MATLAB for Medical Physics: Real-life Clinical Scenarios and Projects

288 Pages·2023·8.134 MB·English

by  Jidi Sun

Jidi Sun
MATLAB
for Medical
Physics
Real-life Clinical Scenarios and Projects
MATLAB for Medical Physics
Jidi Sun
MATLAB for Medical
Physics
Real-life Clinical Scenarios and Projects
Jidi Sun
Peter MacCallum Cancer Centre
Melbourne, VIC, Australia
ISBN 978-981-19-9856-0 ISBN 978-981-19-7565-3 (eBook)
https://doi.org/10.1007/978-981-19-7565-3
© The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature
Singapore Pte Ltd. 2023
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To my wife Qiusi Li and our daughter
Jacqueline Sun
I love you forever
Preface
During the past 13 years of researching, teaching, clinical training and work, I have
been using MATLAB to find effective and efficient solutions to daily problems and
to create multiple open-source automatic image quality assurance software. In mid-
2019, I had this idea to share my MATLAB experiences with the medical physics
community through some of the work that I have done over the past years.
MATLAB is a mature, well-resourced, constantly maintained and updated
commercial programming software. It allows users to perform numerical analysis,
but more importantly MATLAB comes with a large collection of toolboxes that are
designed for solving standard problems in different areas. Because of this, MATLAB
has been widely used in the scientific and engineering areas. As a result, MATLAB
becomes one of the mandatory undergraduate courses at many universities. The best
way to learn MATLAB is by solving problems. Often the undergraduate course
briefly introduces the basics of MATLAB and teaches students using some general
mathematical problems as examples. For medical physics postgraduate students and
clinical medical physicists, the clinical scenarios are more relevant because they
are the daily problems that physicists face. Therefore, this book uses the clinical
scenarios as examples to introduce and demonstrate MATLAB with supplied data
files.
This book is structured into two main parts. The first part (Chap. 1) introduces the
fundamentals of the MATLAB software, so that the readers can be confident to use
MATLAB to solve simple problems. This part is designed for readers who has no or
limited experiences in MATLAB. It first introduces the MATLAB software layout to
help readers to orient around the software. Then it showed readers various ways to
get help. Finally, the basics of MATLAB is introduced systematically with over 100
examples. In terms of the knowledge introduced in this part, it is not too different
from other MATLAB introduction textbooks. However, I have used clinically relevant
problems in some examples where are appropriate. The intermediate and advanced
MATLAB users can skip the first part. The second part of the book (Chaps. 2–4)
focuses on using MATLAB to solve routine clinical problems that medical physicists
may face on daily basis. A total of 18 real-life clinical scenarios were included to
demonstrate how to use MATLAB to solve complex problems. The scenarios cover
vii
viii Preface
areas including DICOM file manipulation, film dosimetry, brachytherapy application,
linac and CT quality assurance and their automations. Some of these 18 scenarios
were further modified to expand to additional 23 clinical scenario expansions. For
all the examples and clinical scenarios and their expansions in this book, the step-
by-step solutions are provided as well as coding explanations. The data files (e.g.
DICOM) used for all clinical scenarios are provided. The code and data files can
be downloaded from one of the following links (https://www.dropbox.com/sh/t9r
xtglw8yz0yaf/AADHHVwxSiga3gGlBIN75lFOa?dl=0 or https://drive.google.com/
drive/folders/1ZjZyfB9fFIBNiJ9qOdWE7KRQKd__58TT).
I have a medical physics background rather than computer science, so the solutions
given in this book are limited by my knowledge and experiences. With my best effort,
I have minimised bugs in the solution code to make sure they are runnable. There is
often no unique solution to a problem. The solutions in this book are not necessarily
the most efficient ones but rather one of many ways to solve the problem. Some of the
solutions were deliberately made more complicated than needed just to demonstrate
some of MATLAB functions where applicable. Readers are encouraged to modify,
improve and find better solutions. Learning by doing and have fun. English is my
second language, so some paragraphs may not be concise. I apologise in advance for
the grammar mistakes that cause readers trouble while reading this book.
This book is primarily written for medical physics students and clinical medical
physicists. As a potential textbook for medical physics students, the clinical back-
grounds at the beginning of the clinical scenarios briefly introduce the relevant
medical physics knowledge. For clinical medical physicists who want to learn
MATLAB, hopefully the clinical scenarios in this book can put the programming
problems into context they are familiar with.
Melbourne, Australia Jidi Sun
Contents
1 Introduction of MATLAB ....................................... 1
1.1 MATLAB Window Layout ................................. 1
1.2 Where to Get Help ........................................ 4
1.2.1 In-software Help ................................... 5
1.2.2 Online Community Support ......................... 10
1.3 MATLAB Basic ........................................... 11
1.3.1 Data Types and Manipulations ....................... 11
1.3.2 File and Directory ................................. 27
1.3.3 Graph Plotting ..................................... 31
1.3.4 Image Display ..................................... 37
1.3.5 Basic Image Processing ............................. 41
1.3.6 Basic Data Analysis ................................ 51
1.3.7 Control Flows ..................................... 56
1.3.8 User-Defined Function .............................. 64
1.4 DICOM-RT File Reading and Manipulation ................... 67
1.4.1 Types of DICOM-RT File ........................... 67
1.4.2 Read DICOM Attributes ............................ 68
1.4.3 Extract DICOM Image ............................. 69
1.4.4 Write DICOM File ................................. 69
1.4.5 Search DICOM Attribute ........................... 70
Reference ...................................................... 71
2 Data Reading, Manipulation and Displaying ...................... 73
2.1 Varian RPM VXP File ..................................... 73
2.1.1 Clinical Background ............................... 73
2.1.2 Clinical Scenario .................................. 73
2.1.3 Clinical Scenario Expansion A ....................... 77
2.1.4 Clinical Scenario Expansion B ....................... 79
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x Contents
3 DICOM File Functions in MATLAB ............................. 83
3.1 Compare Specific DICOM Attribute Among Different
DICOM Files ............................................. 83
3.1.1 Clinical Background ............................... 83
3.1.2 Initial Clinical Scenario ............................. 83
3.1.3 Clinical Scenario Expansion A ....................... 88
3.1.4 Clinical Scenario Expansion B ....................... 89
3.2 Differentiate DICOM Files in a Folder Based on Specific
DICOM Header Information ................................ 92
3.2.1 Clinical Background ............................... 92
3.2.2 Initial Clinical Scenario ............................. 92
3.2.3 Clinical Scenario Expansion A ....................... 97
3.2.4 Clinical Scenario Expansion B ....................... 100
3.2.5 Clinical Scenario Expansion C ....................... 104
3.3 Anonymise DICOM File ................................... 107
3.3.1 Clinical Background ............................... 107
3.3.2 Initial Clinical Scenario ............................. 107
3.4 Modify DICOM-RT QA Plan File ........................... 109
3.4.1 Clinical Background ............................... 109
3.4.2 Initial Clinical Scenario ............................. 110
3.4.3 Clinical Scenario Expansion A ....................... 112
3.5 Invert Pixel Values on All DICOM Images in a Folder .......... 114
3.5.1 Initial Clinical Scenario ............................. 114
3.6 Check Whether the Planned MU Has Been Completely
Delivered on an EPID Image ................................ 117
3.6.1 Clinical Background ............................... 117
3.6.2 Initial Clinical Scenario ............................. 117
References ..................................................... 121
4 Image Display, Processing and Analysis .......................... 123
4.1 Dosimetry: Scanner Reproducibility .......................... 123
4.1.1 Clinical Background ............................... 123
4.1.2 Initial Clinical Scenario ............................. 123
4.1.3 Clinical Scenario Expansion A ....................... 129
4.1.4 Clinical Scenario Expansion B ....................... 131
4.2 Dosimetry: Film Calibration ................................ 134
4.2.1 Clinical Background ............................... 134
4.2.2 Initial Clinical Scenario ............................. 134
4.2.3 Clinical Scenario Expansion A ....................... 142
4.2.4 Clinical Scenario Expansion B ....................... 144
4.2.5 Clinical Scenario Expansion C ....................... 148
4.3 Brachytherapy: HDR Source Position QA Using Film .......... 151
4.3.1 Clinical Background ............................... 151
4.3.2 Initial Clinical Scenario ............................. 152
Contents xi
4.4 OBI: KV Imager Centre versus Gantry Angle ................. 159
4.4.1 Clinical Background ............................... 159
4.4.2 Initial Clinical Scenario ............................. 161
4.4.3 Clinical Scenario Expansion A ....................... 170
4.5 OBI: Leeds Phantom High-Contrast Spatial Resolution Test ..... 176
4.5.1 Clinical Background ............................... 176
4.5.2 Initial Clinical Scenario ............................. 177
4.5.3 Clinical Scenario Expansion B ....................... 196
4.6 EPID: EPID Centre and Scaling QA Using Graticule ........... 200
4.6.1 Clinical Background ............................... 200
4.6.2 Initial Clinical Scenario ............................. 202
4.6.3 Clinical Scenario Expansion A ....................... 213
4.7 MLC: EPID Picket Fence QA ............................... 217
4.7.1 Clinical Background ............................... 217
4.7.2 Initial Clinical Scenario ............................. 217
4.8 CT: MAR (Metal Artefact Reduction) Image Analysis .......... 227
4.8.1 Clinical Background ............................... 227
4.8.2 Initial Clinical Scenario ............................. 228
4.8.3 Clinical Scenario Expansion A ....................... 235
4.8.4 Clinical Scenario Expansion B ....................... 238
4.8.5 Clinical Scenario Expansion C ....................... 242
4.9 CT: Catphan QA HU Reproducibility Test .................... 245
4.9.1 Clinical Background ............................... 245
4.9.2 Initial Clinical Scenario ............................. 246
4.9.3 Clinical Scenario Expansion A ....................... 252
4.10 CT: Automatically Find Catphan QA Sections ................. 254
4.10.1 Clinical Background ............................... 254
4.10.2 Initial Clinical Scenario ............................. 255
4.11 X-ray QA Using Step Wedge ................................ 268
4.11.1 Clinical Background ............................... 268
4.11.2 Initial Clinical Scenario ............................. 268
4.11.3 Clinical Scenario Expansion A ....................... 274
4.11.4 Clinical Scenario Expansion B ....................... 275
References ..................................................... 278