UNIVERSITI PUTRA MALAYSIA

HASAN HADI KHALEEL

FSKTM 2012 10

3D SURFACE RECONSTRUCTION OF CORONARY ARTERIES FROM CARDIOVASCULAR ANGIOGRAPHY

TO DETECT LOCATION OF HEART VESSELS

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3D SURFACE RECONSTRUCTION OF CORONARY ARTERIES FROM CARDIOVASCULAR ANGIOGRAPHY

TO DETECT LOCATION OF HEART VESSELS

By

HASAN HADI KHALEEL

Thesis Submitted to the School of Graduate Studies, Universiti Putra Malaysia, in Fulfillment of Requirements for the Degree of Doctor of Philosophy

March 2012

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Dedicated to my parents, siblings, and good friends

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Abstract of thesis presented to the Senate of Universiti Putra Malaysia in fulfillment of the requirement for the degree of Doctor of Philosophy

3D SURFACE RECONSTRUCTION OF CORONARY ARTERIES FROM CARDIOVASCULAR ANGIOGRAPHY

TO DETECT LOCATION OF HEART VESSELS

By

HASAN HADI KHALEEL

March 2012

Chairperson: Rahmita Wirza O.K. Rahmat, PhD

Faculty: Computer Science and Information Technology

Complications and difficulties are common in the medical field. One of the important

difficulties that a surgeon may face nowadays is that when a vessel or more vessels

goes inside the surface of the heart. Coronary artery vessels naturally lie on the

surface of the heart but sometimes a coronary artery vessel goes inside the heart

muscle and stays there for awhile and then comes out again. In this case a surgeon

will not be able to locate the artery during a bypass operation. Working on 2D

projections can easily mislead the comprehension and the interpretation of the

structures like in the case of stenosis quantification. Different acquisition techniques

make it possible to obtain 3D models of the vessels network reconstructed from 2D

angiographies. The problem is that the coronary angiograms can show the arteries

through contrast dye projection but still cannot show the exact location of a coronary

artery vessel.

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The proposed procedure to solve this problem in this thesis consists of three steps.

The first step is the coronary artery trees extraction. We proposed an algorithm to

extract tree vessels from cardiovascular angiography by removing the background

and highlighting the coronary artery tree vessels. The second step is 3D

reconstruction for coronary artery tree vessels. Since extracted vessels from step one

will be in 2D which will offer little information to surgeons and is difficult to study

as well, we need to reconstruct them in 3D to simplify their diagnosing and

analyzing. The third step in the procedure is the surface fitting. The 3D model

reconstructed from step two will offer more information about the coronary artery

tree vessels but it will again be difficult to decide whether a vessel is in or out the

heart’s surface. Therefore, we need to build a 3D surface out of the 3D cloud of

points obtained from step two to simplify the detection of said vessels.

To best confirm the location of a vessel and determine the depth of that vessel inside

the heart, we added a step at the end of the research to measure the curvatures of the

reconstructed surface and the maximum depth of a vessel inside that surface as well.

This step will measure the depths of all curvatures and highlight the maximum. To

surgeons, 1 cm (10 mm) depth of a vessel inside the heart could cause a problem

during surgery; therefore, our approach would set out an alarm to warn the surgeon if

that depth (10 mm) or more is present. We have tested the approach to raw of clinical

data sets and the results show that our proposed approach is capable of detecting the

location of vessels in about 98%. From those results we can conclude that our

approach is robust and can act as a tool in surgery planning and scientific researches

purposes.

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Abstrak of tesis yang dikemukakan kepada Senat Universiti Putra Malaysia sebagai memenuhi keperluan untuk ijazah dari Doktor Falsafah

3D SURFACE RECONSTRUCTION OF CORONARY ARTERIES FROM CARDIOVASCULAR ANGIOGRAPHY

TO DETECT LOCATION OF HEART VESSELS

Oleh

HASAN HADI KHALEEL

Mac 2012

Pengerusi: Rahmita Wirza O.K. Rahmat, PhD

Fakulti: Sains Komputer dan Teknologi Maklumat

Komplikasi dan kesukaran merupakan perkara biasa dalam bidang perubatan. Salah

satu kesukaran yang sering dihadapi oleh ahli bedah masa kini ialah apabila satu atau

lebih saluran memasuki dalaman jantung. Saluran arteri koronari umumnya berada

pada permukaan jantung tetapi dalam keadaan tertentu, saluran arteri koronari

memasuki ruangan otot jantung, menetap sementara dan keluar semula. Dalam kes

ini, pakar bedah akan gagal menentukan kedudukan arteri semasa pembedahan

pintasan jantung. Pengunjuran 2D boleh mengakibatkan kesalah fahaman dan

kesilapan interpretasi terhadap struktur sebagaimana penjumlahan kes aliran keluar

berbalik. Teknik perolehan yang berbeza memungkinkan imej 3D bagi rangkaian

saluran vesel dibina semula daripada Sinaran-X imej 2D angiografi. Masalahnya

ialah, koronari berupaya menunjukkan arteri melalui unjuran pewarnaan, namun ia

tidak dapat menunjukkan lokasi sebenar saluran arteri koronari.

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Prosedur yang dicadangkan bagi mengatasi permasalahan ini dalam tesis ini terdiri

daripada tiga langkah. Langkah pertama ialah pemisahan pepohon arteri koronari.

Kami mencadangkan satu algoritma untuk memisahkan pepohon saluran vesel dari

angiografi kardivaskular dengan menyingkirkan latar belakang dan menonjolkan

saluran pepohon arteri koronari. Langkah kedua adalah pembangunan semula 3D

untuk saluran pepohon arteri koronari. Memandangkan saluran yang

diekstrak/pengasingan daripada langkah pertama merupakan 2D, yang akan

menawarkan sedikit maklumat kepada pakar bedah dan agak sukar untuk dikaji, kita

perlu membangunkan semula 3D bagi memudahkan mereka mendiagnos dan

menganalisa. Langkah ketiga dalam Prosedur adalah padanan-permukaan.

Pembangunan model 3D daripada langkah kedua menawarkan lebih banyak

maklumat berkenaan saluran pokok arteri koronari tetapi sekali lagi menjadi sukar

untuk menentukan samada saluran tersebut berada di dalam atau di luar permukaan

jantung. Oleh itu, kita perlu membangunkan permukaan 3D di luar daripada titik

awan 3D yang diperolehi daripada langkah kedua untuk mengesan lokasi saluran

dengan mudah.

Untuk memastikan secara optimum lokasi saluran dan menentukan kedalaman

saluran dalam jantung, tambahan satu lagi langkah di penghujung penyelidikan iaitu

mengukur lengkungan yang membina permukaan dan juga kedalaman maksimum

sesuatu saluran di bahagian dalam permukaan. Langkah ini akan mengukur

kedalaman bagi setiap lengkungan dan mengetengahkan nilai kedalaman yang

maksimum. Menurut ahli bedah, 1 cm (10mm) kedalaman saluran dalam jantung

boleh memberi masalah untuk membuat pembedahan, maka, pendekatan kami akan

menetapkan suatu penggera untuk memberi amaran kepada ahli bedah sekiranya

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mencapai kedalaman 10 mm atau lebih. Kami telah menguji pendekatan terhadap

beberapa set data mentah klinikal dan keputusan menunjukkan pendekatan yang

kami cadangkan mampu mengesan lokasi saluran sekitar 98%. Daripada keputusan

ini, kita boleh membuat kesimpulan bahawa pendekatan ini kukuh dan boleh

bertindak sebagai alat dalam pengurusan pembedahan dan kegunaan penyelidikan

saintifik.

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ACKNOWLEDGEMENTS

I would like to thank the almighty Allah for everything during the voyage of

knowledge exploration. First and foremost, I would like to express my sincere

gratitude to my supervisor Associate Professor Dr. Rahmita Wirza O.K. Rahmat

for giving me the opportunity to start off this project. Through the course of my

study, I have had the great fortune to get to know and interact with her. Her

comments and suggestions for further development as well as her assistance during

the whole project and during writing this thesis are invaluable to me. Her talent,

diverse background, interest, teaching and research style have provided me an

exceptional opportunity to learn and made me a better student. I would like to

express my sincere thanks and appreciation to the supervisory committee members

Professor Dr. Ramlan Mahmod, Professor Dr. Mohd Zamrin, and Associate

Professor Dr. Norwati Mustapha for their guidance, valuable suggestions and

advice throughout this work in making this success.

My deepest appreciation is to my parents and siblings, who have been very

supportive and patiently waiting for me to complete my study.

My sincere appreciation to PPUKM hospital and the staff of OT room for making my

mission easy in getting information and data.

For the others who have directly or indirectly helped me in the completion of my

work, I thank you all.

Hasan Hadi Khaleel

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I certify that a Thesis Examination Committee has met on 1 March 2012 to conduct the final examination of Hasan Hadi Khaleel on his thesis entitled “3D Surface Reconstruction of Coronary Arteries From Cardiovascular Angiography to Detect Location of Heart Vessels” in accordance with the Universities and University Colleges Act 1971 and the Constitution of the Universiti Putra Malaysia [P. U.(A) 106] 15 March 1998. The Committee recommends that the student be awarded the Doctor of Philosophy. Members of the Thesis Examination Committee were as follows: Ali Mamat, PhD Associate Professor Faculty of Computer Science and Information Technology Universiti Putra Malaysia (Chairman) Lili Nurliyana Abdullah, PhD Associate Professor Faculty of Computer Science and Information Technology Universiti Putra Malaysia (Internal Examiner) Fatimah Khalid, PhD Lecturer Faculty of Computer Science and Information Technology Universiti Putra Malaysia (Internal Examiner) Sudhir Pandurang Mudur, PhD Professor Faculty of Engineering and Computer Science Concordia University Canada (External Examiner) SEOW HENG FONG, PhD Professor and Deputy Dean School of Graduate Studies Universiti Putra Malaysia Date:

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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted as fulfillment of the requirement for the degree of Doctor of Philosophy. The members of the Supervisory Committee were as follows: Rahmita Wirza O.K. Rahmat, PhD Associate Professor Faculty of Computer Science and Information Technology Universiti Putra Malaysia (Chairperson) Ramlan Mahmod, PhD Professor Faculty of Computer Science and Information Technology Universiti Putra Malaysia (Member) Mohd Zamrin, PhD Professor Faculty of Medicine Universiti Kebangsaan Malaysia (Member) Norwati Mustapha, PhD Associate Professor Faculty of Computer Science and Information Technology Universiti Putra Malaysia (Member) BUJANG BIN KIM HUAT, PhD Professor and Dean School of Graduate Studies Universiti Putra Malaysia Date:

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DECLARATION

I declare that the thesis is my original work except for quotations and citations which have been duly acknowledged. I also declare that it has not been previously, and is not concurrently, submitted for any other degree at Universiti Putra Malaysia or at any other institution. HASAN HADI KHALEEL

Date: 1 March 2012

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TABLE OF CONTENTS

Page DEDICATION ii ABSTRACT iii ABSTRAK v ACKNOWLEDGEMENTS viii APPROVAL ix DECLARATION x LIST OF TABLES xiv LIST OF FIGURES xvi LIST OF ABBREVIATIONS xxi CHAPTER

1. INTRODUCTION 1.1 Background 1-1

1.1.1 The Heart Anatomy 1-2 1.1.2 Coronary Arteries Diseases and Treatment

Procedures 1-3 1.1.3 Cardiac Imaging Technologies 1-6

1.1.3.1 Ultrasound 1-7 1.1.3.2 Computerized Tomography

Angiography (CTA) 1-8 1.1.3.3 Magnetic Resonance Angiography

(MRA) 1-9 1.1.3.4 Angiograms 1-10

1.1.4 C-arm System 1-11 1.2 Motivation 1-17 1.3 Problem Statement 1-20 1.4 Significance of Research 1-21 1.5 Objectives of Research 1-22 1.6 Scope of Research 1-23 1.7 Thesis Organisation 1-23

2. LITERATURE REVIEW 2.1 Coronary Artery Trees Extraction 2-2

2.1.1 Summary of the Coronary Artery Trees Extraction 2-11

2.2 Three-Dimensional (3D) Reconstruction of Coronary Artery Trees 2-11 2.2.1 Summary of the 3D Reconstruction of

Coronary Artery Trees 2-19 2.2.2 Centre of Gravity (CoG) 2-19

2.2.2.1 Summary of the Centre of Gravity 2-23 2.3 Surface Reconstruction 2-23

2.3.1 Spline Fitting Techniques 2-24 2.3.2 Summary of the Surface Reconstruction 2-45

2.4 Chapter Summary 2-46

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3. RESEARCH METHODOLOGY 3.1 Research Methodology 3-1 3.2 Data Acquisition 3-5

3.2.1 Preparation for Coronary Angiography 3-6 3.2.2 Procedure of Coronary Angiography 3-7

3.3 Data Pre-processing 3-8 3.4 Coronary Artery Trees Extraction 3-12 3.5 3D Reconstruction of Coronary Artery Trees 3-14 3.6 Centre of Gravity in 3D Data 3-15 3.7 Surface Reconstruction of a 3D Cloud of Points 3-17

3.7.1 Surface Curvatures Estimation 3-18 3.8 Summary 3-19

4. CORONARY ARTERY TREES EXTRACTION 4.1 Introduction 4-1 4.2 Proposed Methodology 4-7

4.2.1 Gaussian Matched Filter 4-7 4.2.2 Threshold Estimation 4-10

4.2.2.1 Variance ( ) Value 4-14 4.2.2.2 Lighting Effect 4-16

4.2.3 Angiogram Images 4-18 4.3 Implementation 4-28 4.4 Experiments, Results and Discussion 4-31 4.5 Advantages and Limitations 4-47 4.6 Summary 4-47

5. 3D RECONSTRUCTION OF CORONARY ARTERY TREES

5.1 Introduction 5-1 5.2 Proposed Methodology 5-6

5.2.1 Masking 5-7 5.2.2 Data files 5-11 5.2.3 3D Reconstruction Algorithm 5-14

5.3 Implementation 5-16 5.4 Experiments, Results and Discussion 5-19 5.5 Advantages and Limitations 5-33 5.6 Summary 5-34

6. CENTER OF GRAVITY IN ANGIOGRAMS AND 3D DATA

6.1 Introduction 6-1 6.2 Proposed Methodology 6-5

6.2.1 CoG for Real Objects and Images 6-7 6.2.2 Recursive Division of Angiograms 6-9 6.2.3 Finding the Number of Points (NoP) 6-12 6.2.4 Calculation of the CoG 6-13 6.2.5 Linking CoG points by lines 6-21

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6.3 Implementation 6-23 6.4 Experiments, Results and Discussion 6-25 6.5 Advantages and Limitations 6-42 6.6 Summary 6-43

7. SURFACE RECONSTRUCTION OF 3D CLOUD OF POINTS

7.1 Introduction 7-1 7.2 Proposed Methodology 7-8

7.2.1 Euclidean Distance Calculations 7-10 7.2.2 Oriented Data Structuring 7-14 7.2.3 Poisson Surface Reconstruction 7-26

7.2.3.1 The Poisson Problem 7-27 7.2.3.2 Continuity 7-29

7.2.4 Curvature Estimates 7-30 7.3 Implementation 7-38 7.4 Experiments, Results and Discussion 7-41 7.5 Advantages and Limitations 7-58 7.6 Summary 7-59

8. CONCLUSION

8.1 Concluding Remarks 8-1 8.1.1 Coronary Artery Trees Extraction 8-2 8.1.2 3D Reconstruction of Coronary Artery Trees 8-3 8.1.3 Centre of Gravity in 3D Data 8-4 8.1.4 Surface Reconstruction of a 3D Cloud of

Points 8-6 8.2 Contributions of the Research 8-8 8.3 Recommendations for Future Work 8-10

REFERENCES R1 APPENDIX A A APPENDIX B B LIST OF PUBLICATIONS P1 BIODATA OF STUDENT O