MRI-Chilkulwar.pptx

An Introduction to
Magnetic Resonance Imaging
R. H. Chilkulwar
Bhabha Atomic Research Centre

MRI Synopsis
• History of NMR
• Physics of NMR
• MRI Machine  Components
• Imaging Better Contrast & Brightness
• Safety Magnet+RF
• References

How MRI is done?
1) Put subject in big magnetic field
2) Transmit radio waves into subject [2~10 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 of 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

Nuclear magnetic resonance (NMR)
• NMR is a magnetic property of the nucleus mainly used in
spectroscopic studies.
• Proton and Neutron have magnetic field associated with
their nuclear spin and charge distribution.
• Resonance is an energy coupling in the strong magnetic
field where nuclei absorbs and releases energy which is
unique to nuclei and surrounding.
• Magnetic field gradients used to localize NMR signal.
• Pros: High contrast sensitivity to soft tissue, Non-ionizing
radiation
• Cons: High equipment & siting cost, Scan Acquisition complexity
Long imaging time Significant Artefacts
Patient Claustrophobia MR safety concern

• Selection of Magnets is based on Field strength, Temporal
Stability, Field Homogeneity etc.
• Air Core Magnets (High Fringe Fields)
• Solid Core Magnets (Permanent or Electromagnet or
Hybrid, Less Fringe Fields)

Electromagnet Core Wires needs to be Super conductive
for Bo > 1 Tesla (Nb-Ti alloy at Liquid He of 4 deg Kelvin)

• Shim Coils- Improves homogeneity of main magnetic
fields.
• RF coils – Transmit & Receive RF energy
• Gradient coils: Linear variation of magnetic field strength
(~ 5 mT/m magnetic field variation)

• Magnetic Susceptibility of a material is an extent it gets
magnetized when placed in a magnetic field.
• Induced magnetization may opposes or align in the same
direction of external magnetic field Bo which will reduce
or increase local magnetic field surrounding the material.
• Diamagnetic Subs: Oppose Bo due to paired electrons (Ca,
H2O, Organic material etc)
• Paramagnetic Subs: Distort NMR a little due to unpaired
electrons (O2, De-oxy-hemoglobin, Gd based contrast
agents etc)
• Ferromagnetic subs– Distort NMR due to unpaired
electrons (Fe, Ni, Co etc.)

• Magnetic properties of Protons and Neutrons are
influenced by SPIN & CHARGE distribution
• Magnetic dipole is created for proton due to spin and
charge
• Subnuclear charge inhomogeneities and spin of neutron
result in magnetic field in opposite direction
• NUCLEAR MAGNETIC MOMENT (magnetic
characteristics of the nucleus.)
• If P & N are EVEN – magnetic moment is zero
• If P & N are ODD – spin generates magnetic moment.
• Individual nucleus does not generate a large mag. moment
but 10^15 nuclii will give enough mag. moment in non-
random orientation

• TORQUE = magnetic moment * ext. mag. field. strength (Bo)
• ↊ = m * Bo or m = ↊/Bo (J/T)
• Magnetic dipole moment = m/2l
• Hydrogen is a best candidate for clinical utility due to its
magnetic moment and abundance in water and fat.
• Na & P have been used for imaging in limited situation.
• Classically spinning Proton is considered as dipole magnet
(undetectable for individual nucleons)
• In the presence of strong static magnetic field Bo, Proton align
in parallel and antiparallel directions in two discrete energy
levels.
• Excess protons in low energy are approx. 3 Protons per million.

• In addition to the alignment, Proton experiences a Torque in
perpendicular direction called as Precession (wobbling) which is
directly proportional to Bo.
• LARMER EQUATION
where γ/2π is a Gyromagnetic ratio in MHz/T.
This is unique to the element of nonzero nuclear magnetic moment.
ω0 = γ * Bo
fo = γ/2π * Bo

• Brief exposure of RF pulse of Larmor frequency (resonance
with Proton precession) shifts parallel oriented protons from
low energy to antiparallel high energy state.  Mo shrinks
• Subsequently sample returns to equilibrium condition and
releases RF of same frequency which is detected by sensitive
RF antenna.

• Proton Precession is 42.58 MHz/T for 0.3-4.0 Tesla
• Precision in determining in precessional frequency is very
important and is in the order of cycle/s)
• FRAME OF REFERENCES
• Laboratory frame
• Rotating frame (Larmer frequency)

• Net magnetization vector – M have 3 components
• Longitudinal magnetization – Mz along z direction and parallel
to Bo. At equilibrium, Mz is maximum i.e. Mz = Mo
• Transverse magnetization – Mxy is perpendicular to Bo. It
appears only after RF absorption.
• Application of RF energy at precessional frequency of the
protons cause absorption of energy and displacement of sample
magnetic moment from equilibrium conditions. The return to
equilibrium, results in the emission of energy proportional to
the number of excited protons in the volume.
• EXCITATION DETECTION ACQUISITION
• Equilibrium magnetization displaced to perpendicular due to
magnetization component of RF excitation pulse (B1) which is
precisely matched with precessional frequency of protons.

Excitation by Quantum Mechanical Model
• It explains energy absorption and emission (not Mxy)
• Protons will transmit from low to high energy level (∆E) when
RF pulse is equal to proton precessional frequency
• Number of protons undergoes an energy transition are depend on
Amplitude and Duration of pulse.

Classical Physics Model
• Two magnetic field vectors of RF pulse i.e. clockwise and
anticlockwise rotating vectors produce constructive and
destructive magnetic field variation.

Classical Physics Model
• A Larmor frequency, one of the vector rotates in synchronous
with rotating frame and another one not.
• RF (B1) applied to rotating frame.
• If RF energy is not applied at Larmor frequency, B1 will not
interact with Mz.

FLIP ANGLES
• Flip angles represent the degree of Mz rotation by the
B1 field as it is applied along the x’-axis (or the y’-axis)
perpendicular to Mz.
• A torque is applied at Mz to rotate it from longitudinal
to transverse plane.
• Rate of rotation will have angular frequency-(Larmor
equation)
and
Displacement Angle
t –pulse time
ω1 = γ * B1
Ɵ = ω1 t = γ B1 t

FLIP ANGLES
• Common flip angles are 90 & 180 deg. However,
smaller and larger flip angles are chosen to enhance
tissue contrast.
• 90 deg angle provides largest possible Mxy &
detectable MR signal
• 45 deg angle takes half of the time that of 90 deg but
produces 70% of the signal (sin45 = 0.707)
• Fast MRI techniques uses small displacement angles
like 10 deg or so.

Free Induction Decay
• After a 90 deg RF pulse is applied to a magnetized
sample at the Larmor frequency, an initial phase
coherence of the individual protons is established and
maximum Mxy is achieved
• Rotating at the Larmor frequency, the transverse
magnetic field of the excited sample induces signal in
the receiver antenna coil (Laboratory ref.)
• A damped sinusoidal electronic signal known as the
Free induction decay (FID) is produced.
• FID amplitude decay is caused by loss of Mxy phase
coherence due to intrinsic inhomogeneities in sample.
• Phase coherence is lost over time in exponential decay

T2 RELAXATION TIME
(intrinsic spin-spin interaction)
• Elapsed time between maximum transverse signal (Mxy
at 90 deg pulse) and 37% of peak (1/e) is called T2
relaxation time.
𝑀𝑥𝑦 𝑡 = 𝑀𝑜 𝑒−𝑡/𝑇2
(Transverse magnetic moment at time t for a sample of Mo
at t=0)
At t = T2, then e-1 = 0.37  Mxy = 0.37 Mo

T2 RELAXATION TIME
• T2 decay value is strongly get affected by molecular
structure and bound water protons.
• CSF or highly edematous tissues contains rapid
molecular motion of mobile molecules. With no
structural constrain, these tissues do not support
intrinsic magnetic field inhomogeneities and thus
LONG T2 values.
• On the contrary, the large molecules of constrained
molecular motion produce magnetic field and increase
spin dephasing and which causes more rapid decay with
the result of SHORT T2 (e.g. BONE)

• Extrinsic inhomogeneities due to imperfect main
magnetic field Bo or agents like MR contrasts,
para or ferromagnetic objects results into more
loss of phase coherence in addition to the intrinsic
inhomogeneities and further reduce decay
constant known as T2*
T2* RELAXATION TIME
(intrinsic + extrinsic interaction)

• Longitudinal magnetization begins to recover
simultaneously with transverse decay (longer
process)
• Spin-lattice relaxation is the release of energy
back to the lattice (molecular arrangement &
hydration layer) and re-growth of Mz exponentially
• T1 is the time needed to recover 63% of Mz after
90 deg pulse
t=0  Mz=0
t=T1  Mz=0.63 Mo
t=5T1  Mz ~ Mo
T1 RELAXATION TIME
(Spin-Lattice interaction)
𝑀𝑧 𝑡 = 𝑀𝑜 (1 − 𝑒−𝑡/𝑇1)

T1 RELAXATION TIME
(Spin-Lattice interaction)

• Since Mz does not generate an MR signal directly,
specific sequence of RF pulses are used for
specific tissue to determine T1 with delay time.

• After a delay time ∆T, between two 90 deg pulse,
recovered Mz component is converted to Mxy by second
90 deg pulse & the resulting peak amplitude is recorded.
• By repeating the sequence from equilibrium with different
delay time, data points are fitted in exponential equation
& T1 is estimated.
• T1 relaxation time is depend on rate of energy
dissipation in the lattice and varies for different tissues &
pathologies
• For unstructured tissue & bulk water fluid, T1 is LONG
(Aqueous tissue (CSF)-1-4 sec)
• Structured/moderately sized Proteins/Fatty tissue have
T1 SHORT (0.1 – 1 sec)
• GADOLINIUM CHELATE IS USED TO DECREASE T1

T1 vs T2
• T1 > T2 (5-10 times)
• T1 & T2 are influenced by molecular motion, size
& interaction
• Tissues of interest for clinical MR applications are
intermediate to small-sized molecules.

T1 vs T2
• T1 increases with Bo
• T2 is unaffected by Bo
• Usually Longer T1 then Longer T2 and Shorter T1 then
Shorter T2

T1 vs T2
• Values varies widely due to Bo, measurement methods
and biological variation
• Paramagnetic Blood Degradation products, Elements
with unpaired electron spins (Gd) causes a significant
reduction in T2*.
• T1 > T2 > T2*
• Thus, T1, T2, T2* and Proton Density(PD) are the
fundamental properties of tissues and can be exploited
by machine dependent ACQUISITION TECHNIQUES.

TIME OF REPETITION (TR)
(90 to 90)
• The time of repetition (TR) is the period between
B1(RF) excitation pulse.
• Acquisition of an MR image relies on the repetition
of a sequence of event in order to sample the VOI
and periodically build the complete dataset.
• During TR, T2 decay & T1 recovery occurs in the
tissue, TR range is few ms to 10,000 ms as per the
time of sequence.

TIME OF ECHO (TE)
(90 to 180)
• The time of Echo (TE) is the time between
excitation pulse and the appearance of the peak
amplitude of an induced echo determined by 180
deg RF inversion pulse or gradient polarity
reversal at time equal to TE/2.

TIME OF INVERSION (TI)
• TI is the time between an inversion/excitation (180
deg) RF pulse and 90 deg readout pulse
• During TI, Mz recovery occurs and readout pulse
converts Mz into Mxy, which is then measured with
an echo at TE.

SPIN ECHO
• Excitation of magnetized Proton with 90 deg RF pulse
produces FID.
• It is followed by 180 deg RF pulse to produce echo signal
called as SPIN ECHO.
• 90 deg converts Mz into Mxy at largest phase coherence
that immediately begins to decay at a rate of T2* relaxation.
• 180 deg RF pulse at TE/2 inverts the spin system and
induces phase coherence at TE (in rotating frame of
reference)
• Inversion of spin cause proton experience extrinsic
magnetic inhomogeneities before TE/2 and cancellation of
inhomogeneities & associated dephasing effect at TE.
• In rotating frame of reference, echo magnetization vector
reforms in the opposite direction from the initial Mxy.

SPIN ECHO
Repetition of 180 deg RF pulses during TR interval
produce corresponding echoes with peak amplitude
reducing by T2* decay and do not change by extrinsic
inhomogeneities.
𝑆 ∝ ρ𝐻 1 − 𝑒
𝑇𝑅
𝑇1 𝑒−𝑇𝐸/𝑇2

T1 WEIGHTING
• A T1-weighted SE sequence is designed to produce
contrast chiefly based on the T1 characteristics of tissues,
with reduced emphasis of T2 & PD contributions to the
signal.
• This is achieved by using a relatively SHORT TR to
maximize the differences in Mz recovery & SHORT TE to
minimize T2 decay during signal acquisition.

T1 WEIGHTING
TR= 400-600 ms & TE = 3-10 ms (typ.)

Proton Density Weighting
TR (2000-4000ms) & TE (3-30ms)
• Depends on differences in the number of magnetized
protons per unit volume of tissue.
• At equilibrium, Lipids, Fats and CSF have large Mz
compared to other soft tissues
• Reducing contributions of T1 recovery and T2 decay.
• LONG TR (~2400ms) to reduce T1 difference and SHORT TE
(~30ms) for T2 difference
• CONTRAST : CSF > Fat > Gray matter > White matter
• Fat & CSF shows relatively bright signal
• Highest overall signal intensity and largest SNR
• Contrast is low, Contrast to noise ratio is less than T1&T2
weighting

Proton Density Weighting
TR (2000-4000ms) & TE (3-30ms)

Proton Density WEIGHTING
TR= 2000-4000 ms & TE = 3-30 ms (typ.)

T2 Weighting
TR (2000-4000ms) & TE (80-120ms)
• T2 contrast weighting follows directly for PD weighting
sequence
• LONG TR AND LONG TE
• T2 weighted signal is generated from second echo with long TR,
where first echo is PD weighted with short TE
• T2 contrast is achieved by allowing Mxy signal decay
• T2-weighted image gives high tissue contrast as compared to that
of T1 and PD
• As TE increases more T2 contrast less signal/noise is more
• With image processing algorithm can remap the signals so that
overall brightness is similar for all images.

T2 Weighting
TR (2000-4000ms) & TE (80-120ms)

Magnetic Field Gradients
• Special localization is essential for MR images
• Superimposition of linear magnetic field variations on
the Bo to generate position dependent variations.
• Gradient polarity reversals are achieved by reversing the current
direction in the coils.

GRADIENT ECHO
• GE technique uses a magnetic field gradient applied in
one direction and then reversed to induce the formation
of an echo, instead of the 180 deg inversion pulse.

Magnetic and Electromagnetic Fields
• Magnetic fields generate the substance we “see”: magnetization
of the H protons in H2O.
• Magnetic fields also let us manipulate magnetization so that we
can make a map [or image] of its distribution inside the body’s
tissue
• Static magnetic fields change slowly (< 0.1 ppm / hr):main field;
static inhomogeneities
• Gradient magnetic fields change quickly (switching up to
thousands of times per second)
• RF fields are electromagnetic fields that oscillate at Radio
Frequencies (tens of millions of times per second)
– transmitted radio waves into subject
– received signals from subject

Introduction
• The combination of nuclear angular
momentum and the gyroscopic effects will
lead us to the resonance (R) part of NMR.
• Resonance here refers merely to the change
in energy states of the nuclei caused by
absorption of a specific radiofrequency.
• MRI uses the signal from the hydrogen
nuclei (proton) for image generation.

Introduction
• Both protons and neutrons have the same
spin and therefore the same spin angular
momentum.
• The angular momentum of the nucleus is
determined by the spin of unpaired particles
and by the orbital angular momentum of the
neutrons and protons.

Introduction
• A is odd: Nuclear spin I is a multiple of 1/2 (one
unpaired nucleon), A is even and Z is even: I =
0 (no unpaired nucleons), A is even and Z is
odd: I is a whole number 1,2,3,4,5 (Two
unpaired nucleons)
• Proton possesses positive charge as well as spin
(rotation about its axis like a spinning top).
• Thus, it has angular momentum. Spinning
proton acts like a spinning top that strives to
retain the spatial orientation of its rotation axis
(only allowed alignment as per QM).

Introduction
• MRI uses Magnetic field and RF signals
Anatomical Structures; Disease; Biological Functions
• In Magnetic field, tissue getsmagnetizedResonance
• Resonance Absorb & Re-radiate RF at Larmor Freq.
• NMR Resonance of Nuclei (change in Energy States)

Introduction
• MRI is a different imaging modality
Superior soft tissue contrast
• Image Contrast
Adjustment to Acquisition Parameters (Timing)
• Angular Momentum of Nucleus
• P  Spin of unpaired particles and Orbital
Angular Momentum of Nucleons
• Nuclear Spin, I = ½, 0, 1-5
(Unpaired nucleon can only participate in NMR)
γ = ω0/Bo

Introduction
• Nucleus a tiny magnet Allowed limited Alignment in Bo
• Nucleus has Torque Magnetic Moment (only with spin)
• No Bo  µ is randomly oriented  Zero Magnetization
• Appl.of Bo  µ Align Parallel(up) or Antiparallel(down) toBo
= 1.000010 at Bo =1.5 T
• LARMOR FREQUENCY A resonant frequency of a
nucleus where RF that has identical frequency with
precession frequency in the presence of Bo.
ω = γ Bo/2π

Introduction
• Net Magnetization Vector (Mz) is the collection of spins
in entire voxel aligned along Bo (z).
• Mz is aligned at Bo; Stationary/do not Precess.
• Application of RF
• Mz precess about B1 in XY plane till RF is present.
• For Signal, B1 is long enough to have 90o rotation.
• On RF removal Mz precess about Bo at Larmor Freq.
• Signal generated and detected by RF coil.
Bo z (Longitudinal)
M
y
x (Transverse plane)

MR Image
• Strong Magnetic Field results in Magnetisation in Tissue
• Image  Change in Magnetic field during Acquisition
• Image Acquisition  Cyclic process Brightness
• Imaging Protocol  Adjustment of Magnetisation/Contrast

NMR Parameter
• Proton Density (PD)
• Magnetic Relaxation Time
• T1-Relaxation (Spin-Lattice Interaction)
• T2-Relaxation (Spin-Spin Interaction)
• Relaxation – Excited Nucleus  Torque due to B 
Realign  Transfer Excess Energy to Structure
• Relaxation is not Instantaneous  Tissue type decides
• Nuclear Relaxation Time/Rate  Tissue Contrast

T1-Relaxation
• On 90o RF Pulse No component of M along Bo
• Excess Nuclei at Low Energy State  Absorb Energy 
Flip to Higher Energy State
• At the End of 90o RF Pulse  Energy Transfer to
Structure/Lattice  Return to Lower Energy State
• T1 is the Time Constant  Depend on Lattice Mobility and
Efficiency of Energy Transfer

T1-Relaxation
(FREE INDUCTION DECAY) FID Signal

T1-Relaxation
T1-Weighted Images
• Fat – Short T1 (Brighter)
Fluid (CSF) – Long T1 (Darker)
• Rigid Structure-No Rapid Relaxation-Long T1 (Darker)
• Fluid (small molecules) -

• Rotating mass with an electrical charge always has
magnetic dipole moment (B) and behaves like a small
magnet.
• Therefore, proton is affected by external magnetic
fields/electromagnetic waves and induces voltage in a
receiver coil on motion.
• Intrinsic angular momentum/spin of proton is invisible
to us and hence orientation of its rotation axis from the
magnetization vector B can be identified as it generates
a signal in a receiver coil just like a magnet.

Common nuclei with NMR property
Examples:
1H, 13C, 19F, 23N, and 31P with gyromagnetic ratio of
42.58, 10.71, 40.08, 11.27 and 17.25 MHz/T resp.
Since hydrogen protons are the most abundant in
human body, we use 1H MRI most of the time.

Effect of external
strong magnetic
field
• For example, the Earth’s gravitational field acts on a
spinning top and tries to alter the orientation of its
rotational axis. The top begins to wobble which is called
a precession.
• When hydrogen nuclei, a Proton, exposed to external
magnetic field, its magnetic moments/spins (B0) align
with the direction of the field like compass needles.
• It do not only get aligned but also undergo precession.

Larmor frequency
• Precession of the nuclei occurs at a
characteristic speed that is proportional to the
strength of the applied magnetic field (B0 in
Tesla) and is called as Larmor or precession
frequency (in MHz)-
n = g Bo
where, g is the gyromagnetic ratio which is a
characteristic property of a particular nuclei (in
MHz/T).
and g = 42.58 MHz/T for proton
 n = 63.9 MHz at B0= 1.5 T.

A Single Proton
+
+
+
There is an electric
charge
on the surface of the
proton, thus creating a
small current loop and
generating magnetic
moment m.
The proton also
has mass which
generates an
angular
momentum
J when it is
spinning.
J
m
m = g J where g is the gyromagnetic ratio

Protons in Free Space
What happens if they are in a magnetic field ?

Protons in a Magnetic Field
Bo
Parallel
(low energy)
Anti-Parallel
(high energy)
Spinning protons in a magnetic field will assume two states.
If the temperature is 0o K, all spins will occupy the lower
energy state.

• The spins tend to align parallel or anti-parallel
to the magnetic field with parallel alignment
being slightly preferred because it is equivalent
to spins residing in a more favourable energy
state.
• Under steady-state conditions, a slightly larger
fraction aligns parallel to the main magnetic
field (B0).
•It is this small difference that actually produces
the measurable net magnetization Mz (net
magnetization vector).

Net Magnetization
Bo
M
M α B0

Spin System Before RF Irradiation
Bo
Lower Energy
Higher Energy

The Effect of RF Irradiation to the Spin
System
Lower
Higher

 Small B0 produces small net magnetization M
 Thermal motions try to randomize alignment of
proton magnets
 Larger B0 produces larger net magnetization M, lined
up with B0
 At room temperature, the population ratio is roughly
100,000 to 100,006 per Tesla of B0

Knowing the energy difference allows us to use
electromagnetic waves with appropriate energy
level to irradiate the spin system so that some
spins at lower energy level can absorb right
amount of energy to “flip” to higher energy level.

• Energy can be introduced into a stable spin system by
applying RF of same frequency. This is called the
resonance condition.
•The required RF wave is generated in a powerful radio
transmitter and applied to the object to be imaged by
means of an antenna coil.
• The process of energy absorption is known as
excitation of the spin system and results in the
longitudinal magnetization being more and more tipped
away from the z-axis toward the transverse plane.

• All of the longitudinal magnetization is rotated into the
transverse plane by RF pulse that is strong enough and
applied long enough to tip the magnetization exactly 900.
• The resulting magnetization is now denoted by Mxy in
xy plane.
• Whenever transverse magnetization is present, it rotates
or precesses about the z-axis, which has the effect of an
electrical generator and induces an alternating voltage of
the same frequency as the Larmor frequency in a receiver
coil (MR signal).

Relaxation
• The MR signal rapidly fades due to two independent
processes that reduce transverse magnetization and
thus cause a return to stable state.
Spin-spin interaction
Magnetic field inhomogeneties
Magnetic susceptibility
Chemical shift effects
• T1 relaxation
• T2 relaxation
• T2* relaxation

T1-Relaxation (Longitudinal)
• The transverse magnetization vector decreases slowly
and the MR signal fades in proportion.
• As transverse magnetization decays, the longitudinal
magnetization Mz is slowly restored.
• This process is known as longitudinal relaxation or T1
recovery.
• The T1 time of a tissue is the time it takes for the
excited spins to recover and be available for the next
excitation.

T1-Relaxation (Longitudinal)
• Nuclei return to ground state only by dissipating their
excess energy to the surrounding (spin-lattice
relaxation).
• Time constant (Tl) for this recovery is dependent on
the B0 and internal motion of molecules (Brownian).
• Biological tissues have T1 values 0.5 to several
seconds at 1.5 T.
• The T1 time mostly determines how quickly an MR
signal fades after excitation.

T2-Relaxation (Transverse)
• Phase (in terms of angle) refers to the position of a
magnetic moment on its circular precessional path.
• Immediately after excitation, some spins have 0o
phase, then it is called as phase coherence.
• Phase coherence gradually decreases as some spins
advances while others fall behind in precession.
• Transverse magnetization disappears as vectors begin
to cancel each other.

• De-phasing: Transverse relaxation is the decay of
transverse magnetisation because spins lose coherence.
• Unlike T1-relaxation, T2-relaxation do not dissipate
energy instead exchange energy with each other.
• T1 & T2 relaxation are completely independent to
each other but occurs simultaneously.
• Complete recovery of longitudinal magnetization Mz
due to T1 takes 0.5-5 sec while decrease in MR signal
due to T2 takes 0.1-0.3 sec.

• Loss of coherence (dephasing) depends on:-
1. Spin-spin interaction:
1. Local changes in the particle magnetic field due
to energy transfer between spins. Spins precess
faster or slower according to mutual magnetic
field variations they experience.
2. Overall cumulative loss of phase (dephasing)
and having time constant T2.
3. Independent of B0 (more or less).

• Loss of coherence (dephasing) depends on:-
2. Time-independent in-homogeneties of B0
1. These are intrinsic inhomogeneties occurs due to
magnetic field generators itself and the patient body.
2. This contributes in dephasing and signal decay even
faster than earlier cases.
3. Signal decay occurs with time constant T2* (< T2).
4. Inhomogeneties mostly observed at tissue borders
e.g. air/tissue interfaces etc.
5. Also induced by local magnetic fields say due to iron
particles.
6. Loss of MR signal due to T2* is called as Free
Induction Decay (FID) –rectified by “spin-echo seq.”

Image Contrast
• Three intrinsic features of a biological tissue contribute
to its signal intensity/brightness on MR image/contrast--
1. Proton density: number of excitable spins per unit
volume minimizing T1 & T2 (Proton density-
weighted/proton density images).
2. Images contrast mainly determined by T1 are called
T1-weighted Images (T1w).
3. Images with contrast that is mainly determined by T2
are called as T2-weighted images (T2w).
• Proton density and T1 & T2 being a intrinsic features of
tissues, widely vary from one tissue to other. The
resulting images differ in their tissue-tissue contrast.
• Tissues that are virtually indistinct on CT scans can be
differentiated by MRI without contrast medium.

Image Contrast
• Repetition Time (TR) & T1 Weighting
• It is defined as the interval between two excitations of
the same slice.
• Long TR (> 1500 msec), more growth in longitudinal
magnetization and thus larger MR signal due to next
pulse (less T1 weightage).
• Short TR (< 600 msec), image contrast is strongly
affected by T1.
• So, thus, tissues with short T1 relax quickly and
give large signal after next RF pulse and appear
bright on the image  T1-weighted image (T1 info)
• Tissues with long T1, gives less signal and appear
dark.

Image Contrast
• Repetition Time (TR) & T1 Weighting
Short TR  strong T1 weighting
Long TR  low T1 weighting
Tissues with a short T1 appear bright because they
regain most of their longitudinal magnetization during
the TR interval and thus produce stronger MR signal.

Image Contrast
• Echo Time (TE) and T2 Weighting
• Different gradients magnet are used to induce
controlled magnetic field inhomogeneities which is
needed to encode the spatial origin of MR signals.
• However, it also contribute to spin dephasing. This
has to be rectified by applying a refocusing pulse
before an adequate MR signal is obtained.
• Receiver coil receives signal induced after phase
coherence, known as spin echo (SE).
• Echo time is the interval between application of the
excitation pulse and collection of the MR signal.
• Echo time determines the influence of T2 on image
contrast.

Image Contrast
• Echo Time (TE) and T2 Weighting
• If short echo time is < 30 msec, tissue-wise signal is not
much different  image has low T2-weighting.
• Looses most of their signal & appear dark on the image.
• If longer echo time (> 60 msec), tissue-wise signal
intensities are different  image has strong T2 weighting.
• Appear bright on the image.
• Cerebrospinal fluid (CSF) with its longer T2 is brighter
on T2-weighted images.
• Operator can select appropriate TE to control the degree
of T2 weighting of the resulting MR image.

Image Contrast
• Proton density-weighted images (PD images): MR image
which is a combination of T1 as well as T2 effects.
• PD images have a higher signal-to-noise ratio than T1 and
T2-weighted images because of long TR and short TE.
• Intermediate-weighted images: PD images with TE = 40ms
• Typical T1-weighted SPIN ECHO (SE) sequence is
acquired with TR/TE = 340/13 msec.
• T2-weighted FAST SPIN ECHO (FSE) image is acquired
with TR/TE = 3400/120 msec.
• Typical PD-weighted SE image acquisition at TR/TE =
2000/15 ms.
• Typical PD-weighted FSE image acquisition at TR/TE =
4400/40 ms.

Image Contrast
• PD sequences are especially used for evaluating structures
with low signal intensities viz. Bones, ligaments & tendons.
• PD-weighting is often used for high resolution imaging.
• During PD imaging SE sequences are preferred over FSE
since SE images are less prone to distortion.
• Generally, PD sequences are mainly used for imaging of
brain, spine and musculoskeletal system.

Parts of a MR Scanner
BIAC 1.5T Scanner

MRI Pictures
2D slices extracted from a 3D image
[resolution about 111 mm]
axial coronal sagittal

Magnetic resonance imaging, commonly known as
MRI, can non-invasively provide high resolution
anatomical images of human structures, such as brain,
heart and other soft tissues. It is used routinely in
clinical diagnosis.
Functional MRI advances from the traditional static
scans to image dynamic time course of the brain signal
during specific tasks. It is widely used now in studying
the working mechanism of the human brain. Clinical
application is mainly seen in presurgical planning.

Things needed for a typical MRI scanner
Strong magnetic field, usually from
superconducting magnets.
RadioFrequency coils and sub-system.
Gradient coils and sub-system.
Shimming coils and sub-system.
Computer(s) that coordinate all sub-
systems.

Transmit Receive
rf
coil
rf
coil
main
magnet
main
magnet
gradient
Shimming
Control
Computer

Types of Magnets:
Superconducting Magnets
• This is a most common magnet used in MRI which is
better in producing much stronger and stable magnetic
field.
• Superconducting magnet is consisting of electrical wire
conductor whose electrical resistance is zero. Thus, very
small conducting wires can carry very large current
without over-heating.

Superconducting Magnets
• The requirements of superconductivity are the conductor
must be of special alloy (Nb-Ti) imbedded in Cu and then
cooled to a very low temperature (liquid He which needs to
be replenished periodically).
• The Cu has a resistance so it acts as an insulator around the
superconductors. If the superconductivity fails, current in
the conductor produces heat which in turns rapidly reduces
the current. This will collapse magnetic field. This is
called as quench.
• Superconducting magnets in MRI are in the form of
cylindrical or solenoid coils with strong field in the internal
bore. This causes claustrophobia in some patients.

Resistive Magnets
• This type of magnets is made up of Cu wire. Resistive terms
indicate resistance to the current which produces heat.
• Because of this use of resistive magnets are limited to only
low field strengths.
Permanent Magnets
• Permanent magnets can also be used for MRI and there is no
need of coolant as well as conductor wire conducting current
using electrical power.
• However, use of this magnet is also limited to low field
strengths.
Both resistive and permanent magnets are designed to produce
vertical magnetic line between two poles. In this case more
space may be provided to reduce claustrophobia.

 If M is not parallel to B, then
it precesses clockwise around
the direction of B.
 However, “normal” (fully
relaxed) situation has M parallel
to B, which means there won’t
be any precession
Precession of Magnetization M
• Magnetic field causes M to rotate (or precess) about the
direction of Bo at a frequency proportional to the size of Bo —
42 million times per second (42 MHz), per Tesla of Bo. To
visualize the rotation, the magnetization M is tipped away
from the Bo direction.
 N.B.: part of M parallel to Bo
(Mz) does not precess

How to Make M not be Parallel to B?
• A way that does not work:
– Turn on a second big magnetic field B1 perpendicular
to main B0 (for a few seconds)
– Then turn B1 off; M is now not parallel to magnetic
field B0
• This fails because cannot turn huge (Tesla)
magnetic fields on and off quickly
– But it contains the kernel of the necessary idea:
A magnetic field B perpendicular to B
B0
B1
B0+B1
 M would drift over to be
aligned with sum of B0 and B1

 The effect of the tiny B1 is
to cause M to spiral away
from the direction of the
static B field
 B110–4 Tesla
 This is called resonance
 If B1 frequency is not close to
resonance, B1 has no effect
RF Coil: Transmitting B1 Field
• Left alone, M will align itself with Bo in about 2–3 s
• So don’t leave it alone: apply (transmit) a magnetic
field B1 that fluctuates at the precession frequency
and points perpendicular to B0 (how do we achieve
this? – by making a coil)
Time = 2–4 ms

Another Mechanical Analogy: A Swingset
• Person sitting on swing at rest is “aligned” with
externally imposed force field (gravity)
• To get the person up high, you could simply
supply enough force to overcome gravity and
lift him (and the swing) up
– Analogous to forcing M over by turning on a huge
static B1
• The other way is to push back and forth with a
tiny force, synchronously with the natural
oscillations of the swing
– Analogous to using the tiny RF B1 to slowly flip M
over
g

RF Coil: Signal
Receiver
• When excitation RF is turned off, M is left
pointed off at some angle to B0 [flip angle]
• Precessing part of M [Mxy] is like having a
magnet rotating around at very high speed (at RF
frequencies)
• Will generate an oscillating voltage in a coil of
wires placed around the subject — this is
magnetic induction

RF Coil: Signal
Receiver
This voltage is the RF signal whose
measurements form the raw data for MRI
 At each instant in time, can measure one voltage V(t),
which is proportional to the sum of all transverse Mxy
inside the coil
 Must find a way to separate signals from different
regions

Various RF Coils
• Separated by function:
Transmit / receive coil (most common)
Transmit only coil (can only excite the system)
Receive only coil (can only receive MR signal)
• Separated by geometry
Volume coil (low sensitivity but uniform coverage)
Surface coil (High sensitivity but limited coverage)

Gradient Coils: Spatially Nonuniform B:
 Extra static magnetic fields (in addition to B0)
that vary their intensity in a linear way across the
subject
 Precession frequency of M varies across subject
x-axis
f
60 KHz
Left = –7 cm Right = +7 cm
Gx = 1 Gauss/cm = 10 mTesla/m
= strength of gradient field
Center
frequency
[63 MHz at 1.5 T]

A 3-D gradient field (dB/dx, dB/dy, dB/dz) would
allow a unique correspondence between the spatial
location and the magnetic field. Using this
information, we will be able to generate maps that
contain spatial information – images.

Gradient Coils
Gradient coils generate varying magnetic field so that
spins at different location precess at frequencies unique
to their location, allowing us to reconstruct 2D or 3D
images.
X gradient Y gradient Z gradient
x
y
z
x
z z
x
y y

Spatial Encoding – along x
x

Spatial Encoding of the MR Signal
0.8
w/o encoding w/ encoding
Constant
Magnetic
Field
Varying
Magnetic
Field

Spatial Encoding of the MR Signal
Fourier Transform

Spatial Encoding – along y
y

History of Magnetic
Resonance Imaging

Timeline of MR Imaging
1920 1930 1940 1950 1960 1970 1980 1990 2000
1924 - Pauli suggests
that nuclear particles
may have angular
momentum (spin).
1937 – Rabi measures
magnetic moment of
nucleus. Coins
“magnetic resonance”.
1944 – Rabi wins
Nobel prize in
Physics.
1946 – Purcell shows
that matter absorbs
energy at a resonant
frequency.
1946 – Bloch demonstrates
that nuclear precession can be
measured in detector coils.
1952 – Purcell and
Bloch share Nobel
prize in Physics.
1972 – Damadian
patents idea for large
NMR scanner to
detect malignant
tissue.
1959 – Singer
measures blood flow
using NMR (in
mice).
1973 – Lauterbur
publishes method for
generating images
using NMR gradients.
1973 – Mansfield
independently
publishes gradient
approach to MR.
1975 – Ernst
develops 2D-Fourier
transform for MR.
NMR becomes MRI
MRI scanners
become clinically
prevalent.
1990 – Ogawa and
colleagues create
functional images
using endogenous,
blood-oxygenation
contrast.
1985 – Insurance
reimbursements for
MRI exams begin.

Discovery of Nuclear Magnetic
Resonance Absorption (1946)
• Bloch and Purcell independently
discovered how to measure nuclear
moment in bulk matter (1946)
– Determined relaxation times.
• They showed that energy applied
at a resonant frequency was
absorbed by matter, and the re-
emission could be measured in
detector coils
• They shared the 1952 Nobel Prize
in Physics
Felix Bloch
Edward Purcell

Early Uses of NMR
• Most early NMR was used for chemical analysis
– No medical applications
• 1971 – Damadian publishes and patents idea for using
NMR to distinguish healthy and malignant tissues
– “Tumor detection by nuclear magnetic resonance”, Science
– Proposes using differences in relaxation times
– No image formation method proposed
• 1973 – Lauterbur describes projection method for creating
NMR images
– Mansfield (1973) independently describes similar approach

The First ZMR NMR Image
Lauterbur, P.C. (1973). Image formation by induced local interaction: Examples employing
nuclear magnetic resonance. Nature, 242, 190-191.

Early Human MR
Images (Damadian)

Mink5 Image – Damadian (1977)

Using MRI to Study Brain Function
Somatosensory Cortex: Hammeke, et al., 1994
Visual Cortex: Kwong, et al., 1994

Relaxation Characteristics
About the NMR Signal

Relaxation: Nothing Lasts Forever
• In absence of external B1, M will go
back to being aligned with static field B0
this is called relaxation.
• Part of M perpendicular to B0 shrinks [Mxy]
– This part of M is called transverse magnetization
– It provides the detectable RF signal
• Part of M parallel to B0 grows back [Mz]
– This part of M is called longitudinal magnetization
– Not directly detectable, but is converted into transverse
magnetization by externally applied B1

Relaxation Times and Rates
• Times: ‘T’ in exponential laws like e–t/T
Rates: R = 1/T [so have relaxation like e–Rt]
• T1: Relaxation of M back to alignment with B0
– Usually 500-1000 ms in the brain [lengthens with
bigger B0]
• T2: Intrinsic decay of the transverse magnetization over
a microscopic region ( 5-10 micron size)
– Usually 50-100 ms in the brain [shortens with bigger
B0]
• T2*: Overall decay of the observable RF signal over a
macroscopic region (millimeter size)
– Usually about half of T2 in the brain [i.e., faster
relaxation]

T2* Relaxation
S = So * e –t/T2*

Material Induced Inhomogeneities Will Affect
T2*
• Adding a nonuniform object (like a person) to B0 will
make the total magnetic field B nonuniform
– This is due to susceptibility: generation of extra magnetic
fields in materials that are immersed in an external field
– Diamagnetic materials produce negative B fields
– Paramagnetic materials produce positive B fields
– Size about 10–7B0 = 1–10 Hz change in precession f
• Which makes the precession frequency nonuniform,
affecting the image intensity and quality
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
– Nonuniformities in B bigger than voxel size affect whole
image
– Nonuniformities in B smaller than voxel size affect voxel

Frequency and Phase
• RF signals from different regions that are at
different frequencies will get out of phase and
thus tend to cancel out
– Phase = the t in cos(t) [frequency f = /2]

Sum of 500 Cosines with Random Frequencies
Starts off large when all phases are about equal
High frequency gray curve is at the average frequency
Decays away as different
components get different phases

T2* relaxation (decay) and NMR Signal
• Random frequency differences inside intricate
tissue environment cause RF signals (from Mxy) to
dephase
– Measurement = sum of RF signals from many places
 Measured signal decays away over time [T2*40 ms
at 1.5 T]
– At a microscopic level (microns), Mxy signals still
exist; they just add up to zero when observed from
outside (at the RF coil)
• Contents of tissue can affect local magnetic field
 Signal decay rate depends on tissue structure and
material

Hahn Spin Echo: Retrieving Lost Signal
• Problem: Mxy rotates at different rates in different
spots
• Solution: take all the Mxy’s that are ahead and
make them get behind (in phase) the slow ones
– After a while, fast ones catch up to slow ones  re-
phased!
Fast & slow
runners
Magically “beam”
runners across track
Let them run the
same time as before

 The “magic”
trick: Flip of
the magnetization
M
 Apply a second
B1 pulse to
produce a flip
angle of 180
about the y-axis
(say)
 Time between
first and second B1
pulses is called

Spin Echo:
 Excite
 Precess
& dephase
 180 flip
 Precess
& rephase

T2 Relaxation (Decay)
• Spin echo doesn’t work forever (TE can’t be too
big)
– Main reason: water molecules diffuse around
randomly
• About 5-10 microns during 10-100 ms readout window
 They “see” different magnetic fields and so their
precession frequency changes from fast to slow to
fast to ................
– This process cannot be reversed by the inversion RF
pulse
• Time scale for irreversible decay of Mxy is called T2

T1 Relaxation
 Longitudinal relaxation of Mz back to
“normal” (T1)
 Caused by internal RF magnetic fields in
matter
 Thermal agitation of H2O molecules
 Can be enhanced by magnetic impurities in
tissue
 S = So (1-et/T1)

Factors Influencing Relaxation Rates
• Magnetic impurities
* In general, it will shorten the relaxation time such as T2*,
T2 and T1
• Local physiological and chemical environment changes
* For example, bounded water molecules will have shorter
T2 then free water molecules
• Strength of the magnetic fields
* Usually stronger field prolongs T1, however, shortens T2*
and T2 due to increased susceptibility-induced magnetic
inhomogeneities

Contrast Agents that Affects Relaxation
Rate
Drugs containing certain impurities can alter T1,
T2, and T2* — contrast agents (e.g., CuSO4, Gd-
DTPA)

Outline
• Why use MRI to image?
• Key concepts of MRI
• History of MRI
• Parts of a MR scanner
• MR safety

What is MRI?
• A technique for measuring changes in
activity over time using principles of
magnetic resonance.

Why the Growth of MRI?
• Powerful
– Improved ability to understand cognition
– Better spatial resolution than PET
– Allows new forms of analysis
• High benefit/risk ratio
– Non-invasive (no contrast agents)
– Repeated studies (multisession, longitudinal)
• Accessible
– Uses clinically prevalent equipment
– No isotopes required
– Little special training for personnel

Cheng, Waggoner, & Tanaka (2001) Neuron Sakai, Rowe, & Passingham (2002) Nature Neuroscience

Image provided by Dr. James Voyvodic (Duke BIAC)

Key Concepts
• Contrast
• Spatial Resolution
• Temporal Resolution

Anatomical Contrast
Definition: The ability to distinguish between two (or more)
different properties of tissue.

Blood Oxygenation Level Dependent
(BOLD) Contrast
From Mosley & Glover (1995)

Design Effects on Functional Contrast
Contrast should really be considered as “contrast to noise”: how effectively can
we decide whether a given brain region has property X or property Y?

Spatial Resolution: Voxels
Voxel: A small rectangular prism that is the basic sampling unit of MRI.
Typical functional voxel: (4mm)3. Typical anatomical voxel: (1.5mm)3.

Spatial Resolution: Examples
~8mm2
~4mm2 ~2mm2
~1.5mm2 ~1mm2

Temporal Resolution
• Importance depends upon research question
– Type I: Detection
• Temporal resolution is only indirectly important if your study
investigates whether or not a given brain region is active.
– Type II: Estimation
• Temporal resolution is extremely important when attempting to
understand the properties of an active region.
• Determining factors
– Sampling rate, usually repetition time (TR)
– Dependent variable, usually BOLD response
• BOLD response is sluggish, taking 2-3 seconds to rise above
baseline and 4-6 seconds to peak
– Experimental design

Functional Resolution
The ability of a measurement technique to identify
the relation between underlying neuronal activity
and a cognitive or behavioral phenomenon.
Functional resolution is limited both by the intrinsic
properties of our brain measure and by our ability
to manipulate the experimental design to allow
variation in the phenomenon of interest.

MRI Safety
Issue: The appropriate risk level for a research participant is
much lower than for a clinical patient.

Hospital Nightmare
Boy, 6, Killed in Freak MRI Accident
July 31, 2001 — A 6-year-old boy died after
undergoing an MRI exam at a New York-
area hospital when the machine's powerful
magnetic field jerked a metal oxygen tank
across the room, crushing the child's
head. …
ABCNews.com

MR Incidents
• Pacemaker malfunctions leading to death
– At least 5 as of 1998 (Schenck, JMRI, 2001)
– E.g., in 2001 an elderly man died in Australia after being twice
asked if he had a pacemaker
• Blinding due to movements of metal in the eye
– At least two incidents (1985, 1990)
• Dislodgment of aneurysm clip (1992)
• Projectile injuries (most common incident type)
– Injuries (e.g., cranial fractures) from oxygen canister (1991, 2001)
– Scissors hit patient in head, causing wounds (1993)
• Gun pulled out of policeman’s hand, hitting wall and firing
– Rochester, NY (2000)

Issues in MR Safety
• Magnetic Field Effects
• Known acute risks
– Projectiles, rapid field changes, RF heating,
claustrophobia, acoustic noise, etc.
• Potential risks
– Current induction in tissue at high fields
– Changes in the developing brain
• Epidemiological studies of chronic risks
– Extended exposure to magnetic fields
• Difficulty in assessing subjective experience
– In one study, 45% of subjects exposed to a 4T scanner
reported unusual sensations (Erhard et al., 1995)

Possible Effects of Magnetic Fields
• Physiological
– Red blood cells (especially sickled) may alter shape in a
magnetic field
– Some photoreceptors may align with the field.
• Sensory (generally reported in high-field)
– Nausea
– Vertigo
– Metallic taste
– Magnetophosphenes

Risks of MRI
• Projectile Effects: External
• Projectile Effects: Internal
• Radiofrequency Energy
• Gradient field changes
• Claustrophobia
• Acoustic Noise
• Quenching

Projectile Effects: External
“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 Chaljub (2001)
Chaljub (2001)
Schenck (1996)

Radiofrequency Energy
• Tissue Heating
– Specific Absorption Rate (SAR; W/kg)
• Pulse sequences are limited to cause less than a one-degree rise in
core body temperature
• Scanners can be operated at up to 4 W/kg (with large safety margin)
for normal subjects, 1.5 W/kg for compromised patients (infants,
fetuses, cardiac)
– Weight of subject critical for SAR calculations
• Burns
– Looped wires can act as RF antennas and focus energy in a small
area
• Most common problem: ECG leads
• Necklaces, earrings, piercings, pulse oximeters, any other cabling

Projectile/Torsion Effects: Internal
• Motion of implanted medical devices
– Clips, shunts, valves, etc.
• Motion or rotation of debris, shrapnel, filings
– Primary risk: Metal fragments in eyes
• Swelling/irritation of skin due to motion of
iron oxides in tattoo and makeup pigments

Acoustic Noise
• Potential problem with all scans
– Short-term and long-term effects
• Sound level of BIAC scanners
– 1.5T: 93-98 dB (EPI)
– 4.0T: 94-98 dB (EPI)
• OSHA maximum exposure guidelines
– 2-4 hours per day at BIAC levels
• Earplugs reduce these values by 14-29 dB,
depending upon fit.

Gradient Field Changes
• Peripheral nerve stimulation
– May range from distracting to painful
– Risk greatly increased by conductive loops
• Arms clasped
• Legs crossed
• Theoretical risk of cardiac stimulation
– No evidence for effects at gradient strengths
used in MRI

Claustrophobia
• Most common subject problem
– About 10% of patients
– About 1-2% of BIAC subjects
• Ameliorated with comfort measures
– Talking with subject
– Air flow through scanner
– Panic button
– Slow entry into scanner

Quenching
• Definition: Rapid decrease in magnetic field strength due to
loss of superconductivity
– Only initiated voluntarily due to danger to participant’s life or health
• Effects
– Magnets heat up with loss of current
– Cryogenic fluids (Helium) boil off and fill the scanner room
• Displaces breathable air from room
• Cooling of room, condensation reduces visibility
– Physical damage to the scanner may occur
– Safety personnel must be cognizant of room conditions

Image Contrast
• Saturation at Short Repetition Times

Nucleus Abundance in body
(%)
Spin Gyromagnetic ratio
γ = ω0/Bo (MHz/T)
Sensitivity
per nuclei
H-1 63 ½ 42.58 1
C-13 0.13 ½ 10.71 0.016
F-19 0.0012 ½ 40.05 0.83
Na-23 0.037 3/2 11.26 0.093
P-31 0.14 ½ 17.23 0.066
K-39 0.031 3/2 1.99 ~ 5x10-4

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