WRITING THE CODE 133
10.5 WHILE WRITING THE CODE 137
10.6 AFTER WRITING THE CODE 138
10.7 SUMMARY OF VALIDATION PROCESS AND OUTCOMES 139
10.8 REGARDING CERTIFICATION 140
10.9 CONCLUSION 140

Chapter 11  Automating quality control tests and evaluating ATCM in

computed tomography 141
PATRIK N OWIK
11.1 INTRODUCTION 141
11.2 ANALYZING CT PHANTOM IMAGES 142
11.3 APPLICATIONS IN CONSTANCY TESTS 144
11.4 APPLICATIONS IN AUTOMATIC TUBE CURRENT MODULATION 149
11.5 CONCLUSIONS 152

Chapter 12  Parsing and analyzing Radiation Dose Structured

Reports 153
R OBERT B UJILA
12.1 INTRODUCTION 153
12.2 STRUCTURE OF RDSR OBJECTS 154
x  Contents

12.3 PARSING RDSR OBJECTS 157

12.4 ANALYZING PARSED RDSR DATA 159
12.5 CONCLUSIONS 162

Chapter 13  Methods of determining patient size surrogates using CT

images 163
C HRISTIANE S ARAH B URTON
13.1 INTRODUCTION 163
13.2 STRUCTURE OF THE CODE 164
13.3 CALCULATING SIZE METRICS FROM CT AXIAL IMAGES 166
13.4 CALCULATING THE SIZE-SPECIFIC DOSE ESIMATE 169
13.5 CONCLUSION 170

Chapter 14  Reconstructing the geometry of x-ray interventions 171

A RTUR O MAR
14.1 INTRODUCTION 171
14.2 ELEMENTARY VECTOR ALGEBRA 173
14.3 RECONSTRUCTING THE PATIENT-BEAM ALIGNMENT 174
14.4 RECONSTRUCTING THE SOURCE-TO-SURFACE DISTANCE 176
14.5 CALCULATING THE INCIDENT AIR KERMA 180
14.6 CONCLUSION 181

Chapter 15  Mammography and breast tomosynthesis simulation us-

ing Perlin noise 183
M AGNUS D USTLER
15.1 INTRODUCTION 184
15.2 GENERATING THE NOISE 186
15.3 FRACTAL NOISE 192
15.4 PRE-GENERATION 194
15.5 THE FINAL TISSUE MODEL 195
15.6 CONCLUSION: GENERATING BREAST TISSUE 196

Chapter 16  xrTk: a MATLAB toolkit for x-ray physics calculations 197

TOMI F. N ANO AND I AN A. C UNNINGHAM
16.1 INTRODUCTION 198
16.2 OPTIMIZING IMAGE QUALITY 200
16.3 DISCUSSION 209
16.4 CONCLUSIONS 209

Chapter 17  Automating daily QC for an MRI scanner 211

S VEN M ÅNSSON
17.1 INTRODUCTION 211
 Contents  xi

17.2 AUTOMATIC ANALYSIS OF QUALITY CONTROL IMAGES 212

17.3 THE MAIN FUNCTION 221
17.4 CONCLUSION 222

Chapter 18  Image processing at scale by containerizing’ MATLAB 223

J AMES D ’A RCY, S IMON J D ORAN AND M ATTHEW O RTON
18.1 INTRODUCTION 224
18.2 IMPROVED DICOM SUPPORT BY MATLAB-JAVA INTEGRATION 224
18.3 RUNNING MATLAB IN A CONTAINER 230
18.4 EXAMPLE PROBLEM FOR CONTAINERIZATION 233
18.5 XNAT: ORCHESTRATING THE IMAGE ANALYSIS OF LARGE
PATIENT COHORTS 238
18.6 CONCLUSION 238

Chapter 19  Estimation of arterial wall movements 239

M AGNUS C INTHIO, J OHN A LBINSSON , TOBIAS E RLÖV , TOMAS J ANSSON and
Å SA RYDÉN A HLGREN
19.1 THE LONGITUDINAL MOVEMENT OF THE ARTERIAL WALL 240
19.2 BLOCK MATCHING 241
19.3 ARTERIAL WALL MOVEMENT MEASUREMENTS 246
19.4 CONCLUDING REMARKS 247

Chapter 20  Importation and visualization of ultrasound data 249

TOBIAS E RLÖV, M AGNUS C INTHIO and TOMAS J ANSSON
20.1 INTRODUCTION TO ULTRASOUND DATA 249
20.2 STRUCTURE OF A DATA FILE 250
20.3 READ DATA INTO MATLAB 252
20.4 GENERATING AND VISUALIZING B-MODE IMAGES 253
20.5 CONCLUSION 256

Index 269
Foreword

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

Helmenkamp, Robert Bujila and Gavin Poludniowski is the second book in the Series in
Medical Physics and Biomedical Engineering dedicated to software used by clinical medical
physicists.
Given the ongoing and accelerating development of medical device technology and user
protocols, fulfilling the mission and delivering the full competence profile of the clinical
medical physicist has become a daunting task (Caruana et al. 2014; Guibelalde et al. 2014).
However, well-written software and programming skills can help in a multitude of ways (Fer-
ris et al. 2005; Lyra et al. 2011; Donini et al. 2014; Nowik et al. 2015). Regrettably, few suit-
able texts are available, with the result that the acquisition of high-level programming skills
by students and clinical scientists is often a hit-or-miss affair. Few books include exemplary
scripts illustrating application to the clinical milieu whilst didactic approaches are insuffi-
ciently comprehensive or low in communicative power. Diagnostic Radiology Physics with
MATLAB ® : A Problem-Solving Approach aims to fill this gap with the use of MATLAB® in
Diagnostic radiology physics. In this book, the university tutor will find structured teach-
ing text and real-world case study examples (‘examples from the trenches’) with which to
enhance presentations and to set as learning tasks. On the other hand, the student will find
a pedagogically appealing and engaging manuscript for individual study whilst the practic-
ing clinical medical physicist will find a learning tool for further development of his or her
own skills. The authors have included much practical advice ranging from the importation,
manipulation and display of DICOM Data in MATLAB to integration of MATLAB with
other programming languages, regulatory issues when deploying software in the clinical
environment and the sharing and licensing of software.
Johan Helmenkamp, Robert Bujila and Gavin Poludniowski are busy medical physicists
with lots of experience in using MATLAB and I sincerely thank them for finding the time
within their busy schedule to dedicate to this important educational initiative and to share
their expertise with the readers of this book. I also thank the excellent team of contributors
who have presented us with an exciting kaleidoscope of relevant real-world applications. I
am sure it has not been easy and I appreciate it. Finally, I would like to wish readers of
this text many happy programming hours—and to remind them that programming is power!

Carmel J. Caruana, PhD, FIPEM

Professor and Head, Medical Physics Department, University of Malta
Past Chair, Education and Training Committee, European Federation of Organizations for
Medical Physics
Past Associate Editor for Education and Training: Physica Medica—European Journal of
Medical Physics
Past Member, Accreditation Committee: International Medical Physics Certification Board

xiii