Lecture 4: fMRI Methods - Basic Principle of MR Image Formation Flashcards
If the magnetic field was uniform, the RF pulse would … which would not allow you to.. - (2)
the RF pulse would excite all spins.
This would not allow you to discriminate the spatial arrangement of the sample
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)
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
The gradient coils changes/manipulate the
strength of static magnetic field in x,y and z direction
Changes in the gradient coils are important for
generating spatial information about the stimulus
Changes in the gradient coils are important for generating spatial information about the stimulus
For example,
by changing the static magnetic field in the z direction, it is possible to measure the response to a slice through the brain
How do we measure specific regions of the brain in MRI scanner? - (2)
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
What does the diagram show? - (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
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
A. top of the brain would be different to the bottom
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?
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
Once excited slice of brain along z axis we can also excite it on the
x and y axis gradient coils and change the spins along slice = give info of spatial arragnment of brain in x,y plane
MR pulse sequences is sequence of events of
creating an MR image
Diagram of MR Pulse sequences explained - (4)
- 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
What does these graphs of T1 recovery and T2 decay show in terms of MR pulse? - (3)
- 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)
Use the principles of differences between T1 recovery and T2 decay in different types of tissuese
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
By varying two variables (TR, TE) in an MRI pulse sequence, it is possible to
distinguish between regions whose spins differ in both number and relaxation properties (T1, T2).
Different MRI pulse sequences leading to different
types of images
Different types of MRI images you can obtain - (3)
- Proton density imaging
- T1 contrast
- T2 contrast
For proton density imagining we would want in terms of TE and TR - (2)
long TR
short TE
A single proton is a charged particle in centre of
hydrogen’s nucleus
In proton density imagning, all we are interested in is the…
the amount of hydrogen there is in different parts of our sample (the brain)
Proton density images provide information on the total
number of hydrogen atoms (protons) in a voxel.
To maximise proton density images pulse sequences are used that have a long TR and a short TE. This
minimizes T1 and T2 differences.
What does this diagram show (proton density imagning) - (8)
- 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
The most commonly used contrast for anatomical images of the brain is
is T1 weighting
The T1 contrast used for ..
anatomical images of the brain
Tissues with long T1 values such as water appear in T1 contrast
dark
Tissues with short T1 values such as fat in white matter in T1 contrast appear
white
Grey matter in T1 contrast has what?
intermediate T1 value
T1 contrast looks at the different rate
at which hydrogen atom going to be knocked down to going back to z direction
T1 dependent pulse sequences typically have an - (2)
an intermediate TR
and a short TE.
In proton density imagning we weren’t concerned which is what T1 is concerned.. - (2)
- 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
We can’t do proton density in T1 contrast as - (2)
- 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
What does this graph show for T1 contrast? - (2)
- 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
T2 contrast has long and intermediate
long TR and intermedite TE
Why do T2 dependent pulse sequences typically have a long TR and an intermediate TE?
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.
T2* pulse sequences are used in fMRI to show
differences in the concentration of oxy/deoxy-haemoglobin.
We have long TR in T2 contrast as…
we have intermediate TE as.. - (4)
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
TE gives biggest difference between
T1 and T2
T2 used most clinically as picks up … and also sued for
a lot of fluied and used in fMRI
Oncograph measures expansion of a
somatosensory cortex when the sciatic nerve from the leg was stimulated
Whats a kymograph?
measures an increase in blood flow
Experiment by Roy and Sherrington in which revealed
link between blood flow and brain function
Experiment by Roy and Sherrington Did a oncograph did oncograph and kymograph and showed.
change in blood flow goes along the activity in region of somatosensory cortex (expansaion)
Experiment by Roy and Sherrington showed that
The somatosensory cortex receive info from sciatic nerve which is to do with
touch
The core sources of energy we have for brain is - (2)
glucose and oxygen
Although the brain is only 2% of body weight, it consumes
20% of the oxygen and 20-25% glucose
Neurons require a constant energy supply to maintain the
the resting membrane potential
Neurons require a constant energy supply to maintain the resting membrane potential
However, when nuerons become active they
they become active and generate postsynaptic/action potentials they use even more energy
The brain does not store energy
Therefore,
when a region in the brain becomes active it needs more glucose and oxygen
Anaerobic respiration is when
glucose is only used for energy reserve
Aerobic uses both glucose and blood oxygen
glucose not that efficient in
producing energy by itself
Aerobic (oxygen + glucose) resp produces more ATP (34) than
anaerobic respiration (glucose)
Oxygenated haemoglobin (Hb) has no
magnetic momement - dimagnetic
Haemglobin is a protein that can allows to
carry oxygen around body
Diagram of MRI signal when oxygenated vs deoxygenated
deoxygenated haemoglobin is paramagnetic and disrupt the
MRI signal
The magnetic properties of deoxyHb causes spin dephasing (loss of syncrhonisation) of
hydrogen atoms in the transverse direction.
The magnetic properties of deoxyHb causes spin dephasing of hydrogen atoms in the transverse direction.
This results in the
T2 decay being significantly shorter in the presence of deoxyHb than oxyHB (T2* decay)
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
the Blood Oxygen Level Dependent (BOLD) signal.
If there is less oxygen in Hb then less
MRI signal
BOLD stands for
blood oxygen level dependent
When region is active in brain in MRI there is a higher concentration of
oxygenated Hb than dexoygenated Hb
In BOLD response, - (2)
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
Oxygen is carried in the blood which is attached to
haemoglobin molecules.
Before neurons become active, there is ratio of
oxy/deoxyHB
Increased blood flow occurs in areas of high neuronal activity reducing the
relative amount of deoxyHb
This causes an increase in MR signal – the BOLD response
MR signal is higher when there is
more oxyHb
Blood oxygen level dependent (BOLD) response
has
increase and decrease in the magnetic signal in visual cortex when a light is turned on and off
The principle of cognitive subtraction underpins most experiments in
cognitive psychology and cognitive neuroscience
Example of cognitive subtraction experiment Donders 1868 - (5)
- 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.
