week 5.1 - fMRI 1

Question 1

What does fMRI stand for?
What is fMRI aka?

Answer 1

functional magnetic resonance imaging
BOLD MRI = blood oxygen level dependent MRI

Question 2

What do activation maps show?

Answer 2

show activation in areas in response to an assigned task

Question 3

What does fMRI signal detect in the brain?
What biological concept it this know as

Answer 3

detects changes in blood flow due to changes in neuronal activity

NVC = haemodynamic response due to changes in neuronal activity or stimulus

Question 4

How does the properties of blood change the fMRI signal?
How does the haemodynamic response change the fMRI signal?

Answer 4

due to the magnetic properties of oxy and deoxy red blood cells
Oxygenated = weakly diamagnetic: weakly REDUCES magnetic signal
Deoxy = strong paramagnetic: increases magnetism

-increased blood flow to area, blood going to area is oxy -> increases fMRI signal

Question 5

In MRI, what happens to proton spin as magnetism increases?

Answer 5

protons spins gets faster as magnetism increases (proportionately)

Question 6

Why is oxygenated blood weakly diamagnetic?
What does diamagnetic mean?

Answer 6

when is oxygenated, the iron core is shielded and hidden (iron gives rbcs their magnetism)
decreases magnetism

Question 7

What are the magnetic properties of oxy and deoxy rbcs?

Answer 7

oxy = weakly diamagnetic, weak reduction
deoxy = paramagnetic, strong increase

Question 8

What happens to proton spin as you go from oxy to deoxy blood?

Answer 8

protons spin faster as magnetism increases from oxy to deoxy

Question 9

Although deoxy blood is paramagnetic, why is there a decrease in fMRI signal in areas of deoxy blood?

Answer 9

deoxy -> magnetisation increases -> magnetic field disruptions -> protons spins precess at slightly different frequencies in the gradient field -> increased
dephasing (spread out in the x-y plane) -> decreases T2* signal

Question 10

What does precess mean?
What object can precess in MRI?

Answer 10

the movement or rotation of an object around an axis due to an external force
proton

Question 11

Why is T2* imaging used mostly for fMRI?

Answer 11

because T2* is sensitive to changes in magnetic field due to deoxygenated blood

Question 12

How does oxygenated blood increase T2* signal even tho its weakly diamagnetic? (explain this on a capillary level)

Answer 12

task is set -> OVERsupply of oxy blood sent to capillary -> oxy weakly decreases magnetism -> no magnetic field distortions -> less dephasing -> higher T2* signal

Question 13

During a task, why is the capillary made up of mostly oxy blood instead of deoxy? (you would think its deoxy as it using up oxygen in task)

Answer 13

body gives oversupply of oxy given to area during task -> mostly oxy in capillary

Question 14

What is the activation contrast?

Answer 14

the difference in T2* signals between at rest and task

Question 15

In the capillary, what are the proportions of oxy and deoxy blood at rest and during a task?

Answer 15

at rest: about equal of both
task: majority oxy

Question 16

How do you maximise the BOLD effect* with signal decay curves of rest and task?
(have largest change in T2 signals from rest to task)

Answer 16

you choose the optimal echo time= the greatest change in signal between rest and task curves BUT also not without losing too much signal (compromise)

Question 17

What type of lines are the signal decay curves of rest and task?

Answer 17

exponentials (negative/decreasing)

Question 18

Why must you try to not decrease the signal too much (choose optimal echo) to maximalise the BOLD effect?

Answer 18

because if signal is too low then you will be just measuring noise

Question 19

What is the typical fMRI voxel dimensions?

Answer 19

4 x 4 x 4 = 64mm3 (cubed)

Question 20

What is k space?

Answer 20

intermediate mathematical space where frequency data is stored before final MRI is constructed

Question 21

How is the Fourier transform involved in k space?

Answer 21

Fourier transform is used to convert the frequency-based data, stored in k space into an image

Question 22

For gradient echo MRI, what is the direction of k space movement dictated by?

Answer 22

direction of movement in k space -> area of the phase- and frequency-encoding gradients
(area under graph)

Question 23

For gradient echo MRI which xyz plane direction is the phase-encoding gradient and the frequency-encoding gradient in?
Which one happens first?

Answer 23

phase-encoding gradient = y direction
frequency-encoding gradient = x direction
(the transverse planes)

happen in order listed

Question 24

What does the phase-encoding gradient and frequency-encoding gradient do to collect the frequency data for kspace?

For gradient echo, how many horizontal lines of kspace are filled per TR?

Answer 24

1. FIRST before readout/signal acquisition: phase-encoding gradient varies from negative to positive to fill in rows of kspace in a vertical direction
2. THEN during readout/signal acquisition: frequency-encoding gradient encodes spatial information along the x-axis of MRI image

the above 1 and 2 = fills one full row of k-space per TR

Question 25

How many horizontal lines/rows are there in kspace? How does kspace affect image resolution?

Answer 25

-number determined by researcher eg 64 or 256 -as the number of horizontal lines in kspace increases, the image resolution increases.

Question 26

What is the issue with using gradient echo for fMRI? What is this issue caused by? How can this be fixed experimentally?

Answer 26

-BOLD signal happens a lot quicker than the speed at which images are acquired by gradient echo -data for each row of kspace takes one excitation/TR to collect -using echo planar imaging sequence (EPI)

Question 27

What is the key difference between gradient echo and echo planar EPI?

Answer 27

gradient echo takes as many TRs as there are horizontal kspace rows whereas echo planar only requires one TR/one excitation to acquire data for the whole kspace echo planar is lot quicker!!

Question 28

How is echo planar imaging sequence (EPI) able to be a lot quicker than gradient echo sequencing? How long is a typical EPI image take to acquire?

Answer 28

-EPI uses rapid, alternating gradient pulses in the frequency (x) and phase (y) directions -less than 100ms

Question 29

Is gradient echo sequence MRI suitable for FMRI imaging?

Answer 29

no! too slow image acquisition to show the BOLD effect

Question 30

What is the advantage of gradient echo over EPI? What are the disadvantages of using EPI?

Answer 30

-gradient echo has higher spatial resolution than EPI -EPI has lower resolution, MORE sensitive to artefacts and lower quality image

Question 31

What are the two different ways to acquire slices (one image) with BOLD MRI? Which method is more accurate? why?

Answer 31

sequential or interleaved ascending/descending (4 different ways) interleaved because 1. it reduces signal contamination caused by RF interference between neighboring slices Interleaving gives slices more time to relax. 2. prevents the first and last slices from being acquired far apart in time -> makes timing of BOLD signals across the brain more consistent.

Question 32

How does interleaved acquisition differ from sequential acquisition?

Answer 32

interleaved: odd-numbered slices first: 1, 3, 5, then even-numbered slices: 2, 4, 6. whereas sequential is 123456 (vice versa for ascending/descending)

Question 33

For EPI: Why is imaging the BOLD effect susceptible to drop out of signal? What helps to alleviate signal drop out in fMRI imaging? However, what is the consequence of trying to alleviate the signal drop out?

Answer 33

-because fMRI is very sensitive to differences in magnetisation of all the other brain structures (not just blood) -> signal drop out -reducing echo time TE and lowering the flip angle -as TE and flip angle decreases, BOLD effect decreases BUT dropout decreases -> compromise between dropout signal and BOLD effect/contrast

Question 34

What is the BOLD effect?

Answer 34

difference in the contrast between at rest and task?????

Question 35

What is the point of doing a few dummy scans first in EPI fMRI?

Answer 35

to allow the image signal to reach a steady state -> so changes are only due to blood oxygenation levels and NOT due to the MR effect

Question 36

What is the issue with interleaved acquisition of FMRI images? What are the two reasons which cause this?

Answer 36

-it can lead to stripe artefacts -due to the signal changing during acquisition of the volume, or if there is subject motion.

Question 37

How woul you investigate the effect of the BOLD signal from fMRI images? What is a good BOLD signal from this investigation?

Answer 37

by investigating changes in signal intensity as time increases (and switches between at rest and task) in each individual voxel good BOLD signal has clear increase from rest to task

Question 38

What is the simplest model for fMRI data analysis?

Answer 38

linear regression eg. general linear model GLM

Question 38

What is the point of modelling FMRI data?

Answer 38

to show where the bold effect is and which is noise

Question 39

In fMRI modelling, why do we use the haemodynamic response FUNCTION hrf? How is it used? What is the result of hrf use?

Answer 39

There is a delay from the start of the task to the haemodynamic response. So instead of just arbitrarily shifting the model to fit the data better, we can use hrf hrf is convolved with model -> we get a more realistic estimate of the expected signal change from rest to task HENCE the gradient increase in the model

Question 40

For fMRI modelling, how do you combat the residual signal drift? what is it in layman's terms?

Answer 40

residual signal drift is where the waves between rest and task start to move upwards and get a higher signal -> add a linear ramp to the model

Question 41

What are the three steps to linearly modelling fMRI data?

Answer 41

make linear model square wave hrf convolved with square wave add linear ramp

Question 42

What is flip angle? What is the range of the flip angle? Why is the value of the flip angle important? give an example

Answer 42

-the angle by which magnetization is tipped into the transverse plane by an RF pulse - 0 to 180 degrees - value of the flip angle affects the signal strength, contrast, scan speed and the signal-to-noise ratio. For example, lowering the flip angle helps alleviate signal drop out in EPI

Question 43

What are the flip angles <90, 90 and 180 degrees used for?

Answer 43

<90 gradient echo, EPI 90 spin-echo 180 inversion recovery