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: January 14, 2013
Last Course: Psychology 9223, W2013
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?
Most likely explanation:
“Nuclear” has bad connotations
Less likely but more amusing explanation:
Subjects got nervous when fast-talking doctors suggested an NMR
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 Delivery
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
Robarts Research Institute
Siemens 3T Tim Trio
Main field = B0
x 60,000 =
B0
MRI Scanner: Three Key Components
3T magnet
RF
Coil
gradient
coil
(inside)
Necessary Equipment
Magnet
Gradient Coil
Source for Photos: Joe Gati
Radiofrequency
Coil
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 32channel head coil instead of a 12-channel head coil
Coils are Application-Specific
12-channel
head coil
32-channel
head coil
16-channel
breast coil
Images from: https://www.medical.siemens.com
8-channel
knee coil
16-channel
peripheral coil
Parallel Imaging
Siemens
Total Imaging Matrix
(Tim) system
Coils
Head coil
Surface coil
• homogenous signal
• moderate SNR
• highest signal at hotspot
• high SNR at hotspot
Photo source: Joe Gati
Phased Array (Parallel Imaging) Coils
•
•
•
SNR of surface coils with the coverage of head coils
OR… faster parallel imaging
modern scanners come standard with 8- or 12-channel head coils and capability
for up to 32 channels
12-channel coil
32-channel coil
90-channel prototype
Mass. General Hospital
Wiggins & Wald
32-channel head coil
Siemens
Photo Source: Technology Review
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
1H, 13C, 19F, 23Na, 31P
1H 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
Field Strength (Tesla)
7.0
Radio Frequency
Protons: Within Magnetic Field
longitudinal
axis
z
Longitudinal
magnetization
Mz
y
Transverse
magnetization
Mxy
B0
sum of red
vectors along
longitudinal axis
Mz > 0
x
Now imagine
viewing the spins from
above
sum of red
vectors in
transverse plane
Mxy~0
transverse
plane
Step 3: Apply Radio Waves
longitudinal
axis
M=~0
z
Longitudinal
magnetization
Mz
y
B0
sum of red
vectors along
longitudinal axis
Mz ~ 0
90 RF Pulse
Transverse
magnetization
Mxy
x
Now imagine
viewing the spins from
above
sum of red
vectors in
transverse plane
Mxy > 0
transverse
plane
Step 4: Measure Radio Waves
Measure during recovery period
longitudinal
axis
Longitudinal
z
magnetization
Mz
z
y
Transverse
magnetization
Mxy
x
Before
90° pulse
z
y
y
transverse
plane
x
x
Immediately after
90° pulse
Long after
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
Short T1
(e.g., fat)
1.0
Transverse
Magnetization Mxy
Longitudinal
Magnetization Mz
By selecting TR and TE, we can choose T1- vs. T2-weighting
Long T1
(e.g., CSF)
0.5
0
Long T2
(e.g., CSF)
1.0
0.5
Short T2
(e.g., fat)
0
0
1
2
3
Time to Repetition = TR (s)
0
100
200
Time to Echo = TE (ms)
T1 measures how quickly the protons
realign with the main magnetic field
T2 measures how quickly the protons give
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
(The differences
aren’t actually
this large)
B0
gradient
gradient of
field strength
3.1 T
1H Larmor freq
= 132.0 MHz
2.9 T
1H Larmor freq
= 123.5 MHz
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
Step 6: Convert Frequencies to Brain
Space
k-space contains
information about
frequencies in image
We want to see brains,
not frequencies
The Mona Lisa in K-Space
Original Mona
Source: Traveler’s Guide to K-space (C.A. Mistretta)
•
•
•
low frequencies in centre
high frequencies in surround
different orientations around the clock
The Mona Lisa in K-Space
Original Mona
Source: Traveler’s Guide to K-space (C.A. Mistretta)
Low-Frequency Mona
High-Frequency Mona
A Walk Through K-space
single shot EPI
single shot spiral
(forgive the hand-drawn 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
T2*
Source:
Adapted from Jorge Jovicich
gradient echo sequences
-sensitive to T2+T2* effects
time
Spin Echo Sequence
Goebel (2007) book chapter
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
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
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 nonuniformities 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
sinuses
ear
canals
Susceptibility Artifact
-occurs near junctions between air
and tissue
• sinuses, ear canals
-spins become dephased so quickly
(quick T2*), no signal can be
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
At Rest:
Mxy
Signal
Mo
sin
T2* task
T2* control
Stask
Scontrol
Active:
S
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
Very Serious Risk
Source: http://www.fmrib.ox.ac.uk/%7Epeterj/safety_docs/fda_primer.html
Magnet Safety
1.
2.
3.
4.
5.
Principal Investigators should be sure all lab members are aware of hazards.
Make sure that anyone who is about to enter the magnet room has been filled
out consent and screening forms (subjects, lab members, visitors).
Remove all metal, coins, credit cards etc. as soon as you enter the magnet area.
Think! Train yourself to mini-screen yourself every time you approach the
magnet room.
Do not enter the magnet room with any tools (e.g., scissors). Use only magnetfriendly 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