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Magnetic Resonance Imaging. Presented by: Mahyar Nirouei. Synopsis of MRI. 1) Put subject in big magnetic field 2) Transmit radio waves into subject [2~10 ms] 3) Turn off radio wave transmitter 4) Receive radio waves re-transmitted by subject 0 5) Convert measured RF data to image.

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Presented by: Mahyar Nirouei

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Presented by mahyar nirouei

Magnetic Resonance Imaging

Presented by: Mahyar Nirouei

Synopsis of mri

Synopsis of MRI

1) Put subject in big magnetic field

2) Transmit radio waves into subject [2~10 ms]

3) Turn off radio wave transmitter

4) Receive radio waves re-transmitted by subject0

5) Convert measured RF data to image

Siemens allegra 3t scanner

Siemens Allegra 3T Scanner

B0 = 3 T = 30,000 gauss

Earth’s magnetic field = 0.5 gauss

Mri hardware

MRI Hardware

Rf coil

RF Coil

  • RF Coils are used to excite the spins and to receive the signal

  • A typical coil is a tuned LC circuit and may be considered a near field antenna

Many factors contribute to mr imaging

Many factors contribute to MR imaging

  • Quantum properties of nuclear spins

  • Radio frequency (RF) excitation properties

  • Tissue relaxation properties

  • Magnetic field strength and gradients

  • Timing of gradients, RF pulses, and signal detection

What kinds of nuclei can be used for nmr

What kinds of nuclei can be used for NMR?

  • Nucleus needs to have 2 properties:

    • Spin

    • charge

  • Nuclei are made of protons and neutrons

    • Both have spin ½

    • Protons have charge

  • Pairs of spins tend to cancel, so only atoms with an odd number of protons or neutrons have spin

    • Good MR nuclei are 1H, 13C, 19F, 23Na, 31P

Hydrogen atoms are best for mri

Hydrogen atoms are best for MRI

  • Biological tissues are predominantly 12C, 16O, 1H, and 14N

  • Hydrogen atom is the only major species that is MR sensitive

  • Hydrogen is the most abundant atom in the body

  • The majority of hydrogen is in water (H2O)

  • Essentially all MRI is hydrogen (proton) imaging

A single proton

A Single Proton


There is electric charge

on the surface of the proton, thus creating a small current loop and generating magnetic moment m.

The proton also has mass which generates an

angular momentum

J when it is spinning.





Thus proton “magnet” differs from the magnetic bar in that it

also possesses angular momentum caused by spinning.

Presented by mahyar nirouei

Magnetic Moment





m= tmax / B

= IA




t = mB

= m B sinq


t = IBLW = IBA



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Angular Momentum

J = mw=mvr

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The magnetic moment and angular momentum are vectors lying along the spin axis

m = gJ

g is the gyromagnetic ratio

g is a constant for a given nucleus

How do protons interact with a magnetic field

How do protons interact with a magnetic field?

  • Moving (spinning) charged particle generates its own little magnetic field

    • Such particles will tend to line up with external magnetic field lines (think of iron filings around a magnet)

  • Spinning particles with mass have angular momentum

    • Angular momentum resists attempts to change the spin orientation (think of a gyroscope)

Presented by mahyar nirouei


Presented by mahyar nirouei

The energy difference between

the two alignment states depends on the nucleus

  • D E = 2 mz Bo

    D E = hn

  • n = g/2p Bo

    known as Larmor frequency

g/2p = 42.57 MHz / Tesla for proton

Resonance frequencies of common nuclei

Resonance frequencies of common nuclei

Note: Resonance at 1.5T = Larmor frequency X 1.5

Electromagnetic radiation energy

Electromagnetic Radiation Energy

X-Ray, CT


Mri uses a combination of magnetic and electromagnetic fields

MRI uses a combination of Magnetic and Electromagnetic Fields

  • NMR measures the net magnetization of atomic nuclei in the presence of magnetic fields

  • Magnetization can be manipulated by changing the magnetic field environment (static, gradient, and RF fields)

  • Static magnetic fields don’t change (< 0.1 ppm / hr):

    The main field is static and (nearly) homogeneous

  • RF (radio frequency) fields are electromagnetic fields that oscillate at radio frequencies (tens of millions of times per second)

  • Gradient magnetic fields change gradually over space and can change quickly over time (thousands of times per second)

Presented by mahyar nirouei

Radio Frequency Fields

  • RF electromagnetic fields are used to manipulate the magnetization of specific types of atoms

  • This is because some atomic nuclei are sensitive to magnetic fields and their magnetic properties are tuned to particular RF frequencies

  • Externally applied RF waves can be transmitted into a subject to perturb those nuclei

  • Perturbed nuclei will generate RF signals at the same frequency – these can be detected coming out of the subject

Presented by mahyar nirouei

Basic Quantum Mechanics Theory of MR

The Effect of Irradiation to the Spin System



Presented by mahyar nirouei

Basic Quantum Mechanics Theory of MR

Spin System After Irradiation

Presented by mahyar nirouei

Net magnetization is the macroscopic measure of many spins



Net magnetization

Net magnetization

  • Small B0 produces small net magnetization M

  • Larger B0 produces larger net magnetization M, lined up with B0

  • Thermal motionstry to randomize alignment of proton magnets

  • At room temperature, the population ratio of anti-parallel versus parallel protons is roughly 100,000 to 100,006 per Tesla of B0

Quantum vs classical physics

Quantum vs Classical Physics

One can consider the quantum mechanical properties of individual nuclei, but to consider the bulk properties of a whole object it is more useful to use classical physics to consider net magnetization effects.

To measure magnetization we must perturb it

To measure magnetization we must perturb it

  • We can only measure magnetization perpendicular to the B0 field

  • Need to apply energy to tip protons out of alignment

  • Amount of energy needed depends on nucleus and applied field strength (Larmor frequency)

  • The amount of energy added (duration of the RF pulse at the resonant frequency) determines how far the net magnetization will be tipped away from the B0 axis



  • Precession refers to a change in the direction of

  • the axis of a rotating object.

  • It occurs when spinning objects experience a moment outside the plane of rotation

Presented by mahyar nirouei


Slope = gyromagnetic ratio


  • Larmor freqency, and is dictated by

  • The speed of precession of a spinning body in a field is called the Larmor frequency, and we know a few things about it

    • Zero when B0 = 0

    • Increases as magnetic field increases

    • We could do an experiment and plot the relationship between B0 and precessional frequency

  • For protons wL is approximately 42 MHz/Tesla


Presented by mahyar nirouei

Derivation of precession frequency

  • = m× Bo

  • = dJ / dt

    J = m/g

    dm/dt = g (m× Bo)

m(t) = (mxocos gBot + myosin gBot) x + (myocos gBot - mxosin gBot) y + mzoz

This says that the precession frequency is the

SAME as the larmor frequency

Recording the mr signal

Recording the MR signal

  • Need a receive coil tuned to the same RF frequency as the exciter coil.

  • Measure “free induction decay” of net magnetization

  • Signal oscillates at resonance frequency as net magnetization vector precesses in space

  • Signal amplitude decays as net magnetization gradually realigns with the magnetic field

  • Signal also decays as precessing spins lose coherence, thus reducing net magnetization

Nmr signal decays in time

NMR signal decays in time

  • T1 relaxation – Flipped nuclei realign with the magnetic field

  • T2 relaxation – Flipped nuclei start off all spinning together, but quickly become incoherent (out of phase)

  • T2* relaxation – Disturbances in magnetic field (magnetic susceptibility) increase the rate of spin coherence T2 relaxation

  • The total NMR signal is a combination of the total number of nuclei (proton density), reduced by the T1, T2, and T2* relaxation components

T2 decay

T2* decay

  • Spin coherence is also sensitive to the fact that the magnetic field is not completely uniform

  • Inhomogeneities in the field cause some protons to spin at slightly different frequencies so they lose coherence faster

  • Factors that change local magnetic field (susceptibility) can change T2* decay

Presented by mahyar nirouei

Different tissues have different relaxation times. These relaxation time differences can be used to generate image contrast.

  • T1 - Gray/White matter

  • T2 - Tissue/CSF

  • T2* - Susceptibility (functional MRI)

Spatial localization

Spatial Localization

  • Slice selection

    • In a homogeneous magnetic field (B0), an magnetic field (B1) oscillating at or very near the resonant frequency, w, will excite nuclei in the bore of the imaging magnet (Larmor equation):

w = g Bo


Spatial localization1

Spatial Localization

  • Slice selection(continued)

    • We can selectively excite nuclei in one slice of tissue by incorporating a third magnetic field: the “gradient” magnetic field. A gradient magnetic field is a small magnetic field superimposed on the static magnetic field. The gradient magnetic field produces a linear change in the total magnetic field.

    • Here, “gradient” means “change in field strength as a function of location in the MRI bore”.


Spatial localization2

Spatial Localization

  • Slice selection(continued)

    • Since the gradient field changes in strength as a function of position, we use the term “gradient amplitude” to describe the field:

    • Gradient amplitude = D (field strength) / D (distance)

    • Example units: gauss / cm


Spatial localization3

Spatial Localization

  • Slice selection(continued)

    • To recap, we use these magnetic fields in MRI:

    • B0 – large, homogeneous field of superconducting magnet.

    • B1 – temporally-oscillating, RF magnetic field that excites nuclei at resonance.

    • Bg – spatially-varying, small field responsible for the linear variation in the total field.


Spatial localization4

Spatial Localization

  • Slice selection(continued)

    • The linear change of the gradient field can be along the Z axis (inferior to superior), the X axis (left to right), the Y axis (anterior to posterior), or any combination (an “oblique” scanning prescription).

    • Switching the gradient magnetic fields on/off produces the MRI acoustic noise.


Superconducting magnet




Superconducting Magnet

In a typical


magnet having a

a horizontal bore,

the Z axis is down

the center of the

bore, the X axis is

horizontal and the

Y axis is vertical.


Spatial localization5

Spatial Localization

  • Slice selection example:

    • Q: How does the gradient field affect the resonant frequency?

    • A: The resonant frequency will be different at different locations.

    • Consider a gradient magnetic field of 0.5 Gauss / cm, using a Z gradient superimposed on a 1.5 T static magnetic field (1.5T = 15,000 Gauss).


Spatial localization6

Spatial Localization

  • Here’s a picture of the total magnetic field as a function of position:


Presented by mahyar nirouei

Spatial Localization

  • Recall the Larmor equation:

  • w = g Bo

  • For hydrogen:

  • = 42.58 MHz/Tesla = 42.58 x 106 Hz/Tesla

  • Calculating the center frequency at 1.5 Tesla:

  • w = g Bo

  • w = (42.58 MHz / Tesla)(1.5 Tesla)

  • w = 63.87 MHz


Presented by mahyar nirouei

Spatial Localization

What are the frequencies at Inferior 20cm and Superior 20cm?

At I 20cm, Btot = 1.499 T:

  • wI = g Btot

  • wI = (42.58 MHz / Tesla)(1.499 Tesla)

  • wI = 63.827 MHz

    At S 20cm, Btot = 1.501 T:

  • wS = g Btot

  • wS = (42.58 MHz / Tesla)(1.501 Tesla)

  • wS = 63.913 MHz

Difference in


.086 MHz


Rf bandwidth

RF Bandwidth

  • The RF frequency of the oscillating B1 magnetic field has an associated bandwidth. Rather than oscillating at a single frequency of 63.870 MHz, a range or “bandwidth” of frequencies is present. A typical bandwidth for the oscillating B1 magnetic field is + 1 kHz, thus RFfrequencies from 63.869 MHz to 63.871 MHz are present. The bandwidth of RF frequenciespresent in the oscillating B1 magnetic field is inversely proportional to the duration of the RF pulse.


Rf bandwidth continued

RF Bandwidth(continued)

  • There are actually two RF bandwidths are associated with MRI:

  • Transmit and Receive

  • RF Transmit bandwidth ~ +1 kHz affects

  • slice thickness (we are discussing this)

  • RF Receive bandwidth ~ +16 kHz is

  • sometimes adjusted to optimize

  • signal-to-noise in images (more in a later lecture)


Rf bandwidth continued1

RF Bandwidth(continued)


Rf bandwidth continued2

RF Bandwidth(continued)

  • Where will excited nuclei be located, assuming an 63.87 MHz (+ 1 kHz) RF bandwidth and a 0.5 Gauss / cm gradient field superimposed on a 1.5 Tesla static magnetic field?

  • At the inferior-most position of excitation, w is:

  • (63.87 – 0.001) MHz = 63.869 MHz

  • = (42.58 MHz/Tesla)(B inferior)

    B inferior = 63.869 MHz/(42.58 MHz/T)

  • = 1.4999765 Tesla = 14999.765 Gauss


Rf bandwidth continued3

RF Bandwidth(continued)

So, change of field from center to the inferior extent of excitation = (15000 – 14999.765) Gauss

= -0.235 Gauss

The gradient imposes a field change of

0.5 Gauss/cm, so a change of –0.235 Gauss occurs at the following distance from the center:

  • - .235 Gauss

  • .5 Gauss / cm

 - .47 cm


Rf bandwidth continued4

RF Bandwidth(continued)

  • Same is true of the superior position:

    63.871 MHz = (42.58 MHz / Tesla)(B superior)

  • B superior = 1.5000235 Tesla = 15000.235 Gauss

.235 Gauss

.5 Gauss / cm

 .47 cm


Rf bandwidth continued5

RF Bandwidth(continued)



Rf bandwidth continued6

RF Bandwidth(continued)

  • A + 1 kHz RF pulse at 63.870 MHz will excite a 9.4 mm thick slice in the presence of a 0.5 Gauss/cm gradient at 1.5 Tesla.

  • The maximum gradient on the GE LX Horizon Echospeed+ is 3.3 Gauss/cm. The maximum gradient on the Siemens Vision is 2.5 Gauss/cm.

  • Slice thickness can be changed with RF bandwidth or gradient magnetic field or both.


Rf bandwidth continued7

RF Bandwidth(continued)

At a specific RF bandwidth (D w), a high magnetic

field gradient (line A) results in slice thickness (D zA).

By reducing the magnetic field gradient (line B), the

selected slice thickness increases in width (D zB).


Rf bandwidth continued8

RF Bandwidth(continued)

  • An increase in the RF bandwidth applied at a constant magnetic field gradient results in a thicker slice

  • (D zB > D zA).


Slice location rf frequency

Slice Location (RF frequency)

  • The location of the selected slice can be moved by changing the center RF frequency (w0B > w0A).


Two dimensional fourier transform mri 2dft

Two-Dimensional Fourier Transform MRI (2DFT)

  • Planar imaging - a plane or slice of spins has been selectively excited as shown previously. After the Z gradient and RF pulse have been turned off, (and after a brief rephasing with the Z gradient) all spins in the slice are precessing in phase at the same frequency.

  • A 2Dimensional Fourier Transform (2DFT) technique can now be used to image the plane.

  • After imaging a plane, the RF frequency can be changed to image other planes in order to build up an image volume.


Two dimensional fourier transform mri 2dft1

Two-Dimensional Fourier Transform MRI (2DFT)

Q: Once spins in a slice are excited, how does the scanner “observe” the data?

A: The receive coil in the scanner detects the TOTAL transverse magnetization signal in a particular direction, resulting from the SUM of ALL excited spins.

Example #1: one spin case

Receiver Coil


Transverse received signal over time


Two dimensional fourier transform mri 2dft2

Two-Dimensional Fourier Transform MRI (2DFT)

Receiver Coil

Example #2: two spin case, with different frequencies

Spin #1


Spin #2


Summed signal can be complicated…but, this is useful.


2d fourier imaging

Raw data

Processed data

Fourier transform

2D Fourier Imaging

Fourier transform basics

Fourier Transform Basics

In 1-D, we can create a wave with a complicated shape by adding periodic waves of different frequency together.






In this example, we could keep going to create a square wave, if we wanted.






Fourier transform basics1

Fourier Transform Basics

This process works in reverse as well: we can decompose a complicated wave into a combination of simple component waves.

The mathematical process for doing this is known as a “Fourier Decomposition”.


Fourier transform basics2

Fourier Transform Basics

For each different frequency component, we need to know the amplitude…

…and the phase, to construct a unique wave.




Amplitude change

Phase change


Fourier transform basics3

Fourier Transform Basics

So, if spins in an excited slice were prepared such that they precess with a different frequency and phase at each position, the resulting signal could only be constructed with a unique set of magnetization amplitudes from each position.

Thus, we could apply a Fourier transform to our total signal to determine the transverse magnetization at every position.

So, let’s see how we do this…


Phase and frequency encoding

Phase and Frequency Encoding

  • Consider an MRI image composed of 9 voxels

  • (3 x 3 matrix)

  • All voxels have the same precessional frequency and are all “in phase” after the slice select gradient and RF pulse.


Phase and frequency encoding continued

Phase and Frequency Encoding(continued)

  • 1. Apply a Y gradient or “phase encode gradient”

  • 2. Nuclei in different rows experience different magnetic fields. Nuclei in the highest magnetic field (top row), preceses fastest and advance the farthest (most cycles) in a given time.


Frequency encoding

Frequency encoding

During signal reception, a gradient is applied in one direction:

B= B0 + Gxx



The resonant frequency depends on location, so a Fourier transform of the signal tells us where the nuclei are in one dimension

Phase and frequency encoding continued1

Phase and Frequency Encoding(continued)

  • When the Y “phase encode gradient” is on, spins on the top row have relatively higher precessional frequency and advanced phase. Spins on the bottom row have reduced precessional frequency and retarded phase.


Phase and frequency encoding continued2

Phase and Frequency Encoding(continued)

  • 3. Turn off the Y “phase encode gradient”

  • 4. All nuclei resume precessing at the same frequency

  • 5. All nuclei retain their characteristic Y coordinate dependent phase angles


Phase and frequency encoding continued3

Phase and Frequency Encoding(continued)

  • 6. A “read out” gradient is applied along the X axis, creating a distribution of precessional frequencies along the X axis.

  • 7. The signal in the RF coil is now sampled in the presence of the X gradient.


Phase and frequency encoding continued4

Phase and Frequency Encoding(continued)

  • While the frequency encoding gradient is on, each voxel contributes a unique combination of phase and frequency. The signal induced in the RF coil is measured while the frequency encoding gradient is on.


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Phase and Frequency Encoding(continued)

Phase-encode gradient

Phase-encoding of these rows occurs by turning a gradient on for a short period of time…

Total magnetic field

Frequency-encode gradient


Presented by mahyar nirouei

Phase and Frequency Encoding(continued)

Phase-encode gradient

…then, frequency-encoding of the columns occurs by turning a gradient on for a different axis and leaving it on during the readout.

Total magnetic field

Frequency-encode gradient


Phase and frequency encoding continued5

Phase and Frequency Encoding(continued)

  • 8. The cycle is repeated with a different setting of the Y phase encoding gradient. For a 256 x 256 matrix, at least 256 samples of the induced signal are measured in the presence of an X frequency encoding gradient. The cycle is repeated with 256 values of the Y phase encoding gradient.

  • 9. After the samples for all rows are taken for every phase-encode cycle, 2D Fourier Transformation is then carried out along the phase-encoded columns and the frequency-encoded rows to produce intensity values for all voxels.


Phase and frequency encoding continued6

Phase and Frequency Encoding(continued)

  • A 2DFT can be accomplished around any plane, by choosing the appropriate gradients for slice selection, phase encoding and frequency encoding.


K space

k - space

The Fourier transformation acts on the observed “raw data” to form an image. A conventional MRI image consists of a matrix of 256 rows and 256 columns of voxels (an “image matrix”).

The “raw data” before the transformation ALSO consists of values in a 256 x 256 matrix.


K space1

k - space

This “raw data” matrix is affectionately known as “k-space”. Two-dimensional Fourier Transformation (2DFT) of the “k-space” produces an image.

  • Each value in the resulting image matrix corresponds to a grey scale intensity indicative of the MR characteristics of the nuclei in the voxels. Rows and columns in the image are said to be “frequency encoded” or “phase encoded”.


K space2

k - space

For an MRI image having a matrix of 256 rows and 256 columns of voxels, acquisition of the data requires that the spin population be excited 256 times, using a different magnitude for the phase encoding gradient for each excitation.


K space continued

k - space(continued)

  • The top row of k-space would be measured in the presence of a strong positive phase encode gradient.

  • A middle row of k-space would be measured with the phase encode gradient turned off.

  • The bottom row of k-space would conventionally be measured in the presence of a strong negative phase encode gradient.


K space continued1

k - space(continued)

  • While the frequency encoding gradient is on, the voltage in the RF coil is measured at least 256 times. The 256 values measured during the first RF pulse are assigned to the first row of the 256 x 256 “raw data” matrix. The 256 values measured for each subsequent RF pulse are assigned to the corresponding row of the matrix.


Presented by mahyar nirouei


K space continued2

k - space(continued)

  • There are many techniques of “filling” or “traversing” k-space, each of which may convey different imaging advantages. These techniques will reviewed in subsequent sections.


K space continued3

k - space(continued)

  • The central row of k-space is measured with the phase encode gradient turned off. An FFT of the data in the central row produces a projection or profile of the object.


Presented by mahyar nirouei


by row


by column

Plot A-t

Presented by mahyar nirouei


by row


by column

Plot A-t

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