Data Analysis - MRI/fMRI/DTI

Question 1

What are examples of structural data quality?

Answer 1

1. DTI - spin echo EPI
   - distortions (cm)
   - ghosting
   - resolution ~mm
2. Structural MRI
   - distortions (mm or less) in readout direction
   - resolution 1mm (isotropic)
3. CT
   - little distortion
   - faster to acquire than structural MRI
   - poor brain tissue visibility
   - radiation dose

Question 2

What needs to be considered, especially in clinical decision making?

Answer 2

When combining data from different modalities - limitations

Question 3

Why is putting data together from different modalities potentially very powerful?

Answer 3

It allows the understanding of structural and functional data as a whole

Question 4

What does encoded FA map in DTI give?

Answer 4

The direction of white matter orientations

Question 5

What regions does DTI suffer from distortion?

Answer 5

1. Frontal region

2. Temporal regions

Question 6

Structural MRI

Answer 6

Much higher resolution - see details in the stratium and detail in the cortex and white matter

Good for localising different parts of the cortex

Question 7

What are examples of functional data quality?

Answer 7

1. fMRI - gradient echo EPI
   - distortions (cm)
   - dropout
   - resolution ~mm
   - temporal resolution (seconds, HRF + MR limits)
2. ESI -EEG source localisation
   - resolution (cm ‘inverse problem’)
   - resolution/ visibility location dependant
   - high temporal resolution (ms)
   - attenuation didn’t to head structure
3. MEG
   - resolution poor (cm ‘inverse problem’)
   - resolution/ visibility location dependent
   - high temporal resolution (ms)
   - orientation dependent

Question 8

What is gradient echo EPI data quality: dropouts?

Answer 8

1. Tissue in B0 - magnetisation grows along z
2. RF pulse > magnetisation in x/y plane
3. Magnetisation rotates w=yB0

Question 9

What is the gradient echo EPI data quality: dropouts?

Answer 9

Looking just after the application of the RF pulse that flips onto the x/y plane

Looking at different bunch of spins but have the same magnetic field - there is no Variation in the magnetic field

The spins for now we will assume they are not interacting with each other and is purely independently

Over time, they are processing at the same frequency - strong signal which will not decay

There will be a slow signal decay along T2*

Question 10

What do distortions affect?

Answer 10

Both gradient and spin eco - this acquires k-space

Alteration in k-space leads to local distortion
You can acquire field map in a separate image - that will help undo some of the distortions

Question 11

Where does the drop out occur?

Answer 11

Between RF pulse and acquisition

That is in the gradient echo

Question 12

Where does distortion occur?

Answer 12

During acquisition itself and that is true for both spin echo and gradient echo even though the gradient echo has the worst distortion

Question 13

What can be used for distortion correction?

Answer 13

In Anterior-posterior (AP) there is compression whereas on the other side it is stretching it out

Question 14

What are the two options for distortion correction, both of which require acquisition of additional Images?

Answer 14

1. Field maps

2. Images acquired with negated phase encode direction

Question 15

What is distortion correction?

Answer 15

It may not be possible to fully-correct regions where signal had been compressed into a small area

If possible, it is preferable to minimise distortion when setting up the acquisition protocol
- limit echo spacing to reduce Accrual of phase

Question 16

What is used in invasive monitoring of epilepsy patients?

Answer 16

Depth electrode

The images were acquired on a phantom containing an electrode sometimes implanted in the brain of epilepsy patients for seizure localisation

Question 17

Why is gradient-echo EPI susceptible to drop out ?

Answer 17

Due to local inhomogeneities in the magnetic field

Question 18

What suffers from distortions caused by accumulation of phase during read-out?

Answer 18

Both gradient-echo EPU and spin-echo EPI

Question 19

What can both gradient-echo EPI and spin-echo EPI suffer from?

Answer 19

1. Local distortion due to air-tissue boundaries (e.g. in frontal and temporal areas), inconsistencies in main magnetic field, foreign objects (e.g. dental work)
2. Can minimise effect by minimising echo spacing (reducing time available for phase accumulation) during acquisition
3. Can correct using a field map or second image with reverse encoding ( but cannot completely recover image where signal is compressed into a small region)

Question 20

What are the practical considerations for functional MRI?

Answer 20

1. Tasks
   - task too easy/difficult?
   - task type
   - is the participant doing what you want them to?
2. Accessing task performance
   - feedback
   - measure responses
   - video
   - eye tracking

Question 21

What do we not measure directly in fMRI?

Answer 21

Brain activity

We measure changes in blood oxygenation

Question 22

What are two considerations of functional MRI?

Answer 22

1. Cardiac noise
   - heart rate (relative to TR)
   - BOLD changes due to cardiac cycle
   - pulsation-related effects
   - task related effects
   - task related changes to heart rate
2. Respiratory noise
   - breathing changes blood oxygenation and flow
   - breathing changes local fields
   - task related changes in breathing
   - interaction between heart rate and breathing

Question 23

What is fMRI: processing and analysis?

Answer 23

Potentially get rid of any distortion on and realign images

Form normalisation - our subject into a template space - 2 step process: align them to their structural image and align that to a template m

You can smooth the data and use design/model to get parameter estimate

You get a lot of boobs - some of them would be real and some Aren’t - there will be plenty of false positives given the number of multiple comparisons performed

Few boobs to pass significant threshold

The main problems are normalisation and statistical inference