(ebook) mri for dummies

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Section 2Basic fMRI Physics

Other ResourcesThese slides were condensed from several excellent online sources. I have tried to give credit where appropriate.

If you would like a more thorough introductory review of MR physics, I suggest the following:

Robert Cox’s slideshow, (f)MRI Physics with Hardly Any Math, and his book chapters online.

http://afni.nimh.nih.gov/afni/edu/See “Background Information on MRI” section

Mark Cohen’s intro Basic MR Physics slideshttp://porkpie.loni.ucla.edu/BMD_HTML/SharedCode/MiscShared.html

Douglas Noll’s Primer on MRI and Functional MRIhttp://www.bme.umich.edu/~dnoll/primer2.pdf

For a more advanced tutorial, see:Joseph Hornak’s Web Tutorial, The Basics of MRI

http://www.cis.rit.edu/htbooks/mri/mri-main.htm

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Recipe for MRI

1) Put subject in big magnetic field (leave him there)2) Transmit radio waves into subject [about 3 ms]3) Turn off radio wave transmitter4) Receive radio waves re-transmitted by subject

– Manipulate re-transmission with magnetic fields during this readoutinterval [10-100 ms: MRI is not a snapshot]

5) Store measured radio wave data vs. time– Now go back to 2) to get some more data

6) Process raw data to reconstruct images7) Allow subject to leave scanner (this is optional)

Source: Robert Cox’s web slides

History of NMRNMR = nuclear magnetic resonance

Felix Block and Edward Purcell1946: atomic nuclei absorb and re-emit radio frequency energy1952: Nobel prize in physics

nuclear: properties of nuclei of atomsmagnetic: magnetic field requiredresonance: interaction between magnetic field and radio frequency

Bloch PurcellNMR → MRI: Why the name change?

most likely explanation: nuclear has bad connotations

less likely but more amusing explanation: subjects got nervous when fast-talking doctors suggested an NMR

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History of fMRIMRI-1971: MRI Tumor detection (Damadian)-1973: Lauterbur suggests NMR could be used to form images-1977: clinical MRI scanner patented-1977: Mansfield proposes echo-planar imaging (EPI) to acquire images faster

fMRI-1990: Ogawa observes BOLD effect with T2*

blood vessels became more visible as blood oxygen decreased-1991: Belliveau observes first functional images using a contrast agent-1992: Ogawa et al. and Kwong et al. publish first functional images using BOLD signal

Ogawa

Necessary Equipment

Magnet Gradient Coil RF Coil

Source: Joe Gati, photos

RF Coil

4T magnet

gradient coil(inside)

4

x 80,000 =

4 Tesla = 4 x 10,000 ÷ 0.5 = 80,000X Earth’s magnetic field

Robarts Research Institute 4T

The Big Magnet

Very strong

Continuously on

Source: www.spacedaily.com

1 Tesla (T) = 10,000 Gauss

Earth’s magnetic field = 0.5 Gauss

Main field = B0

B0

Magnet SafetyThe whopping strength of the magnet makes safety essential.Things fly – Even big things!

Screen subjects carefullyMake sure you and all your students & staff are aware of hazzardsDevelop stratetgies for screening yourself every time you enter the magnet

Do the metal macarena!

Source: www.howstuffworks.com Source: http://www.simplyphysics.com/flying_objects.html

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Subject SafetyAnyone going near the magnet – subjects, staff and visitors – must be thoroughly screened:

Subjects must have no metal in their bodies:• pacemaker• aneurysm clips• metal implants (e.g., cochlear implants)• interuterine devices (IUDs)• some dental work (fillings okay)

Subjects must remove metal from their bodies• jewellery, watch, piercings• coins, etc.• wallet• any metal that may distort the field (e.g., underwire bra)

Subjects must be given ear plugs (acoustic noise can reach 120 dB)

This subject was wearing a hair band with a ~2 mm copper clamp. Left: with hair band. Right: without.

Source: Jorge Jovicich

Protons

Can measure nuclei with odd number of neutrons1H, 13C, 19F, 23Na, 31P

1H (proton)abundant: high concentration in human bodyhigh sensitivity: yields large signals

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Protons align with fieldOutside magnetic field

Inside magnetic field

• randomly oriented

• spins tend to align parallel or anti-parallel to B0• net magnetization (M) along B0• spins precess with random phase• no net magnetization in transverse plane• only 0.0003% of protons/T align with field

Source: Mark Cohen’s web slides

M

M = 0 Source: Robert Cox’s web slides

longitudinalaxis

transverseplane

Longitudinalmagnetization

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Larmor Frequency

Larmor equationf = γB0γ = 42.58 MHz/T

At 1.5T, f = 63.76 MHzAt 4T, f = 170.3 MHz

Field Strength (Tesla)

ResonanceFrequency for 1H

170.3

63.8

1.5 4.0

RF Excitation

Excite Radio Frequency (RF) field• transmission coil: apply magnetic field along B1(perpendicular to B0) for ~3 ms• oscillating field at Larmor frequency• frequencies in range of radio transmissions• B1 is small: ~1/10,000 T• tips M to transverse plane – spirals down• analogies: guitar string (Noll), swing (Cox)• final angle between B0 and B1 is the flip angle

B1

B0


Transversemagnetization

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Cox’s Swing Analogy


Relaxation and Receiving

Receive Radio Frequency Field• receiving coil: measure net magnetization (M)• readout interval (~10-100 ms)• relaxation: after RF field turned on and off, magnetization returns to normal

longitudinal magnetization↑ → T1 signal recoverstransverse magnetization↓ → T2 signal decays


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T1 and TR


T1 = recovery of longitudinal (B0) magnetization• used in anatomical images• ~500-1000 msec (longer with bigger B0)

TR (repetition time) = time to wait after excitation before sampling T1

Spatial Coding:GradientsHow can we encode spatial position?

• Example: axial slice

Use other tricks to get other two dimensions• left-right: frequency encode

• top-bottom: phase encode

excite only frequencies

corresponding to slice plane

Field Strength (T) ~ z position

Freq

Gradient coil

add a gradient to the main magnetic

field

Gradient switching – that’s what makes all the beeping & buzzing noises during imaging!

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Precession In and Out of Phase


• protons precess at slightly different frequencies because of (1) random fluctuations in the local field at the molecular level that affect both T2 and T2*; (2) larger scale variations in the magnetic field (such as the presence of deoxyhemoglobin!) that affect T2* only.

• over time, the frequency differences lead to different phases between the molecules (think of a bunch of clocks running at different rates – at first they are synchronized, but over time, they get more and more out of sync until they are random)

• as the protons get out of phase, the transverse magnetization decays

• this decay occurs at different rates in different tissues

T2 and TE


T2 = decay of transverse magnetizationTE (time to echo) = time to wait to measure T2 or T2* (after refocussing with spin echo or gradient echo)

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Echos


Echos – refocussing of signal

Spin echo:

use a 180 degree pulse to “mirror image” the spins in the transverse plane

when “fast” regions get ahead in phase, make them go to the back and catch up

-measure T2

-ideally TE = average T2

Gradient echo:

flip the gradient from negative to positive

make “fast” regions become “slow” and vice-versa

-measure T2*

-ideally TE ~ average T2*

pulse sequence: series of excitations, gradient triggers and readouts

Gradient echopulse sequence

t = TE/2

A gradient reversal (shown) or 180 pulse (not shown) at this point will lead to a recovery of transverse magnetization

TE = time to wait to measure refocussed spins

T1 vs. T2


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K-Space

Source: Traveler’s Guide to K-space (C.A. Mistretta)

A Walk Through K-spaceK-space can be sampled in many “shots”(or even in a spiral)

2 shot or 4 shot• less time between samples of slices• allows temporal interpolation

both halves of k-space in 1 sec

1st half of k-spacein 0.5 sec

2nd half of k-spacein 0.5 sec

vs.

single shot two shot

1st volume in 1 sec interpolatedimage

Note: The above is k-space, not slices

1st half of k-spacein 0.5 sec

2nd half of k-spacein 0.5 sec

2nd volume in 1 sec

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T2*


time

Mxy

Mo sinθT2

T2*

T2* relaxation

• dephasing of transverse magnetization due to both:

- microscopic molecular interactions (T2)

- spatial variations of the external main field ∆B

(tissue/air, tissue/bone interfaces)

• exponential decay (T2* ≈ 30 - 100 ms, shorter for higher Bo)

Susceptibility


Adding a nonuniform object (like a person) to B0 will make the total magnetic field nonuniform

This is due to susceptibility: generation of extra magnetic fields in materials that are immersed in an external field

For large scale (10+ cm) inhomogeneities, scanner-supplied nonuniform magnetic fields can be adjusted to “even out” the ripples in B — this is called shimming

Susceptibility Artifact-occurs near junctions between air and tissue

• sinuses, ear canals-spins become dephased so quickly (quick T2*), no signal can be measured

sinuses

earcanals

Susceptibility variations can also be seen around blood vessels where deoxyhemoglobin affects T2* in nearby tissue

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Hemoglobin

Source: http://wsrv.clas.virginia.edu/~rjh9u/hemoglob.html, Jorge Jovicich

Hemoglogin (Hgb):- four globin chains- each globin chain contains a heme group- at center of each heme group is an iron atom (Fe)- each heme group can attach an oxygen atom (O2)- oxy-Hgb (four O2) is diamagnetic → no ∆B effects- deoxy-Hgb is paramagnetic → if [deoxy-Hgb] ↓ → local ∆B ↓

BOLD signal

Source: fMRIB Brief Introduction to fMRI

↑neural activity ↑ blood flow ↑ oxyhemoglobin ↑ T2* ↑ MR signal

Blood Oxygen Level Dependent signal

time

MxySignal

Mo sinθ T2* task

T2* control

TEoptimum

StaskScontrol

∆S


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BOLD signal

Source: Doug Noll’s primer

First Functional Images

Source: Kwong et al., 1992

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Hemodynamic Response Function

% signal change= (point – baseline)/baselineusually 0.5-3%

initial dip-more focal and potentially a better measure-somewhat elusive so far, not everyone can find it

time to risesignal begins to rise soon after stimulus begins

time to peaksignal peaks 4-6 sec after stimulus begins

post stimulus undershootsignal suppressed after stimulation ends

Review

Tissue protons align with magnetic field(equilibrium state)

RF pulses

Protons absorbRF energy

(excited state)

Relaxation processes

Protons emit RF energy(return to equilibrium state)

Spatial encodingusing magneticfield gradients

Relaxation processes

NMR signaldetection

Repeat

RAW DATA MATRIX

Fourier transform

IMAGE

Magnetic field


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