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CUI-THESIS-2017.Pdf MAGNETIC RESONANCE ELASTOGRAPHY FOR APPLICATIONS IN RADIATION THERAPY A Thesis Submitted to the College of Graduate and Postdoctoral Studies In Partial Fulfillment of the Requirements For the Degree of Master of Science In the Division of Biomedical Engineering University of Saskatchewan Saskatoon By Lumeng Cui Copyright Lumeng Cui, August 2017. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfillment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. DISCLAIMER Reference in this thesis to any specific commercial products, process, or service by trade name, trademark, manufacturer, or otherwise (CIRS Inc., Eclipse, GE, ImageJ, MATLAB, Mayo Clinic, MRE/Wave, Resoundant®, Resoundant Inc., Saskatchewan Cancer Agency, Siemens, Varian Medical Systems, and 3D Slicer), does not constitute or imply its endorsement, recommendation, or favoring by the University of Saskatchewan. The views and opinions of the author expressed herein do not state or reflect those of the University of Saskatchewan, and shall not be used for advertising or product endorsement purposes. Requests for permission to copy or to make other uses of materials in this thesis in whole or part should be addressed to: Head of the Division of Biomedical Engineering University of Saskatchewan Saskatoon, Saskatchewan S7N 5A9 Canada OR Dean College of Graduate and Postdoctoral Studies University of Saskatchewan Room 116 Thorvaldson Building 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i ABSTRACT Magnetic resonance elastography (MRE) is an imaging technique that combines mechanical waves and magnetic resonance imaging (MRI) to determine the elastic properties of tissue. Because MRE is non-invasive, there is great potential and interest for its use in the detection of cancer. The first part of this thesis concentrates on parameter optimization and imaging quality of an MRE system. To do this, we developed a customized quality assurance phantom, and a series of quality control tests to characterize the MRE system. Our results demonstrated that through optimizing scan parameters, such as frequency and amplitude, MRE could provide a good qualitative elastogram for targets with different elasticity values and dimensions. The second part investigated the feasibility of integrating MRE into radiation therapy (RT) workflow. With the aid of a tissue- equivalent prostate phantom (embedded with three dominant intraprostatic lesions (DILs)), an MRE-integrated RT framework was developed. This framework contains a comprehensive scan protocol including Computed Tomography (CT) scan, combined MRI/MRE scans and a Volumetric Modulated Arc Therapy (VMAT) technique for treatment delivery. The results showed that using the comprehensive information could boost the MRE defined DILs to 84 Gy while keeping the remainder of the prostate to 78 Gy. Using a VMAT based technique allowed us to achieve a highly conformal plan (conformity index for the prostate and combined DILs was 0.98 and 0.91). Based on our feasibility study, we concluded that MRE data can be used for targeted radiation dose escalation. In summary, this thesis demonstrates that MRE is feasible for applications in radiation oncology. ii ACKNOWLEDGEMENTS I first would like to express my gratitude to my supervisors, Dr.’s Niranjan Venugopal, Paul Babyn, and Francis Bui for their extremely generous support and selfless mentoring. Their professionalism always encourages and inspires me in an academic setting. In life, each of them is a man with a good soul. I could have never finished this work without their guidance and help. It is and will always be a great honor for me to be their student. They will always have my respect. I also want to thank my committee members, Dr.’s Emily McWalter, Andrew Alexander, and Mark Eramian for taking their time to read my thesis and sharing their professional views on my thesis. To me, there was no doubt that their invaluable opinions will help me improve myself in the long term. I am also grateful to the staff from Royal University Hospital, particularly Shawn Kisch, Alain Lalonde, Elaine Roesler, and Dawn Senko for providing technical assistance on the MRI equipment. In the meantime, I would also like to extend my thanks to Dr. Gavin Cranmer-Sargison, the Director of Medical Physics Department in Saskatchewan Cancer Agency, for offering the research resources in the cancer centre. I appreciate the technical support from our industrial partners, in particular Dr. Gerald Moran from Siemens Canada and Dr. Ted Lynch from CIRS Inc. I would also like to acknowledge Mr. Conrad Yuen from British Columbia Cancer Agency for his help on my project during his Sabbatical. I would like to express my appreciation to the sources of my funding source, U of S-BIT Master Scholarship and Prostate Cancer Canada Network – Regina. Lastly, I want to give my very special thanks to my parents, all my family and friends, and Shuyu Shang. I could have never made it this far without their support, encouragement, and love. iii TABLE OF CONTENTS PERMISSION TO USE .................................................................................................................. i ABSTRACT ....................................................................................................................................ii ACKNOWLEDGEMENTS ......................................................................................................... iii TABLE OF CONTENTS .............................................................................................................. iv LIST OF TABLES ...................................................................................................................... viii LIST OF FIGURES ....................................................................................................................... ix LIST OF ABBREVIATIONS ......................................................................................................xii Thesis Overview ........................................................................................................................... xiv Peer Reviewed Abstracts and Manuscripts................................................................................ xv Chapter 1 Introduction ............................................................................................................. - 1 - 1.1. What is Magnetic Resonance Elastography? ................................................................ - 1 - 1.2. Historical Development of Elastography Techniques and MRE’s Applications .......... - 5 - 1.3. Research Objectives ...................................................................................................... - 9 - Chapter 2 Magnetic Resonance Imaging .............................................................................. - 11 - 2.1. Spins, Magnetic Fields, and Relaxation ...................................................................... - 11 - 2.2. Gradient Fields and Encoding Techniques .................................................................. - 18 - 2.2.1. Slice Selection ..................................................................................................... - 18 - 2.2.2. Frequency Encoding ............................................................................................ - 20 - 2.2.3. Phase Encoding ................................................................................................... - 22 - 2.2.4. K space ................................................................................................................ - 25 - 2.3. Reconstruction and the Fourier Transform.................................................................. - 26 - 2.4. Pulse Sequence ............................................................................................................ - 27 - 2.4.1. Spin Echo Pulse Sequence .................................................................................. - 28 - 2.4.2. Gradient-Recalled Echo Pulse Sequence ............................................................ - 32 - 2.4.3. Echo Planar Imaging Pulse Sequence ................................................................. - 33 - 2.5. Summary ..................................................................................................................... - 36 - Chapter 3 Magnetic Resonance Elastography ...................................................................... - 37 - 3.1. Elasticity ...................................................................................................................... - 37 - 3.1.1. Stress ................................................................................................................... - 37 - 3.1.2. Strain ..................................................................................................................
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