Medical Imaging Systems - Lecture Material

CMPUT616 Fundamentals of Medical Imaging

CMPUT616 - Autumn 2011 Fundamentals of Medical Imaging Every Monday, 15h00 to 17h30 Room 349

General Description:

The course starts by reviewing signal processing theory with example from medical imaging. We will then study six general medical imaging modalities: projection radiography, computed tomography, magnetic resonance imaging, nuclear imaging, ultrasound, and confocal microscopy. The goal will be to understand these modalities in terms familiar to a computer scientist. Following the study of modalities, we will then review basic 3D image processing such as filtering, registration, segmentation, and data driven physical simulation. Flexibility exists for the instructor to vary the depth of each topic area after determining the general background and experience of the students.

Syllabus:

Lecture 1: History of Modalities:  Powerpoint files: Introduction.ppt,

Lecture 2: Basics of Linear Systems:  Powerpoint files: LinearSystems-I.ppt,

Lecture 3: Convolution and 1-D Fourier Transform:  Powerpoint files: LinearSystems-II.ppt,

Lecture 4: 2-D Fourier Transform:  Powerpoint files: LinearSystems-III.ppt,

Lecture 5: Sampling Theorem:  Powerpoint files: LinearSystems-IV.ppt,

Lecture 6: Discrete Fourier Transform:  Powerpoint files: LinearSystems-V.ppt,

Lecture 7: Hankel Transform:  Powerpoint files: LinearSystems-VI.ppt,

Lecture 8: 3-D Slicer  Powerpoint files: Slicer3Minute_SPujol.pdf,  3D Slicer website  Tutorials

Lecture 9: Fundamental of X-Ray Physics-I:  Powerpoint files:xRayPhysics-I.ppt,  Movies: XRay General.avi

Lecture 10: Fundamental of X-Ray Physics-II:  Powerpoint files: xRayPhysics-II.ppt,  Movies: Source Obliquity.avi  XRay Depth Dependence.avi

Lecture 11: X-Ray Distortion and Non-linearity:  Powerpoint files: xRayPhysics-III.ppt  Movies: xray source blurring.avi

Lecture 12: Statistical Model of X-Ray Images:  Powerpoint files: xRayPhysics-IV.ppt  Movies: screem capture.avi  xray_contrast_and noise.avi

Lecture 13: X-ray CT-I:  Powerpoint files: CT-I.ppt  Movies: CTscanBasic.avi  CTbackProjDivx.avi

Lecture 14: X-ray CT-II:  Powerpoint files: CT-II.ppt

Lecture 15: Fundamental of MRI:  Powerpoint files: MR-I.ppt  Movies: MR Proton Precession.avi  MR Transceiver Signal.avi

Lecture 16: MRI Image Formation Overview:  Powerpoint files: MR-II.ppt,  Movies: MR Gradient Coil Fields.avi  MR spin vector field.avi  Moviews: MXY under gradient vector fields  MXY with effects of B0 inhomogeneity  Moviews: MXY with effects of B0 inhomogeneity  MXY with B0 inhomogeneity with spin echo

Lecture 17: Nuclear Imaging:  Powerpoint files: Nuclear.ppt

Lecture 18: Ultrasound Imaging Systems:  Powerpoint files: Ultrasound.ppt

Lecture 19: Fluoroscopy and Confocal Microscopy  Powerpoint files: Confocal.ppt

Lecture 21: Multi-modal Non-linear Filtering  Powerpoint files: Filtering.ppt

Lecture 22: Multi-modal Registration  Powerpoint files: Registration.ppt

Lecture 23: Multi-modal Segmentation  Powerpoint files: Segmentation.ppt

Lecture 24: From Segmentation to Physical Simulation and Surgical Planning  Powerpoint files: Simulation.ppt

Textbook:

The following textbook is used to provide both the engineering, mathematical, and physics background necessary for this course. I will lecture from the class notes but I will refer to the textbook from time to time and some of the assignment will be from the textbook.

J.L. Prince and J.M. Links, Medical Imaging: Signals and Systems, Pearson Prentice Hall Bioengineering Homework Homework will generally be handed out during a lecture and will be due on the following week. Some parts of the homework may involve SLICER exercises. There will be approximately 5 problem sets. Don't be misled by the relatively few points assigned to homework grades in the final grade calculation. While the grade that you get on your homework is at most a minor component of your final grade, working the problems is a crucial part of the learning process and will invariably have a major impact on your understanding of the material.

SLICER-Based Project and Exercises One of the best ways of learning much of the material in this course is by exploring many of the concepts with Slicer. In addition to traditional homework problems, this subject will have a computer exercise component based on the Slicer software package.

Course Project There will be an individual semester project, culminating in a final 8 pages report in IEEE format and a 20 minutes presentation during a one day workshop in December. Progress and check points before the final due date will count toward the final grade. Course Grade The final grade for the course is based on our best assessment of your understanding of the material, as well as your commitment and participation. The SLICER project, problem sets, and the final projects are combined to give a final grade: ACTIVITIES WEIGHT

Final Project 60%

Problem Sets 20%

SLICER Project(s) 20%

Links:

 Introduction to various technologies from HowStuffWorks.com o X-rays o CT o MRI o Ultrasound  Joseph Hornak, The Basics of MRI  Online resource, available at http://www.cis.rit.edu/htbooks/mri/ (Introduction to MRI)  MRI safety (flying objects) [simplyphysics.com]  The Ottawa Medical Physics Institute has a series of interesting and relevant Seminars  The Visible Human Project  Interactive Visible Human Viewer  The Computer Vision Test Image Database has many databases relevant to image processing. Some contain medical images  The MedPix Database has X-ray and CT and MRI images.  Physionet.org / Images  digimorph.org X-Ray CT views of living and extinct vertebrates.  Online Computer vision books  P. K.Kaiser; The Joy of Visual Perception, Online book, 1996.  Kak, M. Slaney. Principles of Computerized Tomographic Imaging, Society of Industrial and Applied Mathematics, 2001.  Martin Spahn Flat detectors and their clinical applications Eur Radiol (2005) 15: 1934-1947