Jungwoo Kang Extended Essay MRI

IB Extended Essay - Mathematics
An investigation into the mathematics of the transformation of signals from protons of hydrogen
atoms in magnetic resonance imaging into an image
Jungwoo Kang
Candidate Number: 000717-0036
Supervisor: Mr. Joseph Khan
Anglo-American School of Moscow
September 9, 2014
Word Count: 3998
1
Abstract
This investigation assesses the question How are the magnetically-induced signals from
protons of hydrogen atoms in a magnetic resonance imaging scan converted into an image?
To investigate this question, the essay examined the nuances of Magnetic Resonance
Imaging (MRI) by researching the magnetically induced physical properties of hydrogen atoms
used in MRI. The methods that could induce and change the signal from this physical
phenomenon, Free Induction Decay (FID), to create different image types were investigated.
However, the investigation focused on how FID signals are mathematically converted to an
image, and found that the mathematical principles used were specifically of one branch of
mathematics: Fourier analysis, the study of how functions can be approximated with the sum of
simpler trigonometric functions. To examine this, the Fourier series and the complex form of the
Fourier series were derived, which was used to derive the Fourier Transform and Inverse Fourier
Transform (used to transform information from the spatial domain into the spatial frequency
domain and vice versa). Next, the ideas of the Fourier Transform and Inverse Fourier Transforms
were applied again to MRI technology to reach a conclusion.
It was concluded that the Fourier and Inverse Fourier Transforms are used in
transforming Free Induction Decay signals from protons of hydrogen atoms to form an image.
These signals (waves) in the spatial domain are first Fourier Transformed into k-space, the raw
data space, to the frequency domain, and then Inverse Fourier Transformed back into the spatial
domain to sinusoidal waves, which are stored in a computer. Using these sinusoidal waves, and
the corresponding phase and amplitude data, an image is constructed. Finally, deeper
implications of the applications of Fourier analysis and how it can be used in other fields of
medicine and engineering were briefly considered.
Word Count: 293 Words
2
Table of Contents
Abstract ................. 1
Table of Contents ... 2
Introduction .... 3
Overview of the Process of Magnetic Resonance Imaging ... 4
Longitudinal Magnetization of Hydrogen Nuclei .. 4
Radiofrequency Pulses ... 6
Signal Modification .... 8
Spatial Encoding 10
Fourier Transform .. 13
Fourier Series . 13
Complex Exponential Form of the Fourier Series . 19
Approximation Example 21
Deriving the Fourier Transform and Inverse Fourier Transform .. 24
Sample Fourier Transform Calculation . 26
Application of the Fourier Transform to Magnetic Resonance Imaging ... 28
MR Signal Fourier Transform ... 28
Fourier Transform of FID Signal Example ... 30
Signals in K-Space 32
Inverse Fourier Transform of K-Space Data 32
Conclusion .... 34
Bibliography . 35
3
Introduction
Medical imaging techniques have evolved throughout history. Starting with the discovery
of X-Rays in 1895 to more complex types of imaging that exist today, a variety of methods, such
as radiation and nuclear magnetic resonance, are utilized. With this evolution of medical imaging
techniques, their mathematical applications have developed concurrently. Whether it is the use of
exponential functions in estimating half-lives of radiotracers to ensure a safe dose or the use of a
variety of mathematical transforms in translating signals into images, mathematics is always
prominent in medical imaging.1
Magnetic Resonance Imaging (MRI) is one of the most revolutionary medical
technologies in history that relies heavily on mathematics. First commercially available in 1981,
10 years after the first Computed Tomography (CT) scanner was released, MRI provided a
versatile method of soft-tissue imaging that had a higher level of resolution compared to a CT
scan without using ionizing radiation, which can damage DNA and cause cancer.2 This is
achieved through the mathematical transformation of a magnetically induced signal from protons
of hydrogen atoms. Hence, it is essential to investigate the elegant mathematical applications in
MRI techniques to fully understand the mechanism of its function.
Thus, the focus of this extended essay will aim to answer the following question: How
are the magnetically-induced signals from protons of hydrogen atoms in a magnetic resonance
imaging scan converted into an image?
Infinity. 2014. A History of Medical Imaging. Accessed July 10, 2014. http://www.infinityugent.be/researchdevelopment/a-history-of-medical-imaging.
2
Ibid.
4
Overview of the Process of Magnetic Resonance Imaging
MRI is a scanning technique based on the principle of Nuclear Magnetic Resonance
(NMR), a physical phenomenon where atomic nuclei in a static magnetic field absorb and reemit
electromagnetic radiation when applied an electromagnetic (usually radiofrequency, RF) pulse.
This phenomenon however, only occurs in atomic nuclei with spin (intrinsic angular momentum),
such as hydrogen nuclei.3 As hydrogen atoms are the most abundant atoms in the human body,
MRI utilizes the NMR properties of hydrogen to image the human body.4
Longitudinal Magnetization of Hydrogen Nuclei
A nucleus of the hydrogen atom consists of a single proton, a positively charged particle
that spins and produces a magnetic field (magnetic moment).5 6 Although the protons are charged,
their random orientation leads to a lack of a magnetic field. Hence, in order to utilize the NMR
properties of the hydrogen nuclei, a magnetic field must be applied.
The Primary Magnetic Field (B0) of an MRI, usually of strength 1, 1.5 or 3 Tesla (SI unit
of magnetic strength), causes protons to align with B0.7 Most protons are parallel to B0 and are in
a low-energy state; however, some protons, due to increased regional energy (possibly from
increased heat) line up antiparallel to B0 and are in a high-energy state. Protons aligned in B0 do
not simply point parallel or antiparallel to B0, rather, they precess (spin at an angle) around the z-
Scientific American. 1999. What exactly is the 'spin' of subatomic particles such as electrons and protons? Does it
have any physical significance, analogous to the spin of a planet? October 21. Accessed July 11, 2014.
http://www.scientificamerican.com/article/what-exactly-is-the-spin/.
4
Earl Frieden. 1972. "The Chemical Elements of Life." Scientific Amerian 52-60.
5
National Health Services. n.d. NHS. Accessed July 8, 2014. http://www.nhs.uk/Conditions/MRI-scan/Pages/Howdoes-it-work.aspx.
6
R Nave. n.d. Nuclear Magnetic Resonance. Accessed July 15, 2014. http://hyperphysics.phyastr.gsu.edu/hbase/nuclear/nmr.html.
7
Introduction to MRI Physics, YouTube video, 8:39, posted by "Lightbox Radiology Education," September 24,
2011, http://www.youtube.com/watch?v=Ok9ILIYzmaY
5
axis at a rate, Larmor Frequency (LF), of 42.58MHz per 1 Tesla.8 Nonetheless, this proton
alignment creates a Net Magnetic Vector (M) in the direction of B0. The creation of M in the
long axis (z-axis) is called longitudinal magnetization.
Diagram 1: Normal proton orientation (left) versus parallel/antiparallel proton orientation

with B0 (right)
10
Diagram 2: Proton precessing around z-axis
R Nave. n.d. Nuclear Magnetic Resonance. Accessed July 15, 2014. http://hyperphysics.phyastr.gsu.edu/hbase/nuclear/nmr.html.
9
Introduction to MRI Physics, YouTube video, 8:39, posted by "Lightbox Radiology Education," September 24,
2011, http://www.youtube.com/watch?v=Ok9ILIYzmaY
10
Ibid.
6
Radiofrequency Pulses
After protons align with B0, transverse magnetization is created to achieve resonance.
Thus, a continuous 90o RF pulse equal to the LF of the protons is transmitted from the RF coil to
the protons. As protons absorb energy from the 90o RF pulse, 50% of them move into the high
energy state, and longitudinal magnetization disappears. Then, protons begin to precess in-phase
rather than out-of-phase, creating transverse magnetization and a weak, but measurable current.
Subsequently, the 90o RF pulse is removed and protons return to thermodynamic equilibrium in a
process called relaxation. There are two types of relaxation that occurs: Spin-Spin (transverse)
and Spin-Lattice (longitudinal).11
Spin-Spin relaxation occurs first as protons, with same positive charge, repel each other
and precess out-of-phase, leading to transverse magnetization decay which is modelled by an
1
exponential decay curve. The time required to reach strength (37%) of transverse
magnetization with 90o RF pulse is time constant T2 (a tissue-specific value unaffected by field
strength).12
Then, Spin-Lattice relaxation occurs as some protons in the high-energy state revert to
their original low-energy state, releasing RF energy as heat to the surrounding lattice and leading
to longitudinal magnetization recovery which is modelled by an exponential curve. The time
1
required to reach 1 strength (63%) of the original longitudinal magnetization is time

constant T1 (a tissue-specific value that increases with stronger magnetic fields).13 Overall,
11
Dennis Hoa. n.d. MRI step-by-step, interactive course on magnetic resonance imaging. Accessed August 27, 2014.
http://www.imaios.com/en/e-Courses/e-MRI.
12
Ibid.
13
Ibid.
7
relaxation produces a signal called Free Induction Decay (FID) that can be measured by the RF
coil.
14
Diagram 3: Graph of FID

However, as MRI utilizes magnetic gradients (later discussed in the Spatial Encoding
section), the resulting inhomogeneity in the magnetic field causes FID signals to actually decay
faster than T2 predicts because of the destructive interference it creates.15
Thus, a modified T2* time constant takes into consideration both tissue-specific times of
normal T2 decay and accelerated spin dephasing due to inhomogeneities. Yet, an 180o RF pulse
(antiparallel to B0) can also reverse the effect of static magnetic field inhomogeneities by
rephasing spins.16
During Spin-Spin relaxation, field inhomogeneities cause some protons to spin faster than
others and dephase at time TE/2 after the 90o RF pulse. To counter this, applying an 180o RF
14
FDA. 2014. A Primer on Medical Device Interactions with Magnetic Resonance Imaging Systems. May 8.
Accessed July 16, 2014.
http://www.fda.gov/medicaldevices/deviceregulationandguidance/guidancedocuments/ucm107721.htm.
15
16
Ibid
8
pulse causes protons to flip vertically, causing M to shift from Z+ to Z-. Hence, protons moving
faster lag behind protons moving slower, and at time TE after the 90o RF pulse, the spins are
back in phase, but shortly after begin to dephase. However, at TE (Echo Time), the signal
sampled is not as strong as the initial intensity as the relaxation is entirely due to Spin-Spin
relaxation.17
18
Diagram 4: Graph of FID with T2 and T2* decay

Signal Modification
The process of repetitively applying the 90o and 180o RF pulses is called a Spin Echo
sequence and contains 2 parameters: TR (repetition time: the time between two 90o RF pulses)
and TE (echo time: the time between 90o RF pulse and MR signal sampling). Through
manipulation of the two parameters, tissue signals can be modified.
T1-weighting emphasizes differences in T1 by shortening TR and TE, limiting complete
Spin-Lattice relaxation. As different tissues have varied T1, tissues with shorter T1 recover
longitudinal magnetization more than tissues with longer T1 and thus has greater transverse
17
18
Ibid.
9
magnetization amplitude after a subsequent excitation. Therefore, tissue contrast depends largely
on T1 differences. 19
Contrastingly, T2-weighting lengthens TR and TE to highlight differences in T2. Longer
TR allows tissues to achieve full Spin-Lattice relaxation, thus accentuating variances in SpinSpin relaxation. Then, the longer TE is able to pick up dissimilar Spin-Spin relaxations between
tissues. Therefore, T2 differences affects tissue contrast.20
Finally, proton density-weighting (PD-weighting) lengthens TR but shortens TE,
delineating proton density differences. As higher proton density leads to faster transverse
magnetization decay (by lengthening TR and allowing full Spin-Lattice relaxation) the short TE
recognizes differences in proton density. Thus, PD variance influences tissue contrast.21
Diagram 5: Graphs of MR Signal with different weightings

Nonetheless, MRI images do not completely rely on one weighting type; rather, the
produced images are a combination of effects of T1, T2 and PD. For instance, a tissue in a
predominantly T1-weighted image, a tissue with long T1 and T2 (water) is dark while a tissue
19
20
Ibid.
21
Ibid.
10
with short T1 and long T2 (fat) is bright. However, in a predominantly T2-weighted image, the
former is bright and the latter is grey.22
Spatial Encoding
In order to create an image from MR signals, the precise location of FID must be isolated
through spatial encoding. This process consists of 3 steps: slice selection, phase encoding, and
frequency encoding.
First, a slice-selection gradient (SSG) is applied orthogonal to the slice plane, causing
protons to precess in a frequency relative to SSG in each slice. Then, a RF wave (selective pulse)
with frequency equal to the precession frequency of the desired slice is applied. The selective
pulse only excites the protons in the desired slice, shifting magnetization and thus, isolating the
slice.23 However, in the case of a selective pulse less than 180o, the dispersion of the resonance
frequency causes protons begin to dephase. To counteract this, an antiparallel gradient in the
same axis that is half the surface (amplitude x time) of the original gradient is applied.24
Secondly, a phase encoding gradient (PEG) is applied to the slice for a short amount of
time, which encodes by utilizing different rates of change of phase for the various signal
measurements. The PEG changes spin resonance frequencies and causes dephasing, resulting in
protons antiparallel to PEG to spin out-of-phase. This is important as this can be used to find the
rate of change of phase (equal to frequency), thus pseudo-frequency encoding the image slice
and utilizing a FEG twice would not allow the derivation of the image, since multiple voxels
22
23
Ibid.
24
Ibid.
11
would have the same frequency).25
26
Diagram 6: Demonstrates why the frequency encoding cannot be used for both dimensions.
Finally, a frequency encoding gradient (FEG) is applied to the slice for a limited period.
The FEG (orthogonal to both PEG and SSG) acts like the PEG, causing dephasing by changing
spin resonance frequencies, making protons antiparallel to the FEG spin out-of-phase. Hence, in
a slice 1 proton thick, each proton precesses at a different speeds and thus, FID can be isolated in
the image. These signals are transferred into K-Space (the representation of spatial frequency
information in using amplitude, frequency and phase information), and then from K-Space into
an image.27
25
26
D M Higgins. 2014. The How K-Space Works Tutorial. Accessed September 10, 2014.
http://www.revisemri.com/tutorials/how_k_space_works/.
27
12
Diagram 7: K-Space is the transformed values of the MR signal, with the x-axis representing
the FEG and the y-axis representing the PEG
These signals are transformed through the Fourier Transform and Inverse Fourier
Transforms. The former translates the spatial information of the signals from the protons of
hydrogen nuclei into spatial frequency, while the latter does the opposite. Therefore, before any
further description takes place about the processes of MRI, it is essential to discuss the Fourier
transform and its related components.
13
Fourier Transform
Fourier Series
In mathematics, series of simpler functions can represent a more complex function. For
example, Taylor series, utilize powers of x to represent other functions and thus are called power
series. Contrastingly, Fourier series utilizes trigonometric functions (cosine and sine) to represent
other functions and thus are called trigonometric series. Simply put, the Fourier series is a
method to represent a wavelike function through the decomposition of a periodic function (or
signal) to an infinite set of sine and cosine waves (and thus, complex exponentials).
The principle of linear superposition states that the total output equals the linear
combination of the corresponding outputs of individual inputs. Thus, an infinite series of
sine/cosine functions expressing some periodic function f with period T, constants a, b and
integer n (shown below) was first described by Joseph Fourier.
(x) = a0 + a1 cos
+ a2 cos
+ + b1 sin
+ b2 sin
The above equation can further be simplified by substituting the value of
with 0, the symbol
for angular frequency.

(x) = a0 + a1 cos 0 + a2 cos 20 + a3 cos 30 +
+ b1 sin 0 + b2 sin 20 + b3 sin 30 +
And finally, the above equation can be expressed as a summation.
(x) = a0 + (a cos 0 + b sin 0 )

=1
(1)
14
The use of n0 leads to another essential aspect of the Fourier series: harmonics. Harmonics are
the integer multiple of fundamental frequency
, where the nth harmonic is the nth multiple of
the fundamental frequency. The more harmonics there are, the better the approximation becomes.
0 =
( = 0, 1, 2, 3, )
One aspect to consider is the properties of the summation even and odd functions. The
sum of odd functions yields an odd function and the sum of even functions yields an even
function. However, the sum of both odd and even functions yields a function that neither odd nor
even. Thus, if f(x) is odd, its Fourier series only includes sine terms; if f(x) is even, its Fourier
series only includes cosine terms; and if f(x) is neither odd nor even, its Fourier series includes
both sine and cosine terms.
Next, evaluating coefficient values of a0, an, and bn, the Fourier series can be used to
approximate a function. The value of a0 can be determined by integrating Equation 1 over a
period,
to 2.
2 () = 2 a0 + 2
=1(a cos 0 + b sin 0 )
2
= a0 +
=1 a cos 0 + =1 b sin 0
= a0 +
(
=1 a ) (sin 0 2
sin (0 2)) + (
=1 b ) (cos 0 2 +
cos (0 2))
= a0 + (
=1 a ) (sin + sin()) + (=1 b ) (cos + cos())
= a0 ( , sin = 0)
1 2
a0 = ()

2
(2)
15
To determine an for n1, Equation 1 is multiplied by cos 0mx (for m1) and
integrated from
to 2 for period T.
2 () = 2 a0 + 2
=1(a cos 0 + b sin 0 )
2
() cos 0 = a0 2 cos 0 +
=1 a cos 0 cos 0 +
=1 sin 0 cos 0
(3)
From Equation 3, an is isolated by solving each term.
1) a0 2 cos 0
2 cos 0 = sin (0 2) sin (0 2)
= sin() + sin()
=0
2
2)
=1 a cos 0 cos 0
a. For n m, the second term equals:
cos 0 cos 0 = 2 (2 cos(( )) + 2 cos(( +
)0 ) )
= 2 ([
1
= 2(
sin(()0 )
sin(()(0 )( ))
+[
sin((+)0 )
+
sin(()(0 )( ))
2
+
16
sin((+)(0 )( ))
sin(())
sin((+)(0 )( ))
sin((+))
+
= 0( , , )
b. For n = m, cos 0 is substituted for cos , and the third term equals:
cos 0 cos 0 = (1 + cos 20 )

2
1
= 2 [ +
1
= 2 (2 +
1
sin 20
= 2 (2 +
sin(20 ( ))
2
sin(2)
2
( 2 +
+2 +
sin(20 ( ))
2
))
sin(2)
= 2 ( , sin(2) = 0)
0
c. 2 cos 0 cos 0 = {
=
2
2
2
3)
=1 sin 0 cos 0
sin 0 cos 0 = 2 (
sin(( + )0 ) +
sin(( )0 ) )
= 2 ([
1
= 2(
cos((+)0 )
+
= 2 (
cos((+))
+
cos((+)(0 )( ))
cos(()(0 )( ))
+[
cos(()0 )
cos((+)(0 )( ))
+
cos(()(0 )( ))
cos((+))
+
cos(())
cos(())
=0
Thus, using these values, Equation 3 is simplified to the below equation (only the value for n =
m is used, as it yields the only nonzero value).
17
() cos 0 =
If n is then substituted for m, the coefficient an is found.
2 2
= () cos 0

(4)
Finally, to determine bn for n1, Equation 1 is multiplied by sin 0mx (for m1) and integrated
from
to 2 .
() = a0 +
=1(a cos 0 + b sin 0 )
2
2 () sin 0 = a0 2 sin 0 +
=1 a cos 0 sin 0 +
=1 sin 0 sin 0
(5)
Once again, bn of Equation 5 is isolated by solving the equation term-by-term.
1) a0 sin 0
= cos(n) + cos()
=0
2)
sin 0 = cos (0 2 ) + cos (0 2 )
=1
2
cos 0 sin 0
18
cos 0 sin 0 = 2 (
sin(( + )0 ) sin(( )0 ) )
= 2 ([
1
= 2(
cos((+)0 )
+
cos((+)(0 )( ))
+
cos(()(0 )( ))
= 2 (
cos(()0 )
cos((+)(0 )( ))
cos(()(0 )( ))
cos((+))
cos((+))
cos(())
cos(())
=0
3)
=1 b sin 0 sin 0
2
a. For n m, the third term equals:
2 sin 0 sin 0 = 2 (2 cos(( )0 ) 2 cos(( +
)0 ) )
= 2 ([
1
= 2(
sin(()0 )
+
sin(())
sin(()(0 )( ))
sin((+)(0 )( ))
sin((+)0 )
sin(()(0 )( ))
sin((+)(0 )( ))
+
sin((+))
+
= 0( , , )
b. For n = m, sin 0 is substituted for sin and the second term equals:
sin 0 sin 0 = 2 (1 cos 20 )

1
= 2 [
sin 20
2
19
= 2 (2
sin(20 )
2
( 2
sin(20 ( ))
2
))
c.
0
sin 0 sin 0 = {
=
2
Thus, using these values, Equation 5 is simplified to the below equation. Like simplifying
Equation 3, only the values for n = m are used, as it yields the only nonzero value.
() sin 0 =
If n is then substituted for m, the coefficient an is found.
2 2
= () sin 0

(6)
Complex Exponential Form of the Fourier Series

To simplify the Fourier series, the coefficients an and bn are combined by expressing the
series in a complex exponential form. Using Eulers identity, = cos + sin , and replacing
with 0nx, one can derive the following.
ei0 nx = cos 0 + sin 0
(7)
ei0nx = cos(0 ) + sin(0 )

= cos 0 sin 0
cos 0 =
0 + 0
2
(8)
(9)
20
0 0
sin =
2
(10)
These values can be directly substituted into Equation 1 to convert the Fourier series into a
complex form.
(x) = a0 +
=1 (a
0 + 0
2
a b
0
= a 0 +
(
=1 [
+ b
0 0
2
a +b
) + 0 (
)]
(11)
Let cn and its conjugate, c-n, equal:
c =
a b
2
(12)
c =
a + b
2
(13)
If these values are substituted into Equation 11, f(x) is expressed as a summation of c e0 ,
and therefore, as the complex exponential form of Fourier series.
0
(x) = a0 +
+ c 0 ]
=1[c
0 (as
=
a0 c0 because for n = 0, () = c0 )
= c
Then, cn is computed by substituting the values of an and bn into Equation 12.

c =
a b
2
2
( 2 () cos 0 2 () sin 0 )

2
2
2
1
= ()(cos 0 sin 0 )
(14)
21
Finally, the values of cos 0 and sin 0 from Equations 9 and 10 are substituted to further
simplify the equation.
1
c = 2 ()(cos 0 sin 0 )
= () (
1
= 2 () (
0 + 0
2
0 + 0
2
= ()( 0 )
0 0
2
0 0
2
(15)
Approximation Example
Using the coefficients, the Fourier series can approximate a periodic function or a nonperiodic function (over a period). For instance, take the square wave shown in Diagram 8.
Diagram 8: Square wave with amplitude of 1 unit and wavelength/period of 2 units

The function is defined as:
1 0 < <
(x) = { 0 = 0,
, (x) = (x + 2)
1 < < 0
22
First, taking into consideration that the function is odd, the Fourier series expansion of this
square wave consists of solely sine terms. Thus, these values of f(x), are plugged into the
formulas for bn.
a0 = 2 ()
= 2 ()
= 0 ( (x) )
b = 2 () sin 0
=
() sin

=
2
2
() sin ( 2
0
)
= 0 (1) sin
2
= [ cos ]
0
2
= [cos cos 0]
2
= [(1) 1]
0 =
={4
=
Likewise, the same is done with the complex form of Fourier series.
1
c = ()( 0 )
1
= 2 (0 )
= 2 (0 )
23
i
= 2 (( 1) (1 ))
i
= 2 ( + 2)
0 =
= {2i
=
Thus, f(x) is expressed as:

4
(x) =
=1( (21) sin((2 1)))
2i
(21)
=
= (21)
Taking the 1, 3 and 10 harmonics, the Fourier series approximation expresses the square wave
more accurately as number of harmonics increases.
Diagram 9: Fourier approximations of diagram 8. Note how the approximation improves as

the number of harmonics increases from 1 (red) to 3 (purple) to 10 (blue)
If infinitely many harmonics are used to approximate, the series will converge to f(x), given that
f(x) is integrable. Convergence theory states: if f(x) is piecewise smooth over period [-T, T], then
the Fourier series converges to average value
(0 +)+(0 )
2
at the point of discontinuity, x0, and
to the periodic extension through 2T of f(x) if f(x) = f(x + 2T).

Deriving the Fourier Transform and Inverse Fourier Transform
One problem that mathematicians faced was that, while the Fourier series provided a way
to approximate periodic functions, it is limited as it cannot approximate non-periodic functions
24
beyond a period. Thus, mathematicians derived the Fourier Transform from the complex
exponential form of the Fourier Series, which can approximate non-periodic functions from - to
.
Taking the complex exponential Fourier series from Equation 14 and substituting the value
of cn (Equation 15), the result is:
0
() =
= c
1
2
0
=
) ) 0
=( ()(
Then, is replaced with 20 (definition of angular frequency).
0 2
0
() =
) ) 0
=( 2 ()(
Now, take into consideration the definition of the nth harmonic.

0 =
2
( = 0, 1, 2, 3, )
From this, the separation of these frequencies can be calculated.

0 ( 1)0 = 0 =
As T approaches , the frequency separation () decreases, nears 0 and all the frequency
harmonics are represented, corresponding to a Riemann sum. Therefore, the function can be
simplified into a double integral representation as 0 is replaced with and the summation of
n0 (discrete frequencies) is replaced by an integral over all frequencies. Now, n0 is replaced
with a general variable of frequency, .
1
() = ( ()( ) )
2
(16)
25
The inner integral of Equation 16 can be expressed as (), representing a function dependent
on frequency, (when integral is evaluated for x = , x disappears and only remains).
() = ()( )
(17)
Equation 17 is the Fourier Transform (FT) that shifts information in the time dimension, x, into a
information the frequency dimension, . When Equation 17 is plugged back into Equation 16,
the result is the Inverse Fourier Transform (IFT) which transforms information in the frequency
domain, , to information in the time domain, x.
() =
1
()
2
(18)
When information is in the frequency domain, the y-value (amplitude) of the matching xvalue (frequency) denotes the amplitude of the frequency forming the part of the approximation.
28
Diagram 10: The FT transforms the sinusoidal wave (blue) in the time domain to the
frequency domain (red), while the IFT does the opposite. Note that amplitude does not change
and that both graphs are equivalent but are in different domains.
Sample Fourier Transform Calculation

28
26
Take the function (graphed above) in the time domain, x, () = {
0
.
< 0
Plugging this into the FT, it yields:
() = 0 ( ) + ( )
= 0 (1+) + (1)
(1+)
= [ (1+) ]
(1)
0
+ [ (1) ]
0

= [0 (1+)] + [(1) 0]
1
= (1+) + (1)
1++1
= (1+)(1)
2
= 1+2
Hence, for the values of frequencies () that are plugged in, the value of F() corresponds to the
amplitudes of the frequencies, yielding the graph below.
27
Diagram 11: Graph of the frequency (x-axis) of f(x) calculated above, against the amplitude
(y-axis).
Application of the Fourier Transform to Magnetic Resonance Imaging

As the Fourier Transform has been derived, the original problem of the conversion of MR
signals into, and out of k-space can be investigated. The reason that the FT is used is because it
can turn MR signals information, which is in the space domain, and transform it into the
frequency domain, which is temporarily stored into k-space. Then, using the IFT, information in
the frequency domain is transformed back into the spatial domain to reconstruct the image in a
computer. Furthermore, another benefit of this method is that it provides a shorter and more
efficient way of transformation. Rather than superimposing all frequencies, which would require
65536 calculations for a 256*256 pixel image, the Fourier transforms provide a shortcut to
construct the image.
MR Signal Fourier Transform
28
First, in order for the Fourier Transform to be applied to MR Imaging, the time domain is
replaced with a space domain (time variable becomes x-coordinate) and the frequency becomes
spatial frequency. As frequency is the inverse of the time it takes for a sinusoidal wave to repeat
(period), the spatial frequency is the inverse of the space required for the intensity of an image to
change.
29
Diagram 12: On the left, the image requires a long distance to change in intensity (low
spatial frequency). On the right, the image requires a short distance to change in intensity
(high spatial frequency).
Through this transformation of MR Signals, its 3 essential points of information can be
found: amplitude (determines signal strength); frequency (determines relative position in slice);
and phase (determines relative position in slice). First, the FID signal is Fourier transformed in
the frequency encoding direction (X-axis) to derive the frequency. Subsequently, the signal is
Fourier transformed in the phase encoding direction(Y-axis), to derive the location of the signal
in the PEG.
29
29
30
Diagram 13: The Fourier Transform process of a wave visualized. Notice in the middle how
the frequencies are identical, yet, they are different as the phase information is different and
hence must be treated separately.
Fourier Transform of FID Signal Example
31
Take this voxel located in (3,3). The raw data of the signals for this specific voxel is shown
below: notice how the frequency is the same for all the signals.
30
D M Higgins. 2014. The How K-Space Works Tutorial. Accessed September 10, 2014.
31
Hornak, Joseph P. 2014. The Basics of MRI. Henrietta, NY: Interactive Learning Software.
30
32
Fourier transforming in the frequency encoding direction, the result is the following: note how
the x-value of the frequency of the peaks are in line with the x-value of the voxel.
33
Taking into account the oscillation of the amplitudes of the frequencies, they can be represented
as a wave to make it more visible.
32
33
Ibid.
31
34
Now, Fourier transforming this wave in the phase encoding direction results in a single peak. Its
location is equal to the location of the voxel.
35
Signals in K-Space
34
35
Ibid.
32
K-Space stores the FT data, recording frequency, phase, and amplitude information. By
definition of k-space, the data near the middle of k-space contains the majority of information.
This is because the lowest spatial frequency data tends to have the largest amplitudes, as they
give the greatest changes in contrast. On the other hand, periphery data has higher frequency but
lower amplitudes since they code for finer details that do not require vast changes in contrast.
These amplitudes are portrayed in k-space by the grayscale color that is given to them, with
white as higher amplitudes and black as low/zero amplitudes.
Inverse Fourier Transform of K-Space Data
The final step in the MRI Image Formation process is performing an IFT on k-space data.
Due to the single-dimensional nature of IFT, it must be done line by line in one direction and
then repeated in another direction. This leads to information returning to the spatial domain and
these sinusoids are used to construct an image using frequency, phase and amplitude information.
The process, while it may sound almost impossible, is visualized below.
36
Diagram 14: The progression of an image that has been constructed with 9, 36, 64 and 1024
spatial frequencies.
Every picture is made of waves - Sixty Symbols, YouTube video, 9:42, posted by "Sixty Symbols," June 4,
2014, http://www.youtube.com/watch?v=mEN7DTdHbAU
36
33
Conclusion
Hence, it is evident that the magnetically-induced FID signals from protons of hydrogen
atoms are converted into an image through the use of two mathematical transforms: FT and IFT.
The isolated FID signals of the slice being imaged is are transformed into k-space with the FT
and information in the spatial domain is converted into the spatial frequency domain (while other
variables such as amplitude and phase remain constant). Then, the data is transformed out of kspace into a computer through the IFT, converting information from the spatial frequency
domain into the spatial domain. Finally, the data (consisting of sinusoidal waves and its
amplitude and phase) is used to reconstruct the image.
By investigating this issue, the elegant and unseen mathematical elements of medical
imaging were uncovered. Yet, while this investigation did explore the mathematics of the
conversion of the signals of protons to images, it did not uncover the more intricate mathematical
concepts such as the Fast Fourier Transform, and different types of MRI such as MRI
angiography, which also utilizes complex integrals.37 These applications of mathematics only
serve to demonstrate the prominence of mathematics in other scientific fields such as engineering
and medicine. Yet, this notion becomes even more evident since the Fourier Series and Fourier
Transform can be used in a variety of fields. For instance, it can be used in seismology to
determine the seismic activity of a volcano, be used to measure cosmic background radiation and
differentiate it from the random signals that are in the universe or be used to model the process of
how the human ears hear sound (consequently digital music encoding). These examples suggest
the elegance and importance of mathematics, as it is the basis of almost all fields of research.
37
Nave, R. n.d. Nuclear Magnetic Resonance. Accessed September 20, 2014. http://hyperphysics.phyastr.gsu.edu/hbase/math/fft.html
34
Bibliography
FDA. 2014. A Primer on Medical Device Interactions with Magnetic Resonance Imaging
Systems. May 8. Accessed July 16, 2014.
http://www.fda.gov/medicaldevices/deviceregulationandguidance/guidancedocuments/uc
m107721.htm.
Frieden, Earl. 1972. "The Chemical Elements of Life." Scientific Amerian 52-60.
Hesselink, John R. n.d. Basic Principles of MR Imaging. Accessed August 20, 2014.
http://spinwarp.ucsd.edu/neuroweb/Text/br-100.htm.
Higgins, D M. 2014. The How K-Space Works Tutorial. Accessed September 10, 2014.
Hoa, Dennis. n.d. MRI step-by-step, interactive course on magnetic resonance imaging.
Accessed August 27, 2014. http://www.imaios.com/en/e-Courses/e-MRI.
Infinity. 2014. A History of Medical Imaging. Accessed July 10, 2014.
http://www.infinityugent.be/research-development/a-history-of-medical-imaging.
Introduction to MRI Physics, YouTube video, 8:39, posted by "Lightbox Radiology
Education," September 24, 2011, http://www.youtube.com/watch?v=Ok9ILIYzmaY
National Health Services. n.d. NHS. Accessed July 8, 2014. http://www.nhs.uk/Conditions/MRIscan/Pages/How-does-it-work.aspx.
Nave, R. n.d. Nuclear Magnetic Resonance. Accessed July 15, 2014. http://hyperphysics.phyastr.gsu.edu/hbase/nuclear/nmr.html.
Nave, R. n.d. Nuclear Magnetic Resonance. Accessed September 20, 2014.
http://hyperphysics.phy-astr.gsu.edu/hbase/math/fft.html
Scientific American. 1999. What exactly is the 'spin' of subatomic particles such as electrons and
protons? Does it have any physical significance, analogous to the spin of a planet?
October 21. Accessed July 11, 2014. http://www.scientificamerican.com/article/whatexactly-is-the-spin/.
Every picture is made of waves - Sixty Symbols, YouTube video, 9:42, posted by "Sixty
Symbols," June 4, 2014, http://www.youtube.com/watch?v=mEN7DTdHbAU

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IB Extended Essay - Mathematics

Diagram 1: Normal proton orientation (left) versus parallel/antiparallel proton orientation

Diagram 2: Proton precessing around z-axis

required to reach 1 strength (63%) of the original longitudinal magnetization is time

Diagram 3: Graph of FID

Diagram 4: Graph of FID with T2 and T2* decay

Diagram 5: Graphs of MR Signal with different weightings

The above equation can further be simplified by substituting the value of

with 0, the symbol

for angular frequency.

(x) = a0 + (a cos 0 + b sin 0 )

, where the nth harmonic is the nth multiple of

From Equation 3, an is isolated by solving each term.

2 cos 0 = sin (0 2) sin (0 2)

a. For n m, the second term equals:

cos 0 cos 0 = 2 (2 cos(( )) + 2 cos(( +

cos 0 cos 0 = (1 + cos 20 )

If n is then substituted for m, the coefficient an is found.

Once again, bn of Equation 5 is isolated by solving the equation term-by-term.

sin 0 = cos (0 2 ) + cos (0 2 )

a. For n m, the third term equals:

2 sin 0 sin 0 = 2 (2 cos(( )0 ) 2 cos(( +

sin 0 sin 0 = 2 (1 cos 20 )

If n is then substituted for m, the coefficient an is found.

Complex Exponential Form of the Fourier Series

ei0nx = cos(0 ) + sin(0 )

Let cn and its conjugate, c-n, equal:

Then, cn is computed by substituting the values of an and bn into Equation 12.

Diagram 8: Square wave with amplitude of 1 unit and wavelength/period of 2 units

Thus, f(x) is expressed as:

Diagram 9: Fourier approximations of diagram 8. Note how the approximation improves as

at the point of discontinuity, x0, and

to the periodic extension through 2T of f(x) if f(x) = f(x + 2T).

Then, is replaced with 20 (definition of angular frequency).

Now, take into consideration the definition of the nth harmonic.

From this, the separation of these frequencies can be calculated.

Sample Fourier Transform Calculation

Take the function (graphed above) in the time domain, x, () = {

Plugging this into the FT, it yields:

Application of the Fourier Transform to Magnetic Resonance Imaging

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