MRI SIMPLIFIED

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MRI SIMPLIFIED
Parth Patel MIV, USC SOM
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LET US PROBE INSIDE THE MAGNET
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IT'S ALL ABOUT PHYSICS

• Recall that molecules are made of atoms and atoms
  have a standard structure.
• Electrons are at the periphery and nucleus is in
  the center.
• The nucleus contains protons and neutrons.
• Electrons, protons and neutrons (elementary
  particles) all have unique properties.

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• ONE OF THESE UNIQUE PROPERTIES IS SPIN.
• Spin is a quantized phenomena that occurs due to
  angular momentum.
• Think of it as a planet spinning on its axis or a
  spintop.
• The spin is mathematically described as a
  magnetization vector.
• The reason for not manipulating the spin of
  electrons is that they are usually paired since
  most atoms exist in a stable state in nature.

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SPIN WOBBLING EFFECT

• Spins wobble or precess about the plane of
  magnetic field (B0).

• This spin frequency is called the Larmor
  frequency (?0) and it is directly proportional to
  the strength of magnetic field.
• ?0 ? B0

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MAGNETIZATION VECTOR

• The spins can be broken down into two
  perpendicular components a longitudinal or
  transverse component.

• In a B0 magnetic field, the precession
  corresponds to rotation of the transverse
  component along the longitudinal axis.

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RESONANCE

• Resonance relates to the transfer/exchange of
  energies between two systems at a specific
  frequency.
• It is analogous to talking to someone on your
  cell phone.
• In magnetic resonance, only protons with the same
  frequency as the RF pulse will respond.
• During RF pulse delivery nuclei become excited
  and then return to equilibrium.
• During equilibrium, they emit energy in the form
  of electromagnetic waves.

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ELECTROMAGNETIC WAVES

• In brief, this can be thought of as the light we
  see but with different frequencies.
• The frequency is directly proportional to the
  energy and inversely proportional to the
  wavelength.
• This is the crux of wireless communications that
  we encounter in our daily lives.

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EXCITATION

• During excitation, protons jump to a higher
  energy level.
• Also, the net magnetization vector spirals down
  to the transverse plane (XY plane).
• The degree to which the net vector moves down is
  called the flip angle.
• The flip angle is a function of strength and
  duration of the RF pulse.

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RELAXATION

• After excitation, the protons emit RF pulse of
  their own.
• This is the nuclear magnetic resonance signal in
  the form of electromagnetic waves (ie raw data)
• Longitudinal relaxation and transverse relaxation
  are the two different mechanisms by which this
  occurs.

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RELAXATION - T1

• One can see that T1 measures the duration by
  which the magnetization vector reverts to the
  natural longitudinal direction in a B0 magnetic
  field. This duration measures the degree to which
  the spins are being disrupted by the surrouding
  tissue (a.k.a. spin-lattice relaxation)

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RELAXATION - T2

• One can see that T2 time is the duration in which
  the magnetization vector decays in the transverse
  direction since the spins interact with each
  other causing them to be out of phase (a.k.a.
  spin-spin relaxation)

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RECEIVING THE SIGNAL

• When the protons emit RF signal (Electromagnetic
  radiation) as they relax,
• the signal induces a current in the receiving
  coil and this is the manner in which raw data in
  MRI is obtained.
• Recall from physics that changes in magnetic flux
  induces an electromotive force (i.e. voltage).
  This physical law (Faraday's law) absolutely runs
  our 24/7 economy! We couldn't generate
  electricity efficiently in a large magnitude
  without this law.
• Electromagnetic waves have both an electric and
  magnetic field components perpendicular to each
  other. When the EM waves strike the receiver coil
  in the MRI machine, the change in magnetic flux
  induces a current.

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SUMMARY OF NMR SIGNAL

• In brief, we apply an initial magnetic field, B0
  and the protons align with the field while
  processing at a frequency proportional to the
  magnetic field strength.
• We then send RF pulse in the transverse plane
  (like pinging a wine glass) and the protons align
  and process accordingly.
• Thereafter, protons relax in different two ways
  via emitting RF pulses.
• This allows us to recognize environmental
  differences of protons in a given tissue sample.

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MAKING USE OF NMR DATA

• The key to obtaining an MRI image is to impart
  spatial resolution, use the data from resonance
  to fill up a matrix of voxels, and perform a
  mathematical calculation called Fourier
  transform.
• First let us talk about spatial resolution.
• The way we do this is by applying a gradient of
  magnetic field in order to obtain spatial
  information.

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SPATIAL RESOLUTION

• If we didn't have a magnetic field gradient, our
  image would just look like one big 'blob' without
  obtaining any anatomical information. This would
  be called free induction decay. We will learn
  this a bit later but one needs to have more than
  one frequency peak (shown below) to obtain an
  image.

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SPATIAL RESOLUTION CONT'D.

• Spatial resolution achieved through gradient
  field is nicely depicted in this figure below.

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FILLING UP K-SPACE

• Simply put, k-space is a matrix usually 512x512
  that is used to store data acquired from magnetic
  resonance of protons. The math is complex but
  there is an analogy to this.
• Recall that CT scan uses a similar matrix and
  then calculates the numbers to add up photons
  received in both x and y planes.

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K-SPACE

• The k-space is filled up in iterations by using
  the resonance data obtained from magnetic field
  gradients.
• First, we select a slice (in millimeters) by
  applying a field gradient in the horizontal
  plane.
• Within this slice we try to map out objects in
  both x and y planes by collecting raw data in
  these planes.
• The y-plane is called phase encoding direction.
  To obtain this one has to apply field gradient in
  the vertical (or y-plane) direction.
• The x-plane is called frequency encoding
  direction. To obtain this one has to apply field
  gradient in the horizontal (or x-plane)
  direction.

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K-SPACE

• This is an example of how the matrix is filled
  with data during each slice.

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K-SPACE

• The top image shows process of slice selection,
  and bottom left shows the phase encoding data
  where as bottom right shows frequency encoding
  data.

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K-SPACE

• The phase encoding direction acts as a sieve
  which is sensitive to only vertically distributed
  data. In real life, the filters will obviously be
  many more than depicted in the last slide.
• Vice-versa, the frequency encoding direction acts
  as a sieve which is sensitive to only
  horizontally distributed data.
• One can imagine that if we continued to do this
  for slices upon slices then we would get a stack
  of data which we can scroll through hence
  creating a vivid image.

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K-SPACE ? IMAGE FORMATION

• Now that we have completed the daunting task of
  obtaining data in different planes, how can we
  make an image?...Fourier transform, of course!
• I would like to briefly talk about music since
  this analogy eases the pain of learning Fourier
  transform rigorously.
• Imagine the following say, we have a sound
  tracing of a song and we know what instruments
  (including the voice box) were involved in making
  the final song. Suppose we wanted to know what
  instruments were being played at what time in the
  sound tracing so that we could create a mental
  picture of how the music was composed (i.e.
  arrangement)

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FOURIER TRANSFORM (FT) ANALOGY

• Observe the sound tracing below. Each tracing
  corresponds to a different harmonic (or
  frequency). Instruments are 'tuned' to different
  frequencies and when various instruments are
  played in unison, our brains perceive it as
  melody. We have to use FT in order to dissect the
  sound tracing into its corresponding harmonics

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FOURIER TRANSFORM

• Fourier transform is an efficient method to
  convert time domain data into frequency domain.
  Meaning that you give me any kind of a curve
  (tracing in this case) and I can transform or
  represent the curve into its sine and cosine wave
  components.
• That's it! Now, we won't get into how this is
  done for this lecture.
• Now, the MR data obtained in our magnificent
  k-space can be transformed into wave functions
  representing different frequencies to give us a
  high-resolution image of the body.

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IMAGE FORMATION

• One can see this being done in the axial brain
  image below. We can even do this with counting
  photons (in the visible range) and perform
  Fourier transform to make an image. Your digital
  camera does something similar but with a
  different method!

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THE SECRET IS IN THE K-SPACE

• One can see below that the center of k-space is
  where the contrast information is stored. The
  periphery is where the fine details of the images
  are stored. This is nicely depicted in the
  airplane images below.

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RECALL RELAXATION

• Recall the two types of relaxation T1 and T2.
  Here's a diagram to help you. Z longitudinal
  axis corresponding to T1 relaxation Y transverse
  axis corresponding to T2 relaxation.
• B0 vector is shown in the initial magnetic field
  direction.

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MRI SEQUENCES

• Now that we know how images are formed, let us
  talk about how we can create different images to
  view pathologies by using various sequences.
• For simplicity, we will only talk about basic T1,
  T2, STIR, and FLAIR sequences.
• Note There are hundreds of pulse sequences (each
  manufacturers even have their own!) that you
  don't need to know about unless you want to be an
  expert at MRI.

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TISSUE COMPOSITION

• Hydrogen atoms are ubiquitous in nature as well
  as in our body. Fats whether in the form of
  triglycerides, cholesterol, fatty acids all
  contain hydrogen atoms. Indeed the same applies
  for water.
• It turns out that fat has shorter T1 time
  (100-150 ms) and longer T2 time (10-100 ms)
  compared to water.
• Conversely, water has longer T1 time (1.5-2.0 s)
  and longer T2 time (40-200 ms)range compared to
  fat.
• This turns out to be crucial in distinguishing
  different pathologies and it will be discussed at
  the end of this lecture.

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PULSE SEQUENCE DIAGRAM

• Usually sequences are depicted in the following
  way. You have the RF pulse delivery, then the
  next line shows slice selection gradient, then
  the phase gradient, then the frequency gradient
  and then the readout echo signal. There are two
  main parameters in MRI imaging. You can select
  the time that you want to repeat your RF pulse
  delivery called TR (repetition time) and the time
  you want the receiver coil to receive the signal
  from proton resonance called TE (echo time).
  Usually, the RF pulse is at 42.58 MHz, which is
  the frequency at which proton in the hydrogen
  atoms resonate.

Spin Echo Sequence
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SPIN ECHO

• This is a classic pulse sequence. In Spin Echo,
  we apply a RF pulse 90o relative the initial
  magnetic field, B0 and then apply a RF pulse 180o
  relative to the B0 field to obtain our image. The
  reason for applying 90o pulse is to dephase
  proton spins so that we can 'see' the differences
  in tissues. Moreover, an 180o pulse is applied to
  rephase spins of protons so that we can measure
  an accurate T2 echo since all spins will be
  rephased in the transverse axis.
• One may ask how can180o pulse rephase spins if
  they are all out of phase. Consider a race
  between a turtle and rat. When the race starts
  (relaxation begins), both are in the same place.
  As the rat runs faster, the distance between them
  widens. Then they both have to turn around and go
  back (180o pulse) at the same speed to reach the
  finish line. Both will arrive at the same time
  (rephase) to the finish line.
• Remember Longitudinal axis (T1 relaxation)
  Transverse axis (T2 relaxation)

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SPIN ECHO

• One can already see that the echo signal after
  90o pulse is due to T1 and T2 relaxation since
  protons will attempt to align with the B0
  magnetic field in the longitudinal axis (T1) as
  well as show decay in the transverse axis (T2).
• Conversely, the echo signal after 180o pulse is
  due to T2 decay since the spins have been
  rephased and there is a net vector of all the
  spins in the transverse axis. Hence, 180o pulse
  is applied in order to obtain accurate T2
  measurement as stated previously.
• Thereafter, the spins will realign in the
  longitudinal axis and one can then accurately
  measure T1 time. In this way, one can obtain T1
  and T2 weighted images based on this spin echo
  sequence by modifying the TR and TE time.

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T1 AND T2-WEIGHTED IMAGES

• As we have already discussed, the origin of T1
  and T2 time is due to relaxation of protons in
  different planes.
• If we want a T1 weighted image then the TR and TE
  time will have to be short. This image will show
  fat brighter relative to water.
• If we want a T2 weighted image then the TR and TE
  time will have to be long. This image will show
  water brighter relative to fat.

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T1-WEIGHTED IMAGE
In the figure below, patient on the left is a
normal control vs. patient on the right who has
MS. The patient with MS has significant loss of
myelin due to autoimmune destruction.
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T2-WEIGHTED IMAGE

• In the figure below, one can see the bright CSF
  signal as well as a cyst in the arachnoid space.
• T2-weighted images are generally a good starting
  place when searching for pathology since it has
  some component of edema.

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STIR AND FLAIR

• STIR (Short Time Inversion Recovery) is a pulse
  sequence where one suppresses the fat signal by
  applying a pulse 180o relative the initial B0
  magnetic field and then quickly applying a pulse
  90o relative to B0 field direction. The time
  between is called TI (Inversion Time).This
  combination of pulses doesn't allow the fat to
  relax in the longitudinal plane hence negating
  signal from surrounding tissues containing fat.
• FLAIR (Fluid Attenuated Inversion Recovery) is a
  pulse sequence where one suppresses signal from
  fluid to make surrounding pathology appear
  brighter. This is used frequently in MS. Since
  classic location of plaques in MS is around the
  ventricles, nulling the signal from CSF allows
  for easy visualization of plaques. FLAIR
  sequence uses a TI that is long (close to that of
  T2-weighted image) to suppress fluid from CSF and
  other fluid filled cavities in the body.

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TISSUE CHARACTERISTICS REFERENCE

• Here are the T1 and T2 times for different
  tissues in the human body.

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THAT'S IT!

• Now you should be able to explain MRI in basic
  terms to someone who doesn't know anything about
  obtaining images using magnetic resonance.
• Remember if you forget you can always say this
• Protons resonate or wobble at a certain
  frequency and when you excite them they relax and
  emit energy in the form of electromagnetic
  radiation. The body has different numbers and
  location of protons in various tissues. When you
  receive the emitted energy you can map the data
  onto a matrix. Then you can extrapolate using
  sine and cosine waves what the body looks like
  based on the mapped RF pulses emitted by
  different numbers of protons residing in various
  tissues (kind of like picturing the music
  arrangement by looking only at the sound signal
  on your audio receiver!).