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G16.4428 Practical Magnetic Resonance Imaging II

Part 2: Medical Image Analysis

Henry Rusinek, Artem Mikheev and Jelle Veraart

Tuesdays 2:00, Fridays 1:00

The second part introduces the basics of medical image representation

and analysis. This includes post-processing algorithms that are highly

relevant in clinical radiology: tissue/organ segmentation, coregistration

and kinetic modeling of dynamic MRI. During laboratory sessions and

homework, students will use Matlab and FireVoxel to implement and test

image reconstruction methods, perform image segmentation and

coregistration.

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Part 2 consists of six lectures and four labs:

lecture #9 Fri 10/24 HR imaging modalities

lab #7 Tue 10/28 HR image representation & formats

lecture #10 Fri 10/31 AM nonuniformity correction

lab #8 Tue 11/4 HR image processing, FireVoxel

lecture #11 Fri 11/7 AM organ/tissue segmentation

lab #9 Tue 11/11 HR segmentation at work

lecture #12 Fri 11/14 JV noise & parametric mapping

lecture #13 Tue 11/18 HR dynamic MRI & models

lecture #14 Fri 11/21 HR intro to image coregistration

lab#10 rm chnge Tue 11/25 HR coregistration at work

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Imaging plays a key role in modern medicine

Image data are found in many clinical

specialties:

orthopedics (x-ray, CT)

pulmonology (x-ray, CT)

cardiology (nuclear medicine)

cardiac intervention (fluoroscopy)

urology and gastro-intereology (ultrasound

and endoscopy)

In addition to diagnosis and therapy, imaging

methods are vital for basic biomedical research

and drug development.

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Medical imaging modalities

In addition to MRI, today the most important medical imaging modalities are: planar X-ray

CT

ultrasound

gamma cameras

PET/SPECT scanners

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Basics of CT

CT scanner consists of an array of x-ray detectors opposing an

x-ray tube. This gantry rotates around the object being

imaged.

The attenuation profile changes

depending on the object and the

rotation angle when an x-ray passes

a volume element of length ds

having an attenuation coefficient μ

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Relationship between detected & emitted x-rays flux

The exit x-ray intensity I (detected flux) is related to the emitted intensity by the

equation:

𝐼𝑑𝑒𝑡𝑒𝑐𝑡 = 𝐼𝑒𝑚𝑖𝑡 e−μds [1]

where μ is the attenuation coefficient, ds is the path length. If we divide the object in a

discrete pixels indexed with i, equ.[1] can be refined as:

𝐼𝑑𝑒𝑡𝑒𝑐𝑡 = 𝐼𝑒𝑚𝑖𝑡 e− i μi ds i [2]

After a logarithmic transformation:

ln(𝐼𝑒𝑚𝑖𝑡 /𝐼𝑑𝑒𝑡𝑒𝑐𝑡 ) = i μi dsi [3]

Thus we can capture the unknown attenuation coefficients in a LINEAR system of

equations. The system is sparse, which facilitates accurate solution.

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Reconstruction of CT image from projections

Back in 1917 an Austrian mathematician Johann Radon derived an analytic solution

for reconstructing an image from its projections. This solution, termed "filtered

backprojection" was rediscovered in 1970's and used in the first generation CT scanner

developed by a British engineer Hounsfield.

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Non-filtered vs filtered back-projection

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The first EMI CT developed by Hounsfield at

Godfrey Hounsfield (1919 – 2004) was an English engineer who shared the

1979 Nobel Prize for Physiology or Medicine with Allan Cormack for his part in

developing at EMI Ltd. the computed tomography.

His name is immortalized in the quantitative measure of attenuation coefficient μ.

The scale is defined in Hounsfield units (HU), running from air at −1000 HU,

through water at 0 HU (dense cortical bone ~1000 HU).

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CT scanner generations

1st Gen -- translate and rotate, single detector, 5 mins/slice 2nd Gen -- fan beam and multiple detectors, translations, 20 secs/slice 3rd Gen -- curved detector, no translation, tube and detector rotate 4th Gen -- 360° detector ring -- too expensive!

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Spiral (helical) CT

Earlier x-ray CT scanners imaged one slice at a

time while the patient remained static. In spiral

CT, the patient is being moved axially at a

uniform rate, the x-ray source describes a

helical trajectory relative to the patient body.

The helical scan method reduces the x-ray dose

to the patient required for a given resolution

and scan is faster. There is however greater

complexity in the reconstruction of the image.

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Multi-detector CT

Since its invention by Kalender in the 1980s, spiral CTs have increased the number of

rows of detectors. The prototype 16-slice scanner was introduced in 2001. In 2004, 64-

scanners became available, that can produce a chest volume image in a few sec. This is

important for imaging the heart and coronary vessels.

512 x 512 x 340

(1/2 mm)3

in 3 sec

cardiac vessel imaging

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CT image artifacts

CT is prone to artifacts, as it depends on consistency of millions of measurements:

Streaking

Shading – defect in a group of channels

Ring – detector failure

Beam hardening -- x-ray physics

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Nuclear medicine imaging

fundamental difference from CT: radiation source is introduced to patient

instruments: gamma camera, SPECT, PET

radioactivity: unstable elements 99m-TC or 123-I emit gamma radiation

radiochemistry: science of binding radioactive elements with important

molecules that are taken up by tumors or body organs due to their chemical

properties

radioactive quantity is tiny: "tracer" method

nuclear medicine images show body function, unlike CT that show structure.

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Half-life of common radioactive isotopes

Half-life ( h ) is the time required for a quantity to fall to half its value:

𝑁 𝑡 = 𝑁0 1

2

𝑡

ℎ or 𝑁 𝑡 = 𝑁0𝑒

−𝑡𝜌 where ℎ =ln(2)

𝜌

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Conventional 2D gamma camera – Anger camera

Invented by Hal Anger (1920-2005)

a large area crystal made of NaI(Tl)

collimator placed in front of the crystal

behind the collimator – a 2D array of photo multiplier tubes (PM)

signal from PM used to resolve gamma incidence -- event locator

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SPECT camera

SPECT imaging is performed by using a several

gamma cameras to acquire 2-D images

(projections) at defined points during the

rotation, typically every 3–6 degrees. Typical

time taken to obtain each projection is ~20

seconds, yielding a total scan time of ~20 min.

A tomographic reconstruction algorithm, similar

to CT reconstruction, yields a 3-D image.

Typical spatial resolution is ~8mm. Camera cost

= $200,000, exam cost ~$200.

Multi-headed gamma cameras can provide

accelerated acquisition. For example, a

dualheaded camera can be used with heads

spaced 180 degrees apart, allowing 2 projections

to be acquired simultaneously, with each head

requiring 180 degrees of rotation. Triplehead

cameras with 120-degree spacing are also used.

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Example of a cardiac SPECT study

The SPECT cardiac stress images are

standard heart exams. Patient is imaged

at rest and after exercise (causing dilated

the coronary arteries). The most

common tracers are Thallium-201 or

Technetium Sestamibi.

SPECT camera detects significant

coronary artery blockages that result in

lower perfusion to a segment of the

heart. If both the resting and stress

images show defects, the tissue is dead

(the patient had a heart attack).

Images are generally displayed in three

different projections, with stress images

directly next to resting images.

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Solid state gamma camera technology

Research is being done on solid state detector

technology, mostly based on cadmium

telluride (CdTe) and cadmium zinc telluride

(CdZnTe) crystals. Compared to Anger

cameras based on NaI crystals, these solid state

detectors provide better photon energy

discrimination. They may be also more sensitive

(faster acquisition) and since they

don’t require photomultiplier tubes, they are more

compact.

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Positron (β+) emitters for PET imaging

atoms with excess # of protons used as tracers

Release of a β+ and a neutrino

2 gamma in exactly opposite directions, 511 keV each

coincidence time window: ~ 5 nsec

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PET camera

PET is similar to SPECT in its use of

radioactive tracer material and detection

of gamma rays. In contrast with

SPECT, PET tracers emits two gamma

photons to be emitted in opposite

directions. A PET scanner detects these

emissions coincident in time, which

provides better localization and higher

resolution than SPECT. Typical spatial

resolution is ~5mm. PET cameras are

significantly more expensive

(~1,500,000$) than SPECT. The cost of

each exam is high, ~$2,000. PET camera uses shorter-lived and

less easily-obtained radioisotopes than SPECT. PET/CT are common. PET/MR are now

becoming available.

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PET coincidence circuitry

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Positron emitters in medical imaging

Isotope Half-life

(min)

Spec.

activity

106 Ci/mmol

Max energy

(MeV)

Range

(mm)

Product

F-18 110 1.71 0.63 2.4 Oxygen-18

C-11 20.4 9.22 0.96 4.1 Boron-18

O-15 2.1 90.8 1.72 8.2 Nitrog-15

N-13 9.96 18.9 1.19 5.4 Carbon-13

These four isotopes are used more than any others.

The development of labeled 2-fluorodeoxy-D-glucose (2FDG) by the

Brookhaven group under the direction of Al Wolf and Joanna Fowler

was a major factor in popularizing PET imaging. FDG has

broadest utility, 90% of PET procedures use FDG.

18F NaF PET -- bone cancer

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Review: SPECT versus PET

SPECT PET

single gamma tracer positron emitter

50-250 keV 512 keV

collimation coincidence circuitry

Attenuation correction + Attenuation correction -

Scatter correction + Scatter correction -

Low cost scanner Expensive scanner

Low cost tracer Expensive tracer

Poor image resolution Moderate resolution

Note: CT, SPECT and PET expose patients to ionizing radiation

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Medical Ultrasound Imaging

A sound wave is typically produced by a piezoelectric transducer

made of ceramic that emits strong, short pulses at frequencies 2-18

MHz. The sound is focused to produces an arc-shaped sound wave

from the face of the transducer. The wave travels into the body and

comes into focus at a desired depth.

Newer transducers use phased array techniques to change the

direction and depth of focus. The face of the transducer has a

rubbery coating to let the sound to be transmitted efficiently into

the body. A water-based gel is placed between the patient's skin

and the probe.

The sound wave is partially reflected from the layers between

different tissues. Specifically, sound is reflected anywhere there

are density changes in the body: e.g. blood cells in blood plasma, small structures in

organs, etc. Some of the reflections return to the transducer.

The return of the sound wave to the transducer results in the same process that it took to

send the sound wave, except in reverse. The return sound wave vibrates the transducer,

the transducer turns the vibrations into electrical pulses that travel to the ultrasonic

scanner where they are processed and transformed into a digital image.

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Forming an ultrasound image

The sonographic scanner determines three things from

each received echo:

1. How long it took the echo to be received from

when the sound was transmitted. From this the

focal length for the phased array is deduced,

enabling a sharp image of that echo at that depth.

2. How strong the echo was. Noted that sound wave

is not a click, but a pulse with a specific carrier

frequency.

3. Moving objects inside the body will change the carrier frequency on reflection &

receiver’ electronics can measure the frequency of the echo sound. This is called

Doppler (or color) sonography.

From 1. and 2. the ultrasonic scanner locate which pixel in the image to light up,

corresponding pixel intensity (and at what hue, if frequency 3. is processed).

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Ultrasound Noise and Artifacts

Enhancement artifact: fluid structures (as the cyst on the

right) allow sound to pass easily, absorbing only a

minimal amount of energy. The region that lies behind

will receive more sound than expected for that depth &

will appear brighter.

Shadowing artifact: some tissues will absorb

relatively more of the sound, causing the area

behind to appear darker. In theis gallbladder

image, with a (dense) gallstone casting a shadow.

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Ionizing radiation (Xray CT SPECT PET)

Major impact of ionizing radiation: generation of free radicals

DNA molecules get damaged

most of DNA damage can be repaired, but some cells lose their

capacity and are destroyed

high radiation sensitivity: ovule, sperm, mucose cells,

lymphocytes

low sensitivity: liver, muscle

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Examples of radiation exposure

Exposure Dose [mSv]

USA-Europe round-trip air flight 0.1

Annual cosmic background radiation 1.0

Annual average natural and human-caused 3.6

Nuclear weapon test, effect over 50 years 1.5

Single radiation sterilization procedure 30,000

Local cancer therapy 60,000

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Examples of medical radiation exposure

Exposure Dose [mSv]

Chest x-ray 0.1

Dental x-ray 0.01

mammography 2

Head CT 3

Standard chest CT 20

Local cancer therapy 60,000

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Damage after exposure to acute radiation

Time after 1 Sv

Critical dose

4 Sv

Lethal dose

7 Sv

1st week low white blood cells low white blood

cells Heavy diarrhea,

vomiting, fever

2nd week no symptoms no symptoms

3rd week hair loss, diarrhea hair loss, diarrhea,

internal bleeding

4th week recovery 50% fatality 100% fatal