1. By Prof. Youssri Gaweesh
Prof of colorectal surgery
Alexandria University

2. Historical background
 The story of MRI starts in about 1946 when Felix
Bloch proposed that the nucleus behaves like a
magnet.
 In the late 60s Raymond Damadian discovered that
malignant tissues had different NMR parameters than
normal tissues
 Clinical Magnetic Resonance Imaging (MRI) uses the
magnetic properties of hydrogen and its interaction
with both a large external magnetic field and
radiowaves to produce highly detailed images of the
human body.

3. One(1) Tesla is equal to 10,000 Gauss. The magnetic field of
the earth is approximately 0.5 Gauss. Given that
relationship, a 1.0 T magnet has a magnetic field
approximately 20,000 times stronger than that of the
earth.
Hydrogen has a significant magnetic moment and is nearly
100% abundant in the human body. For these reasons, we use
only the hydrogen proton in routine clinical imaging, and that
is where we will focus our attention from here on.

4. Why MRI
 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

5. The hardware
 The MAGNET
 The RF Coils
 The Computer (Data Processing)

8. To understand physics explore the characters
of the following

9. Some physical properties

13. What is Spin?
Spin is a fundamental property of nature like electrical
charge or mass. Spin comes in multiples of 1/2 and can
be + or -. Protons, electrons, and neutrons possess spin.
Individual unpaired electrons, protons, and neutrons
each possesses a spin of ½ or - ½.
• Two or more particles with spins having opposite signs
can pair up to eliminate the observable manifestations of
spin.
• In nuclear magnetic resonance, it is unpaired nuclear
spins that are of importance

26. Nuclear Spin
A nucleus consists of protons and neutrons
• When the total number of protons and
neutrons (=mass number A) is odd or the
total number of protons is odd, a nucleus
has an angular momentum (phi) and
hence spin
– Ex. Hydrogen (1^H) (1 proton), 13^C
• The spin of a nucleus generates a
magnetic filed, which has a magnetic
moment (mu)
• The spin causes the nucleus
behave like a tiny magnet with a
north and south pole

27. Nuclear Spin System
Collection of identical nuclei in a given sample of
material (also known as spin packet, a voxel in the
imaged volume)
• In the absence of external magnetic field, the spin
orientations of the nuclei are random and cancel each
other
• When placed in a magnetic field, the microscopic spins
tend to align with the external field, producing a net bulk
magnetization aligned with the external field

28. • The hydrogen proton
can be looked at as if it
were a tiny bar magnet
with a north and a
south pole.
• Why Hydrogen ???
• WE HAVE A LOT OF
IT
• IT HAS GOT THE
HIGHEST
GYROMAGNETIC
RATIO 42.6 MHz/T

29. When we put a person
in a magnet some
interesting things
happen to the
hydrogen protons:
1. They align with the
magnetic field
2. They precess or “wobble”
out of phase due to the
magnetic momentum of
the atom.
• ω0 = γ Β0

30. Precession
Spins PRECESS at a single
frequency(w0), but incoherently
, they are not in phase, so
that the sum of x-y components is
0, with net magnetization vector
in z direction
W0=gamma B_0: Larmor freq.

32. How do we get an image?
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.
The following steps can be divided into:
Excitation
Relaxation
Acquisition
Computing and Display.

33. Excitation

34. The field of the RF coil B1 is perpendicular to B0
original field

35. Relaxation
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.
Protons 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 and T2 relaxation.

36. T1 Relaxation

37. T2 Relaxation
• When we apply the 90o RF pulse something
interesting happens. Apart from flipping the
magnetization into the X-Y plane, the protons
will also start spinning in-phase!!

39. 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.
•T2 is much quicker than T1
•Every tissue has its built in T1 and T2
relaxation times.
•T2 is much smaller than T1
– For tissue in body, T2: 25-250ms, T1: 250-
2500 ms

40. Formation of Spin Echo
By applying a 180 degree pulse, the dephased spins can recover their
coherence, and form an echo signal

41. Pulse Sequences, THE ECHO

42. Sequence Parameters:
TR= Repetition time
TE= Echo time
Flip Angle
Matrix
Field of View
Slice thickness

43. Spin echo sequence
T_R (pulse repetition time)
• Multiple π pulses create “Carr-Purcell-Meiboom-Gill (CPMG)” sequence
• Echo Magnitude Decays with time constant T2

44. Acquisition and imaging

45. Basic Principle of MRI
The hydrogen (1^H) atom inside body possess “spin”
• In the absence of external magnetic field, the spin directions of all
atoms are random and cancel each other.
• When placed in an external magnetic field, the spins align with the
external field.
• By applying an rotating magnetic field in the direction orthogonal to
the static field, the spins can be pulled away from the z-axis with an
angle alpha
• The bulk magnetization vector rotates around z at the Larmor
frequency (precess)
• The precession relaxes gradually, with the xy-component reduces in
time, z-component increases
• The xy component of the magnetization vector produces a voltage
signal, which is the NMR signal we measure

46. Process Involved in MRI
Put patient in a static field B_0 (much stronger than the earth’s field)
• (step 1) Wait until the nuclear magnitization reaches an equilibrium
(align with B_0)
• Applying a rotating magnetic field B_1 (much weaker than B_0) to
bring M to an initial angle alpha with B_0 (rotating freq=Larmor
freq.)
• M(t) precess around B_0 at Larmor frequency around B_0 axis (z
direction) with angle alpha
• The component in z increases in time (longitudinal relaxation) with
time constant T1
• The component in x-y plane reduces in time (transverse relaxation)
with time constant T2
• Measure the transverse component at a certain time after the
excitation (NMR signal)
• Go back to step 1
• By using different excitation pulse sequences, the signal amplitude
can reflect mainly the proton density, T1 or T2 at a given voxel

47. Image Weighting
Hydrogen in fat recovers faster than that in
water in the Z axis and loses phase faster in the
X-Y axis.
T1 & T2 time in fat is shorter than water
T2 time of fat is 80ms and water is 200ms
T1 Contrast and T2 contrast
Long TR and TE….T2W image
Short TR and TE….T1W image
Long TR and Short TE….PD image

48. T1 & T2 weighting
•Fat and Water are hyperintense on T2 images
•Most pathological processes have T1 hypointense
and T2 hyperintense (altered fluid contents).
•Air, cortical bone, dense fibrous structures are
hypointense on T1 & T2 images.
•T1 hyperintense signal in:
•Fat
•Calcium (sometimes)
•Melanin
•Subacute blood (metHb)
•High protein fluid
•Flowing fluid

49. T1 weighted image
Fat is bright
Water/simple fluid is dark
Cerebral gray matter is grey
Cerebral white matter is white
Other materials are also bright : acute
hemorrhage (1-3 days old) , melanine , hydrated
calcium, proteinaceous material and gadolinium

50. T2 weighted image
Fat is bright (less than that in T1)
Water/simple fluid is bright
Cerebral grey mater is grey
Cerebral white matter is dark

51. Normal anatomy
a Axial T2-weighted of the pelvis depicting the layers of the rectal wall. The mucosa
and submucosa can be visualized as a relatively hyperintense band (arrows). The
hypointense line (arrowheads) represents the muscularis propria. b Axial T2-
weighted sequence. The mesorectal fascia can be visualized as a thin line
(arrowheads), enveloping the mesorectal compartment, containing the
rectum, mesorectal fat, bloodvessels, lymphatic vessels and nodes

52. A coronal diagram depicting the two anatomical levels (1 and 2) of the distal
rectum to help define the surgical approach

53. Coronal T2-weighted MR
image shows the normal anatomy of
the rectum. The white line indicates
the lower limit of the rectum at the
insertion of the levator ani muscle
(arrows) on the rectal wall. The
levator ani muscle forms the ceiling
of the ischiorectal fossa.

54. Normal anatomy of the mesorectum.
(a) Axial T2- weighted MR image
shows the mesorectal fascia as a
thin, hypointense layer (white
arrowheads)
surrounding hyperintense
mesorectal fat. On the anterior
aspect, the mesorectal fascia appears
more thickened and is difficult to
differentiate from the Denonvillier
fascia (black arrowheads (b)
Photograph of a section of the
explanted rectum shows
perirectal fat surrounded by the
mesorectal fascia.

55. Coronal T2-weighted MR image
obtained with a phased-array surface
coil shows a normal anal sphincter
complex. The levator ani muscle
(straight arrows) appears as a funnel-
shaped muscular layer that extends
from the obturator ani muscle to the
anal canal. The puborectalis muscle
(arrowheads) is depicted at the
insertion of the levator ani muscle onto
the anal canal. The external (curved
arrows) and internal (*) sphincter
muscles are also seen.

56. On MRI the mesorectal fat has a high signal intensity on T1- and T2-weighted
images.
The mesorectal fat is bounded by the mesorectal fascia, which is seen as a fine line
of low signal intensity (red arrows).
.

57. Normal male anatomy. Drawing (a)

58. T2-weighted MR image (b) show the normal male anatomy of the perineum
at the level of the mid anal canal (AC in b) in the axial plane. In b, ES =
external sphincter, IA = ischioanal fossa, InS = intersphincteric space, IS =
internal sphincter.

59. Normal female anatomy. Drawing (a)

60. T2-weighted MR image (b) show the normal female anatomy of the perineum
at the level of the proximal half of the anal canal (AC in b) in the axial plane.
In b, ES = external sphincter, InS = intersphincteric space, IO = internal
obturator muscle, IR = ischiorectal fossa, IS = internal sphincter, U =
urethra, V = vagina.

61. Drawing shows the normal anatomy of the
anal canal in the coronal plane.

62. Suggested orientation for axial MR imaging of the anal canal. Sagittal T2-
weighted image through the midline is used to obtain images that are truly
axial relative to the anal canal

63. Suggested orientation for coronal MR imaging of the anal canal. Coronal MR
imaging is performed at 90° relative to the axial plane to obtain images
parallel to the long axis of the anal canal.

64. Anal clock. Axial T2-weighted MR image of the male perineum shows the
anal clock diagram used to correctly locate anal fistulas with respect to the
anal canal. AP = anterior perineum, L = left aspect of the anal canal, NC =
natal cleft, R = right aspect of the anal canal.

65. Parks classification. Drawing of the anal canal in the coronal plane shows
the Parks classification of perianal fistulas. A = intersphincteric, B =
transsphincteric, C = suprasphincteric, D = extrasphincteric. The external
sphincter is the keystone of the Parks classification.

66. St James’s University Hospital Classification
The classification grades fistulas into five
groups: grade 1, simple linear
intersphincteric fistula; grade
2, intersphincteric with abscess or
secondary track; grade 3, transsphincteric;
grade 4, transsphincteric with abscess or
secondary track in ischiorectal or
ischioanal fossa; grade 5, supralevator and
translevator

67. Grade 1: simple linear intersphincteric fistula. (a) Drawing of the anal
canal in the axial plane shows a simple intersphincteric fistula at the
2-o’clock position (arrow).

68. (b) Axial contrast-enhanced fat-suppressed T1- weighted MR image shows
the left intersphincteric fistula (arrow) bounded by the external sphincter
without a secondary fistulous track or abscess.

69. Grade 1: simple linear intersphincteric fistula (same patient as in pevious
Fig). (a) Drawing of the anal canal in the coronal plane shows the
simple intersphincteric fistula to the left of the anal canal.

70. (b) Coronal contrast-enhanced fat-suppressed T1-weighted MR image
shows the highly enhancing intersphincteric fistula (arrow) confined by
the external sphincter.

71. Grade 2: intersphincteric fistula with an abscess. (a) Axial drawing of
the anal canal shows a right posterolateral abscess (arrow).

72. (b) Axial T2-weighted MR image shows the high-signal-intensity fluid
collection along the right posterolateral aspect of the anal canal
(arrow).

73. (c) Axial contrast-enhanced fat-suppressed T1-weighted MR image shows the
abscess in the right posterolateral aspect of the intersphincteric space
(arrowhead), bounded by the external sphincter.

74. Grade 2: intersphincteric fistula with an abscess (same patient as in previous Fig
). (a) Coronal drawing of the anal canal shows the abscess in the
intersphincteric space (arrow), bounded by the external sphincter.

75. (b) Coronal contrast-enhanced fat-suppressed T1-weighted MR image shows
the right intersphincteric abscess (arrow) without a fistulous track or abscess
in the right ischiorectal fossa.

76. Grade 3: transsphincteric fistula. (a) Axial drawing of the anal canal
shows a posterior transsphincteric fistula (arrow) with the internal
opening at the 6-o’clock position. (

77. (b) Axial contrast-enhanced fat-suppressed T1- weighted MR image
shows the transsphincteric fistula (arrow) crossing the external
sphincter.

78. Grade 3: transsphincteric fistula (same patient as in previous Fig ). (a)
Coronal drawing of the anal canal shows the right transsphincteric
fistula.

79. (b) Coronal contrast-enhanced fat-suppressed T1-weighted MR image
shows the highly enhancing transsphincteric fistula (arrow) from the
dentate line to the skin, passing through the ischioanal fossa and
piercing the external sphincter.

80. Grade 4: transsphincteric fistula with an abscess or secondary track in the
ischiorectal or ischioanal fossa. (a) Axial drawing of the anal canal
shows a posterior transsphincteric fistula with an abscess in the right
ischiorectal fossa.

81. (b) Axial T2-weighted MR image shows the transsphincteric fistula
crossing the external sphincter at the 6-o’clock position (arrow) and a
high-signal-intensity fluid collection in the right ischiorectal fossa
(arrowheads).

82. (c) Axial contrast-enhanced fat-suppressed T1- weighted MR image
shows the posterior transsphincteric fistula (straight arrow), the
abscess in the right ischiorectal fossa with nonenhancing pus in the
cavity (arrowheads), and a secondary extension in the left ischiorectal
fossa (curved arrow).

83. Grade 4: transsphincteric fistula with an abscess or secondary track in the
ischiorectal or ischioanal fossa (same patient as in previous Fig ). (a)

84. (b) Coronal contrast-enhanced fat-suppressed T1-weighted MR image
shows the abscess in the right ischiorectal fossa with nonenhancing pus in
the cavity (arrowheads) and the secondary extension in the left ischiorectal
fossa (arrow).

85. Grade 5: supralevator and translevator disease. (a) Axial drawing of the anal
canal shows a supralevator abscess located at the urethra (U), the left side
of the anal canal, and the left internal obturator muscle (IO).

86. (b) Axial contrast-enhanced fat-suppressed T1-weighted MR image shows
the left supralevator abscess with inflammatory changes in the left internal
obturator muscle (arrows).

87. Grade 5: supralevator and translevator disease (same patient as in previous Fig
). (a) Coronal drawing of the anal canal shows the left supralevator
abscess with a left translevator fistula.

88. (b) Coronal contrast-enhanced fat-suppressed T1-weighted MR image
shows the left supralevator abscess with inflammatory changes
surrounding the rectum and the left translevator fistula crossing the
ischiorectal fossa (arrowheads).

89. Horseshoe abscess. Axial T2-weighted MR image shows a horseshoe abscess with
a fluid-fluid level in both ischiorectal fossae (arrowheads). The abscess has high
signal intensity due to pus and a liquid-liquid level due to detritus.

90. Horseshoe abscess (same patient as in previosu Fig ). Axial (a) and coronal (b)
contrast-enhanced fat-suppressed T1-weighted MR images show a
horseshoe abscess in the ischiorectal and ischioanal fossae (arrows in
a, arrowheads in b). The abscess has intense enhancement due to the
presence of active inflammatory tissue.