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Neuroimaging in Mental Health > Week 2 > Flashcards

Week 2 Flashcards

1
Q

What are the main four equipment pieces inside the MRI scanner?

A
  1. Receiver/Head coil - picks up a signal originating in the brain.
  2. Transmitter coil - produce a signal.
  3. Gradient coils - small electromagnets that can alter the magnetic field strength in a number of directions. These are essential to localise signal, that is to know where the signal we are detecting originated.
  4. Main magnetic field.
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2
Q

What is the typical field strength of MRI?

A

from 1.5 to 3 Teslas, the higher field strength the better performance (better signal-to-noise ratio).

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3
Q

What is the wavelength?

A

Distance between peaks of the wave.

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4
Q

What is the frequency?

A

How many cycles there are per second.

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5
Q

How radiofrequency is involved in MRI process?

A

MRI deals with the interaction between certain atomic nuclei, strong magnetic fields and radio frequency energy.

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6
Q

What is a pixel?

A

A single point on a computer screen.

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7
Q

What is a voxel?

A

A three-dimensional pixel.

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8
Q

What does the right hand rule state?

A

If you curl your fingers of your right hand in the direction of the current flow, your thumb will indicate the direction of the magnetic field.

Magnetic field direction is perpendicular to electron flow.

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9
Q

Describe hydrogen atom, what it consists of?

A

Proton in the nucleus and single electron.

Proton rotates on its axis because it is positively charged. By using a right hand rule we can determine the magnetic field.

In effect we have a small bar magnet.

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10
Q

How protons are oriented in normal conditions?

A

Randomly and effectively cancel each other out, so we are generally not magnetic.

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11
Q

What happens with protons if we put them in strong magnet?

A

Most of the protons tend to line up with the main magnetic field in a low energy state. Some of the protons oppose the main magnetic field and aligns against the main magnetic field in high energy state.

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12
Q

Why protons are compared to gyroscope?

A

Because they behave like gyroscope. The axis they are spinning around moves and traces out a circle.

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13
Q

What is a precession?

A

The angle of spin.

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14
Q

What is the relationship between the rate of precession and strength of magnetic field? How it can be described?

A

The rate of precession is proportional to the strength of the magnetic field. Its relationship can be described by Larmour equation (describes the frequency of precession).

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15
Q

What is the longitudinal magnetization?

A

Longitudinal magnetization is the component of the net magnetization vector parallel to the magnetic field.

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16
Q

What will happen if we transmit radio frequency pulse at exactly the same magnetic field frequency?

A

Two things will happen:

  1. Protons will absorb the energy and
  2. Flip some of the protons into the high energy state
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17
Q

How sinusoidal radiofrequency pushes protons to behave?

A

They spin in synchrony - that is the resonance component of MRI.

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18
Q

What is meant by transverse magnetisation?

A

When a net magnetic force aligned horizontally or perpendicular to the longitudinal magnetisation.

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19
Q

What happens when we stop radiofrequency pulse?

A

The spinning of protons de-phase. The net transverse magnetisation reduces to 0. This process is referred as T2 (relaxation or spin-spin relaxation).

20
Q

What is T1 relaxation or spin-lattice relaxation?

A

When the high energy protons relax back in to a low energy state and heat is dissipated. This is when we regrow longitudinal magnetisiation.

21
Q

Why different tissues in the brain can be pictured?

A

Because different tissues (grey, white matter, CSF) have differences in their T1 and T2 relaxation times.

22
Q

What are the two parameters that we can manipulate in the scanner to maximize our signal of interest?

A
  1. Repetition time (TR). By changing how quickly we stimulate the tissue (radiofrequency pulses).
  2. Echo time (TE). By changing how quickly we listen for the signal (from the precessing protons).
23
Q

Why dephasing of protons (T2 relaxation) in fat occurs earlier?

A

Because its rigid structure.

24
Q

What are the basic building blocks of all 2D flat images?

A

Pixels (picture element)

25
Q

What is intensity value?

A

Grey level

26
Q

What are the main three terms mentioned in the methods section of neuroimaging papers?

A
  1. Matrix size
  2. Pixel size
  3. Field of view (FOV)
27
Q

Describe the matrix size

A

It is the size of the pixel grid, which is its number of rows and columns (width and height) 64x64 voxels is the standard size for fMRI data.

28
Q

Describe the pixel size

A

This is dimensions of the pixel themselves (width and height). For example 3,75 mm square.

29
Q

Describe Field of View (FOV)

A

It represents the size of the grid. usually in centimeters

30
Q

What is voxel?

A

Basic element of 3D images (volume element).

31
Q

What are the two main conventions of storing the data?

A
  1. XYZT

2. XYTZ

32
Q

What is time series?

A

If we extract and plot exactly the intensity values for a specific set of coordinated we obtain what’s called time series.

33
Q

What does the spatial resolution provide?

A

It represent the amount of details in the images. The higher the spatial resolution - more details there are.

34
Q

What does the temporal resolution provide?

A

It represents the speed of data acquisition which means how close apart two measurements are.

35
Q

What do the voxel intensities represent?

A

Depends on the type of imaging you do. If you:

  • use qualitative measure like fMRI, the voxel intensity values are arbitrary, and the number measures do not actually mean anything. So we are looking at the differences in intensity between different tasks. Numbers depend on the equipment, acquisition parameters.
  • Quantitative imaging such as T1 and T2 mapping. In this case voxel intensity values represent real physical quantities such as the tissue T1 and T2.
36
Q

What are the two levels of analysis in neuroimaging data?

A
  1. First level - subject level analysis, which means you only analyze the data at the subject level.
  2. Second level analysis - group level analysis. When you want to check for example if the mean response of a group is different from zero or if different groups are different.
37
Q

What is so called the third level analysis?

A

Beyond the blop (results) map. For example looking at the differences at in connectivity between different brain regions.

38
Q

What additional step is needed before statistically analyzing the data?

A

Pre-processing or cleaning the data.

39
Q

What are the major steps in data analysis?

A
  1. Pre-processing
  2. Analysis scope
  3. Statistical tests
  4. The multiple comparison problem
  5. Data modeling
40
Q

What are two main aims when pre-processing data?

A
  • increase the signal to noise ratio (SNR)

- clean up data

41
Q

What type of effects are detrimental to remove when data is pre-processed?

A
  1. Head motion
  2. Background noise
  3. Physiological noise (heartbeat etc)
42
Q

Why do we need a standard reference template?

A

To be able to compare or group brain images. Anatomy is different for different people (brain viability).

43
Q

Why neuroimaging is not exact science?

A

Because pre-processing stage of analysis can make a great variance in the results. As showed by prof. D. Jones, who sent the same data to 20groups world-wide to analyse it. He received different results because everyone followed in house manuals, that were best suited for different type of data.

44
Q

What are the two types of scope in region analysis?

A
  1. Whole brain analysis (exploratory analysis, unbiased, lots of voxels).
  2. Region of interest analysis (more powerful statistically, less voxels, less multiple comparison corrections). Hypothesis is clear in advance.
45
Q

What is circularity double dipping?

A

In particular, ‘double dipping’, the use of the same dataset for selection and selective analysis, will give distorted descriptive statistics and invalid statistical inference whenever the results statistics are not inherently independent of the selection criteria under the null hypothesis.

46
Q

What is imagers fallacy?

A

Saying that two results are the same or different by just looking at them side by side.

47
Q

Why Bonferroni correction is not suited for neuroimaging?

A

Corrected p value is too small and not within the level of significance.

Neuroimaging in Mental Health (8 decks)

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