How do we look inside your brain without slicing you open?

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How do we look inside your brain without slicing
you open?
Structural Imaging with Magnetic Resonance
Imaging (MRI)
From nuclear spins To Structure Slides Elia
Formisano Rainer Goebel Maastricht
University, Netherlands
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The MR scanner to measure brain activation
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Physical Bases of Nuclear Magnetic Resonance

• The nuclei are not always at the same position
  but they rotate or precess like gyroscopes around
  the direction of the field.

Ho
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Collecting a Brain Volume
15 slices/sec Brain Volume 2 Sec
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• Nuclear
• Properties of atomic nuclei
• Spin, electricity, and momentum
• Magnetic
• How protons behave in static magnetic field
• How they behave during field fluctuation
• Resonance
• What the heck does this mean, anyway?
• Imaging
• Forming maps of relative changes in
  electromagnetic energy
• Functional MRI
• Mapping functional localization (I.e., the new
  phrenology) via hemodynamic properties

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• Nuclear
• Properties of atomic nuclei
• Spin, electricity, and momentum
• Magnetic
• How protons behave in static magnetic field
• How they behave during field fluctuation
• Resonance
• What the heck does this mean, anyway?
• Imaging
• Forming maps of relative changes in
  electromagnetic energy
• Functional MRI
• Mapping functional localization (I.e., the new
  phrenology) via hemodynamic properties

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• Nuclear
• Properties of atomic nuclei
• Spin, electricity, and momentum
• Magnetic
• How protons behave in static magnetic field
• How they behave during field fluctuation
• Resonance
• What the heck does this mean, anyway?
• Imaging
• Forming maps of relative changes in
  electromagnetic energy
• Functional MRI
• Mapping functional localization (I.e., the new
  phrenology) via hemodynamic properties

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• Nuclear
• Properties of atomic nuclei
• Spin, electricity, and momentum
• Magnetic
• How protons behave in static magnetic field
• How they behave during field fluctuation
• Resonance
• What the heck does this mean, anyway?
• Imaging
• Forming maps of relative changes in
  electromagnetic energy
• Functional MRI
• Mapping functional localization (I.e., the new
  phrenology) via hemodynamic properties

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• Nuclear
• Properties of atomic nuclei
• Spin, electricity, and momentum
• Magnetic
• How protons behave in static magnetic field
• How they behave during field fluctuation
• Resonance
• What the heck does this mean, anyway?
• Imaging
• Forming maps of relative changes in
  electromagnetic energy
• Functional MRI
• Mapping functional localization (I.e., the new
  phrenology) via hemodynamic properties

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• Nuclear
• Properties of atomic nuclei
• Spin, electricity, and momentum
• Magnetic
• How protons behave in static magnetic field
• How they behave during field fluctuation
• Resonance
• What the heck does this mean, anyway?
• Imaging
• Forming maps of relative changes in
  electromagnetic energy
• Functional MRI
• Mapping functional localization of cognition and
  behavior, in the nervous system, via hemodynamic
  properties

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Functional MRI of Cognition and Behavior

• Two common image formats
• Structural
• e.g., T1-weighted MP-RAGE images
• Functional
• e.g., spin-echo echo-planar images
• sensitive to BOLD contrast (T2)

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Topics for Today

• MR Signal generation
• Spin properties of atomic nuclei, Hydrogen (1H)
• Angular momentum
• Magnetic moments
• Spin properties of 1H in magnetic field
• parallel
• anti-parallel

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Properties of atomic nuclei
Atomic nuclei are composed of a proton
(positively charged particle), or both protons
and neutrons (neutral charge).
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Properties of atomic nuclei
Atomic nuclei are composed of a proton
(positively charged particle), or both protons
and neutrons (neutral charge). Hydrogen, the
most abundant element, has 1 proton, 0 neutrons
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Properties of atomic nuclei
Atomic nuclei are composed of a proton
(positively charged particle), or both protons
and neutrons (neutral charge). Hydrogen, the
most abundant element, has 1 proton, 0
neutrons Protons and neutrons have angular
momentum (spin, J) that is a function of its
mass, and a magnetic moment (?) that is a
function of electrical charge placed in a
magnetic field
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Properties of atomic nuclei
Atomic nuclei are composed of a proton
(positively charged particle), or both protons
and neutrons (neutral charge). Hydrogen, the
most abundant element, has 1 proton, 0
neutrons Protons and neutrons have angular
momentum (spin, J) that is a function of its
mass, and a magnetic moment (?) that is a
function of electrical charge placed in a
magnetic field The orientation of J and ? are
perpendicular to the direction of spin (right
hand rule) and can be thought of as the axis of
spin
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Some basic notations
Three types of magnetic field in fMRI B0 Main
magnetic field B1 Radiofrequency (RF) pulse
used to excite proton spins Gx Gy Gz Gradient
magnetic fields used for localizing signal
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What influences spin?

• Nuclear spin frequency depends on two factors
• gyromagnetic ratio (?)- ratio between charge and
  mass, constant for a given nucleus

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What influences spin?

• Nuclear spin frequency depends on two factors
• gyromagnetic ratio (?)- ratio between charge and
  mass, constant for a given nucleus
• magnetic field strength (B0 B1 Gx Gy Gz)

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What influences spin?

• Nuclear spin frequency depends on two factors
• gyromagnetic ratio (?)- ratio between charge and
  mass, constant for a given nucleus
• magnetic field strength (B0 B1 Gx Gy Gz)

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What influences spin?

• Nuclear spin frequency depends on two factors
• gyromagnetic ratio (?)- ratio between charge and
  mass, constant for a given nucleus
• magnetic field strength (B0 B1 Gx Gy Gz)

Larmor (resonant) Frequency
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Spins align with magnetic field
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Spins align with magnetic field

• Protons that align in the direction of the
  magnetic field (B0)are in low energy state
  (parallel)

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Spins align with magnetic field

• Protons that align in the direction of the
  magnetic field (B0)are in low energy state
  (parallel)
• Protons that align in the direction opposite to
  B0 are in a high energy state (anti-parallel)

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Spins align with magnetic field

• Protons that align in the direction of the
  magnetic field (B0)are in low energy state
  (parallel)
• Protons that align in the direction opposite to
  B0 are in a high energy state (anti-parallel)
• There will always be more protons in parallel
  than in anti-parallel alignment due to thermal
  energy. Decreasing temperature increases spins
  in parallel state.

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Precession axis is perpendicular to force

• Precession axis for a top is perpendicular to
  gravitational force

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Precession axis is perpendicular to force

• Precession axis for a top is perpendicular to
  gravitational force
• Precession axis for a proton in B0 is
  perpendicular to the orientation, or force, of B0

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Net Magnetization (M) is proportional to the
difference in parallel and anti-parallel states
Longitudinal magnetization component parallel -
antiparallel to B0 Transverse magnetization is
perpendicular to B0
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Net Magnetization (M) is proportional to the
difference in parallel and anti-parallel states
Longitudinal magnetization component parallel -
antiparallel to B0 Transverse magnetization is
perpendicular to B0 M increases with number of
spins in parallel state
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Reception (relaxation) is period in which spins
return to low-energy state. This is the period
during which signal is measured
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Spin and Resonance

• An RF signal can push the spin direction away
  from Bo
• Larmor equation determines the resonance
  frequency

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T1 of Tissue

• T1 - time that it takes the longitudinal
  magnetization to grow back to 63 of its final
  value.

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T1 Relaxation Contrast
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T1 Recovery is tissue-dependent
Number of protons differs across tissue types
How does different T1 make MRI imaging more
useful?
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Two Dimensions of Visibility

• If 2 types of tissue have same T1 the image at
  the boarder looks?
• Analogy light and IR field imaging

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Types of relaxation

• After RF pulse is turned off, spins will relax in
  2 ways
• longitudinal relaxation- M vector realigns with
  B0
• transverse relaxation- Spins lose phase coherence
• A) random molecular fluctuations (like cars on
  the highway) and
• B) inhomogeneity in the magnetic field

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Transverse (T2) relaxation

• T2 Dephasing time till all protons at flat
  distribution of phases

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Monitoring from a Distance

• Coil picks up changing magnetic field based on
  the spin of the protons

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MR signal reception via mutual inductance
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T1 Recovery- longitudinal magnetization about 10x
slower than T2 decay (900 vs. 100msec in gray
matter)
x
(arbitrary units)
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Factors that determine timing in MR image
acquisition
Tissue A
Tissue B
Repetition Time (TR) Time interval between RT
pulses, length determined by relative T1 recovery
profiles Echo Time (TE) Time from RF pulse to
data acquisition (DAQ), length determined by
relative T2 decay profiles
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Spin Echo Inverting the T2
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Pulse Sequence Diagram
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Contrast Formation

• Key variables of scan
• TR Repetition Time
• TE Echo Time
• General classes of scans
• T1- weighted image shows T1 tissue contrast
• T2 Functional
• Proton density weighted

T1 structural
T2 Functional
Proton Density Weighting
Proton Density Weighting
T2 Functional
T1 structural
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Example Contrast images
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Which RF excitation will produce the most signal?
M
M
M
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Summary

• (some) Nuclei spin at a frequency that depends on
  their gyromagnetic ratio and the strength of the
  magnetic field (Larmor frequency)
• Spins enter into parallel or anti-parallel state
  in magnetic field
• Net magnetization is the sum of magnetic moments
  of spins in a volume
• Excitation at the Larmor frequency excites some
  spins into anti-parallel state, visualized as M
  entering the transverse plane
• Relaxation is the process of spins returning to
  parallel state, visualized as M realigning with
  the main magnetic field
• Signal is measured during this phase, and has two
  components longitudinal and transverse
• Signal is measured by mutual inductance, in which
  changes in magnetic field produce changes in
  electrical current in a coil (often called a
  radiofrequency coil.

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How to make a 3 D image?

• Challenge, how to read out spins from a point in
  3d space rapidly without getting interference
  from protons in the rest of the space?
• Selection of protons to resonate with
• Reading out data at different frequencies and
  phases to acquire a plane at a time.

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Though questions

• What molecules are tagged in
• Uniform magnetic space (Bo only)
• Plainer field
• Gradient field

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Some basic notations

• Three types of magnetic field in fMRI
• B0 Main magnetic field
• Aligns axes of precession of nuclei
• Sets up net magnetization (M)
• B1 Radiofrequency (RF) excitation at the Larmor
• frequency of a nucleus
• Gx Gy Gz Gradient magnetic fields used for
  localizing signal

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Induction signals in coils near a precessing
magnetic field (dipole)
M
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RF Excitation- Resonance
RF pulse applied at a 90 degree angle to z-axis
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Gradient magnetic fields
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MR Signal Equation (for background only)
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MR Signal Equation
The total MR signal measured at any point in
time reflects the sum across all voxels of the
net magnetization at time point zero, multiplied
by a decay factor based upon T2, with accumulated
phase given by the strength of the static
magnetic field and of the gradient field at that
point in space. p. 82
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Signal equation terms dropped in practice
2nd e term is not used in modern scanners
X
T2 term doesnt inform spatial location, so it
can be dropped
X
X
MR data collected by slice, so z terms can be
dropped
X
X
X
X
X
X
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Simplified MR signal equation
The total signal recorded from a slice depends
upon the net magnetization at every (x, y)
location within that slice, with the phase of
individual voxels dependent upon the strength of
the gradient fields at that location. p. 83
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Recording MR Signal involves k-space

• Signal at each point is transformed by Fourier
  analysis and coded spatially.
• Fourier analysis is breaking a waveform down
  into composite or fundamental frequency
  components (sine and cosine terms) multiplied by
  a magnitude coefficient

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Recording MR Signal involves k-space

• Signal at each point is transformed by Fourier
  analysis and coded spatially.
• Fourier analysis is breaking a waveform down
  into composite or fundamental frequency
  components (sine and cosine terms) multiplied by
  a magnitude coefficient

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Recording MR Signal involves k-space

• Signal at each point is transformed by Fourier
  analysis and coded spatially.
• Fourier analysis is breaking a waveform down
  into composite or fundamental frequency
  components (sine and cosine terms) multiplied by
  a magnitude coefficient

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Some more examples of Fourier transform
1-dimensional waveform and frequency components



2-dimensional waveform and frequency components



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k-space representation, frequency space
B1
B2
B3
B1,2,3



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Remember that spin is dependent upon magnetic
field strength

• Nuclear spin frequency depends on two factors
• gyromagnetic ratio (?)- ratio between charge and
  mass, constant for a given nucleus
• magnetic field strength (B0 B1 Gx Gy Gz)

Larmor (resonant) Frequency
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Images and Fourier transforms
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Images and Fourier transforms
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Images and Fourier transforms
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k-space organized by frequency of image
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k-space organized by frequency of image
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k-space organized by frequency of image
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k-space organized by frequency of image
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Frequency Encoding
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Phase Encoding
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Flip angle, T1, TE, TR
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2-D Gradient-echo pulse sequence
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2-D Gradient-echo pulse sequence
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2-D Gradient-echo pulse sequence




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2-D Gradient-echo pulse sequence
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As field strength increases, so does noise
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As field strength increases, contribution from
small vessels increases, ? spatial resolution
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