MRI

Mourad Edrees
Contents:

 Introduction ………………………………. 2

 MRI Safety ………………………………. 10

 Simple MRI Physics …………………….. 14

 Parameter and MRI Sequences ……. 36

 Planning common scans ……………… 56

 Common Artifacts …...……………….. 112

1
Introduction
Magnetic resonance imaging (MRI) is a spectroscopic imaging
technique used in medical settings to produce images of the inside of the
human body.
MRI is based on the principles of nuclear magnetic resonance (NMR),
which is a spectroscopic technique used to obtain microscopic chemical
and physical data about molecules.
In 1977 the first MRI exam was performed on a human being. It took 5
hours to produce one image.
The magnetic resonance imaging is accomplished through the absorption
and emission of energy of the radio frequency (RF) range of the
electromagnetic spectrum.
MRI was originally called 'NMRI' (nuclear magnetic resonance imaging)
and is a form of NMR, though the use of 'nuclear' in the acronym was
dropped to avoid negative associations with the word. Certain atomic
nuclei are able to absorb and emit radio frequency energy when placed
in an external magnetic field.
In clinical and research MRI, hydrogen atoms are most often used to
generate a detectable radio-frequency signal that is received by antennas
in close proximity to the anatomy being examined.
Over the years Magnetic Resonance Imaging, hereafter referred to as
MRI, has become a popular and widely available means of cross
sectional imaging modality. That is not coincidental; MRI has gone
through a fast paced round of development since its discovery. Now
every self-respecting hospital or clinic has one or more MRI scanners to
battle the conquest for more precise and accurate imaging and diagnosis
of pathology. Even as we speak the development is still in full swing.
Paired with its excellent image contrast resolution, MRI is harmless to
the human body, within reason, through its use of radio waves and a

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magnetic field. This in contrast with X-rays and CT examinations, which
use ionizing radiation.
As MRI becomes more and more accepted the need for more qualified
staff is also increasing. Through the years operation of MRI scanners has
become easier with each new software release, but this does not
eliminate the need for proper understanding of how MRI works. MRI
works with a host of parameters, such as TR, TE, Flip Angle, Phase
Encoding to name but a few. A thorough understanding of these
parameters is vitally important in order to produce a successful MR
image.

A little MRI History

The story of MRI starts in about 1946 when Felix Bloch proposed in a
Nobel Prize winning paper some rather new properties for the atomic
nucleus. He stated that the nucleus behaves like a magnet. He realized
that a charged particle, such as a proton, spinning around its own axis
has a magnetic field, known as a magnetic momentum. He wrote down
his finding in what we know as the Bloch Equations.
It would take until the early 1950s before his theories could be verified
experimentally. In 1960 Nuclear Magnetic Resonance spectrometers
were introduced for analytical purposes.
During the 1960s and 1970s NMR spectrometers were widely used in
academic and industrial research. Spectrometry is used to analyze the
molecular configuration of material based on its NMR spectrum.
In the late 1960s Raymond Damadian discovered that malignant tissue
had different NMR parameters than normal tissue.
He mused that, based on these differences, it should be possible to do
tissue characterization. Based on this discovery he produced the first
ever NMR image of a rat tumor in 1974.

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In 1977 Damadian and his team constructed the first super conducting
NMR scanner (known as The Indomitable) and produced the first image
of the human body, which took almost 5 hours to scan.

At the same time Paul Lauterbur was pioneering in the same field. One
could discuss who was responsible for bringing MRI to us, although, in
all fairness, one could accept that both gentlemen had their contribution.
The name Nuclear Magnetic Resonance (NMR) was changed into
Magnetic Resonance Imaging (MRI) because it was believed that the
word nuclear would not find wide acceptance amongst the public.
The rest is, as they say, history. In the early 1980s just about every major
medical imaging equipment manufacturer researched and produced MRI
scanners. Since then a lot has happened in terms of development.
The hardware and software became faster, more intelligent and easier to
use. Because of the development of advanced MRI pulse sequences
more applications for MRI opened up, such as MR Angiography,
Functional Imaging and Perfusion / Diffusion scanning.
And yet, the end is not in sight. The development of MR is still in full
swing and only time will tell what the future has in store for us.

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 The first MR scanner

One of the first head images 1981

5
Open MRI “Outlook” 1994
MRI Timeline
1946 MR phenomenon -Bloch & Purcell
1952 Nobel Prize -Bloch & Purcell
1950 NMR developed as analytical tool
1972 Computerized Tomography
1973 Backprojection MRI -Lauterbur
1975 Fourier Imaging -Ernst
1980 MRI -Spin Warp imaging
1986 Gradient Echo Imaging, NMR microscope
1988 Angiography
1991 Nobel Prize R.R. Ernst
1992 Functional Imaging
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Why Use MRI?
When using x-rays to image the body one doesn’t see very much. The
image is gray and flat. The overall contrast resolution of an x-ray image
is poor.
In order to increase the image contrast one can administer some sort of
contrast medium, such as barium or iodine based contrast media.
By manipulating the x-ray parameters kV and mA one can try to
optimize the image contrast further but it will remain sub optimal. With
CT scanners one can produce images with a lot more contrast, which
helps in detecting lesions in soft tissue.
The principle advantage of MRI is its excellent contrast resolution. With
MRI it is possible to detect minute contrast differences in (soft) tissue,
even more so than with CT images.
By manipulating the MR parameters one can optimize the pulse
sequence for certain pathology.
Another advantage of MRI is the possibility the make images in every
imaginable plane, something, which is quite impossible with x-rays or
CT. (With CT it is possible to reconstruct other planes from an axially
acquired data set).
However, the spatial resolution of x-ray images is, when using special x-
ray film, excellent. This is particularly useful when looking at bone
structures.
The spatial resolution of MRI compared to that of x-ray is poor.
In general one can use x-ray and CT to visualize bone structures whereas
MRI is extremely useful for detecting soft tissue lesions.

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Advantages
Advantages of MRI include:
Ability to image without the use of ionizing x-rays, in contradistinction
to CT scanning
Images may be acquired in multiple planes (axial, sagittal, coronal, or
oblique) without repositioning the patient. CT images have only
relatively recently been able to be reconstructed in multiple planes with
the same spatial resolution
MRI images demonstrate superior soft tissue contrast as compared to CT
scans and plain radiographs making it the ideal examination of the brain,
spine, joints, and other soft tissue body parts
Some angiographic images can be obtained without the use of contrast
material, unlike CT or conventional angiography
Advanced techniques such as diffusion, spectroscopy and perfusion
allow for precise tissue characterization rather than merely 'macroscopic'
imaging

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Functional MRI allows visualization of both active parts of the brain
during certain activities and understanding of the underlying networks

Disadvantages
Disadvantages of MRI include:
MRI scans are more expensive than CT scans
MRI scans take significantly longer to acquire than CT and patient
comfort can be an issue, maybe exacerbated by:
MR image acquisition is noisy compared to CT
MRI scanner bores tend to be more enclosed than CT with associated
claustrophobia
MR images are subject to unique artifacts that must be recognized and
mitigated against (see MRI artifacts)
MRI scanning is not safe for patients with some metal implants and
foreign bodies. Careful attention to safety measures is necessary to avoid
serious injury to patients and staff, and this requires special MRI
compatible equipment and stringent adherence to safety protocols (see
MRI safety).

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MRI Safety

MRI scanners, although free from potentially cancer-inducing ionizing radiation

found in plain radiography and CT, have a host of safety issues which must be
taken very seriously.
Main magnetic field
The main magnetic field of a 1.5 T magnet is about 30,000 times the strength of
the earth's magnetic field.
It is strong enough to pull fork-lift tines off of machinery, pull heavy-duty floor
buffers and mop buckets into the bore of the magnet, pull stretchers across the
room and turn oxygen bottles into flying projectiles.
Deaths have occurred from trauma as a result of these effects. Smaller objects such
as pagers, bobby pins and pens have been known to be pulled off the person
carrying them.
The strong field also affects common devices such as pacemakers and watches.
The magnetic reed switch in modern pacemakers is disturbed by strong magnetic
fields resulting in possible deleterious effects to the patient with one implanted.
Mechanic watches will "freeze up" in a strong field, sometimes permanently.
Many intracranial aneurysm clips are ferromagnetic and as a result experience a
torque or twisting in a magnetic field.
Not everyone with an aneurysm clip experiences a fatal hemorrhage when placed
in a magnet, but several cases have been reported.
Some types of heart valves (e.g. Starr-Edwards) are torqued in a magnetic field:
however, this torque is less than the stresses that occur normally as a result of
blood flow.
Therefore heart valves are now considered not to be an absolute contraindication
for MRI.
More of an annoyance than a safety problem is the ability of the magnetic field of a
MRI machine to erase the information contained on the magnetic strip on ATM
and credit cards. This may occur a short distance inside of the scanner room of a
MRI machine.

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Some metallic objects that are usually safe near an MRI machine are gold jewelry,
shirt cuff-links and eyeglass frames.
1. Absolute
Pacemaker / defibrillator that is non-MRI compatible
Metallic foreign body in the eye
Deep brain stimulator
Bullets or gunshot pellets
Cerebral aneurysm clips that are non-MRI compatible
Cochlear implant
Drug infusion device - might malfunction
2. Relative
Surgical clips, wire sutures etc.
Joint replacement or prosthesis
Large patients might not fit into scanner
Claustrophobic patient
Significant pain or other conditions that might limit patient's ability to sit still
Surgery in previous 6 weeks
Pregnancy - usually not performed in first trimester
Emergencies
1. Cardiac Arrest
Patient is removed from the magnet on to an MR-compatible trolley and taken
outside the controlled area
Here, resuscitation can commence
Appliances such as oxygen cylinders must not be brought to the patient in the
scanner due to the ferromagnetic missile effect
2. Fire
Non-ferrous carbon dioxide extinguishers should be used

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Fire-fighting equipment should be used only at a distance of 1m or more from the
bore
If fire-fighters definitely need access to the room the magnet must be quenched to
switch it off
3. Quench
If the magnet has to be switched off e.g.:
Person caught between a metal object and the machine
Fire
Quenching the machine involves converting 1000+ liters of liquid helium (which is
necessary to cool the magnet) into gaseous helium
This is a very quick event and the gas needs to be vented out into the atmosphere
as quickly as possible
A quench can cost £10,000 worth of lost helium
Helium displaces oxygen and so oxygen monitors are used and staff should be
evacuated from the whole MR suite as asphyxiation can occur

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Example photos of accidents

13
MRI Physics
Introduction
It is difficult to decide where to start when you want to explain the physics of MRI.
You could say, “Start at the beginning”, and you’re right, that’s where all good
stories start. But with MRI physics it is a bit more difficult, because one first has to
establish where the beginning is or, put in another way, how much you want to
know.
As the title already indicates this story is supposed to entice those people who are
new to the business (MRI Physics) and who need to know the very basics of MRI
physics. In one way this is easy to write up because I can leave out large chunks of
physics. On the other hand it is very difficult because I have to assume you know
nothing and yet I have to explain something complicated in an easy to understand
manner.
Magnetization
Let us start the journey into MRI physics by looking around us. What do we see?
Amongst a host of items which have nothing to do with MRI we see the earth.
There are a few things we know about earth:
The earth is a giant ball that floats in space. Not randomly, but that’s a different
story.
The earth has a moon, which rotates around the earth.
The earth has an electrical charge. Whether it be positive or negative is not
important.
The earth rotates (spins) around its own axis. This is the interesting bit.
There’s a heck of a lot of water on earth, around 70% worth, and most of it seems
to be falling in my back garden while I’m writing this.
This giant, electrically charged and spinning ball is floating in space. Quite
happily: nothing to worry about. From our physics lessons in school we may
remember that a rotating electrical charge creates a magnetic field. And sure
enough, the earth has a magnetic field, which we use to find our way from one
place to another by means of a compass.

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The magnetic field strength of the earth is rather small: 30 micro Tesla at the poles
and 70 micro Tesla at the equator. (Tesla is for magnetic fields what Ampere is for
electric current).
In short we can establish that the earth is a giant spinning bar magnet, with a north
and a south pole. And don’t forget it is wet, very wet.

You may wonder what all this has to do with MRI but I’ll get to that in a moment.
Now let’s have a look at ourselves, the Homo sapiens. What do we have in
common with earth? Well on first sight not a lot, but when we take a bit from our
body and we would put it under an electron microscope we can see things that look
rather familiar.
We see tiny little balls, which rotate around their own axes and also have an
electrical charge and they have moons floating around it. What we are looking at
are atoms. And atoms have everything to do with MRI, because we use them to
generate our MR image.
Another thing we have in common with earth is water. Our body consists of 80%
water.
From our chemistry lessons we know that there are many different elements, 110
to be precise. Because we exist mainly of water let’s have a look at it. Water
consists of 2 Hydrogen and 1 Oxygen atom. The hydrogen atom (the first element
in the periodic table) has a nucleus, called proton, and 1 moon, called electron.
This proton is electrically charged and it rotates around its axis. There we have the
analogy with the earth. Also the hydrogen proton can be looked at as if it were a
tiny bar magnet with a north and a south pole.
Why do we take hydrogen as our MR imaging source?
There are two reasons. First off all we have a lot of them in our body. Actually it’s
the most abundant element we have.
Secondly, in quantum physics there is a thing called Gyro Magnetic Ratio. It is
beyond the scope of this story what it represents; suffice to know that this ratio is
different for each proton.

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It just so happens, that this gyro magnetic ratio for Hydrogen is the largest; 42.57
MHz/Tesla.
For who really wants to know, Hydrogen is not the only element we can use for
MR imaging. In fact any element, which has an odd number of particles in the
nucleus can be used. Some elements, which can be used, are:
MRI Friendly Elements

If we look at a bunch of hydrogen protons (as in a molecule) we see, in fact, a lot

of tiny bar magnets spinning around their own axes. As we may recall from
classes, two north poles and two south poles of two magnets repel each other,
while two poles of opposite sign attract each other.
In our body these tiny bar magnets are ordered in such a way that the magnetic
forces equalize. Our bodies are, magnetically speaking, in balance.
Just as well, otherwise we would attract a lot of metal when we go about.
Now we have established some interesting facts of life, let’s have a look at what
happens when we go ahead and try to make an MRI examination.
As we have seen in the paragraph about the hardware, magnets used for MR
imaging come in various field strengths. The magnetic field strength of a 1.5 Tesla
magnet is ± 30.000 times stronger than the earth gravitational field!

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This indicates that we are working with potentially dangerous equipment (more
about that later).

When we put a person in a magnet some interesting things happen to the hydrogen
protons:

1. They align with the magnetic field. This is done in two ways, parallel or anti-
parallel.

(B0 is the indication for the magnetic field of the MRI scanner)

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2. They process or “wobble” due to the magnetic momentum of the atom.

They process at the Larmor frequency. This Larmor frequency is something, which
needs a little further explanation.
The Larmor frequency can be calculated from the following equation:

Here we see two things, which we discussed before, come together: the Gyro
Magnetic Ratio and the Magnetic field strength.
So, there you have it. A cute little equation, if ever I saw one. But why is this so
important? Well, we need the Larmor frequency to calculate the operating
frequency of the MRI system.
If we have a MRI system of 1.5 Tesla then the Larmor or precessional frequency
is: 42.57 x 1.5 = 63.855 MHz
The precessional frequencies of 1.0T, 0.5T, 0.35T and 0.2T systems would work
out to be 42.57 MHz, 21.285 MHz, 14.8995 MHz and 8.514 MHz respectively.
You can view these values on your own system by checking the Centre Frequency
or similar phrase.
Now we know what happens to the individual protons when we put a victim in the
scanner. Let’s continue the story and see what happens further.

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When the protons experience a strong magnetic field from the scanner we saw that
they can align with the field in two ways: parallel and anti-parallel. You could call
this also Low and High Energy State.
The distribution of the protons for both states is not the same. The protons are, just
like many people, lazy. They prefer to be in low energy state. There are more
protons aligned parallel or low energy state than there are anti-parallel or high
energy state.

In the end we see that there is a net magnetization (the sum of all tiny magnetic
fields of each proton) pointing in the same direction as the system’s magnetic
field.
However, it’s not that big a difference. The excess amount of protons aligned
parallel within a 0.5T field is only 3 per million (3 ppm = parts per million), in a
1.0T system there are 6 per million and in a 1.5T system there are 9 per million.
So, the number of excess protons is proportional with B0. That is also the reason
why 1.5T systems make better images than systems with lower field strengths.

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In order to see what happens with this net magnetization in our MRI experiment in
an easy way, the scientific community came up with the brilliant idea to visualize it
by means of vectors.
A vector (the red arrow in the figure below) has a direction and a force. To see
what happens with the vector (net magnetization) we imagine a frame of rotation,
which is nothing else than a set of axes called X, Y and Z.
The Z-axis is always pointing in the direction of the main magnetic field, while X
and Y are pointing at right angles from Z.
Here we see the (red) net magnetization vector pointing in the same direction as
the Z-axis. The net magnetization is now called Mz or longitudinal magnetization.
It is now possible to make simplified drawings of the net magnetization in motion.

Now you are ready to dig a little deeper into the matter and we continue with our
MRI experiment and see what happens when we start to play around with the net
magnetization.
To obtain an image from a patient it is not enough to put him/her into the magnet.
We have to do a little bit more than that.

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The following steps can be divided into Excitation, Relaxation, Acquisition,
Computing and Display (to be defined later).
Precession
As well as "spinning" about their own axis, when a magnetic field is applied the
nuclei will "rotate" about the axis of the magnetic field. This is called precession.
The example usually given is of a gyroscope. Spinning a gyroscope causes it
to rotate about its own axis, but gravity will also cause it to lean and
spin about another axis dependent on the gravitational field strength.

The frequency of this spinning is the precessional / Larmor / rotational frequency.

In MR imaging we induce precession by applying a magnetic field (conventionally
in the Z axis and called B0, along the long axis of the patient).
This magnetic field is permanently switched on in the MRI scanner.
The precessional frequency is calculated by the Larmor Equation
F = K x B0
F = precessional frequency (Larmor frequency)
K = the gyromagnetic ratio (a constant that is different for different nuclei)
B0 = strength of the static magnetic field
For a field strength of 1 Tesla the Larmor frequency of hydrogen is 42 Megahertz
(MHz) or 42 million cycles per second.
As the main magnetic field (B0) is applied, the nuclei precess in the Z-axis along
the applied magnetic field.

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Most will precess aligned with it (the low energy state) but a few will precess in
the opposite direction (the high energy state).
However, the majority will be aligned, creating a net longitudinal magnetization
(Mz) in the Z-axis direction.

Transverse magnetization
However, we cannot measure the longitudinal magnetization and so we need to
"flip" the magnetization, usually to 90°, in order to be able to measure it and create
our MRI signal.
To flip the magnetization a rapidly oscillating magnetic field at 90° to B0 is
applied (B1 / radiofrequency pulse / RF pulse).
This flips the net magnetization into a transverse plane (Mxy).
In order to do this the B1 magnetic field needs to oscillate at the same frequency as
the precessing nuclei, the resonant frequency as this ensures the most efficient
transference of energy to the nuclei.
Remember, this is 42 MHz for a 1 Tesla scanner, or 63 MHz for a 1.5 Tesla
scanner.

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Preparation

The patient is placed in a static magnetic field produced by the magnet of the MR
scanner.
In living tissues there are a lot of hydrogen atoms included in water molecules or in
many different other molecules.
The proton, the nucleus of Hydrogen, does possess an intrinsic magnetization
called spin.
The spin magnetization vector precesses (rotates) around the magnetic field at a
frequency called Larmor frequency, which is proportional to the magnetic field
intensity.
The resulting magnetization of all protons inside the tissues aligns parallel to the
magnetic field.
The parallel magnetization scales with the magnetic field intensity, basically at 3T
it will be twice the value obtained at 1.5T.
Additional preparation sequences can also be performed to manipulate the
magnetization and so the image contrast, e.g. inversion preparation

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Excitation
Excitation: If an oscillating magnetic field (called a radio frequency pulse) is
applied to nuclei at their resonance frequency, their spins absorb energy, causing
the magnetization of the nuclei to precess in phase about the static magnetic field.
Before the system starts to acquire the data it will perform a quick measurement
(also called pre-scan or survey) to determine (amongst others) at which frequency
the protons are spinning (the Larmor frequency).
This Centre frequency is important because this is the frequency the system uses
for the next step.
Once the Centre frequency is determined the system will start the acquisition. This
time we keep things real simple. No fancy pulse sequences.
For now we only send a radio frequency pulse into the patient and we look at what
happens.
Let us assume we work with a 1.5 Tesla system. The Centre or operating
frequency of the system is 63.855 MHz. In order to manipulate the net
magnetization we will therefore have to send a Radio Frequency (RF) pulse with a
frequency that matches the Centre frequency of the system: 63.855 MHz
Only protons that spin with the same frequency as the RF pulse will respond to that
RF pulse.

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By sending an RF pulse at the Centre frequency, with a certain strength
(amplitude) and for a certain period of time it is possible to rotate the net
magnetization into a plane perpendicular to the Z axis, in this case the X-Y plane

Standard exam
Multiple image sets are obtained in the standard exam (which varies from facility
to facility).
Exam times vary according to the part of the anatomy being studied, pathology
expected, and radiologist preferences.
Occasionally, a contrast medium may be used to enhance images.
Typically, exams are ordered without and with contrast for comparison purposes.
Very rarely, and only in certain circumstances are exams ordered with contrast
only.
After the exam the patient is removed from the scanner and given post-procedure
instructions (information about contrast medium if used, sedation if used, and time
when to expect a report from the examination)
Relaxation
Relaxation is the process whereby nuclear magnetization returns to its resting state
following a disturbance by an RF pulse.
Now it becomes interesting. We rotated the net magnetization 90º into the X-Y
plane. We could also say that we lifted the protons into a higher energy state, same
thing. This happened because the protons absorbed energy from the RF pulse.
This is a situation that the protons do not like.
The protons, prefer to align with the main magnetic field or, in other words, they
would rather be in a low energy state.
Now something happens that is referred to as Relaxation. The relaxation
process can be divided into two parts:

T1 relaxation and T2 relaxation.

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T1 Relaxation
The protons want to go back to their original situation, called equilibrium. They do
so by releasing the absorbed energy in the shape of (very little) warmth and RF
waves.
In principle the reverse of excitation takes place. The net magnetization rotates
back to align itself with the Z-axis.
T1 relaxation describes what happens in the Z direction.
So, after a little while, the situation is exactly as before we sent an RF pulse into
the patient.
T1 relaxation is also known as Spin-Lattice relaxation, because the energy is
released to the surrounding tissue (lattice).
T1 is also called the longitudinal relaxation time because it refers to the time it
takes for the spins to realign along the longitudinal (z)-axis.

After the RF excitation pulse stops, the net magnetization will re-grow along the Z-
axis, while emitting a radio-frequency waves.
T1 Relaxation Curves
T1 relaxation happens to the protons in the volume that experienced the 90º-
excitation pulse.

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However, not all the protons are bound in their molecules in the same way. This is
different for each tissue.
One 1H atom may be bound very tight, such as in fat tissue, while the other has a
much looser bond, such as in water.
Tightly bound protons will release their energy much quicker to their surroundings
than protons, which are bound loosely.
The rate at which they release their energy is therefore different. The rate of T1
relaxation can be depicted

The curve shows at time = 0 that there is no magnetization in the Z-direction right
after the RF-pulse. But immediately the Mz starts to recover along the Z-axis. T1
relaxation is a time constant. T1 is defined as the time it takes for the longitudinal
magnetization (Mz) to reach 63 % of the original magnetization.
A similar curve can be drawn for each tissue. That’s
what Damadian and Lauterbur discovered many moons ago. Each tissue will
release energy (relax) at a different rate and that’s why MRI has such good contrast
resolution.

Effects on T1
Fat and protein: short T1. The molecules are large with low innate energy. This
makes them very effective at absorbing energy causing a quick loss of Mxy and,
therefore, quick recovery of Mz and a short T1.

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Water: long T1. The molecules are small and move quickly making them
inefficient at jostling the nuclei and absorbing energy. This causes a long T1.
Bone / calcium / metal: very long T1. The macromolecules are fixed and rigid and
are the least effective at removing energy from the precessing nuclei.

T2 Relaxation

As said before, the relaxation process is divided into two parts. The second part, T2
relaxation, is slightly more complicated.
T2 is the 'transverse' relaxation time. It is a measure of how long transverse
magnetization would last in a perfectly uniform external magnetic field.
T2 relaxation is also called spin–spin relaxation because it describes interactions
between protons in their immediate surroundings (molecules).
Alternatively, it is a measure of how long the resonating protons remain coherent
or precess (rotate) 'In phase' following a 90 degree RF pulse.
T2 decay is due to magnetic interactions that occur between spinning protons.
It is very important to realize that T1 and T2 relaxation are two independent
processes. The one has nothing to do with the other. The only thing they have in
common is that both processes happen simultaneously. T1 relaxation describes
what happens in the Z direction, while T2 relaxation describes what happens in
the X-Y plane. That’s why they have nothing to do with one another.
Also unlike T1 interactions, T2 interactions do not involve transfer of energy but
only a change in phase, which lead to loss of coherence
Phase Coherence: the vectors align with each other in phase

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Transverse Magnetization
This process of getting from a total in-phase situation to a total out-of-phase
situation is called T2 relaxation.
T2 Relaxation Curves
Just like T1 relaxation, T2 relaxation does not happen at once. Again, it depends on
how the Hydrogen proton is bound in its molecule and that again is different for

each tissue.

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Right after the 90º RF-pulse all the magnetization is “flipped” into the XY-plane.
The net magnetization changes name and is now called MXY. At time = 0 all spins
are in-phase, but immediately start to de-phase. T2 relaxation is also a time
constant. T2 is defined as the time it takes for the spins to de-phase to 37% of the
original value.
The rate of de-phasing is different for each tissue. Fat tissue will de-phase quickly,
while water will de-phase much slower.
One more remark about T2: it happens much faster than T1 relaxation. T2
relaxation happens in tens of mille -seconds, while T1 can take up to seconds.

Effects on T2
Bone / calcium / metal: short T2. The local variation of magnetic field is greatest in
solids and macromolecules that are rigid.
Fat: Long T2.
Water: Very long T2. The lighter molecules are in rapid thermal motion that
smoothies out the local field producing a longer T2.
Remember this:
T1 and T2 relaxation are two independent processes, which happen
simultaneously.
T1 happens along the Z-axis;
T2 happens in the X-Y plane. T
T2 is much quicker than T1
When both relaxation processes are finished the net magnetization vector is aligned
with the main magnetic field (B0) again and the protons are spinning Out-Of-
Phase; the situation before we transmitted the 90º RF-pulse.

During the relaxation processes the spins shed their excess energy, which they
acquired from the 90º RF pulse, in the shape of radio frequency waves.

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In order to produce an image we need to pick up these waves before they disappear
into space.
This can be done with a Receive coil. The receive coil can be the same as the
Transmit coil or a different one. An interesting, but ever so important, fact is the
position of the receive coil.
The receive coil must be positioned at right angles to the main magnetic field (B0).
Failing to do so will result in an image without signal. This is why: if we open up a
coil we see it is basically nothing but a loop of copper wire. When a magnetic field
goes through the loop, a current is induced.
B0 is a very strong magnetic field; much stronger than the RF signal we are about
to receive. That means if we position the coil such that B0 goes through the coil an
enormous current is induced, and the tiny current induced by the RF wave is
overwhelmed. We will only see a lot of speckles (called: noise) in our image.

Therefore, we have to make sure that the receive coil is positioned in such a way
that B0 can’t go through the coil. The only way to achieve this is to position the
receive coil at right angles to B0 as shown below

31
Remember this:
The only proper way to position the receive coil is at right angles to B0.

32
33
 Spatial Encoding

 slice selection

 phase encoding
 frequency encoding

34
35
MRI Parameter

36
Field of view FOV

37
38
Slice Thickness

39
Average

MRI Parameter
Pixel area = field of view / matrix

increasing the matrix size:

- Increases spatial resolution
- Decreases signal
- Increases scan time

Increasing the FOV:

- Increases the signal
- Lower resolution
- Increased viewing area

increasing the slice thickness:

- Increases the signal
- Decreases the resolution
- Increases the partial volume effect
40
- Gives larger object coverage

Increased slice gap:

- Less cross-talk
- Increased coverage

Increasing NEX or NSA:

- Increases signal
- Less noise
- Fewer artefacts due to signal averaging
- Increased scan time

To improve the SNR:

- Increase NEX
- Lower resolution
- Thicker slices
- Larger FOV
- Use surface coils

To improve the resolution:

- Increase the matrix
- Decrease the FOV
- Decrease the slice thickness

41
Phase direction

O Axial Plane {Right to Left (RL) or Anterior to Posterior (AP)}

O Sagittal Plane {Anterior to Posterior (AP) or Head to Feet (HF)}

O Coronal Plane {Head to Feet (HF) or Right to Left (RL)}

NOTE
Phase direction should be invers motion of respiration and same
direction blood flow for decrease artifacts. It is depend on place scan in
body

MRI Sequences
T1 weighted sequence


T2 weighted sequence


MRI contrast


PD weighted sequence


Fat suppression


Diffusion weighted image



In/out-of-phase


Gradient & spin echo sequence



42
The most common MRI sequences are T1-weighted and T2-weighted
scans. T1-weighted images are produced by using short TE and TR
times. The contrast and brightness of the image are predominately
determined by T1 properties of tissue. Conversely, T2-weighted
images are produced by using longer TE and TR times. In these images,
the contrast and brightness are predominately determined by the T2
properties of tissue.
In general, T1- and T2-weighted images can be easily differentiated by
looking the CSF. CSF is dark on T1-weighted imaging and bright on T2-
weighted imaging.
A third commonly used sequence is the Fluid Attenuated Inversion
Recovery (Flair). The Flair sequence is similar to a T2-weighted image
except that the TE and TR times are very long. By doing so,
abnormalities remain bright but normal CSF fluid is attenuated and
made dark. This sequence is very sensitive to pathology and makes the
differentiation between CSF and an abnormality much easier.

43
44
45
T1-weighted imaging can also be performed while infusing Gadolinium
(Gad). Gad is a non-toxic paramagnetic contrast enhancement agent.
When injected during the scan, Gad changes signal intensities by
shortening T1. Thus, Gad is very bright on T1-weighted images. Gad
enhanced images are especially useful in looking at vascular structures
and breakdown in the blood-brain barrier [e.g., tumors, abscesses,
inflammation (herpes simplex encephalitis, multiple sclerosis, etc.)].

The recommended dose of gadolinium DTPA

injection is 0.1 mmol/kg, i.e. 0.2 mL/kg in adults,
children and infants

46
PD weighted image
The proton density (PD) weighted image visualizes the number of
protons per volume. To achieve this, both the T1 and T2 components are
switched off as fully as possible.
Tissues with few protons have low signal intensity, tissues with many
protons have high signal intensity.
Fat has a relatively high signal intensity, however, not as high as in a T1
weighted image.
A PD weighted image is used among other things to evaluate meniscal
tears in the knee

47
Fat suppression
Suppression of fat tissue is one of the many options that can be used in
an MRI sequence.
In virtually all abdominal MRI examinations, suppressing the fat tissue
signal is advisable. The created low signal intensity of fat then contrasts
more strongly with the vessels & pathology (high signal intensity!).
Also in skeletal imaging, it may be useful to make a sequence with fat
suppression. Bone marrow contains fat and may mask bone marrow
edema on a T2 weighted image.
There are several technical options to suppress fat tissue. Frequently
used sequences are the STIR (short-tau inversion recovery) and the SPIR
(spectral pre-saturation inversion recovery) sequences. Both are T2
weighted images.
You can also recognize fat suppression by the abbreviation Fat sat,
meaning Fat Saturation (e.g. T2wFatSat).

48
Diffusion weighted image

Diffusion weighted imaging (DWI) is designed to detect the random

movements of water protons. Water molecules diffuse relatively freely
in the extracellular space; their movement is significantly restricted in
the intracellular space. Spontaneous movements, referred to as diffusion,
rapidly become restricted in ischemic brain tissue. During ischemia, the
sodium - potassium pump shuts down and sodium accumulates
intracellular. Water then shifts from the extracellular to the intracellular
space due to the osmotic gradient. As water movement becomes
restricted intracellular, this results in an extremely bright signal on DWI.
Thus, DWI is an extremely sensitive method for detecting acute stroke.

49
50
51
52
In/out-of-phase
An in/out-of-phase is a gradient sequence used as a tool to detect
microscopic fat in a lesion/organ. It is used in particular to evaluate
adrenal masses (fat-containing adenoma vs adrenal carcinoma) and fatty
infiltration of the liver.
Background: the protons in fat and water have a slight difference in
Larmor frequency, which may cause a so-called chemical shift.
The series has two components: the in-phase sequence and the out-of-
phase sequence. When reading the signal on the in-phase sequence, the
protons of the fat and water are in exactly the same phase (despite the
slight difference in Larmor frequency). The protons are in-phase and
therefore give off signal.
The signal in the out-of-phase sequence is read at a specific different
moment, the moment that the protons of the fat and water are not exactly
in the same phase. This eventually leads to signal loss (Note: the protons
are out-of-phase).
Example: a fat-containing adrenal lesion has high signal intensity on the
in-phase sequence (B) and low signal intensity on out-of-phase (C)

53
Gradient & spin echo sequence
‘Gradient’ and 'spin echo’ are common terms in an MRI context.
Importantly, this is a technique that can be used on a T1, T2 and PD
sequence. The gradient & spin echo technique may be regarded as two
large families in which multiple variations are possible.
In summary: the gradient technique has a shorter scan time than the spin
echo technique and is used among other things for angiography, brain,
heart, abdomen and functional MRI. A significant drawback of the
gradient technique is susceptibility to artifacts (hemoglobin in blood and
prosthesis/osteosynthesis material).
Spin echo technique is an alternative option. The traditional spin echo
was commonly used because of its many applications. Nowadays the
spin echo has been developed into a faster sequence; the fast spin echo
(FSE) and the single shot fast spin echo (SSFSE). Scan time has now
been reduced to a few minutes, resulting in fewer movement artifacts.
Despite the fact that the spin echo is not as fast (as the gradient), the
technique is used frequently because of its image quality. The fast spin
echo sequences are used frequently to image the abdomen (e.g. MRCP),
pelvis (urogenital) and musculoskeletal system (especially in prosthesis

54
material!).
Practical tip:
- gradient is a good choice to detect blood products.
- Spin echo technique has fewer unwanted artifacts in prosthesis and
osteosynthesis material.

Susceptibility artifact
Magnetic susceptibility means that protons with their own internal
magnetization interact with the external magnetic field. In other words:
it is the degree to which tissue becomes magnetic as a result of exposure
to a magnetic field. When two tissues with different magnetic
susceptibilities are close together, local field in homogeneities may
develop. This disruption accelerates dephasing and will eventually lead
to loss of signal or distorted images. These susceptibility artifacts
develop with metals (depending on the metal type) and natural
transitions such as air-tissue (sinuses-brain parenchym) and tissues
surrounding bone. Also the blood product hemoglobin may cause
susceptibility artifacts on a gradient echo sequence. Despite this
undesired phenomenon, it can also be used to characterize lesions. A
frequently used gradient echo is the SWI sequence (Susceptibility
Weighted Imaging).

55
Planning scans
Head (Brain, MRA, MRV, Sella, Petrous Bone, Orbit, PNS and
TMJ).
Neck (Neck and MRA Neck)
Spine (Cervical Spine, Dorsal Spine, Lumber Spine and
Sacroiliac Joint)
Body (Chest, Abdomen, Pelvis, Entrography, MRCP and MRU).
Upper Limbs (Shoulder, Arm, Elbow, Forearm, Wrist and
Hand).
Lower Limbs (Hips, Thigh, Knee, Leg, Ankle and Foot).
Notes
Dynamic scans meaning : imaging during injection contrast
1. MRI Sella
2. MRI Breasts
3. MRI Abdomen -Triphasic (Arterial, portal and Delayed)
4. MRI Entrography -Triphasic
5. MRI Prostatic

56
57
 MRI Brain
Indications for MRI brain
> Transient ischaemic attack (TIA), syncope, collapse , stroke
> Brain Tumor, Suspected brain tumor, metastases, papilloedema
> CNS infection, abscess, meningitis, AIDS,&TB
> Congenital malformation of brain or meninges
> Post-operative follow-up after brain surgery
> Dementia, neurodegenerative disorder- Demyelinating disease of the brain
> Encephalopathy, encephalitis- Cerebellar, or brainstem lesion
> Head trauma, epilepsy, stroke- CVA, altered mental status- Suspected
leukodystrophies
> Ataxia, bipolar disorder- Multiple sclerosis- ENT problems

Planning
Axial plane

Saggital

58
 Coronal

Indications for contrast enhancement brain scans

> Tumor, Metastases, Cranial nerve lesion, Indeterminate intracranial lesion,
IAC mass
> Cavernous angioma, Amyloid angiopathy, Neurocysticercosis
> Meningitis, Encephalitis, Leptomeningeal spread
> Multiple Sclerosis, AVM, HIV, Infection Abscess
> Leukodystrophies, Delayed development
> Syringomyelia(Syrinx)

MRI pituitary fossa(sella turcica).

Basic anatomy

59
Common indications
• Investigation of diseases related to pituitary function
(hyperprolactinaemia,
Cushing’s disease, acromegaly, hypopituitarism,
diabetes insipidus, amenorrhoea)
• Hypothalamic disorders
• Visual field defect
• Post-operative assessment of pituitary adenomas
PLANNING
1) Axial Brain

2) Sagittal

3) Coronal

60
MRI Orbit
Basic anatomy

Common indications
• Proptosis
• Visual disturbance
• Evaluation of orbital or ocular mass lesions

61
Planning
1) T2 Axial Brain

2) Coronal Planning (3 mm )

3) Sagittal Oblique parallel to Optic nerve ( RT & LT )

62
 4) Axial parallel of optic nerve

MRI petrous Bone

Posterior fossa and internal auditory meatus
( IAM )
( CPA ) Cerebellopontine angle

Common indications
• Symptoms that require the exclusion of an acoustic
neuroma
(vertigo, unilateral sensory hearing loss, tinnitus)
• Facial palsy/numbness
• Diagnosis of a posterior fossa lesion
• Haemifacial spasm
• Trigeminal neuralgia

Planning

1) T2 Axial brain

63
2) Coronal Small FOV and Small thickness 3 mm

3) Axial Small FOV and Small thickness 3 mm

64
MRI paranasal sinuses (PNS)

Basic anatomy

Common indications
• Staging of neoplasms prior to resection
• Distinction of inflammation from neoplasm

65
Planning

1) Coronal Small FOV And Small Thickness 3 mm

2) Axial Small FOV And Small Thickness 3 mm

66
MRI Temporomandibular joint (TMJ)
Basic Anatomy

Indications
Irregular jaw movement with difficulty in opening and closing the mouth
> Pain in the ear area when speaking, chewing or opening the mouth wide
> TMJ Headaches (become worse while opening and closing the mouth)
> Clicking sounds in the jaw joint when opening or closing the mouth
> Ear pain in front of or below the ear without any signs of infection
> Pain in the jaw joint area, tooth, neck and shoulders> Jaw pain or toothache
when waking up after sleep
> Feelings of teeth are not fitting together properly
> Difficulty in chewing

67
Planning

1) Axial

2) Coronal RT and LT

3) Sagittal RT and LT

68
MRA Brain
We use technique depend on the motion direction of the
Blood called TOF (Time Of Flight).

69
MRV
Brain Venography
We use technique depend on the speed of the blood called
PS (Phase Shift).

Axial PS
Blue shape is saturation band for block up flow blood (arteries)
And detect down flow blood only ( Veins )

70
MRI Neck

Indications for soft tissue neck MRI scan

> Abnormalities noted on other imaging or endoscopic studies> Upper airway
obstruction
> Staging of known malignancy of head and neck> Presence of a foreign body
> Trauma
> Congenital anomalies (e.g., branchial cleft cyst) > Pre-operative evaluation
of tumours
> Treatment planning for radiation therapy > Evaluation for response to
treatment
> Obstructive thyroid disease > Head/neck abscess> Retropharyngeal abscess
> Tracheal stenosis
> Vocal cord paralysis> Lymphadenopathy> Nasopharynx tumours> Parotid
tumor> Orbital tumours

71
Coronal planning

Axial planning

sagittal planning 4mm 280 -300 FOV

72
Neck MRA
Indications for Magnetic Resonance Angiography of neck
> Cervicocranial arterial dissection > Arterio-venous
malformation> Vertebrobasilar syndrome
> Injury to the carotid artery> Aneurysm> Tumours

73
Neuro MRI Protocol
Spine
Indications for spine MRI scan

> Persistent neck pain or radiculopathy, with 6-week course

of conservative care and inadequate
> response to treatment. > Spinal TB> Spinal cord tumour>
Spinal injury or trauma
> Cancer or tumours of the spine (cancer of the spine, spinal
cord, or meninges)
> Evaluation or monitoring of congenital malformations of
the spinal cord
> Multiple sclerosis or other demyelinating diseases or
myelopathies
> Possible spinal cord injury and post-traumatic neurologic
deficit
> Post-operative evaluation, with new neurologic findings
> Congenital or acquired spinal abnormalities in children
> Fracture evaluation for suspected or known fracture.
> Severe intractable arm pain for more than 6 weeks
> Infectious or inflammatory processes > Evaluation or
monitoring of myelopathy
> Monitoring of previous spinal surgery
> Evaluation or monitoring of syrinx

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Sagittal Spine planning

76
Axial spine planning

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MSK MRI planning
Indications
Marrow abnormalities (e.g. bone contusions, osteonecrosis, marrow
oedema
syndromes, and stress fractures)
> Synovial based disorders ( e.g. synovitis, tenosynovitis, bursitis,
and ganglion cysts) > Soft
tissue masses
> Infections of bone, joint, or soft tissue (eg. osteomyelitis, osteo
arthritis ) > Carpal tunnel
syndrome
> Neoplasms of bone, joint, or soft tissue> Avascular necrosis>
Nerve impingement> Fractures in children Soft tissue masses
> Carpal nonunions > Occult fracture> Ganglion cyst> Ligament tear

Upper Extremity
Shoulder
Positioning

Localizer

78
Axial

Coronal

Sagittal

79
Arm
Positioning

Localizer

Axial

80
Coronal

Sagittal

Elbow
Positioning

81
Localizer

Axial

Coronal

Sagittal

82
Forearm
Positioning
Supine and head first

Localizer

Axial

83
Coronal

Sagittal

Wrist

84
Positioning
Head first prone with arm up (superman position)

Localizer

Axial

Coronal

85
Sagittal

Hand
Positioning
Head first prone with arm up (superman position)

86
Localizer

Axial

Coronal

Sagittal

87
Thumb
Positioning
Have thumb pressed to the hand (by wrapping thumb snugly to the hand)
- Thumb should be parallel to the other hand metacarpals
- Prone in a Superman position

Axial

88
Coronal
Angle parallel to sesamoid plane of thumb

Sagittal
Perpedicular to Coronal and Axial sequences

89
Lower Joints
Sacroiliac joints

Indications
Neoplasms of bone, joint, or soft tissue> Infections of bone,
joint, or soft tissue
> Inflammation of the Sacroiliac joint> Sacroiliac joint
dysfunction> ankylosing spondylitis
> degenerative arthritis > Sacroiliac joint pain> rheumatoid
arthritis> avascular necrosis
> osteoarthritis> Sacroiliitis> psoriasis> gout

90
Positioning
you can use both the Body Matrix Coil (strapped anteriorly
over pelvis) and Spine Coil to reduce burn-out of image
posteriorly
Position the patient in supine position with head pointing
towards the magnet (head first supine)

Localizer

Coronal

91
Axial

Sagittal

92
Hips
Indications
> Intra or extra articular abnormality (e.g., loose body) > Slipped
femoral capital epipysis
> Tears of the acetabular labrum. > Evaluate integrity of hip
cartilage > Degenerative disk disease
> Avascular necrosis > Inflammatory arthritis > Traumatic fracture
> Pathologic fracture> Stress fracture
> Osteoarthritis > Muscle injury> Tendonitis> Myositis > Bursitis>
Cellulitis
Positioning
Position the patient in supine position with head pointing towards the
magnet (head first supine)

Localizer

93
Coronal

Axial

Sagittal

94
Axial oblique small FOV on one side

95
Thigh (femur)
Indications
> Marrow abnormalities: avascular necrosis, marrow edema
syndromes, and stress fractures> Muscle and tendon disorders:
strains, partial and complete tears, tendonitis, tendonopathy>
Congenital and developmental conditions > Neoplasms of bone,
joint or soft tissue> Infections of bone, joint or soft tissue>
Myositis and osteomyelitis> Hamstring injury> Ligament tears>
Acute trauma> fractures> Abcess> Ulcer
Positioning
the patient in supine position with feet pointing towards the
magnet (feet first supine) Position the patient over the spine coil
and place the body coils over the thighs

Localizer

96
Axial

Coronal

Sagittal

97
Knee
Indication
Meniscal disorders: nondisplaced and displaced tears, discoid
menisci, meniscal cysts> Chondromalacia> Marrow abnormalities:
avascular necrosis, marrow edema syndromes, and stress fractures>
Congenital and developmental conditions: blount disease, dysplasia,
normal variants> Acute trauma> Synovial based disorders:
symptomatic plicae, synovitis ,bursitis, and popliteal cysts>
Fractures
> Muscle and tendon disorders: strains, partial and complete tears,
tendonitis, tendonopathy.
> Mechanical knee symptoms: catching, locking, snapping,
crepitus> Osteochondral fractures
> Vascular conditions: entrapment, aneurysm, stenosis, occlusion>
Neoplasms of bone, joint or soft tissue
> Infections of bone, joint or soft tissue> Ligament tears: cruciate,
collateral, retinacular> Osteochondral and articular cartilage
infractions > Osteochondritis> Degenerative chondrosis

Positioning
Feet first supine

98
Axial

Coronal

Sagittal

99
Leg (Tibia and Fibula)
Indication
> Marrow abnormalities (eg. bone contusions, osteonecrosis,
marrow edema syndromes, and stress fractures)> Infections of bone,
joint, or soft tissue (eg. osteomyelitis, osteochondritis ,osteo arthritis
)> Neoplasms of bone, joint, or soft tissue > Avascular necrosis>
Nerve impingement> Fractures in children> Soft-tissue masses >
Occult fracture> Ligament tear> cysts
Positioning
the patient in supine position with feet pointing towards the magnet
(feet first supine)
Position the patient over the spine coil and place the body coils over
the lower leg (knee joint
down to ankle joint)

100
Localizer

Coronal

101
Axial

Sagittal

102
Ankle
Indication
Marrow abnormalities (eg. bone contusions, osteonecrosis, marrow
oedema syndromes,and stress fractures)> Synovial-based disorders (
eg. synovitis, tenosynovitis, bursitis, and ganglion cysts)
> Congenital and developmental conditions ( eg.dysplasia, tarsal
coalition) > Achilles tendon disorders (eg.tears, tendonitis,
tendinopathy) > Infections of bone, joint, or soft tissue (eg.
osteomyelitis) > Neoplasms of bone, joint, or soft tissue
> Osteochondral and articular cartilage abnormalities > Posterior
tibial tendon disorders> Abnormalities of other hindfoot tendons>
Plantar fasciitis, fascial rupture> Peroneal tendon disorders> Intra-
articular loose body > Sinus tarsi syndrome > Avascular necrosis
>Fibromatosis
Positioning
Position the patient in supine position with feet pointing towards the
magnet (feet first supine)

103
Localizer

Axial

Coronal

104
Sagittal

Foot
Indication
Synovial based disorders ( eg. synovitis, tenosynovitis, bursitis, and
ganglion cysts
> Congenital and developmental conditions( eg.dysplasia, tarsal
coalition)
> Infections of bone, joint, or soft tissue (eg. osteomyelitis
,osteoarthritis )> Plantar fasciitis, fascial rupture, and plantar
fibromatosis> Abnormalities of foot tendons> Neoplasms of bone,
joint, or soft tissue> Mortons neuroma > Avascular necrosis

Positioning
Position the patient in supine position with feet pointing towards the
magnet (feet first supine)
Try and center coil at the Metatarsal heads (ball of foot), but make
sure toes are in coil to prevent inhomogeneous Fat Sat.

105
Localizer

Axial

Coronal

Sagittal

106
Breasts

107
Abdomen

If scan with contrast

Injection contrast IV dynamic (Tri phasic)
T1 FS DYN (Arterial, portal and delayed)

108
MRCP

109
MRU

110
Pelvis

111
112
113
114
115
116
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Thank you to everyone who
helped with information that
benefits others and spreads
Knowledge

Best regards
Mourad Edrees

119