Welcome to22481 Introduction to medical imaging
Biomedical EngineeringHealth Tech
Jens E. Wilhjelm°, Markus Nowak Lonsdale¹,Lars G. Hanson² & Mikael Jensen³(with assistance by Mads Fjelbro Klavsen³)
°Biomedical Instrumentation, ²Center for Magnetic ResonanceDepartment of Health Technology
¹Department of nuclear medicine, Bispebjerg Hospital, ³Hevesy laboratory, DTU Nutech (Risø), DTU
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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What is medical imaging?
Tomographic (tomo = slice) images of living tissueProjection (or shadow) images of living tissue
What does the images show?Structure or anatomy:
Organs (lungs, heart, liver, bones, blood vessels, etc)
Functionality:Blood flow (occlusion in vessels, perfusion, etc)
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What does medical imaging reveal?
A broken boneCancerOcclusion of blood vessels (Atherosclerosis)Heart (dis)functionalityMuscle (dis)functionalityPregnancy follow-upBrain functionand much more......
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Imaging modalitiesSound:
Diagnostic ultrasound (acoustical impedance diff)
X-ray:Planar (projection) (density)Computed Tomography (CT) (density)
Radioactive tracers (Nuclear medicine):SPECT (intensity of radioactive tracer)PET (intensity of radioactive tracer)
Radio waves:Magnetic Resonance Imaging (eg. H2O content)
Elec
trom
agne
tic ra
diat
ion
Mec
hani
ncal
vibr
atio
n
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Course objectives
In short:Understand X-ray, CT, PET, US and MRIBe able to work with real images in MATLABDo laboratory work (?)Do independent and team-wise project workWrite an impressive report
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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Looking for the unknown
(Photograph removed)
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An image says a thousand words, but you need to know the words
Sour
ce: W
ikip
edia
(Photograph removed)
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The phantoms
(Photograph removed)
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Tissue in agar block
Fiducial markers(or reference markers)
Agar
Phantom number in binary Tube for radioactive tracer
Tissue
Phantom number
Acrylic lid
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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The main flow of the courseYou will get:
A photograph of the phantom surfaceMedical imaged from Bispebjerg hospital and DTUPhotograps of sliced tissue to make a reference
You will:Maybe do some home experimentsDo some image handling, processing and analysisStudy the physics of the imaging modalitiesMake a final report on the above and based on 4 assignments
(Photograph removed)
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The time lineLectures etc
13-14:30
MRI
PET
X-ray & CT
US
MRI
September
December
Data recording & analysis14:30-17:00
Top photo
MRIX-ray
CT &PET
US
Slicing
AssignmentsHome
0
1
2
3
4
Final report
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Next Thursday
Next module (one week before Bispebjerg):Short lecture on all modalitiesVideo about the same (if I find time to produce)MRI as already planned
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Which objects to identify?
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Which objects to identify?
All things within the limit of the acrylic box
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Which objects to identify?
I 22481
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The main flow of the course
Study the imaging techniques!!!
(Photograph removed)
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Format of the course: Homepage
courses.healthtechnology.dtu.dk/22481
(how to nagivate in these pages)
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Format of the course: The plan
We do not have "grupperegning". We have project work!So all rehearsal for the exam is on your own!
Read in advance to lecture. Otherwise it will be very fustrating for you.
courses.healthtechnology.dtu.dk/2248121/53
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Language
Normally English lecturesAll written material is in EnglishDuring project work, guidance is in Danish/EnglishReport language is your choicePlease consider writing assignments 1 to 4 in English
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The Web Book of Medical Imaging
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Peer-reviewSet-up:
Assignments 1 and 2 are individual and will be peer reviewed.Assignments 3 and 4 are team-wise and will be reviewed by TAs.
Procedure for Assignment 1:All students opload their reportsEach report is then sent to three different students:1. Each student have to use a scoring sheet (Rubric) to score each of
the three reports2. All reviews are meant to be double-blinded so:
No name in text, in properties nor in file name3. I will oversee the entire process4. Problems in Learn or CampusNet (Inside):
Please ask TAs to help.Pease document these!
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Report writing
Reading and writing reports have to be to seperate processes.If citing text, there is only one way: In quotes (that is: "bla bla") with reference immediately after the end-quote. Otherwise, it will be considered plagarism and treated as such!When does the work start?
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Exam
Type:24 problems MC exam lasting 2 hours (in English)Designed so that remembering how to solve a problem does not help much. The idea is that the process of leaning is important!Exam problems and solutions for all previous years are available.
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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COVID-19
Follow general rulesAccess to kitchen - but keep nice and tidy, please
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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The SIS toolbox(self-contained image structure)
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SIS: zoom on 2D example
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SIS: zoom on 2D example
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SIS: zoom on 2D example
distance in mm
dist
ance
in m
m
image values
Data.Images
Data.Axes(2).Axis
Dat
a.Ax
es(1
).Axi
s
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SIS: zoom on 2D example
Data.Images
Data.Axes(2).Axis
Dat
a.Ax
es(1
).Axi
s
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The SIS structureData.Images: [100x200x50 double]Data.ImageType: 'intensity'Data.Axes: [1x3 struct]Data.ImagesLabel: 'Magnitude'Data.ImagesSymbol: 'HV'Data.ImagesUnit: 'HU'Data.Date: 7.3329e+005Data.Object: 'Phantom 1'Data.Operator: 'mnl'Data.Where: 'Bispebjerg Hospital'Data.ScannerType: 'CT'Data.Settings: (e.g. DICOM header)
Main fields:
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SIS: 3D example
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SIS: 3D example
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SIS: 3D example
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SIS: 3D example
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SIS: 3D example
1Data.Images( , , )1
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SIS: 3D example
12
Data.Images( , , )1 2
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SIS: 3D example
12
3
Data.Images( , , )1 2 3
*
* By sis_zoom43/53
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SIS: 3D example
12
3
Data.Images( , , )1 2 3
is fixed for this image3*
* By sis_zoom44/53
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SIS: 3D example
3
3
Data.Images( , , )1 2 3
* By sis_zoom
*
is fixed for this image1
22
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SIS: 3D example
3
3
Data.Images( , , )1 2 3
* By sis_zoom
*
is fixed for this image1
22
( )( )(New image)
1
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SIS: 3D example
DataOut = sis_zoom( DataIn, [45 1 1], [45 50 25], 'iii') output input start stop mode
DataIn.Images is100 by 50 by 25
DataOut.Images is:1 by 50 by 25 which is changed to 50 by 25
Dimension 1 disappearsDimension 2 becomes dimension 1Dimension 3 becomes dimension 2(50 by 25 can be changed to 25 by 50 via sis_reorder)
3 3 3
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SIS: What do you need?
MATLAB (ideal is 2017a, but others may also work)Image processing toolbox (plus more?)
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Teaching assistants-how can they help?
Here you need Oraculus:MyImage = ones(3,3);MyImage = 3*MyInage;
Here you might need a teaching assistant (TA):MyImage = ones(3,3);imagesc( [1 5 6], [22 23 50], MyImage); colorbar;
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ContentMedical imaging and course objectives
The plot
Format of the course
COVID-19
SIS
This afternoon
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This afternoon
349.214 & 215(two phantoms at a time,
starting with teams 1 and 2)
Optical scanning of
phantomJens E. Wilhjelm
349.019,025,034(all other teams)
Treasure hunt(see the plan)
Try examples in SIS guide
Work with data from optical scanning
(homepage)
Mads Fjeldbro Klavsen
Forming teamsYou are
here
17:00
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Team establishment(only for those not in a team)
Procedure:If you are a bachelor from MedTek, try to form teamIf not a bachelor from MedTek OR not forming a team with only MedTek:
Come to me right nowPresentation roundForming of teams
All teams:Within 1 hour, submit to [email protected] a mail with:
Team members name and study IDTeam title, if you so desire
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The last slide of today
My basic philosophy:I hear, and I forgetI see, and I know where to look for it laterI write & draw, and I rememberI do, and I understand
and ...We do not teach biomedical engineering, we teach you to be a biomedical engineer
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