Lecture 4: fMRI Methods - Basic Principle of MR Image Formation

Question 1

If the magnetic field was uniform, the RF pulse would … which would not allow you to.. - (2)

Answer 1

the RF pulse would excite all spins.

This would not allow you to discriminate the spatial arrangement of the sample

Question 2

If the magnetic field was uniform, the RF pulse would excite all spins. This would not allow you to discriminate the spatial arrangement of the sample

However, the

Therfore.. - (2)

Answer 2

Larmor frequency depends upon the strength of the magnetic field.

Therefore, if the static magnetic field was varied slightly across the sample ( brain), spins in different spatial locations would be different and thus be excited by different frequencies

Question 3

The gradient coils changes/manipulate the

Answer 3

strength of static magnetic field in x,y and z direction

Question 4

Changes in the gradient coils are important for

Answer 4

generating spatial information about the stimulus

Question 5

Changes in the gradient coils are important for generating spatial information about the stimulus

For example,

Answer 5

by changing the static magnetic field in the z direction, it is possible to measure the response to a slice through the brain

Question 6

How do we measure specific regions of the brain in MRI scanner? - (2)

Answer 6

Taking slices of brain one after the other to measure signal in the brain

Able to do this with the gradient coils we have in X,Y and Z

Question 7

What does the diagram show? - (7)

Answer 7

• Blue line could be the static magnetic field in Z and dashed is influence of Z gradient coil
• Smaller effect of Z gradient coil at bottom and larger effect at top
• Magnetic field gets higher towards top of brain as compared to bottom of brain in Z direction
• We got X and Y gradient coils and once excited a slice we excite X and Y gradient coils and change spins across slice and give info of spatial arrangment of brain in X and Y plane
• If you increase the magnetic field in Y (yellow) the spins to far end of brain will go faster than one nearest
• If you increase magnetic field in X (red) magnetic field and spins higher at back of brain then front
• That info used to produce image –> spatial encoding

Question 8

If the magnetic field was increased along the z axis (sometimes referred as B0) the RG to excite

A. The top of the brain would be different to the bottom
B. The middle of the brain would be different to the side
C. Diff regions of the brain would be the same

Answer 8

A. top of the brain would be different to the bottom

Question 9

If the magnetic field was increased along the z axis (sometimes referred as B0) the RG to excite top of the brain would be different to the bottom - why?

Answer 9

z gradient changes magnetic field strength from top to bottom

Strength at top of brain is 3.1 T and bottom of brain is 2.9 T and strength in middle is 3 if we are in 3T MRI scanner

What we do in order to excite sample (brain), we apply RF which has to be matched with precession frequency of hydrogen atoms

That precision frequnency determined by strength of magnets

Hydrogen atoms at top at 3.1 T is spinning fastest as compared to middle and bottom

If we change RF we can excite different slices of brain - we go for 128 so 3T so can just exciet hydrogen atoms in middle of brain if we do 3.1* 42.58 then RF is higher than 128 then excite top part of brain and 2.9*42.58 then that RF pulse excite bottom

Question 10

Once excited slice of brain along z axis we can also excite it on the

Answer 10

x and y axis gradient coils and change the spins along slice = give info of spatial arragnment of brain in x,y plane

Question 11

MR pulse sequences is sequence of events of

Answer 11

creating an MR image

Question 12

Diagram of MR Pulse sequences explained - (4)

Answer 12

• This shows MR pulse sequence
• RF = Radio frequency pulse which is matched with particular z gradient (Gz) - hydrogen atoms knocked over
• Apply Z gradient coil that allows to excite a specific brain slice (previous slide of brain slices)
• Apply different levels of x and y gradient which allows spatial info along x,y, plane of that specific brain slice (Gx, Gy)
• Once all gradient coils applied (x,y,z) , we then do the measurement of measuring the magneitc signal as it goes through the pipe which is recording signal going through
• This is repeated
• TE i(short)s time from RF pulse to measurement
• TR (long) is time between succession radio frequency pulses
• Can vary TE and TR to pick out different types of tissue

Question 13

What does these graphs of T1 recovery and T2 decay show in terms of MR pulse? - (3)

Answer 13

• Units are longitudinal magnestisation (magnetic signal along z direction) [ inferred ] and time since excitation along x axis
• In T1 recovery, hydrogen atoms knocked over and gradually go to the top (rise) - long time scale
• In T2 decay, hydrogen atoms knocked off originally pointing in same direction (high magnetic signal) but spread out - spreading out of magnetic signal and become less coherent and causes reduction in the magnetic signal to 0 (facing different directions)

Question 14

Use the principles of differences between T1 recovery and T2 decay in different types of tissuese

Answer 14

e.g., white matter, grey matter to get a picture of what is going on in those tissues as T1 and T2 is different in those tissues

Question 15

By varying two variables (TR, TE) in an MRI pulse sequence, it is possible to

Answer 15

distinguish between regions whose spins differ in both number and relaxation properties (T1, T2).

Question 16

Different MRI pulse sequences leading to different

Answer 16

types of images

Question 17

Different types of MRI images you can obtain - (3)

Answer 17

• Proton density imaging
• T1 contrast
• T2 contrast

Question 18

For proton density imagining we would want in terms of TE and TR - (2)

Answer 18

long TR
short TE

Question 19

A single proton is a charged particle in centre of

Answer 19

hydrogen’s nucleus

Question 20

In proton density imagning, all we are interested in is the…

Answer 20

the amount of hydrogen there is in different parts of our sample (the brain)

Question 21

Proton density images provide information on the total

Answer 21

number of hydrogen atoms (protons) in a voxel.

Question 22

To maximise proton density images pulse sequences are used that have a long TR and a short TE. This

Answer 22

minimizes T1 and T2 differences.

Question 23

What does this diagram show (proton density imagning) - (8)

Answer 23

• Two regions of the brain - blue and red region
• Blue regon lets say located near ventricles and red region is the white matter
• In ventricles, its just water (higher density of hydrogen/protons) and white matter more fat and less water (lower density of hydrogen/protons)
• If we allow long TR we allow (first graph) hydrogen atoms to get back to normal state and precessing around main axis
• More hydrogen atoms in ventricles than white matter so strength of signal is higher in ventricles than white matter - blue bit higher then red bit in first graph at top
• Then apply RF pulse and hydrogen atoms go to x,y plane and measure signal
• Since more hydrogen atoms in blue region the inital signal is high (start of second graph) than red white matter
• The difference in response to blue region higher then red region -= telling more hydrogen atoms in blue then red

Question 24

The most commonly used contrast for anatomical images of the brain is

Answer 24

is T1 weighting

Question 25

The T1 contrast used for ..

Answer 25

anatomical images of the brain

Question 26

Tissues with long T1 values such as water appear in T1 contrast

Answer 26

dark

Question 27

Tissues with short T1 values such as fat in white matter in T1 contrast appear

Answer 27

white

Question 28

Grey matter in T1 contrast has what?

Answer 28

intermediate T1 value

Question 29

T1 contrast looks at the different rate

Answer 29

at which hydrogen atom going to be knocked down to going back to z direction

Question 30

T1 dependent pulse sequences typically have an - (2)

Answer 30

an intermediate TR and a short TE.

Question 31

In proton density imagning we weren't concerned which is what T1 is concerned.. - (2)

Answer 31

* speed at which hydrogenknocked down but all wanted to get back up - TR long * But we measure difference in rate when they get back to main axis in T1 contrast which vary in different regions of brain

Question 32

We can't do proton density in T1 contrast as - (2)

Answer 32

* density of water so signal would be the same * Here is interested in T1 recovery and rate of recovery of hydrogen atoms in different regions

Question 33

What does this graph show for T1 contrast? - (2)

Answer 33

* More hydrogen atoms gone back to vertical position (First graph) in blue than red region * Blue region in second graph has higher signal compared to red region in second graph when knocked down again * T1 contrast between regions

Question 34

T2 contrast has long and intermediate

Answer 34

long TR and intermedite TE

Question 35

Why do T2 dependent pulse sequences typically have a long TR and an intermediate TE?

Answer 35

Because T2 values depend on spin-spin interactions, homogeneous tissues such as fluid in the ventricles will tend to have a longer T2 decay and generate brighter MR images.

Question 36

T2* pulse sequences are used in fMRI to show

Answer 36

differences in the concentration of oxy/deoxy-haemoglobin.

Question 37

We have long TR in T2 contrast as... we have intermediate TE as.. - (4)

Answer 37

not interested in measuring recovery of regions want differences in T2 decay in blue and red region - spreading out magnetic signal in graph below second graph- blue region tend to stick together before dispering out as compared to red region which loses signal faster - first - T2 contrast of blue vs red

Question 38

TE gives biggest difference between

Answer 38

T1 and T2

Question 39

T2 used most clinically as picks up ... and also sued for

Answer 39

a lot of fluied and used in fMRI

Question 40

Oncograph measures expansion of a

Answer 40

somatosensory cortex when the sciatic nerve from the leg was stimulated

Question 41

Whats a kymograph?

Answer 41

measures an increase in blood flow

Question 42

Experiment by Roy and Sherrington in which revealed

Answer 42

link between blood flow and brain function

Question 43

Experiment by Roy and Sherrington Did a oncograph did oncograph and kymograph and showed.

Answer 43

change in blood flow goes along the activity in region of somatosensory cortex (expansaion)

Question 44

Experiment by Roy and Sherrington showed that

Answer 44

Question 45

The somatosensory cortex receive info from sciatic nerve which is to do with

Answer 45

touch

Question 46

The core sources of energy we have for brain is - (2)

Answer 46

glucose and oxygen

Question 47

Although the brain is only 2% of body weight, it consumes

Answer 47

20% of the oxygen and 20-25% glucose

Question 48

Neurons require a constant energy supply to maintain the

Answer 48

the resting membrane potential

Question 49

Neurons require a constant energy supply to maintain the resting membrane potential However, when nuerons become active they

Answer 49

they become active and generate postsynaptic/action potentials they use even more energy

Question 50

The brain does not store energy Therefore,

Answer 50

when a region in the brain becomes active it needs more glucose and oxygen

Question 51

Anaerobic respiration is when

Answer 51

glucose is only used for energy reserve Aerobic uses both glucose and blood oxygen

Question 52

glucose not that efficient in

Answer 52

producing energy by itself

Question 53

Aerobic (oxygen + glucose) resp produces more ATP (34) than

Answer 53

anaerobic respiration (glucose)

Question 54

Oxygenated haemoglobin (Hb) has no

Answer 54

magnetic momement - dimagnetic

Question 55

Haemglobin is a protein that can allows to

Answer 55

carry oxygen around body

Question 56

Diagram of MRI signal when oxygenated vs deoxygenated

Answer 56

Question 57

deoxygenated haemoglobin is paramagnetic and disrupt the

Answer 57

MRI signal

Question 58

The magnetic properties of deoxyHb causes spin dephasing (loss of syncrhonisation) of

Answer 58

hydrogen atoms in the transverse direction.

Question 59

The magnetic properties of deoxyHb causes spin dephasing of hydrogen atoms in the transverse direction. This results in the

Answer 59

T2 decay being significantly shorter in the presence of deoxyHb than oxyHB (T2* decay)

Question 60

the T2 decay being significantly shorter in the presence of deoxyHb than oxyHB (T2* decay) due to magnetic properities in deoxyHb and none in oxy Hb is the basis of

Answer 60

the Blood Oxygen Level Dependent (BOLD) signal.

Question 61

If there is less oxygen in Hb then less

Answer 61

MRI signal

Question 62

BOLD stands for

Answer 62

blood oxygen level dependent

Question 63

When region is active in brain in MRI there is a higher concentration of

Answer 63

oxygenated Hb than dexoygenated Hb

Question 64

In BOLD response, - (2)

Answer 64

Oxygen is carried in the blood attached to haemoglobin molecules. Increased blood flow occurs in areas of high neuronal activity reducing the relative amount of deoxyHb

Question 67

Oxygen is carried in the blood which is attached to

Answer 67

haemoglobin molecules.

Question 68

Before neurons become active, there is ratio of

Answer 68

oxy/deoxyHB

Question 69

Increased blood flow occurs in areas of high neuronal activity reducing the

Answer 69

relative amount of deoxyHb This causes an increase in MR signal – the BOLD response

Question 70

MR signal is higher when there is

Answer 70

more oxyHb

Question 71

Blood oxygen level dependent (BOLD) response has

Answer 71

increase and decrease in the magnetic signal in visual cortex when a light is turned on and off

Question 72

The principle of cognitive subtraction underpins most experiments in

Answer 72

cognitive psychology and cognitive neuroscience

Question 73

Example of cognitive subtraction experiment Donders 1868 - (5)

Answer 73

* Franciscus Donders (1868) was interested in higher cognitive function such as decision making. * He developed a technique for accurately recording response time or reaction time. * To measure the time it took to make a decision, he measured the response time for detecting an isolated light (simple reaction time). * He then compared that response time with the time taken to make a decision about whether a light appeared to the left or right – a different response is required for each (choice reaction time). * He subtracted the response times from each to isolate the time taken to make the decision! The answer is ~100ms.