MRI

Samuel T. (MSc.)
Characteristics of MR image
• including factors that affect the signal-to-noise ratio (SNR), blood flow
effects, and artifacts
• The protons in a material, with the use of an external uniform magnetic
field and RF energy of specific frequency, are excited and subsequently
produce signals with amplitudes dependent on relaxation characteristics
and spin density,
• How to localize the 3d volume ?
Magnetic Field Gradients

• Magnetic fields with predictable directionality and strength are

produced in a coil wire energized with a direct electric current of
specific polarity and amplitude.

• Magnetic field gradients are obtained by superimposing the magnetic

fields of one or more coils with a precisely defined geometry

• With appropriate design, the gradient coils create a magnetic field that
linearly varies in strength versus distance over a pre-defined FOV.
Individual conducting wire coils that are separately
energized with currents of
opposite directions produce
magnetic fields of opposite
polarity. Magnetic field strength
reduces with distance from the
center of each coil. When combined, the magnetic
field variations form a linear change
between the coils, producing a

linear magnetic field gradient.

Properties of gradient system
• Amplitude: The peak amplitude of the gradient field determines the
"steepness" of the gradient field. Gradient magnetic field strength
typically ranges from 1 to 50 millitesla per meter (mT /m) [0.1 to 5
gauss (G)/cm].
• Slewrate: is the time required to achieve the peak magnetic field
amplitude, where shorter time is better. Typical slew rates of gradient
fields are from 5 mT/m/msec to 250 mT/m/msec. Limitations in the
slew rate are caused by eddy currents, which are electric currents
induced in nearby conductors that oppose the generation of the
gradient field
Cont.
• The gradient is a linear, position-dependent magnetic field applied
across the FOV, and it causes protons to alter their precessional
frequency corresponding to their position along the applied gradient in
a known and predictable way.
• Location of protons along the gradient is determined by their
frequency and phase; the gradient amplitude and the number of
samples over the FOV determine the frequency bandwidth (BW)
across each pixel.
Cont.
The gradient field creates a net positive and negative magnetic environment that adds to and
subtracts from the main magnetic field. Associated with the local change in magnetic field is a
local change in precessional frequencies, per the Larmor equation. The frequencies thus
directly vary across the field in proportion to the applied gradient strength.
Cont.
Cont.
• The localization of protons in the three-dimensional volume requires
the application of three distinct gradients during the pulse sequence
• slice select, frequency encode, and phase encode gradients.
• Slice select gradient (SSG):
• Proton precessional frequencies vary according to their distance from
the null of the SSG.
• Slice thickness: determined by two parameters:
(a) the bandwidth (BW) of the RF pulse, and
(b) the gradient strength across the FOV
Cont.

The slice select gradient (SSG)

disperses the precessional
frequencies of the protons
in a known way along the gradient.
A narrow-band radiofrequency (RF)
pulse excites only a
selected volume (slice) of tissues,
determined by RF bandwidth and
SSG strength
Cont.

Slice thickness is dependent on RF

bandwidth and gradient strength.
A: For a fixed gradient strength,
the RF bandwidth determines the
slice thickness.
B: For a fixed RF bandwidth,
gradient strength determines the
slice thickness.
FEG

• Readout gradient, is applied in a direction perpendicular to the SSG.

• For an axial image acquisition, the FEG is applied along the x-axis throughout the
formation and the decay of the signals arising from the spins excited by the slice
encode gradient.

• Spins constituting the signals are frequency encoded depending on their position
along the FEG.
Cont.

A spatial "projection" of the object is

created by summing the signal
amplitude along a column of the tissue;
the width of the column is defined by
the sampling aperture (pixel), and the
thickness is governed by the slice select
gradient strength and RF bandwidth.
Cont.
• Overall signal amplitude is dependent on spin density and T1 and T2
relaxation events.
• This produces a spatial domain profile along the direction of the
applied gradient.
• Frequency encoding can be used to define location within a slice or
between slice
PEG
• Position of the spins in the third spatial dimension is determined with
a phase encode gradient (PEG), applied before the frequency encode
gradient and after the slice encode gradient, along the third
perpendicular axis.

• after the initial localization of the excited protons in the slab of tissue
by the SEG, all spins are in phase coherence (they have the same
phase).
Cont.

The phase encode gradient (PEG) produces a spatially

dependent variation in angular frequency of the excited
spins for a brief duration, and generates a spatially
dependent variation in phase when the spins return to
the Larmor frequency.
Incremental changes in the PEG strength for each TR
interval spatially encodes the phase variations: protons
at the null of the PEG do not experience any phase
change, while protons in the periphery experience a
large phase change dependent on the distance from the
null.
• The incremental variation of the PEG strength can
be thought of as providing specific "views" of the
three-dimensional volume because the SSG and FEG
remain fixed throughout the acquisition.
Signal Generation and Detection

• RF excitation dependent on precessional frequency of proton.

• Cause magnetic moment to displace from equilibrium

• Returning relaxation result in signal emission

• Excitation-> detection -> acquisition form basic process for MRI
Cont.

• Quantum mechanical assumption: Spins oriented parallel and

antiparallel to B0 are separated with ∆E.

• The energy corresponds to specific precessional frequency

• The applied B1 should exactly Match the energy difference to excite

the spins and Generate MR signal.
Cont.
• Classical thinking:
• B1 field is considered the magnetic component of an electromagnetic
wave with sinusoid ally varying electric and magnetic fields.
Cont.
FID and Time Relaxations
• The 90-degree RF pulse phase coherence and maximum transverse
magnetization.
• Mxy rotates at the Larmor frequency,: the receiver antenna coil, free
induction decay (FID) signal
Cont.
T2
• Exponential relaxation decay, T2, represents the intrinsic spin-spin
interactions that cause loss of phase coherence due to the intrinsic
magnetic properties of the sample. The elapsed time between the peak
transverse signal and 37% of the peak level (1/e) is the T2 decay
constant .

where Mxy is the transverse magnetic moment at time t for a sample that has Mo
transverse magnetization at t = O. When t= T2, then e exp(-1) = 0.37, and Mxy =
0.37
Mo
Cont.
• T2 decay mechanisms are determined by the molecular structure of the sample
• Mobile molecules in amorphous liquids (e.g., cerebral spinal fluid [CSF]) exhibit
a long T2, because fast and rapid molecular motion reduces or cancels intrinsic
magnetic in homogeneities.
• As the molecular size increases, constrained molecular motion causes the
magnetic field variations to be more readily manifested and T2 decay to be more
rapid.
• Thus large, nonmoving structures with stationary magnetic in homogeneities have
a very short T2.
Cont.
T1
• The loss of transverse magnetization (T2 decay) occurs relatively quickly,
whereas the return of the excited magnetization to equilibrium (maximum
longitudinal magnetization) takes a longer time.
• Individual excited spins must release their energy to the local tissue (the lattice).
• Spin-lattice relaxation is a term given for the exponential regrowth of M" and it
depends on the characteristics of the spin interaction with the lattice (the
molecular arrangement and structure).
cont.
• The Tl relaxation constant is the time needed to recover 63% of the
longitudinal magnetization, M"after a 90-degree pulse (when Mz = 0).

where Mz is the longitudinal magnetization that recovers after a time t in a material

with a relaxation constant Tl.
Cont.
Cont.
• T1 relaxation depends on the dissipation of absorbed energy into the
surrounding molecular lattice.
• The relaxation time varies substantially for different tissue structures
and pathologies.
• From a classical physics perspective, energy transfer is most efficient
when the precessional frequency of the excited protons overlaps with
the "vibrational" frequencies of the molecular lattice.
Cont.
A classical physics explanation of spin-lattice
relaxation is based on
the vibration of the molecular lattice of a sample
material and its frequency spectrum. Large,
stationary structures exhibit little motion with
mostly low-frequency
vibrations (solid curve). Medium sized, proteinated
materials have increased frequency amplitudes
(short dash curve), and small sized, aqueous
materials have
frequencies distributed over a broad range (long
dash curve). The overlap of the
Larmor precessional frequency (vertical bar) with
the molecular vibration spectrum

indicates the probability of spin-lattice relaxation.

Comparison T1 and T2
• T1 >>T2.
• For instance, in a soft tissue, a T1 time of 500msec has a correspondingT2
time that is typically 5 to 10 times shorter
• Factors: Molecular motion, size, and interactions influence T1 and T2
relaxation
• Small molecules exhibit long T1 and long T2, and intermediate-sized
molecules have short T1 and short T2; however, large, slowly moving or
bound molecules have long T1 and short T2 relaxation times.
Cont.
• It is the differences in Tl, T2, and T2* (along with proton density
variations and blood flow) that provide the extremely high contrast in
MRI.
• A higher magnetic field strength increases the Larmor frequency ωo
=γBo), which reduces the amount of spectral overlap and produces a
longer T1.
• To summarize, T1 > T2 > T2*, and the specific relaxation times are a
function of the tissue characteristics.
Cont.
• The spin density, T1, and T2 decay constants are fundamental
properties of tissues, and therefore these tissue properties can be
exploited by MRI to aid in the diagnosis of pathologic conditions such
as cancer, multiple sclerosis, or hematoma.
 Factors affecting T1 and T2 relaxation
Cont. times of different tissues are generally
based on molecular motion, size, and
interactions. The relaxation times
(vertical axis) are different for T1 and

T2
T1-weighted imaging: higher spatial
resolution
T2-weighted imaging: higher tissue
contrast
typically both time-scales are used
T2 relaxation T1 relaxation
Measuring the MR Signal
• The moving proton vector induces a signal in the RF
antenna
• The signal is picked up by a coil and sent to the
computer system.
• The received signal is sinusoidal in nature
• The computer receives mathematical data, which is
converted through the use of a Fourier transform into
an image.

http://www.cea.fr/english/Pages/News/voyage-aimant-IRM-pr
ojet-iseult.aspx
cont.
2D Fourier Imaging
Raw 2D k-space data Processed data

Magnitude of Fourier transform

Pulse sequences
• Emitted signals in MRI are dependent on T1, T2 and Spin density relaxation
characteristics.
• MRI Pulse sequence: spin echo, inversion recovery, and gradient recalled
echo
• It is all about: timing, order, polarity, and repetition frequency of the RF
pulses and applied magnetic field gradients

• Contrast weighted images are obtained by combining the above pulses with
spatial encoding techniques
Spin Echo parameters
• TR: Time of repetition, TE: time of Echo
Spin echo
• Refocusing the Spin Magnetization
• Spin echo describes the excitation of the magnetized protons in a
sample with an RF Pulse and production of the FID, followed by a
second RF pulse to produce an echo.

• Timing between the RF pulses allows separation of the initial FID and
the echo and the ability to adjust tissue contrast.
Spin echo

Spin echo pulse sequence

timing is initiated with a 90-
degree pulse, followed by a
180-degree pulse applied at
time TE/2. The peak echo
signal occurs at the
echo time, TE. The signal is
acquired during the evolution

and decay of the echo.

Inversion recovery
• Emphasizes Tl relaxation times of the tissues by extending the amplitude
of the longitudinal recovery by a factor of two.
• An initial I80-degree RF pulse inverts the Mz longitudinal magnetization
of the tissues to –Mz.
• After a delay time known as the time of inversion (TI), a 90-degree RF
pulse rotates the recovered fraction of Mz spins into the transverse plane
to generate the FID.
• A second I80-degree pulse at time TE/2 produces an echo signal at TE.
• TR in this case is the time between l80-degree initiation pulses
Inversion recovery (STIR and FLAIR)
 Gradient recalled echo
• For an FID signal generated under a linear gradient, the transverse
magnetization de-phases rapidly as the gradient is continually applied.

• If the gradient polarity is instantaneously reversed after a predetermined

time, the spins will re-phase and produce a gradient echo;

• its peak amplitude occurs when the opposite gradient (of equal strength) has
been applied for the same time as the initial gradient.

• Continually applying this latter (opposite) gradient allows the echo to decay,
during which time the signal can be acquired
Gradient echo
MRI Contrast Formation
• Different values of Tl or T2 (or of PH or f(v)) will change the signal S.

• The signal in adjacent voxels will be different when Tl or T2 changes between

those two voxels, and this is the essence of how contrast is formed in MR!.

• Importantly, by changing the pulse sequence parameters TR and TE, the

contrast dependence in the image can be weighted toward Tl or toward T2.
PH is the spin (proton) density, f(v) is the signal arising from fluid flow, Tl and T2 are physical properties of
tissue, and TR and TE are pulse sequence controls on the MRI machine
T1 weighting
• de-emphasizing T2 contributions
• Short TR to maximize the differences in longitudinal magnetization during the
return to equilibrium, and a short TE to minimize T2 dependency during signal
acquisition.
• In the longitudinal recovery and transverse decay diagram note that the TR
time on the abscissa of Tl-weighted images therefore require a short TR and a
short TE for the spin echo pulse sequence.
T weighted image

The T1-weighted spin

echo axial brain image obtained with TR = 549
msec and TE = 11 msec demonstrates bright
image intensity for short-T1 tissues (white matter
and fat) and dark intensity for long-T1 tissues
(cerebrospinal fluid).
Spin (proton) density weighting

• Image contrast with spin density weighting relies mainly on

differences in the number of magnetizable protons per volume of
tissue.
• Very hydrogenous tissues such as lipids and fats have a high spin
density compared with proteinaceous soft tissues; aqueous tissues such
as CSF also have a relatively high spin density.
• Spin density-weighted images therefore require a long TR and a short
TE for the spin echo pulse sequence.
Cont.
The proton densityweighted axial spin echo
brain image, obtained
with TR = 2,400 msec and TE = 30 msec, shows
reduced contrast compared with the T1-
weighted images (but an overall higher signal
amplitude).
Tissues with higher spin density
(e.g., fat, (SF) have higher image intensity.
T2 weighting
• T2 weighting follows directly from the spin density weighting sequence:
Reduce Tl effects with a long TR, and accentuate T2 differences with a longer
TE.
• Compared with a Tl-weighted image, inversion of tissue contrast occurs (CSF
is brighter than fat instead of darker),

• Tissues with a longT2 (e.g., CSF) maintain transverse magnetization longer

than short-T2 tissues, and thus result in higher signal intensity.
Cont.
The T2-weighted
spin echo axial brain image, obtained
with TR =
2,400 msec and TE = 90 msec, has bright
image
intensity for long- T2 tissues such as
cerebrospinal fluid and dark intensity
for short-T2
tissues such as white matter and fat.
Contrast comparison of SPIN ECHO Sequences
• Comparisons of the contrast characteristics are essential for accurate
differential diagnoses and determination of the extent of pathology.

The images illustrate the characteristics of n with high fat signal; PD with
high signal-to-noise ratio (SNR) yet low contrast discrimination; T2 with high signal and contrast for
long-T2 tissues; and FLAIR, with fluid-containing tissues clearly delineated as a low signal.
All images assist in the differential diagnosis of disease processes.
Image characteristics
• Spatial resolution, contrast sensitivity, and SNR parameters form the basis
for evaluating the MR image characteristics.
• The spatial resolution is dependent on the FOV, which determines pixel
size, the gradient field strength, which determines the
FOV, the receiver coil characteristics (head coil, body coil, various surface
coil designs), the sampling bandwidth, and the image matrix.

• Common image matrix sizes are 128 X 128,256 X 128,256 X 192, and 256
X 256, with 512 X 256,512 X 512, and 1024 X 512 becoming prevalent.
Cont.
• MR provides spatial resolution approximately equivalent to that of CT,
with pixel dimensions on the order of 0.5 to 1.0 mm for a high-
contrast object and a reasonably large FOV (>25 cm).

• In small FOV acquisitions with high gradient strengths and surface

coils, the effective pixel size can be smaller than 0.1 to 0.2 mm

• Slice thickness in MRI is usually 5 to 10 mm and represents the

dimension that produces the most partial volume averaging.
Cont.
• A higher field strength magnet generates a larger SNR and therefore allows thinner
slice acquisition for the same SNR.
• Improved resolution results from the reduction of partial volume effects.
• However, with higher magnetic field strengths, increased RF
absorption (heating) occurs.
• Additional compromises of higher field strengths include increased artifact
production and a lengthening of T 1 relaxation.
• Higher field strength magnets increase the Tl relaxation constant, which decreases Tl
contrast sensitivity because of increased saturation of the longitudinal magnetization.
Contrast
• Contrast sensitivity is the major attribute of MR.
• The spectacular contrast sensitivity of MR enables the exquisite discrimination of
soft tissues and contrast due to blood flow. This sensitivity is achieved through
differences in the Tl, T2, spin density, and flow velocity characteristics.
• Contrast which is dependent upon these parameters is achieved through the
proper application of pulse sequences, as discussed previously.
• MR contrast materials, usually susceptibility agents that disrupt the local magnetic
field to enhance T2 decay or provide a relaxation mechanism for enhanced Tl
decay (e.g., bound water in hydration layers), are becoming important
enhancement agents for the differentiation of normal and diseased tissues.
• The absolute contrast sensitivity of the MR image is ultimately limited by the
SNR and presence of image artifacts.
SNR
• The signal-to-noise ratio (SNR) of the MR image is dependent on a
number of variables,

There are numerous dependencies on the ultimate

SNR achievable by the MR system. The intrinsic
signal intensity based on T1, T2, and spin density
parameters has
been discussed.
Image acquisition and reconstruction algorithm
• It affect SNR
• Point acquisition, line acquisition, two-dimensional Fourier transform
acquisition, and three-dimensional Fourier transform volume
acquisition.
• Reconstruction filters and image processing algorithms will also affect
the SNR.
• High-pass filtration methods that increase edge definition will
generally decrease the SNR,
• while low-pass filtration methods that smooth the image data will
generally increase the SNR at the cost of reduced resolution.
Artifacts
• Machine dependent: field in-homogeneities,
• Susceptibility artifact: the ratio of the induced internal magnetization in a tissue
• to the external magnetic field.
• Gradient field: Proper reconstruction requires linear, matched, and properly sequenced
gradients.
• Radio-frequency and coil artifacts: RF sources, such as TV and radio broadcasts, electric
motors, fluorescent lights, and computers.
• K-space error: Errors in k-space encoding affect the reconstructed image, and cause the
artifactual superimposition of wave patterns across the FOV.
• Motion artifacts: voluntary and involuntary movement, and flow (blood, CSF)
• Chemical shift: Chemical shift refers to the resonance frequency variations resulting from
intrinsic magnetic shielding of anatomic structures.

• Others
QC testing area
QC: Spatial resolution, slice thickness, SNR, distortion, distance
accuracy, and chemical shift artifacts
• SNR is calculated from a region of interest in the images as
average number/standard deviation.
• Various magnetic susceptibility agents are placed in the vials to
produce known T1 and T2 values; of note is the center vial filled
with oil, and the easily recognized chemical shift artifacts.
• A: SPGR (TR = 10.2 msec, TE = 1.8 msec, slice = 2 mm, 256 x
128 image, SNR = 55.7).
• B: Three-dimensional gradient recalled echo (3D GRE) (TR =
31.0 msec, TE= 10.0, slice = 4 mm, 512 x 512 image, SNR =
64.0)
Safety and bio-effect
• Strong magnetic fields, RF energy, time varying magnetic gradient fields,
cryogenic liquids, a confined imaging device (claustrophobia), and noisy
operation (gradient coil activation and deactivation, creating acoustic
noise).

• Patients with implants, prostheses, aneurysm clips, pacemakers, heart

valves, etc., should be aware of considerable torque when placed in the
magnetic field, which could cause serious adverse effects.

• Even nonmetallic implant materials can lead to significant heating under

rapidly changing gradient fields
 Cont.
• Ferromagnetic materials
• With very high field strength magnets (e.g., 4 T or higher),
• there has been anecdotal mention of dizziness and disorientation of personnel
and patients as they move through the field.
• The most common bio-effect of MR systems is tissue heating caused by RF
energy deposition and/ or by rapid switching of high strength gradients.
FDA guideline

Serious bio-effects are

demonstrated with static and
varying magnetic
fields at strengths significantly
Static magnetic field effect

• Very high field strength static magnetic fields have been shown to
increase membrane permeability in the laboratory.

• With systems in excess of 20 T, enzyme kinetic changes have been

documented, and altered bio-potentials have been measured.

• These effects have not been demonstrated in magnetic fields below

10T.
Varying Magnetic Field Effects
• Magnetic fields that vary their strength with time are generally of
greater concern than static fields because oscillating magnetic fields
can induce electrical current flow in conductors.
• At extremely high levels of magnetic field variation, effects such as
visual phosphines (the sensation of flashes of light being seen) can
result because of induced currents in the nerves or tissues.
• Other consequences such cardiac fibrillation have been suggested in
the literature.
Magnetic field, RF exposure, and noise limits
• RF exposure causes heating of tissues.
• There are obvious effects of overheating, and therefore a power
deposition limit is imposed by governmental regulations for various
aspects of MRI and MRS operation.
• The rationale for imposing limit on static and varying magnetic fields
is based on the ability of the resting body to dissipate heat buildup
caused by the deposition and absorption of thermal energy.
Cont.

The principal applications for MRI are

– head and spine (73%),
– bone and joints(17%),
– body (10%)
K-space data acquisitions and image
reconstruction in MRI