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Clinical Radiotherapy Physics with MATLAB: A Problem-Solving Approach [Kõva köide]

  • Formaat: Hardback, 244 pages, kõrgus x laius: 254x178 mm, kaal: 594 g, 61 Tables, black and white; 31 Line drawings, black and white; 18 Halftones, black and white; 8 Illustrations, color; 49 Illustrations, black and white
  • Sari: Series in Medical Physics and Biomedical Engineering
  • Ilmumisaeg: 12-Jun-2018
  • Kirjastus: CRC Press Inc
  • ISBN-10: 1498754996
  • ISBN-13: 9781498754996
Teised raamatud teemal:
  • Formaat: Hardback, 244 pages, kõrgus x laius: 254x178 mm, kaal: 594 g, 61 Tables, black and white; 31 Line drawings, black and white; 18 Halftones, black and white; 8 Illustrations, color; 49 Illustrations, black and white
  • Sari: Series in Medical Physics and Biomedical Engineering
  • Ilmumisaeg: 12-Jun-2018
  • Kirjastus: CRC Press Inc
  • ISBN-10: 1498754996
  • ISBN-13: 9781498754996
Teised raamatud teemal:
The first MATLAB® programming book written specifically for clinical radiotherapy medical physicists and medical physics trainees, this much-needed book teaches users how to create their own clinical applications using MATLAB®, as a complement to commercial software particularly when the latter does not cover specific local clinical needs.

Chapters explore key radiotherapy areas such as handling volumes, 3D dose calculation, comparing dose distributions, reconstructing treatment plans and their summations, and automated tests for machine quality assurance. Readers will learn to independently analyse and process images, doses, structures, and other radiotherapy clinical data to deal with standard and non-standard situations in radiotherapy. This book will also significantly improve understanding of areas such as data nature, information content, DICOM RT standard, and data flow. It will be an invaluable reference for students of medical physics, in addition to clinical radiotherapy physicists and researchers working in radiotherapy.

Features:





Includes real clinical medical physics applications derived from actual clinical problems Provides commented MATLAB® scripts working with sample data and/or own data matching input requirements Promotes critical thinking and practical problem solving skills

Arvustused

"This is a well-structured book! Nothing else to expect from an excellent author on the subject of programming. Pavel Dvorak Ph.D.is a Czech medical physicist who had worked at various places in Austria and the United Kingdom and who summarizes in this book his enormous amount of knowledge to work with MatLab® scripts related to clinical radiotherapy physics that he collected for more than 10 years. The additional web-based resources to the book add up to >900MB as ZIP-file including DICOM sample data files. In the book are MatLab® scripts presented in great detail, that are useful for medical physicists in radiotherapy with ambitions to dig into and/or handle the data themselves for research or quality assurance purpose (clinical use is declined for liability reasons) as well as for students with interests in getting to know clinical radiotherapy physics from the computational side of it. The book starts with lists of "acronyms and abbreviations" and "definition of terms" that each are briefly explained, so a newcomer to this field is not lost by the use of special acronyms or terms later in the text. The subsequent text is divided into 10 chapters, starting with a chapter on the basics of MatLab®Each chapter starts with a list of the intended learning outcomes that will be covered in the following. The literature referenced (not much, but better than nothing!) is also listed at the end of each chapter. This way the chapters could be possibly used as stand-alone modules, e.g.as an instructional text for an inverted-classroom teaching concept of a course.This is a well-structured compendium of in great detail explained useful scripts to be used in the commercial MatLab® scripting environment." Prof. Dr. Markus Buchgeister, Beuth Hochschule für Technik Berlin, in The European Federation of Organizations for Medical Physics Bulletin (Spring 2019)

"This book provides a "dummy" for beginners guide to using MATLAB® to solve common problems in DICOM and imaging post-processing. It also provides guidance on how to manage the preliminary problems of dose calculation and the extrapolation of data from instruments and devices available in modern radiation therapyThe book is intended as an introductory guide to managing simple problems and code in MATLAB® which will be useful in radiation therapy environments. The added value in the book comes from having so many recent references and publications in the field, which will contribute to the training and learning of students and stimulate them to try to improve the state of the art of technology, solving everyday problems even in the absence of software and dedicated technologies, but by developing, if anything, that which is not available in their own radiotherapy department...The book is organized into ten chapters, as the author guides the readers through the problems in DICOM and the typical domain of the TPS, LINAC and images systems available in modern radiation therapy; he tries to provide the reader with the initial tools to understand which parameters, script, or complex codes should be written and how to integrate industrial data with simple interfaces developed in MATLAB®A much needed addition to current literature in the field, this book is tailored to the needs of medical physicists who are problem-solving using scripts and codes in MATLAB. Dr. Dvorak has provided scripts as dummy codes and summarized a sample of problems typically present in radiotherapy related to the use of advanced systems for treatment plansThe book can be used to support MSc programs in medical physics or early-career professionals from different disciplines (physics, engineering, software and medical instruments design, etc.) who need to understand the approach of using MATLAB® codes for problem solving in radiation therapy." Gabriele Guidi, Ph.D., M.Sc, Director of Medical Physics, Az. Ospedaliero-Universitaria di Modena, Italy in The Medical Physics International Journal (MPI), 2018, Vol.6, No. 2

"This introductory programming book demonstrates a series of accessible programming solutions for automating common tasks of the clinical therapy medical physicist. Prior familiarity with brute force solutions to analysis and Quality Assurance allows the reader to appreciate the algorithmic approach of this text. The approach of focusing on the problem/task and algorithmic solution makes the book readable. The readers introduction to coding is supplemented with online examples and the MATLAB online help.. The purpose of this book is to show how many common clinical physics tasks can be tackled through using the MATLAB code. Often, medical physicists have a unique set of circumstances, equipment, or software requiring unique solutions. Rather than applying brute force techniques, this book helps lead the reader to eloquent algorithmic solutions that are easily customizable.

This book is written for clinical radiotherapy physicists, educators, students, and medical physics residentsThe targeted audience for this book is the population having a general knowledge of radiation therapy tasks, with access to MATLAB, and having time to learn how to program in MATLABThe accompanying online resources are a series of short MATLAB scripts that are well-commented. These scripts give the reader the correct syntax of the MATLAB code that can be run "as is" or alteredThis book is well written with thoughtful practical examples of how to use the MATLAB code to solve many clinical problems that need to be customized. If you have the MATLAB software, I recommend this book."

Kenneth Bernstein in Med. Phys. 47 (3), March 2020 "This is a well-structured book! Nothing else to expect from an excellent author on the subject of programming. Pavel Dvorak Ph.D.is a Czech medical physicist who had worked at various places in Austria and the United Kingdom and who summarizes in this book his enormous amount of knowledge to work with MatLab® scripts related to clinical radiotherapy physics that he collected for more than 10 years. The additional web-based resources to the book add up to >900MB as ZIP-file including DICOM sample data files. In the book are MatLab® scripts presented in great detail, that are useful for medical physicists in radiotherapy with ambitions to dig into and/or handle the data themselves for research or quality assurance purpose (clinical use is declined for liability reasons) as well as for students with interests in getting to know clinical radiotherapy physics from the computational side of it. The book starts with lists of "acronyms and abbreviations" and "definition of terms" that each are briefly explained, so a newcomer to this field is not lost by the use of special acronyms or terms later in the text. The subsequent text is divided into 10 chapters, starting with a chapter on the basics of MatLab®Each chapter starts with a list of the intended learning outcomes that will be covered in the following. The literature referenced (not much, but better than nothing!) is also listed at the end of each chapter. This way the chapters could be possibly used as stand-alone modules, e.g.as an instructional text for an inverted-classroom teaching concept of a course.This is a well-structured compendium of in great detail explained useful scripts to be used in the commercial MatLab® scripting environment." Prof. Dr. Markus Buchgeister, Beuth Hochschule für Technik Berlin, in The European Federation of Organizations for Medical Physics Bulletin (Spring 2019)

"This book provides a "dummy" for beginners guide to using MATLAB® to solve common problems in DICOM and imaging post-processing. It also provides guidance on how to manage the preliminary problems of dose calculation and the extrapolation of data from instruments and devices available in modern radiation therapyThe book is intended as an introductory guide to managing simple problems and code in MATLAB® which will be useful in radiation therapy environments. The added value in the book comes from having so many recent references and publications in the field, which will contribute to the training and learning of students and stimulate them to try to improve the state of the art of technology, solving everyday problems even in the absence of software and dedicated technologies, but by developing, if anything, that which is not available in their own radiotherapy department...The book is organized into ten chapters, as the author guides the readers through the problems in DICOM and the typical domain of the TPS, LINAC and images systems available in modern radiation therapy; he tries to provide the reader with the initial tools to understand which parameters, script, or complex codes should be written and how to integrate industrial data with simple interfaces developed in MATLAB®A much needed addition to current literature in the field, this book is tailored to the needs of medical physicists who are problem-solving using scripts and codes in MATLAB. Dr. Dvorak has provided scripts as dummy codes and summarized a sample of problems typically present in radiotherapy related to the use of advanced systems for treatment plansThe book can be used to support MSc programs in medical physics or early-career professionals from different disciplines (physics, engineering, software and medical instruments design, etc.) who need to understand the approach of using MATLAB® codes for problem solving in radiation therapy." Gabriele Guidi, Ph.D., M.Sc, Director of Medical Physics, Az. Ospedaliero-Universitaria di Modena, Italy in The Medical Physics International Journal (MPI), 2018, Vol.6, No. 2

"This introductory programming book demonstrates a series of accessible programming solutions for automating common tasks of the clinical therapy medical physicist. Prior familiarity with brute force solutions to analysis and Quality Assurance allows the reader to appreciate the algorithmic approach of this text. The approach of focusing on the problem/task and algorithmic solution makes the book readable. The readers introduction to coding is supplemented with online examples and the MATLAB online help.. The purpose of this book is to show how many common clinical physics tasks can be tackled through using the MATLAB code. Often, medical physicists have a unique set of circumstances, equipment, or software requiring unique solutions. Rather than applying brute force techniques, this book helps lead the reader to eloquent algorithmic solutions that are easily customizable.

This book is written for clinical radiotherapy physicists, educators, students, and medical physics residentsThe targeted audience for this book is the population having a general knowledge of radiation therapy tasks, with access to MATLAB, and having time to learn how to program in MATLABThe accompanying online resources are a series of short MATLAB scripts that are well-commented. These scripts give the reader the correct syntax of the MATLAB code that can be run "as is" or alteredThis book is well written with thoughtful practical examples of how to use the MATLAB code to solve many clinical problems that need to be customized. If you have the MATLAB software, I recommend this book."

Kenneth Bernstein in Med. Phys. 47 (3), March 2020

Foreword xv
Preface xvii
About the Series xxi
Acknowledgements xxiii
Acronyms and Abbreviations xxv
Definitions of Terms xxvii
Chapter 1 MATLAB Essentials and Principles of Simple Programming
1(30)
All You Need To Start
1(12)
MATLAB Interface
2(1)
Presenting Strategy for This Book
3(1)
First Steps: Using MATLAB as a Pocket Calculator
4(1)
First Steps: Vector Algebra and Composite Commands
5(2)
First Steps: Data Plots and Figures
7(1)
First Steps: Program Development (Scripting)
7(4)
First Steps: Algorithmization
11(1)
Workspace Saving and Loading
12(1)
Variable Saving and Loading
12(1)
Path Setting/Adding
13(1)
Data Types In Matlab
13(2)
Numeric Types
13(1)
Character and String Data
14(1)
Cell Arrays
14(1)
Structure Arrays
14(1)
Basic Output and Export Options
15(3)
Basic Input and Import Options
18(4)
Managing Files and Folders
22(1)
A Simple Case Study
22(8)
Problem Definition
23(1)
Problem Specification
23(2)
Algorithmization
25(1)
Scripting
26(1)
Testing
27(2)
Documentation
29(1)
References
30(1)
Chapter 2 Radiotherapy Physics Related Data Types and Basic Operations
31(28)
Introduction
31(1)
Scalars
32(1)
1D Data
32(11)
Graphical Display
32(1)
Beam Scans
32(1)
Dose Volume Histogram
33(1)
Interpolating Dose Profiles
33(1)
Matching Dose Profiles
34(1)
Finding CAX0
35(1)
Finding CAXc
35(1)
Finding edgeR/edgeL
35(1)
Symmetric Averaging Dose Profile
36(2)
Mirroring Dose Profile
38(1)
Smoothing a Dose Profile
39(1)
DVH: Differential and Integral Format
40(1)
DVH Statistics
41(2)
2D Data
43(8)
Graphical Display
44(1)
Interpolation and Resizing
45(3)
Filtering
48(1)
Rotations, Mirroring, Zoom
48(1)
Regions of Interest
49(1)
Matching 2D Data
50(1)
3D Data
51(3)
Graphical Display
51(1)
Interpolation and Resizing
52(1)
Matching 3D Data
52(1)
Rotations and Mirroring
53(1)
Regions of Interest
53(1)
Histogram
53(1)
4D Data
54(1)
Cell Array
55(1)
Structure Array
55(2)
String
57(1)
References
57(2)
Chapter 3 Reconstructing Basic DICOM RT Data
59(32)
Introduction
59(1)
Dicom: All You Need To Know To Start Working
59(1)
Radiotherapy Specific Module: Dicom RT
60(2)
Importing Dicom Data
62(20)
Image Series
62(8)
Secondary Image Series (MRI, PET, ...)
70(1)
Volumes of Interest (RT Structures)
70(6)
Dose
76(2)
DVH
78(2)
Other DICOM RT Data in Radiotherapy
80(2)
Reconstructing 3D Dose Distribution
82(8)
Matching the Dose with the CT Model
84(3)
Calculating and Comparing DVHs
87(3)
References
90(1)
Chapter 4 Modifying DICOM Data in Radiotherapy
91(22)
Introduction
91(1)
Import and Re-Export Without Modification
92(3)
DICOM Image Data
92(1)
RT Treatment Plan (RTPLAN)
93(1)
RT Structure Set (RTSTRUCT)
94(1)
Dicom UIDs Cross-Referencing Examples
95(2)
Anonymizing Images and Other Dicom Data
97(1)
Examples of Modification of Dicom RT Data
97(6)
CT Image Density Override
98(2)
Modifying DICOM CT and RTSTRUCT
100(2)
Modifying DICOM RTPLAN
102(1)
Case Studies: Problems Solved By Data Modification
103(3)
Series `Too Old'
103(1)
Missing Slice
103(1)
Extending a CT Series
104(1)
Arithmetic Operations with Image Series
105(1)
Dose as the Secondary Image
106(1)
Creating Your Own Phantom Image Series
106(5)
Example CT Phantom: Preparing a 3D Voxel Phantom
107(1)
Example CT Phantom: Metadata Template and DICOM Export
108(3)
References
111(2)
Chapter 5 Simple 3D Plan Sum Using Rigid Registration
113(18)
Introduction
113(1)
Basic Concept
114(1)
Rigid Registration of Two CT Series
115(11)
Image to Image Registration
115(4)
Registration Based on VOI Contours
119(1)
Registration Based on Pairs of Reference Points
119(5)
General Aspects
124(2)
Co-Registration of Dose and Structures -- and Verification
126(1)
Dose Sums and Reporting
126(3)
Radiobiology Aspects
126(1)
A Few Thoughts on the Reporting of Results
127(2)
References
129(2)
Chapter 6 Handling Regions and Volumes of Interest in Radiotherapy
131(20)
Introduction
131(1)
Defining ROIs/VOIs -- A Review
132(1)
Basic ROI/VOI Operations
132(2)
Extending a VOI
132(1)
Interpolation
132(1)
Margins and Wall Extraction
133(1)
Boolean Operators
133(1)
Clinical Examples
133(1)
Crop Structures
134(1)
Expanding and Reducing ROIs/VOIs
134(6)
Comparing ROIs/VOIs
140(3)
Conformity Index and Coverage
141(2)
Internal Target Volume
143(6)
Static Coordinates
143(1)
Dynamic Coordinates -- Tracking
143(6)
References
149(2)
Chapter 7 Three-Dimensional Dose Calculation in Radiotherapy
151(22)
Introduction
151(1)
A Brief Introduction to Dose Calculation
151(2)
Voxel-Based Dose Calculation
152(1)
Factor-Based Algorithms
152(1)
Example of 3D Dose Calculation
153(15)
Organizing Beam Data in Lookup Tables
155(1)
Off-Center Ratio (OCR)
156(1)
Tissue Phantom Ratio (TPR)
157(1)
Output Factors (DM)
158(1)
Equivalent Path Length Correction (deg)
159(1)
Obtaining and Organizing Treatment Beam Parameters
159(1)
Dose Calculation
160(8)
Independent Dose/Mu Check
168(3)
References
171(2)
Chapter 8 Semi-Automated Measurement of the Major Mechanical Parameters of Linacs
173(26)
Introduction
173(1)
Scope of Automation In Radiotherapy Quality Control
174(1)
General Aspects of Linac QC
175(2)
Conventional Medical Linear Accelerators
177(1)
Measuring the Major Mechanical Parameters
178(1)
The Traditional Approach in Brief Examples
179(1)
Image-Based Approach
180(18)
Reference Systems
180(1)
Test Images Import and Common Principles
181(1)
Import Test DICOM Images
182(1)
Detect a Beam Collimation Device Edge
182(1)
Detect a Ball Bearing Center
183(2)
Manual Input of Reference Pixel Indices
185(2)
MV Imager Essentials
187(1)
Collimator Rotation Spoke Test
188(1)
Test Plan
188(1)
Data Acquisition
188(1)
Data Analysis
189(2)
Reference Collimator Rotation Angle 90°
191(1)
Test Plan and Data Acquisition
191(1)
Data Analysis
191(1)
MV Isocenter and Reference Anatomical Planes
192(1)
Test Plan
193(1)
Data Acquisition
193(1)
Data Analysis
193(1)
kV Isocenter
194(1)
Test Plan and Data Acquisition
195(1)
Data Analysis
195(1)
MV Detector, kV Detector (kVD) and kV Source (kVS) Arms
195(1)
Gantry Rotation Scale
196(1)
Test Plan
196(1)
Data Acquisition
196(1)
Data Analysis
196(1)
Couch Translation Orthogonality
196(1)
Couch Translation Scale
197(1)
Couch Rotation Scale
197(1)
Secondary Jaws (X, Y) and MLC Tests
197(1)
References
198(1)
Chapter 9 Comparing Dose Distributions: The Gamma Method
199(30)
Introduction
199(1)
Importance of Comparing Dose Distributions in Clinical Radiotherapy
199(2)
Qualitative and Quantitative Approaches
201(6)
Theoretical Foundations of the Gamma Method
202(1)
Implementation Assumptions, Conditions and Decisions
203(1)
Data Import Formats
204(1)
Dose Normalization
204(2)
Spatial Resolution
206(1)
Threshold
206(1)
Pass/Fail Only or Exact Gamma?
207(1)
Explanation of the Proposed Matlab Scripts to Calculate the Gamma Index For Two Given Dose Distributions
207(9)
Alternatives to the Basic Gamma Calculation Algorithm
210(1)
Calculating Gamma Using Norm
210(1)
Local Normalization of Dose Difference
211(1)
Simple Square Raster Scanning Search Space
211(1)
Dynamically Adapted Search Space
211(1)
Arbitrary Restricting Meaningful Search Space
211(1)
No Threshold Test for Each Evaluated Point
212(1)
No Out-of-Border Test for Each Gamma Calculation
212(1)
Circular Search Space
212(1)
Basic Gamma Calculation in 3D
212(1)
Generalised Gamma Calculation Algorithm
213(3)
Pass/Fail Only Gamma Calculation
216(1)
Demonstrating Matlab Scripts to Calculate the Gamma Index for two Given Dose Distributions
216(6)
Further Processing Gamma Maps
222(2)
Mean Gamma Value of All Evaluated Dose Points
222(1)
Gamma Histogram as a General Extension of Pass Fraction Statistics
222(1)
Inverse Alternative to Gamma Histogram
223(1)
Merits and Limitations of Gamma Analysis
224(4)
Result Interpretation
224(1)
Input Sensitivity and Output Robustness
225(1)
Specification of a Particular Gamma Assessment
225(1)
Clinical Relevance of the Gamma Result
226(1)
Alternative Methods
227(1)
References
228(1)
Chapter 10 Example of Accessory Modeling in Radiotherapy
229(10)
Introduction
229(1)
Applications of Accessory Modeling
229(2)
Collision Avoidance
230(1)
Treatment Couch Attenuation
230(1)
Dosimetry In Vivo
231(1)
Treatment Couch Model Example
232(1)
Clinical Application of the Model
233(3)
Considering General Aspects of in Vivo Dosimetry
236(1)
References
237(2)
Index 239
Pavel Dvorak is a medical physicist with several years experience in managerial clinical positions. Within medical physics, he has worked in education, research, and clinical practice in public and private health institutions in the Czech Republic, Austria, and the United Kingdom. His speciality is implementing novel techniques and technologies, creating and managing efficient workflows, and problem solving in radiotherapy.