Jody Culham

Brain and Mind Institute

Department of Psychology
Western University

http://www.fmri4newbies.com/

fMRI Physics in a Nutshell

Understanding WTF
your MR physicist is talking about

Last Update: September 15, 2014

Last Course: Psychology 9223, F2014
 Magnetic Resonance Imaging
Scanner

Siemens Prisma 3T Siemens Magnetom 7T

The Big Three
 MRI vs. fMRI

Functional MRI (fMRI)

MRI studies brain anatomy.
studies brain
function.
Brain Imaging: Anatomy
CAT

Photography PET

MRI

Source: modified from Posner & Raichle, Images of Mind

 MRI vs. fMRI
MRI fMRI low resolution
high resolution
(1 mm) (~3 mm)

One 3D volume

…
series of 3D volumes (i.e., 4D data)
(e.g., every 2 sec for 5 mins)
 The First “Brain Imaging Experiment” (1884)
… and probably the cheapest one too!

E = mc2

Angelo Mosso
Italian physiologist
(1846-1910)

“[In Mosso’s experiments] the subject to be observed lay on a delicately balanced table
which could tip downward either at the head or at the foot if the weight of either end were
increased. The moment emotional or intellectual activity began in the subject, down went the
balance at the head-end, in consequence of the redistribution of blood in his system.”
-- William James, Principles of Psychology (1890)
 The Man Who Could Hear His Brain

Walter K, 1927
Whenever he opened his eyes, a gurgling
sound could be heard at the back of his skull
 The Rise of fMRI

Friston, 2010,
Science
 History of NMR
NMR = nuclear magnetic resonance
Rabi; Block and Purcell
• atomic nuclei absorb and re-emit
radio frequency energy
nuclear: properties of nuclei of atoms
magnetic: magnetic field required
resonance: interaction between magnetic
field and radio frequency

Felix Bloch Edward Purcell

NMR  MRI: Why the name change?

Less likely but more amusing explanation:

Most likely explanation: Subjects got nervous when fast-talking doctors suggested an NMR
“Nuclear” has bad connotations
 History of MRI
1971: Raymond Damadian uses NMR for tumor detection
1972: Lauterbur suggests NMR could be used to form images using gradients
1977: Peter Mansfield proposes echo-planar imaging (EPI) to acquire images
faster
1977: first MRI scanner (0.05 T) created by Damadian’s FONAR corporation,
named “Indomitable”

1977: First MR image of human body

• Didn’t use EPI
• Each voxel took 2 min; 106 voxels
• 4 hours to get one slice
 History of fMRI
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

Seiji Ogawa
 First Functional Images

Flickering Checkerboard
OFF (60 s) - ON (60 s) - OFF (60 s) - ON (60 s)

Source: Kwong et al., 1992

Five Nobels; One Ig Nobel; One Controversy
1944 Nobel
• Isador Rabi
1956 Nobel
• Felix Bloch and Edward Purcell
2000 Ig Nobel
• for discoveries "that cannot, or should not, be reproduced”
• Pek van Andel, British Medical Journal
2003 Nobel
• Paul Lauterbur and Peter Mansfield
• Damadian protests
 Inside the MRI Scanner

Robarts Research Institute

3T Tim Trio installation
August 2008
 The Big Magnet
Very strong
1 Tesla (T) = 10,000 Gauss
Earth’s magnetic field = 0.5 Gauss
3 Tesla = 3 x 10,000  0.5 = 60,000X Earth’s magnetic field

Continuously on

Main field = B0

x 60,000 =
B0
 Other strong magnets for comparison…

Junkyard Magnet Large Hadron Collider World’s Strongest Magnet (not MRI)
~1 T ~8.4 T ~100 T
Los Alamos National Lab

http://www.webpronews.com/tesla-100t-record-2012-03
 The Main Magnet
inside an 11.7 T scanner
http://spectrum.ieee.org/biomedical/imaging/the-
worlds-most-powerful-mri-takes-shape
How do you make a magnet that strong?
running a current through a coil so just make a really big coil
generates a magnetic field
But doesn’t that take a massive amount of energy?
• no, use a superconducting magnet
• cool magnet using liquid helium
• almost to absolute zero (-273°C = 0 K)
• hope you don’t have to “quench” the scanner
• quenching = releasing all the helium
• magnetic field drops rapidly
• can happen accidentally, during decommission or if
necessary due to accident
• otherwise, never touch the big red button!
• http://www.youtube.com/watch?v=9SOUJP5dFEg
MRI Scanner: Three Key Components

3T magnet

RF
Coil

gradient
coil
(inside)
 Necessary Equipment

Radiofrequency
Magnet Gradient Coil
Coil

Source for Photos: Joe Gati Source for Photo: Siemens

 Improving Data Quality
To get better quality data (higher signal-to-noise, as
we’ll discuss later):

1. Increase field strength (e.g., use a 3 T scanner

instead of a 1.5 T scanner)

and/or

2. Use a coil with more channels (e.g., use a 32-

channel head coil instead of a 12-channel head coil
 Coils are Application-Specific

12-channel 32-channel 16-channel 8-channel 16-channel

head coil head coil breast coil knee coil peripheral coil

Images from: https://www.medical.siemens.com

 Parallel Imaging

Siemens
Total Imaging Matrix
(Tim) system
 Coils

Head coil Surface coil

• homogenous signal • highest signal at hotspot
• moderate SNR • high SNR at hotspot

Photo source: Joe Gati

 Phased Array (Parallel Imaging) Coils
• provides SNR of surface coils with the coverage of head coils
• OR… faster parallel imaging (“iPAT” acceleration factor on Siemens)
• modern scanners come standard with multi-channel head coils
• current capability for up to 128 channels (64 for head and neck on Prisma)

12-channel coil 32-channel coil

90-channel prototype
Mass. General Hospital
Wiggins & Wald

32-channel head coil

Siemens Photo Source: Technology Review
64-channel head and neck coil
for Prisma
 Phased Array Coils

Source: Huettel, Song & McCarthy, 2004,

Functional Magnetic Resonance Imaging
 Step 1: Study Atoms With NMR Spin
Heads have lots of water,
thus lots of protons…
Let’s study a head

Can measure nuclei with odd number of protons or odd number of neutrons
1
H, 13C, 19F, 23Na, 31P
1
H hydrogen (proton)
abundant: high concentration in human body (5 x 1027 protons in 150 lb guy)
high sensitivity: yields large signals
 1H = “proton”

Less common isotopes have

neutrons

The most common form (99.98%)

of hydrogen has one proton and
no neutrons
 Protons: No Magnetic Field

• protons in random orientation (obviously not to scale!)

Step 2: Put Subject in Big Magnet

Protons (hydrogen atoms) have

“spins” (like tops). They have
an orientation and a frequency.
 Protons: Within Magnetic Field

B0

• protons align parallel or anti-parallel to B0 (parallel>antiparallel)

– actually only 0.0003% of protons/T align with field
• phase is random
 Larmor Frequency
Larmor equation
f = B0
 = 42.58 MHz/T for hydrogen

At 1.5T, f = 63.8 MHz

At 3T, f = 127.7 MHz
At 7T f = 298.1 MHz

298.1

Resonance
Frequency for 1H

63.8

1.5 3.0 7.0

Field Strength (Tesla)

Radio Frequency
 Transmit and Receive
12-channel head coil

On the 3T Siemens Prisma:

•Transmission of RF (Tx) is done by a “body” RF coil
• yields good homogeneity
•Reception of RF (Rx) is done by the head coil
• close to brain
 Protons: Within Magnetic Field
longitudinal
axis

z Longitudinal
magnetization
Mz

y
Transverse
B0 magnetization
transverse
plane
Mxy
sum of red x
vectors along Now imagine
longitudinal axis viewing the spins from
Mz > 0
above

sum of red
vectors in
transverse plane
Mxy~0
 Step 3: Apply Radio Waves
longitudinal
axis

z Longitudinal
magnetization
Mz

y
Transverse
transverse
magnetization plane
Mxy
B0 sum of red
vectors along x
longitudinal axis Now imagine
Mz ~ 0 viewing the spins from
above

sum of red
vectors in
90 RF Pulse transverse plane
Mxy > 0
 Step 4: Measure Radio Waves

Measure during recovery period

longitudinal
axis Longitudinal
z magnetization z z
Mz

y y y
Transverse
transverse
magnetization plane
Mxy
x x x
Before Immediately after Long after
90° pulse 90° pulse 90° pulse

• Measure radio waves as protons gradually return to

original configuration within the magnetic field
 Step 4: Measure Radio Waves

Goebel (2007) book chapter

 Step 4: Measure Radio Waves
By selecting TR and TE, we can choose T1- vs. T2-weighting
Long T2
1.0 Short T1 1.0 (e.g., CSF)
(e.g., fat)

Magnetization Mxy
Magnetization Mz
Longitudinal

Transverse
0.5 Long T1 0.5
(e.g., CSF)
Short T2
(e.g., fat)
0 0
0 1 2 3 0 100 200
Time to Repetition = TR (s) Time to Echo = TE (ms)

T1 measures how quickly the protons T2 measures how quickly the protons give
realign with the main magnetic field off energy as they recover to equilibrium

T1-WEIGHTED ANATOMICAL IMAGE T2-WEIGHTED ANATOMICAL IMAGE

 Jargon Watch
• T1 = the most common type of anatomical image
• T2 = another type of anatomical image
• TR = repetition time = one timing parameter
• TE = time to echo = another timing parameter
• flip angle = how much you tilt the protons (90 degrees
in example above)
 Step 5: Use Gradients to Encode Space
Remember the Larmor equation: f = B0

higher
magnetic field;
higher
frequencies 3.1 T
1
H Larmor freq
= 132.0 MHz
B0 (The differences
gradient aren’t actually
this large)

2.9 T
1
H Larmor freq
field strength

= 123.5 MHz
gradient of

lower
magnetic field;
lower
frequencies
 Step 5: Use Gradients to Encode Space

• We’ve seen how gradients can be used to encode one direction of space
(slice selection)
• Other gradients and other tricks (frequency encode and phase encode) can be
used to encode the other two directions, though it’s more complicated
Interlude: A primer on Fourier Analysis
 A Brief Primer on Fourier Analysis
• Sine waves can be characterized by frequency and
amplitude
peak: high point
amplitude
trough: low point

frequency: number of cycles within

a certain time (e.g., cycles per sec
= Hz) or space (e.g., cycles per
peak
cm)

amplitude: height of wave

trough

phase: starting point

• (b) has same frequency as (a) but lower amplitude

• (c) has lower frequency than (a) and (b)
• (d) has same frequency and amplitude as (c) but
different phase
Source: DeValois & DeValois, Spatial Vision, 1990
 Fourier Decomposition
• Any wave form can be decomposed into a series of
sine waves
Frequency spectrum

fundamental

Frequency
space
3rd harmonic (3X freq; 1/3 ampl)
(1D pattern)

5th harmonic (5X freq; 1/5 ampl)

7th harmonic (7X freq; 1/7 ampl)

Source: DeValois & DeValois, Spatial Vision, 1990

 Temporal Analysis

• In a simple “square wave” block design, you expect

the time course to have strong energy at the
fundamental frequency
• changes at other frequencies are noise
 Spatial Analysis
Spatial waveforms
• can be one dimensional
(e.g., sine wave gratings in
vision) or two dimensional
(e.g., a 2D image)
• e.g., image analysis
• e.g., an fMRI slice (k-
space)

Adapted from DeValois & DeValois, Spatial Vision, 1990

Step 6: Convert Frequencies to Brain
Space

k-space contains We want to see brains,

information about not frequencies
frequencies in image
 The Mona Lisa in K-Space

Original Mona • low frequencies in centre

• high frequencies in surround
• different orientations around the clock

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

 The Mona Lisa in K-Space

Original Mona Low-Frequency Mona High-Frequency Mona

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

 A Walk Through K-space
single shot EPI single shot spiral

echo-planar imaging
• sample k-space in a linear zig-zag trajectory
spiral imaging
• sample k-space in a spiral trajectory
 T2 and T2*
Dephasing of transverse magnetization due to both:
1. spin-spin interactions (T2)
2. static magnetic field inhomogeneities (additional T2*
effects)
Mxy spin echo sequences
-sensitive to T2 but not T2* effects

T2 gradient echo sequences

T2* -sensitive to T2+T2* effects

time
Source:
Adapted from Jorge Jovicich
 Spin Echo Sequence

Goebel (2007) book chapter

 Pulse Sequence
• series of excitations, gradient triggers and readouts

Gradient echo Echos – refocussing of signal

pulse sequence
t = TE/2
A gradient reversal (shown) or
180 pulse (not shown) at this
point will lead to a recovery of
transverse magnetization
Source: Mark Cohen’s web slides
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*
TE = time to wait to
measure refocussed spins
Magnetic Field Non-uniformities and Shimming
Adding a non-uniform object (like a person) to B0 will make the total magnetic field
non-uniform

Shimming: applying non-uniform shimming gradients to “even out” coarse non-

uniformities in the magnetic field

If the subject moves after shimming, the

magnetic field uniformity may change
Barry et al., 2010, MRI
 Susceptibility
Susceptibility: generation of extra magnetic fields in materials that are immersed
in an external field

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

 Hemoglobin

Hemoglogin (Hgb):
- can attach up to four oxygen atoms (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   blood flow   oxyhemoglobin   T2*   MR signal

Mxy
At Rest: Signal
Mo sin
T2* task
T2* control
Stask
Scontrol S

Active: TEoptimum time

Source: Jorge Jovicich

Figure Source: Huettel, Song &
McCarthy, 2004, Functional Magnetic
Resonance Imaging
MRI Safety
 Magnetic Fields
• main magnetic field is very strong
• BUT static magnetic fields are less of a concern than changing
magnetic fields
• moving quickly through a magnetic field, especially the head, is
a BAD idea -- like doing whole brain TMS on yourself

• some people experience dizziness, nausea, metallic tastes

– BUT these were also reported in 45% of subjects when the magnet was
OFF!

• typical consent form phrasing: “no known risks”

– you can never prove anything is safe, only that something is unsafe
 Magnet Safety: Big Things

Source: www.howstuffworks.com

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

“Large ferromagnetic objects that were reported as having been drawn into the MR equipment
include a defibrillator, a wheelchair, a respirator, ankle weights, an IV pole, a tool box, sand
bags containing metal filings, a vacuum cleaner, and mop buckets.”
-Chaljub et al., (2001) AJR
 Very Serious Risk

Westchester NY, 2001

Source: http://www.mrireview.com/docs/mrideath.pdf
 Magnet Safety: Little Things

Aneurysm clips can be

pulled off vessels, leading
to death

Flying things can kill people.

Even in less severe incidents, they can fly
into the magnet and damage it or require
an expensive shutdown.
 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 (but fillings are okay) This subject was wearing a hair band with a ~2 mm
copper clamp. Left: with hair band. Right: without.
Source: Jorge Jovicich
Subjects must remove metal from their bodies
• jewellery, watch, piercings
• coins, etc.
• wallet
• any metal that may distort the field (e.g., underwire bra)

Females must not be pregnant or at risk of conceiving

• Some institutions even require pregancy tests for any female, every session

Subjects must be given ear plugs (acoustic noise can reach 120 dB)
 Fall-off of Magnetic Field

actively shielded magnet

 Very Serious Risk

Source: http://www.fmrib.ox.ac.uk/%7Epeterj/safety_docs/fda_primer.html
 Magnet Safety
1. Principal Investigators should be sure all lab members are aware of hazards.
2. Make sure that anyone who is about to enter the magnet room has been filled
out consent and screening forms (subjects, lab members, visitors).
3. Remove all metal, coins, credit cards etc. as soon as you enter the magnet area.
4. Think! Train yourself to mini-screen yourself every time you approach the
threshold of the magnet room.
5. Do not enter the magnet room with any tools (e.g., scissors). Use only magnet-
friendly tools in the toolbox in the magnet room.

Do the “Metal Macarena!”

 Specific Absorption Rate (SAR)
• excess energy heats body tissues
• if body heats faster than natural cooling, temperature
rises
• Specific Absorption Rate (SAR) = amount of heat
absorbed by body
• magnets have SAR limits to prevent overheating
– limited to 1 degree rise in core body temperature
– depends on body size, geometry, thermoregulation
– depends on pulse sequences (e.g., larger flip angles =
greater SAR)
 Other safety issues
• fire safety
– always give subjects a panic button
– make sure that subject can be evacuated quickly if needed
– have an MR-compatible fire extinguisher available
– operator must know safety protocols

• quenching
– rapid decrease in magnetic field strength
– helium boils off and can fill room (displacing oxygen)
– can occur spontaneously
– only voluntarily initiated in extreme situations

• burns
– do not loop any wires or cables
– do not place electrodes on subjects’ skin
 Other safety issues
• claustrophobia
– subject screening

• peripheral nerve stimulation

– rapid switching of gradients can lead to generation of
currents in the body that stimulate the nerves (e.g.,
twitching)
– manufacturers limit rate of gradient switching to avoid
problems

• acoustic noise
– without ear protection, could cause hearing loss
– soundproofing
– earplugs
– headphones