MRI and fMRI

Question 1

Characteristics of the scanner

Answer 1

Relies on electromagnetic field, radio waves and hydrogen in the body
Contain Gradient and radio frequency coils
Contains superconducting magnets
Magnetic field is measured in Tesla - 1.5T, 3T, 4T, 7T
Does not have radiation (like PET)

Question 2

What is the frequency at which protons spin?

Answer 2

Larmor frequency

Question 3

What do gradient coils do?

Answer 3

3 gradient coils generate secondary magnetic field.
Allows the manipulation of the magnetic field and to aquier data in x (left-right); y(anterior-posterior) and z(superior-inferior) directions

Question 4

What do radio frequency coils do?

Answer 4

Used for specific part of the body to get the best SNR;
they disturb the proton alignment by making them to jump up and down; when they relax they give off radio waves measured by the MRI signal

Question 5

Structural Imagining

Answer 5

Creates a static image and gives information about tissue structure, volume, gray-white matter differences, damage, tumours, etc

Question 6

Types of contrast

Answer 6

T1 weighted - 3D volume scans, BBB contrast for leakage, used in anatomical scanning (structural scans)
T2 weighted - lesions and strokes, microtubules. and white matter micro-structures (fMRI)
Proton density (PD) - to calculate quantative T1 and T2
Fluid attenuation by inversion recovery (FLAIR)- stroke, lesions, white matter hypertensities
MPRAGE

Question 7

Regions of Interest (ROI)

Answer 7

Depends on the research question
Allows investigation of local region, but may be affected by selection bias, size and shape of the ROI
planimetry (drawing around something)
stereological technique - sampling a part of a region
MRI is a series of 2D images building a 3D image and therefore may be affected by the slice thickness

Question 8

Protocol for ROI

Answer 8

what size
what shape
criteria for placing it 
how many slices
choose a plane (dorsal, corononal, etc)
inter-rater reliability

Question 9

Types of Atlases

Answer 9

Talarach (1988)

Montreal Neurological Institute (MNI)

Question 10

What are some issues associated with Atlas use?

Answer 10

Using different atlases (and softwares) may give different results. Therefore, need to be careful when comparing data across studies.

Question 11

Talarach Atlas

Answer 11

coordinate system for the human brain based on post-mortem sections of one 60 year old woman.
Smaller than average brain, oddly shaped and can lead to error and distortion after rewrapping
corresponds to Broadmann areas
doesn’t map well of MNI

Question 12

Montreal Neurological Institute (MNI) Atlas

Answer 12

Based on large sample of normal, young subjects of 305 people.
standard atlas used may be slightly larger than the average brain

Question 13

What is a Pipeline?

Answer 13

The series of steps that describe what is a research doing to the data and include everything that is done to the data

Question 14

What are some limitations of MRI

Answer 14

Can answer only certain questions
A lot of poor work done by people who do not understand the method (put garbage in, get garbage out)
cannot make changes to the scanner/software partway through the study
almost everything done to the data introduces error
smoothing increases the chance of finding positive result (type 1 error)
needs a correction for multiple comparisons
expensive as it needs helium

Question 15

Benefits of MRI

Answer 15

Great spatial resolution, anatomical information and tissue contrast
Information about blood flow, functional region and white matter microstructures

Question 16

What is Automatic Segmentation?

Answer 16

Quick and easy, requires relatively less experience BUT:
different results across different software
less accurate than well trained individual
each stage needs to be checked for errors
still requires knowledge of software and pipelines

Question 17

What is fMRI?

Answer 17

Creates dynamic images and measures the changes in local oxygenation of blood, which reflects the amount of local brain activity

Question 18

Blood oxygenation level dependant contrast (BOLD)

Answer 18

Not an absolute measure as it measures difference between two brain states (e.g. oxygenated vs deoxygenated blood);
statistical methods are used to determine the areas that are reliably different in action vs baseline (no action)

Question 19

Why does fMRI has poor temporal resolution

Answer 19

It mesures the hemodynamic response (initial dip - decrease in oxygen in the blood; overshot - compensation for oxygen demand; undershot- back to baseline) and it takes 6sec for the signal to peak, while neural processing happens in the ms range

Question 20

What are the components of fMRI analysis?

Answer 20

Check raw images - orientation etc
distortion correction
motion correction
slice timing correction
spatial normalisation
spatial smoothing
temporal noise filtering
statistical modeling
statistical interference
visualisation

Question 21

fMRI design

Answer 21

Requires comparison between conditions as BOLD is not an absolute measure of neural activity:
Substraction paradigm - task - baseline; 2 subtypes
event related desisgn
block design

Question 22

Problems with substraction based designs?

Answer 22

Assumes that adding a component to a task does not affect already existing processes (e.g. pure deletion);
however no such thing as neutral state, brain is active at rest..

Question 23

Block design

Answer 23

alternating conditions A and B ot A, control B in the same order
certain number of slices is possible per brain image
Blocks are repeated during the experiment
Having a slice several times and combining them increases SNR
higher BOLD contrast

Question 24

fMRI limitations

Answer 24

A lot of poorly planned experiments
poorly defined hypothesis
poorly defined hypothesis relating to brain structures
attenuation and fatigue (Especially block designs)
scanner drift
learning effects and habituation
Dangers with blob spotting
poor temporal resolution
limitations with interpretations of the data
limits to choices of subjects - safety criteria, weight, height, tolerance levels, etc