Introduction to Medical Image Analysis - compute.dtu.dk - week8.pdf · DTU Compute 3 DTU Compute,...
Transcript of Introduction to Medical Image Analysis - compute.dtu.dk - week8.pdf · DTU Compute 3 DTU Compute,...
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DTU Compute
Introduction to Medical Image Analysis
Slides adapted from Jens E. Wilhjelms lectures
Rasmus R. PaulsenDTU Compute
http://www.compute.dtu.dk/courses/02511http://www.compute.dtu.dk/courses/02512
mailto:[email protected]://www.compute.dtu.dk/courses/02511
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Lecture 8 X-ray imaging and CT scanning
9.00 Lecture
Exercises
12.00 13.00 Lunch break
13.00 - Exercises
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What can you do after today? Describe the basic use of X-rays Describe the X-ray as an electromagnetic wave Explain the basic technique in an X-ray tube Estimate how simple materials will look on an X-ray Use Lambert-Beers law to compute material attenuation Compute the attenuation of simple non-homogenous
materials Describe the concept of tomographic reconstruction Describe the relation between Hounsfield units and tissue
types Compute a CT slice using a simple and idealised setup
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X-ray imaging The most used form of
medical imaging Simple Cheap Fast Radiation
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The history of X-ray Discovered by chance
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Wilhelm Conrad Rntgen German physics professor Experimented with a Crookes
tube Discovered that an unknown ray
could be captured on photographic plates
Named them X-rays Other call them Rntgen-rays
Had no idea they were dangerous
Made an X-ray of his wife's hand First medical X-ray
Wilhelm Rntgen's first medical X-ray, of his wife's hand, taken on 22 December 1895
Crookes tube
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Quick popularity X-ray became popular
extremely fast Shoe fitting Examine your bones in coin
machines Wedding pictures
X-ray clinics in small normal apartments
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Dangers People started to realise that
exposure to X-rays could be dangerous
Hands of X-ray pioneer Mihran Kassabian
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Brief history of X-ray and CT 1895 Wilhelm Conrad Rntgen discovered X-ray 1896 Within a week X-ray was not known worlwide 1896 GE and Siemens begin selling X-ray equipment 1904 Dangers of radiation are described 1956 First reconstruction algorithm is described 1958 First prototype CT scanner without computer 1968 Hounsfields method for CT patented 1972 Hounsfields method for CT demonstrated in the US 1989 First spiral CT scanner enters the market
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X-rays as electromagnetic radiation It has a frequency f
(v is used for frequency in notes) Measured in Hertz [Hz]
It has a wavelength (lambda) Measured in meters [m]
It has a speed The speed of light c
http://upload.wikimedia.org/wikipedia/en/1/1a/Wavelength.svg
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Wavelength 10 pm < < 10 nm
pm = picometer = 11012 m nm = nanometer = 1109 m
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Production of X-rays Electrons are accelerated using a cathode Some hit the anode (heavy metal target) Slowed down in the anode material
Generating heat A small part of the energy is transformed
to X-rays The electron comes very close to the
nucleus Electromagnetic interaction causes a
deviation of the trajectory The electron looses energy and an X-ray
photon is emitted.
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Electron volts 1 eV is the energy increase that an electron
experiences, when accelerated over a potential difference of 1 V.
In medical imaging 20 keV < E < 150 keV
keV = kilo-electron-volts
Cathode Anode
- +100 kV
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X-ray tube
The anode rotates to avoid over heating
http://upload.wikimedia.org/wikipedia/en/9/9b/Xraytubeinhousing.png
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X-ray tube
Jackson X-ray tube, 1896. Modern rotating anode tube
http://upload.wikimedia.org/wikipedia/commons/5/51/Rontgenbuis-draaianode.jpg
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Full X-ray system
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X-ray film Until recently real film was
used Being replaced by digital
radiography The first step was to use
phosphor plates that was later scanned
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Contrast in X-ray images Some materials absorb more
X-rays than others We see the X-rays that got
through Dark area high radiation
Air Soft-tissue Fat
Bright area low radiation Metals Bone
Scanned X-ray film
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X-ray attenuation (dmpning) X-rays hits an object and
travels through it is the intensity at the
entrance is what is left on the
other side after a length of x
The rest disappears in several different ways
Computed using Lambert-Beers law
I (x)I 0
I 0
I (x)
x
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Lambert-Beers law Materials can be described
using a linear attenuation coefficient How much do the material
dampen X-rays High coefficient
Metal and bone Low coefficient
Soft tissue and fat
: Linear attenuation coefficient
0 1 2 3 4 5 6 7 8 9 100
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
Distance in object (cm)
exp(
x)
High Low
I (x)I 0
x
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Non-homogeneous material Non-homogeneous not the same everywhere
x1
x2 x5x3
x4
I 0
I 0
I 0
I 0I 1
film
I 2
I 3?
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X-rays in practise Several parameters to tune
KV Exposure time Etc
Settings dependent on body part Radiologists are trained for this Still a lot of human knowledge in
taking good X-rays
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Uhomogentmateriale A) 1
B) 2C) 3D) 4E) 5F) 6
Chart1
1
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Sheet1
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CT scanning
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Invention of Computed Tomography 1972: G.N. Hounsfield, scientist in Middlesex, England
Announced computed axial transverse scanning Presented cross-sectional images of the head showing tissues
inside the brain as separate structures of gray matter, white matter, cerebrospinal fluid, and bone
Pathologic processes such as blood clots, tumors, and infarcts could be easily seen
Dr. Hounsfield's discovery completely revolutionized the practice of medicine: Structures inside the human body that had never been imaged before, could now be visualized.
1979 Nobel Prize in Medicine
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Development of CT Early 70s : Several minutes to acquire single slice Today: Less than a minute for a full body scan
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Basic principle of CT Super Sudoku It is assumed that the object
consists of small cubes of homogeneous material
We want to find the linear attenuation coefficient in each cube
I 0
I 0
I 0 I 0
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Quiz? What is A, B, C, D? Can be formulated as a
system of equations 4 unknowns 4 equations
A
C
B
D
A+B = 13
C+D = 10
B+D = 11A+C = 12 DISCLAIMER: just an illustration not solvable
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Basic principle of CT Super Sudoku It is assumed that the
object consists of small cubes of homogeneous material
We want to find the linear attenuation coefficient in each cube
We measure the radiation that comes through
I 0
I 0
I 0 I 0
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Basic principle of CT Super Sudoku What is ?
I 0
I 0
I 0 I 0
x
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Basic principle of CT Super Sudoku Four equations Four unknowns Can be solved directly
I 0
I 0
I 0 I 0
x
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Real CT More than 4 pixels per slice 512 x 512 pixels Many projections Enormous system of
equations Not solvable by direct
methods
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Hounsfield Units Instead of using a linear
attenuation coefficient Dimensionless Calibrated
Air: -1000 Water: 0
Linear attenuation coefficient in voxel
Different equation used in book (eq (1))
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Hounsfield Units
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Hounsfield Units
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Real CT scanning
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Real CT scanning Many projections Advanced reconstruction
algorithms Filtered back projection Radon transform
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Different versions of CT machines
Rotating detectors
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Rotating source stationary detectors
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Modern CT
High Speed Advantage GE Spiral CT
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Multi-slice CT
128 slice scanner
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What can be seen on the CT image
Photograph of cryosectioned head CT scan
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Uhomogent MaterialeA) 1B) 2C) 3D) 4E) 7
0
11
3
6
0
A B C D E
Chart1
0
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3
6
0
Sheet1
A0
B11
C3
D6
E0
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Todays exercise Automatic algorithm to locate the spleen Mandatory hand in for both 02511 and 02512 Several methods
Pixel classification Morphology BLOB analysis
Training data Validation data why?
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Bonus ChallengeThe Spleen Challenge I have three secret images
Locate the spleen on these Upload your Matlab code on CampusNet
The Spleen Challenge Input: file name of DICOM file Output: Binary image with the Spleen
I will run your function on the images and compare the results to the gold truth
The winner is the algorithm that is closest to the ground truth Give your algorithm a funky name
Deadline 4. April
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Previous highlights
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Epic_SpleenMasterOrz9000Extreme_supreme_premium_Deluxe_Edition
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What can you do after today? Describe the basic use of X-rays Describe the X-ray as an electromagnetic wave Explain the basic technique in an X-ray tube Estimate how simple materials will look on an X-ray Use Lambert-Beers law to compute material attenuation Compute the attenuation of simple non-homogenous
materials Describe the concept of tomographic reconstruction Describe the relation between Hounsfield units and tissue
types Compute a CT slice using a simple and idealised setup
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Next week Geometric transformations
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Exercises
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Introduction to Medical Image AnalysisLecture 8 X-ray imaging and CT scanningWhat can you do after today?X-ray imagingThe history of X-rayWilhelm Conrad RntgenQuick popularityDangersBrief history of X-ray and CTX-rays as electromagnetic radiationSlide Number 11Production of X-raysElectron voltsX-ray tubeX-ray tubeFull X-ray systemX-ray filmContrast in X-ray imagesX-ray attenuation (dmpning)Lambert-Beers lawNon-homogeneous materialX-rays in practiseUhomogentmaterialeCT scanningInvention of Computed TomographyDevelopment of CTBasic principle of CT Super SudokuQuiz?Basic principle of CT Super SudokuBasic principle of CT Super SudokuBasic principle of CT Super SudokuReal CTHounsfield UnitsHounsfield UnitsHounsfield UnitsReal CT scanningReal CT scanningDifferent versions of CT machinesRotating source stationary detectorsModern CTMulti-slice CTWhat can be seen on the CT imageUhomogent MaterialeTodays exerciseBonus ChallengeThe Spleen ChallengePrevious highlightsSlide Number 50Slide Number 51Epic_SpleenMasterOrz9000Extreme_supreme_premium_Deluxe_EditionSlide Number 53Slide Number 54What can you do after today?Next weekExercises