PRECLINICAL AND CLINICAL
IMAGING
,MRI
WHAT MRI CAN MEASURE (WHAT ¹H-MRI TELLS US)
MRI uses hydrogen nuclei (protons) and their interactions with their environment to create
contrast.
MRI can provide:
• Proton density (amount of hydrogen → water/fat content)
• Relaxation times:
o T₁, T₂, T₂* depend on molecular environment
• Diffusion (free motion of water)
• Perfusion (blood flow)
• Blood volume
• Angiography (blood vessels, with/without contrast)
• Functional activation (fMRI: changes in blood oxygenation → brain activity)
• Molecular info (e.g., tracking labeled stem cells)
WHY MRI WORKS WELL FOR THE BRAIN
MRI is excellent for soft tissue contrast (head, neck, spinal cord).
Other nuclei (¹³C, ³¹P) can be used in special cases but ¹H is most common.
MRI HARDWARE: OVERVIEW
MRI involves:
1. Big static magnetic field (B₀)
o Typical strengths:
▪ Vet: 0.2–0.5 T
▪ Humans: 1.5–3 T
▪ Small animals: up to 11.5 T
o Superconducting magnet → coils cooled with liquid helium (≈4 K)
2. RF transmit coil
o Sends radio waves into the body
3. Receiver coil
o Detects radio waves emitted back from the body
4. Gradient coils
o Add small, position-dependent magnetic field changes
o Used for spatial encoding (to form images)
WHICH ATOMIC NUCLEI CAN BE USED FOR MRI?
A nucleus must have:
• Spin
• Charge
Nuclei with even numbers of protons and neutrons cancel out → no net spin.
So only atoms with an odd number of protons OR neutrons are MRI-visible.
Examples:
Element Spin Abundance
¹H (hydrogen) 1/2 0.63 → perfect for MRI
¹³C 1/2 rare
1
,ALL THE BACKGROUND INFORMATION OF HOW THE MRI SIGNAL IS CREATED
1. PROTONS ACT LIKE TINY MAGNETS
Each proton has:
• Spin (it rotates)
• Magnetic moment μ (like a tiny bar magnet)
This creates a magnetic field.
2. IN AN EXTERNAL MAGNETIC FIELD B₀
When protons are placed in the MRI magnet:
1. They can only align parallel (low energy) or
anti-parallel (high energy) to B₀
2. Slightly more spins choose the low-energy
state → tiny imbalance
3. This creates a net magnetization vector (M) along the z-axis
The imbalance is very small:
Only 7 extra spin-up protons per 1 million produce the measurable signal
3. PRECESSION: SPINS ROTATE AROUND B₀
Protons don’t sit still →they precess (wobble) around B₀ like spinning tops
• This motion is caused by torque from B₀
• The rotation frequency is the Larmor frequency
𝜔0 = 𝛾𝐵0
Meaning:
Stronger magnets → faster precession
4. CREATING AN MR SIGNAL
In equilibrium:
• Magnetization M is aligned with B₀ (along z)
• No transverse component (Mxy = 0)
• → No signal
To get a measurable signal:
We must tip M away from the z-axis using an RF pulse at the Larmor frequency.
This creates:
• A transverse component Mxy
• Mxy rotates → generates a changing magnetic field
• Receiver coil detects this → MR signal
5. ENERGY LEVELS & RF EXCITATION
Because spins have two energy states:
• Spin up = low energy
• Spin down = high energy
The energy difference ΔU is very small.
2
, To flip a spin, you must apply an RF pulse with exactly this energy → meaning the RF frequency
must match the Larmor frequency.
RF pulse = Larmor frequency
The spin absorbs energy → flips → creates transverse magnetization
Net Magnetization M
• Each proton has a magnetic moment μ
• Add up all μ in a voxel → net magnetization M
Without B₀ → protons randomly oriented → M = 0
With B₀ → slight excess of low-energy spins → M ≠ 0
M grows with:
1. Proton density
2. Magnetic field strength B₀
EQUILIBRIUM VS NON -EQUILIBRIUM
Equilibrium
• M aligned with B₀
• Mxy = 0
• No signal
Non-Equilibrium
RF pulse tips M into x–y plane:
• Mxy ≠ 0
• M precesses
• Signal is visible
ROTATING FRAME OF REFERENCE
The magnetization precesses extremely fast → hard to visualize.
Solution:
Switch to a coordinate system rotating at the same frequency (the “rotating frame”).
In the rotating frame:
• M appears nearly stationary
• This makes it easy to understand how RF pulses manipulate magnetization
HOW TO PERTURB M?
Magnetization M normally points along B₀ (z-axis).
To create MR signal, we must tilt M away from the z-axis.
How?
• Apply a small oscillating magnetic field B₁ in the x–y plane
• At the Larmor frequency (= natural precession frequency)
= the spins absorb energy and move
What is B₁?
When the scanner sends out an RF pulse, the RF coil generates a tiny, oscillating magnetic field.
That oscillating magnetic field is called B₁.
• It exists only during the RF pulse
• It is much smaller than B₀ (microtesla vs tesla)
• It oscillates at the Larmor frequency
3
• It is oriented perpendicular to B₀ (in the x–y plane)
= B1 tips the magnetization M away from the z-axis
IMAGING
,MRI
WHAT MRI CAN MEASURE (WHAT ¹H-MRI TELLS US)
MRI uses hydrogen nuclei (protons) and their interactions with their environment to create
contrast.
MRI can provide:
• Proton density (amount of hydrogen → water/fat content)
• Relaxation times:
o T₁, T₂, T₂* depend on molecular environment
• Diffusion (free motion of water)
• Perfusion (blood flow)
• Blood volume
• Angiography (blood vessels, with/without contrast)
• Functional activation (fMRI: changes in blood oxygenation → brain activity)
• Molecular info (e.g., tracking labeled stem cells)
WHY MRI WORKS WELL FOR THE BRAIN
MRI is excellent for soft tissue contrast (head, neck, spinal cord).
Other nuclei (¹³C, ³¹P) can be used in special cases but ¹H is most common.
MRI HARDWARE: OVERVIEW
MRI involves:
1. Big static magnetic field (B₀)
o Typical strengths:
▪ Vet: 0.2–0.5 T
▪ Humans: 1.5–3 T
▪ Small animals: up to 11.5 T
o Superconducting magnet → coils cooled with liquid helium (≈4 K)
2. RF transmit coil
o Sends radio waves into the body
3. Receiver coil
o Detects radio waves emitted back from the body
4. Gradient coils
o Add small, position-dependent magnetic field changes
o Used for spatial encoding (to form images)
WHICH ATOMIC NUCLEI CAN BE USED FOR MRI?
A nucleus must have:
• Spin
• Charge
Nuclei with even numbers of protons and neutrons cancel out → no net spin.
So only atoms with an odd number of protons OR neutrons are MRI-visible.
Examples:
Element Spin Abundance
¹H (hydrogen) 1/2 0.63 → perfect for MRI
¹³C 1/2 rare
1
,ALL THE BACKGROUND INFORMATION OF HOW THE MRI SIGNAL IS CREATED
1. PROTONS ACT LIKE TINY MAGNETS
Each proton has:
• Spin (it rotates)
• Magnetic moment μ (like a tiny bar magnet)
This creates a magnetic field.
2. IN AN EXTERNAL MAGNETIC FIELD B₀
When protons are placed in the MRI magnet:
1. They can only align parallel (low energy) or
anti-parallel (high energy) to B₀
2. Slightly more spins choose the low-energy
state → tiny imbalance
3. This creates a net magnetization vector (M) along the z-axis
The imbalance is very small:
Only 7 extra spin-up protons per 1 million produce the measurable signal
3. PRECESSION: SPINS ROTATE AROUND B₀
Protons don’t sit still →they precess (wobble) around B₀ like spinning tops
• This motion is caused by torque from B₀
• The rotation frequency is the Larmor frequency
𝜔0 = 𝛾𝐵0
Meaning:
Stronger magnets → faster precession
4. CREATING AN MR SIGNAL
In equilibrium:
• Magnetization M is aligned with B₀ (along z)
• No transverse component (Mxy = 0)
• → No signal
To get a measurable signal:
We must tip M away from the z-axis using an RF pulse at the Larmor frequency.
This creates:
• A transverse component Mxy
• Mxy rotates → generates a changing magnetic field
• Receiver coil detects this → MR signal
5. ENERGY LEVELS & RF EXCITATION
Because spins have two energy states:
• Spin up = low energy
• Spin down = high energy
The energy difference ΔU is very small.
2
, To flip a spin, you must apply an RF pulse with exactly this energy → meaning the RF frequency
must match the Larmor frequency.
RF pulse = Larmor frequency
The spin absorbs energy → flips → creates transverse magnetization
Net Magnetization M
• Each proton has a magnetic moment μ
• Add up all μ in a voxel → net magnetization M
Without B₀ → protons randomly oriented → M = 0
With B₀ → slight excess of low-energy spins → M ≠ 0
M grows with:
1. Proton density
2. Magnetic field strength B₀
EQUILIBRIUM VS NON -EQUILIBRIUM
Equilibrium
• M aligned with B₀
• Mxy = 0
• No signal
Non-Equilibrium
RF pulse tips M into x–y plane:
• Mxy ≠ 0
• M precesses
• Signal is visible
ROTATING FRAME OF REFERENCE
The magnetization precesses extremely fast → hard to visualize.
Solution:
Switch to a coordinate system rotating at the same frequency (the “rotating frame”).
In the rotating frame:
• M appears nearly stationary
• This makes it easy to understand how RF pulses manipulate magnetization
HOW TO PERTURB M?
Magnetization M normally points along B₀ (z-axis).
To create MR signal, we must tilt M away from the z-axis.
How?
• Apply a small oscillating magnetic field B₁ in the x–y plane
• At the Larmor frequency (= natural precession frequency)
= the spins absorb energy and move
What is B₁?
When the scanner sends out an RF pulse, the RF coil generates a tiny, oscillating magnetic field.
That oscillating magnetic field is called B₁.
• It exists only during the RF pulse
• It is much smaller than B₀ (microtesla vs tesla)
• It oscillates at the Larmor frequency
3
• It is oriented perpendicular to B₀ (in the x–y plane)
= B1 tips the magnetization M away from the z-axis
