HC 4

Question 1

What is the base principle of MRI and fMRI?

Answer 1

Magnets produce magnetic fields. It is based on attraction and repulsion. The most relevant element for brain imaging is hydrogen (H).

Question 2

What is the effect of the MRI machine on the human body?

Answer 2

The effect is not obvious. It has influence on the nuclei. That is why it is also called nuclear magnetic resonance imaging (NMR). That is not the same as radioactivity. It may cause nausea, but it causes no consequent short- or long-term illness.

Question 3

Why do we want to use hydrogen for imaging?

Answer 3

The body is made out of 65% of water. Water molecules contain hydrogen atoms. Every hydrogen atom is a magnet in itself. Hydrogen atoms only contain one single protein. Atoms with uneven, so only one proton, act as dipoles. This means that spinning does not cancel each other out.

Question 4

What is nuclear magnetic resonance imaging?

Answer 4

Part of the nuclei align with the direction of the magnetic field. This happens in MRI and fMRI.

Question 5

What is the Larmor frequency?

Answer 5

Nuclei with odd number of protons/neutrons precess at this. It is the movement that the rotating axis of a rotating object makes under the influence of an external force, in this case the magnetic field strength of the magnet.

If additional magnetic field oscillates with the Larmor frequency, then the nuclei absorbs energy from the field.

Question 6

How do the protons spin when under the MRI machine?

Answer 6

1. No magnetic field
2. Static magnetic field: atoms align with direction of the magnetic field (z-dimension)
3. Oscillating magnetic field: radio frequency (RF) pulse is applied. Now the individual atoms spin the get in phase. Atoms flip and take direction of the oscillating field. There is an increase in energy state (X, Y- dimension).
4. When the RF-pulse is no longer applied, the dephasing of atoms starts. It starts realigning to static magnetic field (flip back to z-dimension. At the same time, energy gets released and picked up. These are small signals in radio frequency range.
5. Small signals over all the re-aligning nuclei integrate. The less dephasing happened, the stronger this signal is.

Question 7

How do we know where a signal comes from in MRI?

Answer 7

Larmor frequency depends on field strength.

If magnetic field strength differs across space, then:
-nuclei in different locations have different Larmor frequency
-RF pulse only affects the nuclei with matching Larmor frequency (thus on specific locations)

So, in different layers/ slices, there are different Larmor frequencies. To reconstruct where the signal comes from, we need other gradients to know the dimensions.

Question 8

How do we reconstruct an image?

Answer 8

There are three orthogonal gradients of field strength on top of the static magnetic field:

-Slice selection gradient: applied at the same time of the RF-pulse (Z). This determines whether the signal comes from the top or bottom.

-Phase encoding gradient: use of dephasing after the RF-pulse (Y). The magnetic field increases and protons spin faster.

-Frequency encoding gradient: applied at the time of read out signal (x). When the RF-pulse is removed, we add the frequency gradient, this changes the frequency, so we can determine left or right?

Question 9

What is the slice selection gradient?

Answer 9

It is applied during the RF-pulse. RF-pulse only affects nuclei that experience a total field strength with matching Larmor frequency.

One slice per RF-pulse if it is a 2D-image. If you want a full 3d-image, then it requires as many RF-pulses as number of slices needed.

Interleaved slice acquistition is used to minimize cumulative effects due to cross-slice excitation.

Question 10

What is a slice?

Answer 10

Volume of excited nuclei.

Question 11

What is the phase encoding gradient?

Answer 11

It is applied after the RF-pulse. The change spin resonance frequency of excited nuclei depends on their location in the gradient, causing dephasing.

When the RF-pulse is removed, resonance frequencies are the same again, but differences in phase persist.

All nuclei at a certain position the gradient have the same phase, thus phase is informative about position.

Question 12

What is frequency encoding gradient?

Answer 12

This is applied during data acquisition. This is the read-out direction.

All nuclei at a certain position in the gradient have the same resonance frequeny, thus frequency read-out is informative about position.

Question 13

What is a pulse sequence?

Answer 13

The succession of RF pulses and gradient changes.

Question 14

What is a voxel?

Answer 14

The smallest unit of space that are shown as pixels on a screen.

The shorter the time in which an image has to be taken, the lower the number of slices that can be imaged.

The number of voxels per row/column in the slice relates back to the number of steps of phase/frequency encoding gradient.

Question 15

How do physical principles give rise to an image with anatomical structure?

Answer 15

The emitted signal decays over time. Signal intensity depends upon several factors: density of H1 protons, T1-recovery and T2-decay.

Factors are different in different tissues, resulting in signal contrast.

Pulse sequence and parameter choice determine which factor has most weight=> T1-weighted .v.s. T2-weighted imaging

Question 16

What is T1-recovery?

Answer 16

Recovery of longitudinal orientation= spin-lattice relaxation.

Time it takes the longitudinal magnetization to grow back to 63% of its final value.

Time to recover depends on the tissue type.

White matter appears as white, because the signal is strong, the protons spin back faster.

Grey matter is dark, because the signal is weaker, the protons spin back slower.

Question 17

What is T2-decay?

Answer 17

Loss of transverse magnetization due to the loss in phase coherence= spin-spin interactions.

Time it takes the transverse magnetization to decrease to 37% of its starting value= spin-spin relaxation time.

Immediately after aplication of the RF pulse, transverse magnetization is maximized. It then begins to dephase due to natural interactions at atomic or molecular levels. The signals from these dephasing protons begin to cancel out => MR signal decreases.

Signal strength is highest for slowest dephase.

White matter appears as grey, because the signal is weaker, because dephasing is faster.

Grey matter appears as white, because the signal is stronger
, because dephasing is slower.

Question 18

Describe the hardware of a scanner.

Answer 18

-Magnet (static magnetic field)
-Gradient coils (varyin magnetic field)
-Radio frequency coil (RF pulse)

Magnet and gradient coild create varying magnetic fields. Radio frequency coil transmits and measures radio frequency waves.

Question 19

How does the magnet work in a MRI?

Answer 19

Electrons flow along a wire.

Faraday’s principle: electric current in a loop wire generates transient magnetic field perpendicular to the loop of wire.

Question 20

What are some structural imaging methods?

Answer 20

Under structural T1-weighted imaging we have voxel-based-morphometry (VBM).

Under structural connectivity we have diffusion weighted imaging (DWI) and tractography.

And magnetic resonance spectroscopy.

Question 21

When do we use CT and when MRI?

Answer 21

CT-scan is mainly used in a clinical context.

There is difference in contrast. MRI is more detailed than a CT.

We use CT when people cannot go into a MRI machine and it is also quicker and cheaper.

Question 22

How is quality check done before structural imaging?

Answer 22

-Image artefacts
-Finding anatomical abnormalities
-Routine pulse sequences

Question 23

What is voxel based morphometry (VBM)?

Answer 23

Morphometry is to quantify specific properties of the brain anatomy.

We compare regional volumes of tissue and produce a map of statisitically significant differences.

Question 24

What are some problems with VBM?

Answer 24

There is the problem of normalization. The solution is to put it on a template, change size or orientation.

Question 25

What is diffusion weighted imaging (DWI)?

Answer 25

It is a non-invasive method in which water molecules are uses to generate a contrast in MR-images.

There is a pattern in action potentials. The paths that can be seen are axons. They are called white-matter pathways or tracts: axons that start and end in each other’s vicinity, stay together.

Question 26

How does diffusion weighted imaging work?

Answer 26

Pulse sequence is adapted to be sensitive for diffusion of molecules. Molecules move from parts with higher to parts with lower concentration.

Cell walls and myelin impede such motion.

Observing characteristics of self-diffusion in particular part of brain provides insight into underlying tissue microstructure.

Question 27

What is isotropic diffusion?

Answer 27

Diffusion in the same direction.

Question 28

What is anisotropic diffusion?

Answer 28

Different diffusion coefficients along different directions,

Question 29

What is tensor in DTI?

Answer 29

Diffusion is described by tensor, which is the mathematical construct used to characterize the diffusion of water molecules in biological tissues.

Question 30

What are the DTI indices?

Answer 30

Mean diffusion (MD)= overall amount of diffusion

Fractional anistropy (FA)= From zero (isotropic diffusion) to 1 (only diffusion along main axis)

Axial and radial diffusivity (AD and RD)= amount of diffusion in certain direction: main axis (AD) or other directions (RD)

Question 31

What is tractography?

Answer 31

Trace a line following main diffusion direction.

Question 32

What is the relevance of doing DWI for behavior?

Answer 32

It is for testing disconnection hypotheses: changes in connectivity or access between mental processes and the underlying brain regions.

Question 33

What is the effect of intended vs unintended variations in frequency (MRS)?

Answer 33

A signal generated by an atom is affected by its local chemical environment.

Each molecule has different resonant frequency=”chemical shift”.

We use the variation in frequency to measure chemical composition of brain tissue.

Question 34

What is the MR spectrum?

Answer 34

Reflects particle resonance of metabolites that are associated with specific neurotransmitters or other substances in the brain tissue.