103
Magnetic Resonance Imaging (MRI)
Yes we know MRI does not use ionizing radiation and it is good for imaging soft tissues including blood.
Is that all for MRI?
MRI has powerful features whereas other imaging techniques, such as CT and PET, are relatively
limited. These features of MRI include several protocol parameters by which indigenous contrast and
image quality can be manipulated in unlimited ways.
For example by changing TE and TR we can
generate different MRI contrasts.
Magnetic Resonance Imaging (MRI)
Selective Tissue Suppression using IR
Other sequences have special parameters such as inversion time in IR sequence
http://mriquestions.com/why-use-ir.html
MRI Protocol Parameters
bad Contrast Bad resolution(partial volume)
It is important to understand MRI protocol parameters and their changes, to do so
the basic physics of MRI must be understood.
Different flip anglesReceiver bandwidth (BW)
Small FOV
Several phenomena (force, velocity etc) in our life can be represented as vectors but in MRI we are only
interested in magnetic fields.
A vector can be represented by an arrow or two components (horizontal and vertical components ).
Review of Vectors
How to reach to this point ?
What is the resultant vector of the following:
2
2
2
2
Out of phase
In phase
(1) Horizontal vector
(2) Vertical vector
(3) Oblique vector
What are the total horizontal and vertical components for these oblique vectors?
MRI Radio Signals
FM 90.4FM 94.5
An MRI scanner uses radio signals with frequencies in the range of megahertz (MHz). You have to
therefore exercise extreme caution in relation to any source of communication systems (mobile, radio, train
..etc) near the MRI scanner or the building.
Let’s imagine a signal as though it was the motion of a hand clock.
time
In MRI, we will see how magnetic field vectors rotate in the same manner as a hand clock.
Signal Representation
One dimensional representation Two dimensional representation
(2) Frequency: How fast the clock’s hand is rotating around the face of the clock (number of cycles per second).
(3) Phase: the location of the clock’s hand at a specific time
Which ones are in phase and which are out of phase ?
Signal Parameters
(Magnitude, Frequency and Phase)
(1) Magnitude
The length of the clock’s hand
Lecture 1
Signal Creation
The Static Magnetic Field (the B0 Field)
Why do we have to place our patient in the bore of the MRI scanner?
There has to be a source of magnetism in our body!
B0
A superconducting electromagnet, which is
immersed in liquid Helium, is capable of
producing a very powerful magnetic field
such as 3 Tesla.
1 Tesla = 10,000 Gauss
Earth’s B field ~ 0.5 Gauss (50 µT)
Refrigerator magnet ~ 5 mT
The blue arrow or vector represents
the magnitude and direction of the
B0 field
Different elements in the human body can be used as the source of magnetism such as
Hydrogen1, Carbon13, Sodium23 and Phosphorus31.
However, due to the abundance of 1H nuclei (spins) in water and fat-based tissues of the
human body, 1H is the most commonly used element in clinical MRI.
Water (H2O)
Nucleus (like the core of the earth)
Spin
Magnetic moment (µ)
The Source of Magnetism in the Human Body
1H possesses:
Spin angular momentum (Spin)
A magnetic dipole moment (µ)
In MRI, hydrogen nuclei are referred to as spins.
MRI active nuclei have a property of spin greater than zero which enables them
to interact with the external B0 field.
Nuclei must have one of the following:
Odd protons.
Odd neutrons.
Odd (protons + neutrons).
Examples: 1H, 23Na, 13C, 31P
Stable nuclei, with nuclear spin equalling zero, cannot undergo an MRI experiment:
Examples: 4He,12C,16O and 32S
Active and Stable Nuclei
The net magnetization (M) = 0
Outside the MRI Scanner
(Spins with Random Orientations)
Outside the MRI scanner, human tissue is
not magnetised
Quantum Behaviour of Hydrogen in the B0 Field
(Energy States)
1H nuclei have only two energy states in the presence of the B0 field; spin up
(lower energy state) or spin down (higher energy state).
Spin up
Spin down
-1/2 γB0h
1/2 γB0h
γB0h
Although there are 2 energy states, we
do not know what the exact state of
the hydrogen is at any time, it is
actually in all possible states
simultaneously (quantum
superposition).
Quantum mechanics can tell us what happens to a large number of 1H
nuclei in the B0 field at the thermal equilibrium.
γ: gyromagnetic ratio and h: Planck's constant
Lower energy state
Higher energy state
Spin up
Spin down
The population is given by the Boltzmann factor:
N+/N− = exp [− γB0h / kT] --- magnetic energy / thermal energy
At absolute temperature (-273.15 Cº) most nuclei reside at the lower energy state.
Increasing the field strength also increases spins in the lower energy state.
Quantum Behaviour of Hydrogen in the B0 Field
(Energy States)
Lower energy state
Higher energy state At thermal equilibrium (body
temperature ~ 27 Cº), there is almost
equal distribution of spins in the two
states but with a very small excess in the
lower energy state.
The small excess in the lower energy
state is only visible for MRI
measurement.
27 Cº -273.15 Cº
The ratio is roughly 100,000 to 100,006 per Tesla of B0
Since there is an excess number of nuclei
in the lower energy state, the thermal
equilibrium magnetisation M (net
magnetisation) > 0
Spin up
Quantum Behaviour of Hydrogen in the B0 Field
The net magnetisation (M) > 0
Since 1H possesses spin, it precesses
around B0 with Larmor frequency which
depends on the field strength:
ω0 = γ * B0γ: gyromagnetic ratio of hydrogen (42.58 MHz/T)
At 3 Tesla ω0 = 127 MHz
Larmor or the precessional frequency equation
(ω0=γ*B0) is the most important equation in
MRI and you should memorize it.
Spin up
Quantum Behaviour of Hydrogen in the B0 Field
(Precession or Larmor Frequency)
B0
spin
http://www.xrayphysics.com/sequences.html
Longitudinal (Mz) and Transverse (Mxy)
Magnetisation Components
Transverse xy plane
Classical mechanic’s view of precession:
• The net magnetization vector (M) of all hydrogen nuclei aligns along the B0 field (z axis) and it is called the longitudinal magnetisation component (Mz).
• In the xy plane, the transverse magnetisation component (Mxy)= 0.
• The precession is said to be frozen or invisible in the classical view.
Mxy=0
Resonance Condition
We place our subject in the MRI scanner to generate some longitudinal magnetization (Mz)
which is parallel to the B0 field.
How do we measure M0 ?
Fact: M0 is extremely small and there is no existing device which can measure it directly.
B0 field
M = 0
Subject out of the MRI bore
Subject in the MRI bore
Mz
We have to manipulate (excite) the system by adding energy.
This is done by applying an oscillating magnetic field (much smaller than B0) known as the B1 field (RF pulse).
Fact: the B1 field is not static like B0 but it alters its direction (+ to -) at Larmor frequency.
When spins absorb this energy (resonance condition),
(1) Spins transfer from lower energy state to higher energy state.
(2) Mz starts to rotate to the xy plane (transverse plane).
(3) Spins are brought into phase in the xy plane
B0 field
M = 0Mz
Mxy
zdirection
Resonance Condition (Excitation)
ω0
= γ
* B
0
B1 field (90° RF pulse)
a) The laboratory frame of reference. b) The rotating frame of reference rotating about z.
Most MRI analyses are performed in the rotating frame to simplify the complex motion of precessing spins.
Frames of Reference
Let us imagine how Mz rotates during the application of B1 field (RF pulse):
On a dark night, imagine you are holding a flash light and standing on a merry go round that is moving. Try to flip/rotate the
flashlight.
If someone from outside is watching you, what is the trajectory of the light (a or b)?
If someone is with you on the merry go round, what is the trajectory of the light (a or b)?
How is the trajectory when the flashlight is rotated 90°?
Mz=0 Mxy = M0
90° RF pulse
Detecting an MRI Signal
We applied a 90° RF pulse (B1 field), for a short period of time, to rotate Mz completely to the transverse plane.
Mz in the transverse plane is called the transverse magnetisation component (Mxy ) which is the only component which is visible for measurement.
Since Mxy in the transverse plane precesses at the Larmor frequency ,by placing a loop of wire around the imaged subject (an MRI coil), we can detect Mxy as a free induction decay signal (FID).
Fact: Mxy is the only component which can be measured by the MRI coil.
MRI coil
Transverse plane (xy)
Mxy
Mxy in the transverse plane is not static but it is rotates or precesses at Larmor frequency. Voltage can then be produced due to the motion of Mxy (Faraday's Law).
Z axis
SI( Mxy)
time
• The received MRI signal (FID) decays quite rapidly due to relaxation.
• The excited spins need to return back to the thermal equilibrium state along the
longitudinal axis (z-axis)– Energy exchange (T1 relaxation).
• However, the rate of decay is much faster than the required time to return to the
thermal equilibrium state.– spin-spin magnetic fields interaction (T2 relaxation)
– field inhomogeneity (T2*)
Free Induction Decay (FID) Signal
The Composed MRI Signal (FID)
What we receive in the MRI coil is only one signal (the composed signal) that is the sum of the contribution
of all 1H nuclei.
What frequency does the FID signal have (spins all see B0 field)? ω0 = γ * B0
Which part of the human body does the FID signal come from (liver, heart, brain, limbs…..etc)?
Lecture 2
MRI Pulse Sequences
As we mentioned, the MR scanner can only detect a single signal (the composed signal) in the transverse plane.
We applied a 90° RF pulse, then after some time (echo time ‘TE’), we recorded the FID signal. The FID signal declines due to the fact that spins need to go back to the lower energy state (T1 relaxation). However, the rate of decay is much faster than T1 relaxation due to T2/T2* relaxation.
The Concept of Echo in MRI
TE
Free Induction ecay )FID)
Initially, we assume all spins experience only the B0 field, so each spin precesses at the same Larmor
frequency (ω0=γ*B0).
• However, in the transverse plane, the magnetic field of each spin can interact with the B0 field and this
causes changes in the precessional frequency of other spins (T2 relaxation).
• Also, the B0 field may not be homogeneous at all points in the space (T2′ relaxation).
The affect of T2 and T2′ (T prime) is called T2*.
Field Inhomogeneity (T2*)
T2T2*
time
Sign
al In
ten
sity
(SI)
This figure shows how the MRI signal decays (T2) even faster due to T2*.
In order to minimise the rate of decay to some degree due to T2′, we can add 180° RF pulse after the 90° pulse to generate an "echo" that occurs later in time. This is referred to as the spin echo. The 180° RF pulse only reduces the rate of decay due to the inhomogeneity in B0 (T2′) and not due to T2.
Please be aware that spin echo sequences can not recover all inhomogeneity in the B0 field.
The Concept of Echo in MRI
FID: free induction decay
Maximum signal
Losing signal
If you are in a cave and start shouting. You will hear your voice come back due to reflection of sound. This is called an echo.
Spin Echo (SE) (Hahn Echo)
Experiment:
(1) Take two pens and flip them to 90° from the longitudinal axis to the transverse plane.
(2) In the transverse plan, move one pen faster than the other. You will notice that they are out of phase (dephased)
(3) After some time (TE/2), rotate the two dephased pens by 180° RF pulse
(4) In this case, the faster pen will be behind the slower pen.
(5) If you wait the same time (TE/2) and the same speed, you will notice that both pens will come back in phase.
http://www.slideshare.net/drpsdeb/mri-basics
Even spin echo minimizes the rate of decay due to T2′, the echo is still affected by the rate of T2.
An MRI pulse sequence consists of several horizontal lines. Each line shows a specific event of when RF-pulses are applied, an MR signal is generated, and gradients are turned on and off. Time is on the horizontal axis.
To generate an MRI image, we have to repeat the excitation process (RF pulse) many times, which depends on the number of phase encoding steps (Nphase). The time used to repeat the excitation is called the repetition time (TR).
The Concept of an MRI Pulse Sequence Timing Diagram
TR: how often we repeat the RF excitation pulseTE: the time between the centre of the RF pulse and the centre of the echo.
NP
has
e
Nfrequency
SignalADC
Echo
ADC: Analogue to Digital Converter
TE
TR
Nphase
http://www.revisemri.com/questions/pulse_sequences/se_ge_differences
The Main Components of an MRI pulse Sequence
Most MRI pulse sequences have the following components:
(1) An RF excitation pulse is applied in the presence of slice selection
gradient (Gss) to generate Mxy from a specific slice
(2) A frequency encoding gradient (Gf) to create a 1D image
(3) A phase encoding gradient (Gp) to create the second dimension in
the image
(4) A signal or ADC where our echo is recorded
SignalADC
Echo
TE
TR
FID
Gradient Recalled Echo (GRE) Pulse Sequence
SE vs GRE
What differences can you observe?
http://www.revisemri.com/questions/pulse_sequences/se_ge_differences
Spin Echo (SE) Pulse Sequence
The spin echo pulse sequence has :
(1) A 90° excitation pulse with Slice selection gradient (Gss) to generate Mxy
from a specific slice
(2) A frequency encoding gradient (Gf) to create 1D image
(3) A phase encoding gradient (Gp) to create the second dimension in the
image
(4) A 180° pulse (refocusing pulse) used to refocus the dephased spins (T2′)
(5) Signal or ADC where our echo is recorded
ADC
Echo
FID
TR
TE
The typical TR in SE is around 2 s and Nphase = 256.
Total scan time to acquire one slice = TR * Nphase = 2 *256 = 8.3 minute
Gradient Recalled Echo (GRE) Pulse Sequence
GRE is identical to SE pulse sequence except that there is no 180° RF pulse. While the SE sequence generates an echo using a 180° RF pulse, in the GRE, the echo is generated using the gradient reversal approach.
Following the 90° RF pulse, the first negative lobe of the gradient (dephasing lobe) causes a rapid phase dispersion of the precessing spins. When this gradient is reversed (rephasing lobe), the spins refocus and form a gradient (recalled) echo.
Although GRE does not correct for T2′,GRE has two main features, the echo can be recorded much more quickly and with less RF power.
dephasing lobe
rephasing lobe
For clarity, other sequence components are not shown.
Multislice Imaging
Free time echo
TR
TE
SE Sequence
Multislice SE Sequence
Since TR in SE sequence is quite long, a large number of slices can be excited in the free time within the same TR.This approach is implemented to speed up the imaging acquisition.
Slice 1 Slice 2 Slice 40 Slice 1
Turbo/Fast Spin Echo (TSE)
TSE is an extension of multislice imaging
TSE uses a series of 180° refocusing pulses after a
single 90° pulse to generate a train of echoes for
the same slice.
The number of echoes acquired in a
given TR interval is known as the echo train
length (ETL) or turbo factor.
If a SE sequence with a certain TR/TE/spatial
resolution takes 8 minutes to perform, a TSE
sequence with ETL=8 would take only 1 minute.
echo1 echo2 echo3 echo4
echo1
FIDEcho1 Echo2 Echo3 Echo4
Turbo/Fast Spin Echo (TSE)
TSE
http://mriquestions.com/fse-parameters.html
http://www.revisemri.com/questions/pulse_sequences/tse
Inversion Recovery (IR) Pulse Sequence
What differences can you observe between SE pulse sequence and the second sequence?
Inversion Recovery (IR) Pulse Sequence
In our SE pulse sequence, what happens if we add a 180° RF pulse at the start of the sequence?
90° RF
B0
B0
-z
IR
180° RF
SE
Inversion Recovery (IR) Pulse Sequence
TI
TE
TRThe time between the first 180° RF pulse and the 90 RF pulse is called inversion time (TI).
TI is one of the most important protocol parameters in MRI by which a signal from any tissue can be suppressed (STIR and FLAIR).
FACT: there was a technique called FIRMFast Inversion Recovery Myeline
which was used to suppress the signal from myelinated brain white matter.
The point where we apply the 90° RF pulse is called the nulling or bouncing point
http://mriquestions.com/why-use-ir.html
Lecture 3
Image Contrasts (T1, T2/T2* and PD) in MRI
Spin Relaxation
Let’s look at the example below.
A heater is similar to the RF excitation pulse. The RF gives energy to spins (hydrogen nuclei).
The heater provides the two cats with heat (energy). Let’s take the heater away.
Where do you think this energy goes?
(1) Energy exchanges between the two cats (2) Energy exchanges between each cat and the surroundings(3) Cats will keep their energy
The process of energy exchange is called relaxation.
Coil
FID: free induction decay
TE
Maximum signal
Losing signal
Spin Relaxation
Once we switch the RF pulse (heater) off, spins need to move back to the lower energy state or thermal equilibrium along the longitudinal z axis.
Keep in mind that we are only able to measure the magnetization (Mxy) in the transverse plan.
While we are busy measuring our FID signal, the relaxation process takes place simultaneously , causing the signal to decay very rapidly.
The excitation trajectory is different to the relaxation trajectory!
M0
Mxy
During excitation
During relaxation
Mz
Spins In phase and Out of Phase
The phase of spins (magnetizations vectors of spins) are one of the most important concepts in MRI by which the signal decay is determined.
• If spins in the transverse plane (xy plane) are in phase (spins point in the same direction), the MRI signal intensity (SI) will be maximum (a).
• If spins in the transverse plane (xy plane) have different orientations (out of phase or dephase), the MRI signal will be weak (b) and it becomes extremely weak as the dephasing aggravates.
time
SI
a
b
c
The spins’ dephasing mainly arises from T2 relaxation and aggravates with T2* relaxation.
Spin-Spin Relaxation (T2 Relaxation)
T2 relaxation is the process by which the transverse component of magnetization (Mxy) decays very rapidly. This is due to the spins’ dephasing (spins get out of step from one another in random ways). This is shown in the figure below (arrows with different orientations).
The exponential decay of Mxy is governed by a time T2. Thus T2 is the time required for the signal to fall to approximately 63% of its initial value (when there is only 37% of the signal left)
+ +
+ +
T2
time
SI
37% of M0
M0
http://mriquestions.com/what-is-t2.html
Spins’ magnetic fields interaction
Once we place our subject in the bore of the MRI scanner, the field becomes inhomogeneous. This is due to the different levels of susceptibility of human tissue. This causes a very slight variation in B0 field strength (variation in the precession frequency) from point to point.
This will cause the transverse magnetisation to decay even faster. In this case, the time governing this decay is not T2 but T2*. The T2* is the sum of T2 and T2′. T2 prime (T2’) is due to the inhomogeneity in the B0 field.
In reality, we measure our signal weighted by T2* relaxation.
Luckily, there is a way to generate an MRI signal weighted by T2. This is done by minimising, to some degree, the affect of T2’ using spin echo with 180° RF pulse.
T2T2*
time
Fact: T2* can be useful in MRI. There are many applications which use MRI based on T2* such as fMRI.
Inhomogeneity in the B0 Field (T2* relaxation)
SI
37% of M0
M0
Spin–Lattice Relaxation (T1 relaxation)
T1 relaxation is the process by which the net magnetisation (M) returns to its initial maximum value (Mo) parallel to Bo.
Mz
63% of M0
tissue
T1The rate of recovery is governed by time T1.T1 can be viewed as the time required for the z-component of Mz to reach about 63% of its maximum value (Mo).
+
time
M0
http://mriquestions.com/what-is-t2.html
Energy exchange between spins and the surroundings.
Spin Relaxation Times (T1, T2 and T2*)
Fact: T1 is much longer than T2/T2*. Each tissue has a unique T1 and T2
I usually like to imagine T1 and T2 curves as a mountain with a slope
It takes a longer time to climb a mountain (T1) than to slide down it (T2/T2*).
When you go to a higher magnetic field, for example from 1.5 T to 3 T,the ‘mountain’ becomes higher. This means the signal is much higher but T1 is longer.
T2/T2*
T1
http://www.slideshare.net/drpsdeb/mri-basics
List of relaxation times by tissue type and main magnetic field strength (Gati et al., 1997; Kruger et al., 2001; Lu et al., 2005; Wu and Wong, 2006).
List of Relaxation Times for some Tissue at 1.5 T and 3 T
ADC Echo
Echo
SE vs GRE
ADC
FIDFID
GRE vs SE
GRE generates an MRI image weighted by T2* (T2,T2′).
SE generates an MRI image weighted by T2.
But why do we have to use GRE if it generates such a low signal?
hemorrhage, calcification, and iron deposition in various tissues and lesions.
Time
MZ
Time
tissue
fat
TRlong
fat
tissue
TE
T2w MRI Long TR Long TE
PD Long TR Short TE
Image contrast is a function of all T1,T2/T2* and PD.The important point is how to minimise one contrast and maximize the other one.
T2/T2* and PD Contrasts
PD T2
With a longer TE there is more T2 contrast but a lower signal
SI (Mxy)
With a shorter TE, we have a higher signal but no T2 contrast
Difference in T1 contrast almost 0
TR
TE
Decay curve
Recovery curve
SE Signal Intensity vs TE
SE brain images with TR = 1500 ms and various TE’s
What do you observe in terms of signal brightness and contrast?
Source from chapter 3 "MRI from picture to proton"
How to Measure T2 Relaxation Time of a Tissue
This is done using SE sequence by acquiring different acquisitions with varying TEs. Each acquisition is applied with the same TR (very long).
For each acquisition and for the same location, we measure the mean signal intensity (SI).
We then plot these values and determine the time where the maximum SI falls to 37% of its initial value.
SI
time
37% of M0
Initial value (M)
T2
T2 T2*Spin echo gradient echo
An example of T2 vs T2*
T2* includes T2 and T2′. T2′ is due to the variability in the B0 field.
While spin echo recovers to some degree T2′, gradient echo accumulates both T2 and T2′.
MZ
Time
tissue
fat
TRshort
fat
tissue
TE
T1 contrast
T1w MRI Short TR Short TE
Image contrast is a function of all T1,T2/T2* and PD.The important point is how to minimise one contrast and maximize the other one
T2+T1T1
Contrast reverse
SI (Mxy)
T1 Contrast
Yes with a short TR we generate a T1 contrast but also a less amount of Mz is rotated to the transverse plane (xy)
Difference in T1 contrast
SE Signal Intensity vs TR
SE brain images with TE = 10 ms and varies TR
What do you observe in terms of signal brightness and contrast?
Source from chapter 3 "MRI from picture to proton"
Some applications require the use of a very short TR to speed up the scan time. In this case, the optimal flip angle to generate a maximum signal is not 90° RF pulse.
The GRE Pulse Sequence and the Modified Flip Angle
http://mriquestions.com/4-or-more-rf-pulses.html
GRE with fixed TR (150 ms) and TE (4.6 ms) and various flip angles
GRE with Short TR and Varying Flip Angles
The exact shape of this curve depends on the specific T1 value of the tissue and the TR interval.
The choice of flip angle is critical for determining both signal intensity as well as image contrast.
Which flip angle gives:(1) the maximum signal intensity for a given tissue?
(2) the maximum contrast?
the Ernst angle provides maximum signal intensity
Source from chapter 3 "MRI from picture to proton"
Contrast Enhanced MRI Image
There are ways to manipulate the relaxation time of tissues. In other words, how to speed up the energy exchange between spins and the surroundings.
For example when gadolinium (Gd) is injected, the T1 relaxation time is dramatically shortened. This causes the MRI signal to be brighter or whiter in the image.
Inject GdTumour
Normal tissue
Effect of contrast agent on images
MZ
tissue
Tumour-Gd
Tumour
Tumour and normal tissue have both almost same T1 (contrast ~ 0)With Gd inserted, the contrast becomes much better
TR
https://en.wikipedia.org/wiki/MRI_contrast_agent
Inversion Recovery (IR) Pulse Sequence
In our SE pulse sequence, what happens if we add a 180° RF pulse at the start of the sequence?
90° RF
B0B0
-z
180° RF
IR SE
Inversion Recovery (IR) Pulse Sequence
Observations:
(1) Since we applied a 180° RF inversion pulse, all the longitudinal magnetization (Mz) will be transferred completely from ‘+z’ to ‘-z’ direction.
(2) Once we switch the 180° RF inversion pulse off, the spins tend to relax back to the lower energy state.
(3) It turns out that spins are relaxed by shrinking along the z direction (- to +). This means that there is no magnetization appearing at the transverse plane (Mxy=0, no signal) at any time.
(4) Since there is no Mxy during and after the 180° RF pulse, a 90 ° RF excitation pulse is then applied to generate Mxy.
During excitation (180°)
During relaxation
TE
Inversion pulse Excitation pulse Refocusing pulse
Selective Tissue Suppression using IR
The time between the 1st 180° and 90° RF pulses is called Time to inversion (TI) or tau (τ). This time determines how much Mxy is generated in the transverse plan.
TI is one of the most important parameters in the MRI protocol for suppressing a signal from a specific tissue.
Short tau inversion recovery (STIR ): it is used to null fat at a very short TI (why).
Fluid attenuation inversion recovery (FLAIR): it is used to null fluid at a very long TI (why).
Fact: if you know the bouncing point of a tissue then you can determine the T1 of the tissue (T1 ≈ TI/ 0.69)
Nulling or bouncing point
FLA
IR
STIR
TI
http://mriquestions.com/why-use-ir.html
Selective Tissue Suppression using IR
This is done by acquiring different acquisitions with varying TIs. Each acquisition is applied with the same TR (usually very long ~ 9000 ms).
For each acquisition and for the same location, we measure the mean signal intensity (SI).
Then we plot these values and determine TI where the curve crosses zero (bouncing or nulling point)
The T1 of a tissue = TIbouncing_point/0.69
SI
TimeTI = Bouncing point
TI
How to Measure T1 Relaxation Time of a Tissue
Lecture 4
Imaging Gradients
The Composed MRI Signal (FID)
What we receive in the MRI coil is only one signal (the composed signal).
If we excite a human body (subject) with a 90° RF pulse for a period of time, then we start measuring
the FID or echo signal:
Which part of the human body does the FID/echo signal come from (liver, heart, brain, limbs…..etc)?
What frequency does the FID/echo signal have?
B0 field Composed signal
The RF coil measures only one signal which is the sum of the contribution from all spins (1H nuclei).
The FID/echo signal comes from everywhere (all spins) and we have absolutely no clue how to tell how much of the signal is coming from the brain, heart, toes, liver etc. This is therefore not a useful piece of information.
In MRI, magnetic field gradients encode spatial position in precessional frequency.
Spatial Encoding
FOVbase
FOV
ph
ase
FOV: Field Of View
The gradient is an additional magnetic field which varies over space.
• Gradient adds to B0, so the field depends on the position
• Precessional frequency varies with position
• Spins at each position precess at a different frequency
• The RF coil hears all of the spins at once
• Differentiate material at a given position by selectively listening to that frequency
Magnetic Field Gradients
(ω = γB0+ γG.r)
B0
Fastprecession
Slowprecession
High field
Low field
The Components of Spatial Encoding
How does an MRI scanner create an MRI image?
1) Select information (Mxy) from a single slice.
2) Then address, in sequence, the localization in the plane of that slice.The in plane localization uses two different techniques:
- Frequency encoding - Phase encoding
Slice Selection
Any MRI scanner comes with three magnetic field gradients:Magnetic field gradient in X direction,Magnetic field gradient in Y direction and Magnetic field gradient in Z direction.
We have to keep in mind that the direction of slice selection will always be perpendicular to the net gradient magnetic field
Slice Selection
How do we:
1) Select a slice in any plane (axial, sagittal, coronal)2) Select a slice in any location in the plane3) Select a slice with a specific thickness4) Select a slice in any orientation
SignalADC
Echo
TE
TR
FID
Slice Selection In GRE Pulse Sequence
Slice selection gradient
Rephase lobe for Gs
0frequency
Gs gradient
RF
excited slice
Slice Selection
Isocenter where all gradient magnetic fields are zero.
Along the bore of the magnet (z direction)
How to write Larmor frequency in the presence of slice selection gradient that varies linearly in z direction:
ω = γB0+ γGz
Slice Selection
Which gradient do you select to image in the coronal or sagittal plane?
In lumbar spine imaging, we usually want slices parallel to disk spaces at different oblique angles.This can be achieved by turning on more than one gradient simultaneously .
http://mriprotocol.blogspot.co.za/2012/01/mri-lumbar-spine-protocol.html
An interslice gap is a small space between two adjacent slices.
Because the resultant slice profiles of the B1 field (90° RF excitation pulse) are not perfectly rectangular, two adjacent slices overlap at their edges when closely spaced.
In this case, the RF pulse for one slice also excites spins in adjacent slices. This interference is known as cross-talk.
Cross-talk produces saturation effects and thus reduces SNR
Most clinical applications use an interslice gap of 25–50% of the slice thickness.
Interslice Gap (Distance Factor)
Effect of cross-talk on image contrast. SE (with (TR/TE 2000/20) image with (a) 50% gap and (b) 0% gap demonstrating impaired contrast.
tails
90
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F p
uls
e
http://mriquestions.com/cross-talk.html
Interleaved Acquisition for 100% gap
The interleaved approach allows us to acquire contiguous slices without cross talk artefacts. This is done firstly by acquiring odd-numbered slices and this is followed by acquiring even-numbered slices.
Slice interleaving to allow contiguous slices without cross-talk. Odd-numbered slices (with 100% gaps) are obtained in one acquisition, followed by a second acquisition of even-numbered slices.
http://mriquestions.com/cross-talk.html
In Plane Localization
Both an RF pulse with Gs is turned on for a period of time to knock the longitudinal magnetization (Mz) from a specific slice to the transverse plane (Mxy). At time (TE), the MRI signal is recorded.
Where does the FID signal come from?
Gs
We know it comes from the excited slice but we have no idea which part of the slice it is originating from.
There are two steps for in plane localisation. One dimension is encoded using the frequency encoding gradient while the other dimension is encoded using the phase encoding gradient.
An MRI image of a slice
Frequency encoding direction
Ph
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Frequency encoding gradient
In Plane Localization
Recipe (spatial frequencies) Real ImageK-space
Fourier Theory
Fourier’s theory can find the receipt of an image.
Fourier demonstrates that an image can be made from ingredients called signals. Each signal has a different spatial frequency.
Signals with different spatial frequencies are generated by magnetic field gradients.
Frequency Encoding Gradient (Gf) (FOVx and base resolution)
B0±Gx.x
1. Gf generates range of frequencies along the frequency encoding direction.
2. The range of frequencies determine the FOVx
3. The period of Gf depends on the base resolution in the frequency encoding direction.
Range of frequencies (FOVx)
SignalADC
Echo
TE
TR
FID
Frequency Encoding in GRE Pulse Sequence
lobe1
lobe2
Time during Gf is on
Spatial frequency:
kx(t) = Gf(t) dt
Phase Encoding to Create the Second Dimension
Now we need to find Fourier’s recipe for the other dimension
One of the most difficult challenges in MRI is phase encoding to locate signals with different frequencies along the phase encoding direction.
Frequency encoding direction
Ph
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A,B and C experience the same frequency (a). The same with D, E and F, they see (b).
a b
http://mriquestions.com/frequency-encoding.html
Phase Encoding Gradient (Gp) (FOVy and phase resolution)
To differentiate each pixel along the phase encoding direction, the excitation process has to be repeated, which depends on the matrix size of the image along the phase encoding direction.
Gp is applied with different amplitudes.
This has several dramatic complications in MRI:
(1) A substantial increase in the scan time,(2) Limiting image resolution,
SignalADC
Echo
TE
TR
FID
Spatial frequency:
ky(t) = Gp (t) dt
In MRI, the normal spatial resolution in the phase encoding direction (Nphase) is about 128 or 256.
Let’s say in spin echo we use a very long TR such as 2 seconds and Nphase=256 (for simplicity we assume we have one slice)
The total scan time = TR * Nphase = 256 * 2 = 8.5 minutes
The time to acquire one slice takes 8.5 minutes. Imagine we have 50 slices.
Do not forget we can still minimize the total scan time using Multislice Imaging (slide 35) or Turbo/Fast Spin Echo (TSE) (slide 36) techniques.
Phase Encoding Gradient (Gp) (FOVy and phase resolution)
Lecture 5
Imaging Formation
Sampling an MRI Signal (Echo)
Using magnetic field gradients in the x, y and z directions, we were able:
(1) To localise our signal to a specific slice (RF excitation pulse together with Gs)
(2) To encode one dimension in that slice using the frequency encoding gradient (Gf).
(3) To encode the other dimension of the slice using the phase encoding gradient (Gp) multiple times.
(4) Each time we repeat (TR) with different Gp, we collect an echo with Gf.
(5) The echo data is placed in a special grid called K-space.
SignalADC
Echo
TE
TR
FID
Remember that what we receive in the MRI coil is only one signal (the composed signal or an echo). Since we are dealing with a digital system, each echo has to be digitized.
Coil
Sampling an MRI Signal (Echo)
Gf
Gp1
RFGS
Coil
Gf
Gp2
RFGS
Where does each pointin the echo come from?
Since each echo is composed of waveforms with different spatial frequencies, to record the echo efficiently we have to sample as fast as possible to avoid aliasing (wrap-around) or chemical shift artefacts.
The protocol’s parameter, which determines the sampling efficiency, is called receiver bandwidth (BW = 1 / td)
Sampling and Receiver Bandwidth (BW)
SignalADC
Echo
TE
TR
FID
We sample an echo while Gf is turning on
Fact: since we work on a digital computer, we have to sample a signal
http://mriquestions.com/receiver-bandwidth.html
Narrow Receiver Bandwidth
Chemical shiftof fat signal
Wrap-around
Sampling in K-space
K-spaceEcho 1
Echo 2
Echo 3
Echo n
Each time we acquire and sample an echo, we place the samples of each echo in a line, in a special grid called k-space.
k-space is an array of numbers representing spatial frequencies in both directions (kx,Ky) of the MR image.
In each pixel in the k-space, where does the signal intensity for each sample come from?
Ky
Kx
Two Dimensional Fourier Transform (2DFT)
Since each sample in k-space represents the Fourier relationship between the signal at a spatial frequency and the signal in real space, by taking the inverse Fourier, we can generate an MRI image.
K-space Real image
In each pixel in the k-space, where does the signal intensity for each sample come from?
What is the total scan time?
What determines how many echoes we have in k-space?
What determines the number of samples in both directions?
Sampling K-space
SignalADC
Echo
TE
TR
FID
We sample an echo while Gf is turning on
Each generated echo is placed in one line in k-space
K-spaceEcho 1
Echo 2
Echo 3
Echo n
Ky
Kx
The Properties of K-space
http://mriquestions.com/locations-in-k-space.html
k-space Image
Full sampling Full-FOV,high-res
Full-FOV,low-res:blurred
Low-FOV,high-res:may be aliased
Reduce kmax
Increase k
2DFT
k-space relations:FOV and Resolution
This is related to the receiver BW. With a smaller BW, a smaller ranges of frequencies are sampled.
http://users.fmrib.ox.ac.uk/~karla/teaching/image_formation.ppt
Partial Fourier in K-space
The k-space data have special properties where the upper part is a mirror to the lower part. This is only correct if there are no aretfacts influencing the acquired data.
With partial Fourier, not all of the phase-encoding values are acquired.
The phase-encoding values that are not collected are approximated from those that are.
This can be translated into a reduction in imaging time.
Example:In the Siemens scanner, If you choose the partial Fourier to be 7/8:We are only acquiring 75 % of the lines of k-space (Nphase)
Total scan time to acquire one slice = TR * Nphase * partial Fourier
K is a constant that is related to the hardware system,FOVx and FOVy are the field-of-view in the x and y directions,Nx and Ny are the number of frequency and phase encoding steps,Δz is the slice thickness,NEX is the number of excitation (number of signal averages), and BW is the receiver bandwidth.
Factors Affecting the Signal-to-Noise Ratio (SNR)
The SNR is defined in terms of voxel volume, number of measurements and
receiver bandwidth.
FOVx
FOV
y
FOV: Field Of View
Δz
In this example Nx =5 Ny = 5
http://link.springer.com/chapter/10.1007%2F978-3-540-37845-7_5#page-1
The matrix should be as large as possible in order to produce high spatial resolution.But the minimum pixel size is limited by the fact that, in general, SNR decreases with the size of thevoxel.
Effect of the FOV on pixel size with the matrix size held constantA smaller matrix size with the FOV held constant resultsin larger pixels and thus a poorer spatial resolution
SNR - Field of View (FOV) and the Imaging Matrix Size
What is the pixel size in each figure?
15 cm FOV
a b c d e
30 cm FOVx 15 cm FOVx
30
cm
FO
Vy
Thinner slices are better for image resolution.
Thinner slices are associated with more noise (↓ SNR).
Thicker slices are associated with other problems such as an increase in partial volume effects.
SNR - Slice Thickness
Increasing receiver bandwidth reduces SNR as more noise is included.
SNR - Receiver Bandwidth
NEX is also called the number of signal averages (NSA).
NSA refers to how many times a signal from a given slice is measured.
The SNR, which is proportional to the square root of the NEX, improves as the NEX increases, but scan time also increases linearly with the NEX.
Scan time = TR × number of phase-encoding steps × number of signal averages (NSA).
SNR – Number of Excitations (NEX)
The SNR increases with the longer TR, but the T1 effect is lost. The SNR decreases as the TE increases, but with a short TE, the T2 contrast is lost.
SNR – TR and TE
At higher field strength the longitudinal magnetisation is increased (more spins align along the B0 field), resulting in an increase in SNR.
The disadvantages of the higher field are RF and longer T1.
SNR – Magnetic Field
There is another way to improve SNR without increasing voxel size or lengthening scan time, this is by selecting an appropriate radiofrequency (RF) coil.
An RF coil should be as close as possible to the anatomy being imaged and should surround the target organ.
SNR – MRI Coils
