MRI basics

Question 1

fMRI

Answer 1

• it works by placing a participant in a static magnetic field, generated by superconducting electromagnet cooled by liquid helium.
• the field strength is 3 tesla (T) or 1.5 T for clinical purposes
• The head coil is used to send radio frequency (RF) pulses and also function as a receiver for the incoming signal.

Question 2

how MRI actually works

Answer 2

• nuclear magnetic resonance (NMR) refers to the atomic nucleus, which contains protons and neutrons
• more than 70% of the brain consists of water, which consists of hydrogen atoms (H+ protons)
• these can be thought as small bar magnets ‘precessing’ like a spinning top about an axis.

Question 3

hydrogen bonds

Answer 3

• the Hydrogen bonds are referred to as protons or ‘spins’, because their ‘precessing’ is often referred to as spinning.
• the protons spin directions are initially random, but in a strong, externally applied magnetic field, like in the MRI scanner, they align parallel or anti-parallel to the magnetic field
• most protons align parallel to the B0 field
• however, they are not perfectly aligned- and they are also not static- they keep ‘precessing’ in a random fashion

Question 4

B0 field

Answer 4

• the B0 field is orientated into the direction of the Z-axis in the scanners coordinated system
• the precession frequency of the protons is also referred to as the larmour frequency
• the precession frequency of protons depends on the strength of the magnetic field. this means, we know the frequency of the spink because we know how strong the magnetic field is
• we can imagine all the protons being aligned with the B0 field. but they would all be in different positions in their precession.

Question 5

RF pulse

Answer 5

• as long as they are aligned in the direction of B0 field we cannot measure the signal with our head coil, which surrounds the head
• the second problem that the signal from each proton in itself is ting, and they are not precessing in phase.
• in order to get a signal, we apply a radio frequency (RF) pulse perpendicular to magnetic field B0 using the head coil
• ## if the frequency of the RF matches the Lamor frequency of the protons, it will affect these protons.

Question 6

the first affect of the RF pulse

Answer 6

• the first effect of the RF pulse is that all protons will start precessing in phase, meaning that their magnetization will all point to the same location in space at the same time.
• this happens because the protons absorb energy from the RF pulse.

Question 6

the second effect of the RF pulse

Answer 6

• the RF pulse is the magnetisation vector (the next magnetisation that the protons have together) is tilted away from the Z-axis
• this means the magnetisation is tilted from the longitudinal direction (of the field Bo) into the transversal plane

Question 6

magnetization vector

Answer 6

• the magnetization vector now ‘rotates’ around in the transversal plane where our head coil is placed
• the head coil will now receive this as a signal, however this signal is still rather meaningless for us, because it comes from the entire brain
• this trick is now switch off the rf pulse after which the transversal magnetization decays very quickly because the protons emit excess energy
• they also lose phase coherence quickly which makes the signal disappear

Question 7

first consequence of turning off the RF signal

Answer 7

• the protons align again with the magnetic field, also referred to as longitudinal relaxation, spin-lattice, relaxation (because it is due to an interaction of ‘spins’, the protons and lattice) or T1 recovery
• T1 refers to a time constant of a function, indicating how long the recovery of the longitudinal magnetization tasks
• importantly for us, this time constant is different for different tissue types

Question 8

second consequence of switching off the RF pulse

Answer 8

• the 2nd consequence of switching off the RF pulse is that the transversal magnetization decays (which is an independent process), also referred to as transversal relaxation, spin-spin relaxation or T2 decay
• T2 is the time constant indicating how long the transversal decay takes
• T2 decay is much faster than T1 recovery

Question 9

phase of relaxation- signal measured

Answer 9

• when the signal is measured during this phase of relaxation, different signals will be emitted from protons in different tissues
• depending on when signals are measured, researchers can use T1 and T2 to get differently weighted images of the brain and clearly see this type of tissue.
• for this, different types of sequences are used that are optimised to capture differences in signal due to T1 recovery and T2 decay
• structural brain images depend on when signal is recorded during this process

Question 10

reconstructing brain images

Answer 10

• in order to get seperate measurements from different locations in the brain, we first need to reconstruct where the signal comes from
• for this we use gradients created by gradient coils
• protons will absorb energy from RF pulses only when the frequency of the RF pulse matches the protons precession frequency
• thus, by causing the magnetic field to vary linearly, we can cause the resonance frequency to vary throughout the brain
• an RF pulse of a specific frequency will not only excite one slice of the brain- precisly the slice where the resonance frequency of the protons matches the RF pulse

Question 11

gradient slicing

Answer 11

• the first gradient we use is called slice selecting gradient
• it varies the gradient field along the Z-axis such that different slices are exposed to different field strengths
• A RF pulse can now be chosen to match precisly the precession frequency of the protons in one slice of the brain

Question 12

second gradient used

Answer 12

• now that we know the ‘slice’ of the signal comes from, the second gradient we use is called the phase encoding gradient
• it changes the precession frequency of the excited protons depndning on their location in the gradient, using de-phasing
• when removed, the resonance frequencies are the same again but the differences in phase persist- their phase is now informative about their position

Question 13

the third gradient

Answer 13

• the third gradient is called to frequency encoding gradient, and it changes the magnetic field within the selected slice
• this happens during read-out of the signal
• becuase all protons at a certain position in the gradient now have same precession frequency, the frequency at read-out is informative about their position

Question 14

characteristics of the slices

Answer 14

• in classical sequencies, one RF pulse is used for each slice, meaning that the time it takes to measure the entire brain depends on the number of slices- usually 1-3 seconds
• the other important parameter is the echo time (TE), which is the interval between excitation and data Acquistion.
• other important parameters are
• the slice thickness, the size of the measurement point