Medical Images, 6 credits (TSBB31)

Medicinska bilder, 6 hp

Main field of study

Electrical Engineering

Level

First cycle

Course type

Programme course

Examiner

Maria Magnusson

Director of studies or equivalent

Lasse Alfredsson
Course offered for Semester Period Timetable module Language Campus VOF
6CMED Biomedical Engineering, M Sc in Engineering 5 (Autumn 2019) 1 1 Swedish Linköping o

Main field of study

Electrical Engineering

Course level

First cycle

Advancement level

G2X

Course offered for

  • Biomedical Engineering, M Sc in Engineering

Entry requirements

Note: Admission requirements for non-programme students usually also include admission requirements for the programme and threshold requirements for progression within the programme, or corresponding.

Prerequisites

Continuous 1-D Fourier transform and its theorem for scaling, translation, derivation, convolution and multiplication. Basic knowledge of Matlab programming. Linear algebra: vector, matrix, determinant and scalar product. One- and multidimensional calculus.

Intended learning outcomes

After completing the course, the student will be able to:

  • Describe the generalization from 1-D to 2-D continuous Fourier transform and related theorems, such as scaling, translation, derivation, convolution and multiplication.
  • Explain the following concepts in 1-D and 2-D: sampling and reconstruction, DFT, the sampling theorem and aliasing, resampling and interpolation.
  • Interpret the results of a 2-D Fourier transform of an image, such as understanding what a spatial frequency means. Describe simple convolution kernels and filters that perform differentiation, low-pass and high-pass filtering.
  • Know of the most common types of medical images, what they show, their underlying physics and technique: ultrasound, x-ray, CT, MRI, gamma-camera, SPECT, PET.
  • Have a deeper understanding the above techniques, with focus on signal- and image processing.

     

Course content

The course consists of two parts. The first part provides fundamental knowledge about 2D signal processing on images. In the second part, these skills are used in the study of various medical imaging techniques. The course aims to give a deeper understanding of ultrasound, CT, MRI, SPECT and PET, with focus on signal- and image processing.

  • The digital image: pixels/size/zoom, storage and quantization, grayscale/color, real/complex. Histogram and gray-scale transformations. Color Tables: grayscale, RGB true, pseudo.
  • Repetition of 1-D Fourier transform. From 1-D to 2-D Fourier transform. Theorems for 1-D and 2-D Fourier transform, such as scaling, translation, derivation, convolution and multiplication. Theorems for the 2-D Fourier transform such as the rotation and projection theorem. Looking at images and their Fourier transforms and relating them to the theorems.
  • The Dirac impulse. Sampling and reconstruction. Effects on the image during aliasing in the spatial or Fourier domain.
  • 1-D and 2-D DFT and FFT. Discrete 1-D and 2-D convolution. Convolution kernels/filters in the spatial and Fourier domain: low-pass (gauss), high-pass (Laplace), derivative (Sobel). Edge detection using the magnitude of the gradient.
  • Resampling and interpolation, especially up- and down-sampling. Ideal up-sampling by zero-padding.
  • Some simple image analysis tools: threshholding, erosion, labelling.
  • Important measurements on images such as: contrast, MTF, resolution, SNR.
  • Ultrasound.
  • Briefly on different imaging techniques: digital radiography, angiography, fluoroscopy, mammography.
  • Briefly on the physics for plain radiography and CT: X-ray spectrum, physical interactions such as photoelectric effect, Compton and Rayleigh radiation, noise. The idea is to show how the physics influence the image quality.
  • CT: the projection theorem, 2-D reconstruction using the direct Fourier method, 2-D reconstruction using filtered back projection, parallel beam and fanbeam, rebinning, briefly on 3-D reconstruction.
  • PET and SPECT. CT-PET and CT-SPECT.
  • Carefully about MRI basics. Overview of some MRI-variants, fMRI, EPI, diffusion.


The computer exercises:

  • 1) The digital image: pixels/size/zoom, quantization and storage, grayscale/color, real/complex. Histogram and grayscale transformations. Color tables: grayscale, RGB true, pseudo. 2-D Fourier transform of the images: appearance, properties. Simple convolution kernels in the spatial domain. Linear filters in the Fourier domain.
  • 2) Resampling and interpolation. Effects of sampling in the spatial and Fourier domain. Extra exercise on dowsampling and aliasing.
  • 3) CT reconstruction: How do you do a CT image?
  • 4) Basic MRI. Design of pulse sequences.
  • 5) How do you do an ultrasound image? Rf-signal => envelope detection => downsampling => histogram transformation => scan conversion (resampling) => ultrasound image
  • 6) Measurement of noise. Some simple image analysis methods. Preparation for computer exercise 7.
  • 7) Measurements on SPECT/CT-volumes. Example volumes form healthy and COPD patients.


Study visit: The course includes a study visit to CMIV, where we will look at a CT-scanner and an MRI-camera. We will also listen to a lecture about how medical images are used today at the University Hospital in Linköping

 

Teaching and working methods

The course consists of lectures, tutorials and laboratory sessions based on Matlab.

Examination

LAB1Laboratory workU, G2 credits
TEN1Written examinationU, 3, 4, 54 credits

Grades

Four-grade scale, LiU, U, 3, 4, 5

Other information

Admission courses: Courses within the image profile.

Department

Institutionen för systemteknik

Director of Studies or equivalent

Lasse Alfredsson

Examiner

Maria Magnusson

Education components

Preliminary scheduled hours: 71 h
Recommended self-study hours: 89 h

Course literature

Books
Prince, J.L., Links, J.M., (2008) Medical Imaging: Signals and Systems (Prince, J.L. and Links, J.M.; 2006) [Book Review]
Compendiums
Maria Magnusson, Grundläggande 1D och 2D signalbehandling för Bilder

(in Swedish)

Other

*) Lecture slides.

*) Lesson material.

*) Laboratory exercise material.

*) Formula collection.

*) Short extract from the PhD-thesis by Maria Magnusson.

*) Short extract from the PhD-thesis by Henrik Turbells.

*) Parts from the Master Thesis by Oscar Grandell.

*) Short on Poisson noise by Theo Fuchs.

*) Parts from the TBMI02 Compendium: "MRI, fMRI, Image Registration, Image Segmentation".

All material above are in pdf-format and are available from the course home page.

Books

Prince, J.L., Links, J.M., (2008) Medical Imaging: Signals and Systems (Prince, J.L. and Links, J.M.; 2006) [Book Review]

Compendia

Maria Magnusson, Grundläggande 1D och 2D signalbehandling för Bilder

(in Swedish)

Other

*) Lecture slides.

*) Lesson material.

*) Laboratory exercise material.

*) Formula collection.

*) Short extract from the PhD-thesis by Maria Magnusson.

*) Short extract from the PhD-thesis by Henrik Turbells.

*) Parts from the Master Thesis by Oscar Grandell.

*) Short on Poisson noise by Theo Fuchs.

*) Parts from the TBMI02 Compendium: "MRI, fMRI, Image Registration, Image Segmentation".

All material above are in pdf-format and are available from the course home page.

LAB1 Laboratory work U, G 2 credits
TEN1 Written examination U, 3, 4, 5 4 credits

Course syllabus

A syllabus has been established for each course. The syllabus specifies the aim and contents of the course, and the prior knowledge that a student must have in order to be able to benefit from the course.

Timetabling

Courses are timetabled after a decision has been made for this course concerning its assignment to a timetable module. A central timetable is not drawn up for courses with fewer than five participants. Most project courses do not have a central timetable.

Interrupting a course

The vice-chancellor’s decision concerning regulations for registration, deregistration and reporting results (Dnr LiU-2015-01241) states that interruptions in study are to be recorded in Ladok. Thus, all students who do not participate in a course for which they have registered must record the interruption, such that the registration on the course can be removed. Deregistration from a course is carried out using a web-based form: www.lith.liu.se/for-studenter/kurskomplettering?l=sv. 

Cancelled courses

Courses with few participants (fewer than 10) may be cancelled or organised in a manner that differs from that stated in the course syllabus. The board of studies is to deliberate and decide whether a course is to be cancelled or changed from the course syllabus. 

Regulations relating to examinations and examiners 

Details are given in a decision in the university’s rule book: http://styrdokument.liu.se/Regelsamling/VisaBeslut/622678.

Forms of examination

Examination

Written and oral examinations are held at least three times a year: once immediately after the end of the course, once in August, and once (usually) in one of the re-examination periods. Examinations held at other times are to follow a decision of the board of studies.

Principles for examination scheduling for courses that follow the study periods:

  • courses given in VT1 are examined for the first time in March, with re-examination in June and August
  • courses given in VT2 are examined for the first time in May, with re-examination in August and October
  • courses given in HT1 are examined for the first time in October, with re-examination in January and August
  • courses given in HT2 are examined for the first time in January, with re-examination at Easter and in August.

The examination schedule is based on the structure of timetable modules, but there may be deviations from this, mainly in the case of courses that are studied and examined for several programmes and in lower grades (i.e. 1 and 2). 

  • Examinations for courses that the board of studies has decided are to be held in alternate years are held only three times during the year in which the course is given.
  • Examinations for courses that are cancelled or rescheduled such that they are not given in one or several years are held three times during the year that immediately follows the course, with examination scheduling that corresponds to the scheduling that was in force before the course was cancelled or rescheduled.
  • If teaching is no longer given for a course, three examination occurrences are held during the immediately subsequent year, while examinations are at the same time held for any replacement course that is given, or alternatively in association with other re-examination opportunities. Furthermore, an examination is held on one further occasion during the next subsequent year, unless the board of studies determines otherwise.
  • If a course is given during several periods of the year (for programmes, or on different occasions for different programmes) the board or boards of studies determine together the scheduling and frequency of re-examination occasions.

Registration for examination

In order to take an examination, a student must register in advance at the Student Portal during the registration period, which opens 30 days before the date of the examination and closes 10 days before it. Candidates are informed of the location of the examination by email, four days in advance. Students who have not registered for an examination run the risk of being refused admittance to the examination, if space is not available.

Symbols used in the examination registration system:

  ** denotes that the examination is being given for the penultimate time.

  * denotes that the examination is being given for the last time.

Code of conduct for students during examinations

Details are given in a decision in the university’s rule book: http://styrdokument.liu.se/Regelsamling/VisaBeslut/622682.

Retakes for higher grade

Students at the Institute of Technology at LiU have the right to retake written examinations and computer-based examinations in an attempt to achieve a higher grade. This is valid for all examination components with code “TEN” and "DAT". The same right may not be exercised for other examination components, unless otherwise specified in the course syllabus.

Retakes of other forms of examination

Regulations concerning retakes of other forms of examination than written examinations and computer-based examinations are given in the LiU regulations for examinations and examiners, http://styrdokument.liu.se/Regelsamling/VisaBeslut/622678.

Plagiarism

For examinations that involve the writing of reports, in cases in which it can be assumed that the student has had access to other sources (such as during project work, writing essays, etc.), the material submitted must be prepared in accordance with principles for acceptable practice when referring to sources (references or quotations for which the source is specified) when the text, images, ideas, data, etc. of other people are used. It is also to be made clear whether the author has reused his or her own text, images, ideas, data, etc. from previous examinations.

A failure to specify such sources may be regarded as attempted deception during examination.

Attempts to cheat

In the event of a suspected attempt by a student to cheat during an examination, or when study performance is to be assessed as specified in Chapter 10 of the Higher Education Ordinance, the examiner is to report this to the disciplinary board of the university. Possible consequences for the student are suspension from study and a formal warning. More information is available at https://www.student.liu.se/studenttjanster/lagar-regler-rattigheter?l=sv.

Grades

The grades that are preferably to be used are Fail (U), Pass (3), Pass not without distinction (4) and Pass with distinction (5). Courses under the auspices of the faculty board of the Faculty of Science and Engineering (Institute of Technology) are to be given special attention in this regard.

  1. Grades U, 3, 4, 5 are to be awarded for courses that have written examinations.
  2. Grades Fail (U) and Pass (G) may be awarded for courses with a large degree of practical components such as laboratory work, project work and group work.

Examination components

  1. Grades U, 3, 4, 5 are to be awarded for written examinations (TEN).
  2. Grades Fail (U) and Pass (G) are to be used for undergraduate projects and other independent work.
  3. Examination components for which the grades Fail (U) and Pass (G) may be awarded are laboratory work (LAB), project work (PRA), preparatory written examination (KTR), oral examination (MUN), computer-based examination (DAT), home assignment (HEM), and assignment (UPG).
  4. Students receive grades either Fail (U) or Pass (G) for other examination components in which the examination criteria are satisfied principally through active attendance such as other examination (ANN), tutorial group (BAS) or examination item (MOM).

The examination results for a student are reported at the relevant department.

Regulations (apply to LiU in its entirety)

The university is a government agency whose operations are regulated by legislation and ordinances, which include the Higher Education Act and the Higher Education Ordinance. In addition to legislation and ordinances, operations are subject to several policy documents. The Linköping University rule book collects currently valid decisions of a regulatory nature taken by the university board, the vice-chancellor and faculty/department boards.

LiU’s rule book for education at first-cycle and second-cycle levels is available at http://styrdokument.liu.se/Regelsamling/Innehall/Utbildning_pa_grund-_och_avancerad_niva. 

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