Section 2

Basic fMRI Physics

Other Resources
These 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 slides

http://porkpie.loni.ucla.edu/BMD_HTML/SharedCode/MiscShared.html

Douglas Noll’s Primer on MRI and Functional MRI

http://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 transmitter
4) Receive radio waves re-transmitted by subject
– Manipulate re-transmission with magnetic fields during this readout
interval [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 images
7) Allow subject to leave scanner (this is optional)

Source: Robert Cox’s web slides

History of NMR
NMR = nuclear magnetic resonance
Felix Block and Edward Purcell
1946: atomic nuclei absorb and re-
emit radio frequency energy
1952: Nobel prize in physics
nuclear: properties of nuclei of atoms
magnetic: magnetic field required
resonance: interaction between
magnetic field and radio frequency
Bloch Purcell
NMR → MRI: Why the name change?

most likely explanation: less likely but more amusing explanation:

nuclear has bad connotations subjects got nervous when fast-talking doctors suggested an NMR

2
 History of fMRI
MRI
-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
4T magnet

RF Coil

gradient coil
(inside)

Magnet Gradient Coil RF Coil

Source: Joe Gati, photos

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 The Big Magnet
Very strong
1 Tesla (T) = 10,000 Gauss
Earth’s magnetic field = 0.5 Gauss
4 Tesla = 4 x 10,000 ÷ 0.5 = 80,000X Earth’s magnetic field
Continuously on
Main field = B0
Robarts Research Institute 4T

x 80,000 = B0

Source: www.spacedaily.com

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

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

flying_objects.html

Screen subjects carefully

Make sure you and all your students & staff are aware of hazzards
Develop stratetgies for screening yourself every time you enter the magnet

Do the metal macarena!

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 Subject Safety
Anyone 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)

This subject was wearing a hair band with a ~2 mm

Subjects must remove metal from their bodies copper clamp. Left: with hair band. Right: without.
• jewellery, watch, piercings Source: Jorge Jovicich
• 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)

Protons
Can measure nuclei with odd number of neutrons
1H, 13C, 19F, 23Na, 31P

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

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Outside magnetic field
Protons align with field

• randomly oriented

Inside magnetic field

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

Longitudinal
magnetization

transverse
plane
Source: Mark Cohen’s web slides
M=0 Source: Robert Cox’s web slides

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 Larmor Frequency
Larmor equation
f = γB0
γ = 42.58 MHz/T

At 1.5T, f = 63.76 MHz

At 4T, f = 170.3 MHz

170.3

Resonance
Frequency for 1H

63.8

1.5 4.0

Field Strength (Tesla)

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
Transverse
magnetization

B0

B1

Source: Robert Cox’s web slides

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 Cox’s Swing Analogy

Source: Robert Cox’s web slides

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 recovers
transverse magnetization↓ → T2 signal decays

Source: Robert Cox’s web slides

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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

Source: Mark Cohen’s web slides

add a gradient to
the main magnetic
Spatial Coding:Gradients
field How can we encode spatial position?
• Example: axial slice
excite only
frequencies Use other tricks to get other two dimensions
corresponding to
slice plane • left-right: frequency encode
• top-bottom: phase encode

Gradient switching – that’s

Freq

what makes all the beeping

& buzzing noises during
imaging!
Field Strength (T) ~ z position

Gradient coil

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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 Source: Mark Cohen’s web slides

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

Source: Mark Cohen’s web slides

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 Echos
pulse sequence: series of excitations, gradient triggers and readouts

Gradient echo Echos – refocussing of signal

pulse sequence
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
t = TE/2
make “fast” regions become “slow” and
vice-versa
-measure T2*
A gradient reversal (shown) or -ideally TE ~ average T2*
180 pulse (not shown) at this
TE = time to wait to
point will lead to a recovery of
measure refocussed spins Source: Mark Cohen’s web slides
transverse magnetization

T1 vs. T2

Source: Mark Cohen’s web slides

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 K-Space

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

A Walk Through K-space

single shot two shot
K-space can be sampled in many “shots”
(or even in a spiral)

2 shot or 4 shot
• less time between samples of slices
Note: The above is k-space, not slices • allows temporal interpolation

vs.

both halves of k-space 1st half of k-space 2nd half of k-space 1st half of k-space 2nd half of k-space
in 1 sec in 0.5 sec in 0.5 sec in 0.5 sec in 0.5 sec

1st volume in 1 sec interpolated 2nd volume in 1 sec

image

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 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)

Mxy

Mo sinθ
T2
T2*

time

Source: Jorge Jovicich

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

Susceptibility variations can also be seen around

blood vessels where deoxyhemoglobin affects T2*
in nearby tissue

Source: Robert Cox’s web slides

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 Hemoglobin

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 ↓

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

BOLD signal
Blood Oxygen Level Dependent signal

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

Mxy
Signal
Mo
sinθ T2* task
T2* control
Stask
Scontrol ∆S

TEoptimum time

Source: fMRIB Brief Introduction to fMRI Source: Jorge Jovicich

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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 time to rise

= (point – baseline)/baseline signal begins to rise soon after stimulus begins
usually 0.5-3%
time to peak
initial dip signal peaks 4-6 sec after stimulus begins
-more focal and potentially a better
measure
post stimulus undershoot
-somewhat elusive so far, not
signal suppressed after stimulation ends
everyone can find it

Review
Magnetic field

Tissue protons align

with magnetic field
(equilibrium state)
RF pulses

Protons absorb
Relaxation Spatial encoding
RF energy
processes using magnetic
(excited state)
field gradients
Relaxation
processes

Protons emit RF energy

(return to equilibrium state)

NMR signal
detection

Repeat

RAW DATA MATRIX

Fourier transform

IMAGE Source: Jorge Jovicich

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