Comprehensive Guide to Spin Echo MRI Pulse Sequences Explained

hello everybody and welcome back today's talk is the first in a three-part Series where we're going to be looking at

different types of MRI pulse sequences we'll start off today by looking at spin Echo pulse sequences before then moving

on to gradient Echo and inversion recovery sequences now the focus of today's talk is first going to be to

understand what exactly a spin Echo is and why we would want to go about generating an echo within our sequence

and we'll see that the generation of an echo is going to help us to recover some of that signal that's been lost during

free induction Decay or T2 star decay once we understand what exactly a spin Echo is then we're going to move on and

look at three different pulse sequences that utilize this spin Echo phenomenon now if you look at this pulse sequence

here this is the kind of pulse sequence we've been looking at throughout this module now the first thing we do is

apply a radio frequency pulse that will tip the net magnetization Vector out of the longitudinal plane and it will allow

that Vector to gain some transverse magnetization as well as gaining transverse

magnetization it's simultaneously losing longitudinal magnetization now why is this important the signal that we can

measure in MRI is transverse magnetization we can't measure longitudinal magnetization because of

that large magnetic field that we've applied along the patient that is always on there's no way that we can place a

receiver coil and manage to somehow measure this longitudinal magnetization we can only measure what we flip into

the transverse plane now we've applied a slide selection gradient at the same time that we apply

that radio frequency pulse and that just allows us to select a specific slice and if you don't understand that concept go

back to the slice selection talk we've then seen that we've applied a phase encoding gradient one gradient per

complete cycle here to the entire slice and that phase encoding gradient will cause the spins to de-phase along the

y-axis we've then previously touched on why we would apply a 180 degree RF pulse and how that goes about generating an

echo within our sequence and we're going to revise that in a little bit more depth here today

then when that Echo occurs when there's that rephasing of those spins we sample the signal at a time known as t e the

time to Echo and it's enable te because that's where this Echo the spin Echo occurs and that's what we're going to be

looking at today we sample over a period of time and we sample while we are applying the

frequency encoding gradients as that frequency encoding gradient is being applied we're taking multiple discrete

data points and then placing those data points within a single line on K space that corresponds to the specific phase

encoding gradient that we applied for that specific pulse sequence we then wait a long period of time until

we repeat the process again the time to repetition until we then flip those bins back into the 90 degree plane now te is

a certain period of time after we have flipped those spins in this example to 90 degrees

now what causes these spins to lose transverse magnetization it's not those spins returning into the longitudinal

plane that contributes ever so slightly to signal loss the main contribution to loss of that transverse signal is the

phasing of those spins if we were to take two spins here that we have flipped from the longitudinal plane into the

transverse plane we then stop our 90 degree RF pulse those spins are going to D phase they're going to become out of

phase with one another based on their local environments now that D phasing is causing loss of transverse signal

because they are no longer in Phase with one another and that loss of transverse signal we can measure that rate and that

rate is what's known as T2 and in an ideal world that loss of transverse signal from the D phasing would only be

due to spin spin interactions with spins interacting with one another causing D phasing but as we'll see throughout this

talk there are local magnetic field in homogeneities that are actually responsible for the majority of the

dephasing of those spins and the loss of transverse magnetization and that loss of transverse magnetization because of

the local magnetic field in homogeneities is what's known as T2 star or free induction Decay and that happens

much more rapidly than T2 now these spins they've lost phase with one another so there's no longer any

transverse magnetization the net magnetic moments of those spins though they're still in the 90 degree

plane or they may have lost some of that angle there is still magnitude to those vectors if there's some way that we can

cause those spins to re-phase they will start to regain some of that transverse magnetization that free induction Decay

is a loss of transverse signal purely because of de-phasing we are not losing it because those spins have now gone

into the longitudinal plane that's a really important concept to remember that's why T2 Decay happens so much

faster than the longitudinal relaxation or T1 relaxation T1 relaxation takes a lot longer for the

spins to ultimately lie back in parallel with that main magnetic field that's why TR is often so much longer than te so

let's look at transverse Decay take three different tissues CSF fat and muscle

now if this was pure spin spin interaction this would what be known as T2 relaxation or transverse Decay now

once the transverse signal has lost 63 percent of its magnetization that is what's known as the t2 time constant and

we can see that the t2 values for these three different tissues will have different time based values that teach

you value as a constant how quickly are those tissues losing their transverse magnetization

now that loss of transverse magnetization is because of the phasing of those spins these spin spin

interactions in CSF is much less in the spin spin interactions in fat and in muscle and it's this that provides us

contrast within our image if we do a te that's based say at this period of time we can see that the signal from muscle

will be much less in that effect and the signal from fat will be less than that of CSF

now the problem I've mentioned is that local magnetic field in homogeneities caused the signal to be lost much

quicker than the t2 constant and that's what's known as T2 star free induction Decay and you can see here on this graph

just how much quicker that happens and this again occurs because of local magnetic field in homogeneities either

from our machine it's hard to make a machine that has a perfectly uniform magnetic field and when you place

anything into the magnetic field like a patient there are different molecules and atoms within that patient that are

going to ever so slightly distort that magnetic field like we saw in our chemical shift talk

now you might think how big do these magnetic field differences need to be in order to cause such a drastic loss of

transverse magnetization why did the spins defaze so quickly well if we look at the gyromagnetic

ratio of hydrogen if we were to place hydrogen within a one Tesla main magnetic field those hydrogens will

process at a frequency of 42.58 million Hertz 42.58 megahertz and we can use this equation here to

look at two separate spins first is experiencing the main magnetic field and the second is experiencing a

magnetic field that is one millionth of a Tesla difference if this spin is processing at 42.58

million Hertz per second this spin instead of precessing at 42.58 million Hertz it's going to have an extra

42.58 precessions per second it's going to be spinning or it's going to be processing at a frequency that's 42.58

Hertz more now we're talking about million Hertz so that difference is ever so small we can use the rotational frame

to compare how is this spin spinning in comparison to this spin if this bin stayed still as a rotational frame and

we just looked at this spin relative to this spin this spin will process

42.58 Hertz more per second now all it has to do is process 180 degrees more to be completely out of

phase with the spin we flip them into the transverse plane they're both processing in the megahertz millions of

Hertz range but we know that every second this spin is processing 42.58 Hertz more than the spin

it only takes a very small amount of time for the first time for these two spins to be completely out of phase from

one another and it turns out if you use these equations we can see that the time taken for them to be out of Faith with

one another is less than 12 milliseconds it's an extremely small amount of time and that is caused by the most minute

difference in main magnetic field that's why we get this free induction Decay and it's very difficult to measure that

signal so quickly in less than 12 milliseconds at a te that's going to give us accurate measurements and not

only that you can see now that the contrast between these two tissues has been greatly reduced because of this

free induction decay these spins have defaced we need a way of rephasing them and measuring it at t

e and that is the basis of spin Echo pulse sequences so let's go to an example here where

we're looking at some form of tissue we've applied a B1 we've flipped those spins into the 90 degree plane and we

allow them now to lose phase over time now this loss of phase is the t2 relaxation spin spin interactions

causing this dephasing and that actually happens over a very long period of time especially if we're looking at water in

CSF that dephasing that loss of transverse magnetization is very slow now I've said to you that that loss of

transverse magnetization happens much quicker in the real world free induction decay occurs as local magnetic field in

homogeneities cause that signal to be lost very quickly because of that rapid defacing of those spins

now if we were to look at two separate examples here the one on the left here is the laboratory frame how we've been

looking at these spins spinning from the outside the one on the right is the rotational frame which is sometimes more

easy to conceptualize when looking at spin Echo in the laboratory frame as we've seen

now those spins are going to de-phase over time mainly due to those local magnetic field in homogeneities

the rotational frame is going to show you how the spins D phase relative to the Llama frequency the Llama frequency

at this specific location how are some of the spins going to defaze slower some of them D phase faster because of those

slight differences in processional frequencies based on those local magnetic field in homogeneities

now as we play this now with those local magnetic field in homogeneities we are losing signal rapidly compared to how we

were losing signal when it was only spin to spin interaction see now how we've got Fanning out of

that rotational frame those spins are de-phasing relative to one another the laboratory frame those spins have either

gone faster or slower depending on the local magnetic field now we need a way to re-phase those spins to allow

re-accumulation of phase and give us a better transverse magnetization signal now this is what's called a spin Echo

where we regain signal and that signal is ever so slightly less in our true T2 signal what we've done here is accounted

for those local magnetic field in homogeneities and the loss of signal at this time period is generally only due

to spin spin interactions or molecules that have moved within the tissue during this period of time and have experienced

a slightly different magnetic field strength then if we were to allow this to carry

on for a further period of time we will again lose signal at the free induction Decay so let's look at exactly how this

happens we're going to be looking at the rotational frame when we look at these examples because it's much more easy to

conceptualize at least for me so let's now look we've flipped our spins into the 90 degree here we're

looking from the side here we're looking end on as we allow those spins to then defaze

we are losing phase we're losing transverse magnetization because of those local magnetic field in

homogeneities we've said that this happens really quickly in a matter of milliseconds and

it's very difficult to measure any good signal here at te we saw how rapidly that dropped off and even if we did

measure it there wouldn't be much contrast between the tissues what we can do is as we look at this end

on we can apply the 180 degree RF pulse now when we are flipping spins into the 90 degree

we actually need to think of the sample as containing spins in the parallel and spins in the anti-parallel direction and

as we apply that RF pulse those spins can gain transverse magnetization applying an RF pulse that's either

stronger than this 90 degree RF pulse or applying the same strength but for double the period of time will allow

that net magnetization Vector to surpass the 90 degree angle and actually form in a higher energy state in that

anti-parallel side of our longitudinal magnetization that's how we can get past the 90 degree in our 90 degree RF pulse

if we were to apply the 180 degree RF pulse here look what happens to these spins that have defased relative to our

llama frequency some have de-phased slower and some have de-phased faster like this these spins down here are our

leading spins they've de-phased faster these here are lagging spins let's apply a 180 degree RF balls and what that does

is it spins that magnetization Vector 180 degrees along that X Y plane now these were our leading spins they're

de-phasing faster these were our lagging spins also because we have now flipped these spins a full 180 degrees spins

that were processing in say the clockwise direction as we've now flipped them are going to be spinning in the

anti-clockwise direction so these leading spins are now going to be lagging behind the lagging spins but

because they are dephasing faster they're experiencing a high a local magnetic field strength they are going

to re-phase again as time passes by you can see that those leading spins now became the lagging spins and then

re-phased we can now measure that signal at te our time to Echo and we can see how much higher that signal is and that

signal now is much closer to the true T2 signal the signal loss because of spin spin interaction we've accounted for

those local magnetic fields in homogeneities we're not reproducing signals here we're

not adding more energy into the system technically what we are doing is allowing those magnetization vectors to

re-phase and then that accumulation of phase is what's giving us that signal I hope this makes sense as to how we are

accounting for those local magnetic field in homogeneities after all it's those in homogeneities that are causing

this rapid defacing this spin here based on its location is experiencing a different magnetic field strength in

this spin here and because that magnetic field strength is different it's rapidly defacing with the other spin once we

apply that 180 degree RF pulse as long as these spins are in the exact same location this spin is still going to

rapidly defaze but now the dephasing because of this change in orientation actually happens to be a re-phasing and

that is the basis for spin Echo production now once we've generated that spin Echo and we've measured this signal

here this analog signal that we've measured we've converted it to a digital signal we then place that Digital Signal

within one line of k-space we then need to wait till TR so we can redo this entire process and fill another line of

K space we've got many lines of K space to fill and not only that for each line of K space we repeat it multiple times

and get multiple signal averages and then k space only represents one slice of our patient we still need to do that

for all the slices within the patient you can see how if we're waiting a second to three seconds for TR this is

going to start taking a very long time to take our MRI image so if we think about acquisition time we've seen that

the time to take the total scan is the time from our first RF pulse all the way to tr what is our TR value then each

phase encoding step is going to fill a different line of K space and the number of phase encoding steps is going to give

us our resolution in the y-axis but each one requires a repetition of this entire cycle the next represents the number of

excitations or the number of signal averages that we do for each line in case space every time we add another

excitation we add a full TR onto our scan time so we need to account for the number of excitations then we need to do

all of these steps for every single slice so we need to multiply that by the number of slices that's going to give us

our total acquisition time now the three different pulse sequences that we're going to look at here that utilize spin

Echo pulse sequences we're going to see how this downtime between t e and TR is going to be utilized to reduce this

total scan time now before we move on to these pulse sequences you may have noticed some

subtle changes here our D phasing frequency encoding gradient Now lies before the 180 degree pulse and this is

a common site for this frequency encoding gradient to be placed but you see now it's no longer below this line

it's above the line here now why is it here previously we place the frequency encoding gradient below this line a d

phase ingredient prior to our data acquisition time when we applied the frequency encoding gradients along the

x-axis now we apply that D phasing frequency encoding gradient to allow those spins

despite having different frequencies along the x-axis to re-phase at t e and D phase again allow us to increase

signal and decrease signal something we covered in the frequency encoding talk if we were to do that before the 180

degree rfo so we would require that frequency encoding gradient to be in the same direction along the x-axis as when

we reapply it here at our time to Echo and that's because this 180 degree RF pulse causes a flipping of those net

magnetization vectors we can apply our phase encoding gradient prior or after this 180 degree RF pause and I've

Illustrated it here to show you that we can use those two separate timings so let's get into our first pulse sequences

what is known as the multi-eco spin Echo Imaging we've done exactly what we've looked at

in this talk so far flip the spins to 90 allow them to de-phase flip the 180 degrees allow them to reface giving us

an echo at te and we read out that Echo during the frequency encode ingredients we then got all this time to wait until

our TR what we can do here is apply another 180 degree rfos those spins when we first

flip them to 90 degrees started to defaze we flip them 180 degrees and they started to re-phase again boom we read

out our signal at this point now they will defaze at that free induction Decay again they've still got

magnitude we haven't lost the transverse signal it hasn't flipped into the longitudinal plane we've seen that takes

a very long time for T1 relaxation to occur what's happened after that first 180 degree rfls once they've refaced

given us our Echo they are defacing again at T2 star we can apply another 180 degree pulse

and that again is going to cause that rephasing we can generate another Echo here and measure out a separate te

now this te is going to have slightly less signal than our first ee because the spin Echo is only accounting for the

local magnetic field in homogeneities we can't do anything to recover more than T2 Decay T2 Decay true T2 Decay is going

to happen no matter what that spin spin interaction is going to cause loss of transverse magnetization that is

unrecoverable not even by spin Echo Imaging now what have we done here we've created

two separate data acquisition points that have different Tes one a very short te and one a slightly longer te

now which sequences use a very short te well a very short t e is used in proton density Imaging because we haven't

allowed those differences in T2 relaxation to occur and in T1 weighted Imaging because we don't want

differences in T2 to provide contrast to our image the second te here is a longer te like we're using T2 Imaging we've

allowed a longer period of time for that true T2 relaxation to occur and we've separated the contrast in our image

based on those T2 values we can now place this data acquisition into one k space and this data acquisition into a

separate k space during this one pulse sequence now we've created one k space for this specific

slice at this phase encoding gradient we filled one part of K space here our TR is going to be long we are

waiting a long TR and that's what we want in proton density Imaging we want those spins to regain their full

longitudinal relaxation before then flipping them again into the transverse plane so a short t e and a long TR is

going to give us a proton density weighted image in this case space and when we fill this k space with our

second data acquisition we filled now this line here it's the same slice that we've selected with the same phase

encoding gradient the only thing that's changed is our te that slightly longer t e is going to bring out those T2

differences in tissue and we are going to generate a slice that has T2 weighting or more T2 waiting in that

image you can see how we've utilized this downtime to now create two separate images now this is a little bit of an

old technique with the development of flare which we're going to look at when we look at inversion recovery sequences

we generally don't use proton density weighted Imaging especially when we're looking at brain Imaging but this was a

good way to see if there were lesions close to water within the brain we could acquire a T2 image and if the lesion was

T2 bright it's quite difficult to see the difference between the CSF and the lesion and this proton density image

would allow us to tease out some of those differences no longer really used because of flair Imaging which we're

going to look at later but this is the first way that we can utilize some of that spare time we can then repeat the

sequence over and over again the only thing we're changing is the phase encoding gradient here and as we change

the phasing coding gradient we're going to fool the rest of k-space now the next pulse sequence we're going to look at is

a much more common pulse sequence we start again with exactly the same sequence here what are we going to do

with this extra period of time now the slice that we have selected here we've only caused a very specific slice

along our patient to then be flipped into the transverse plane all the other protons within our patient are still

just experiencing the main magnetic field they weren't processing up the frequency of this RF pulse that we

flipped into the 90 degrees we've then generated our spin Echo we've measured that spin Echo from that specific slice

the rest of the tissue is just waiting around processing at the Llama frequency again here the only magnetic field

that's on is the main magnetic field what we can do in multi-slice spin Echo Imaging is apply a different RF pulse

with the same slice selection gradient we are going to create a gradient along the z-axis that causes the spins to

process at different frequencies along that z-axis we can select a different RF pulse with a different RF bandwidth to

select a different slice while this is happening that First Slice is still relaxing waiting for it to get all its

longitudinal relaxation before we flip it again what we're doing here

is firstly we have selected one specific slice we have excited that slice we flip those spins into the 90 degree we've

generated our spin Echo and we've measured that signal in the second signal here we are using a different

rfos a different radio frequency pulse that different frequency is going to then account for a different slice

within our patient these spins in that First Slice are still regaining their longitudinal relaxation and we can now

at the same te this te here is the same as this te here so we've got the same te but on different slices we can now fill

two separate K spaces with these two Echoes and we can repeat this process for multiple different slices while

we're waiting for that next TR to occur the TR here is going to correspond to this First Slice once we repeat this

process again we are going to get a separate TR that's going to correspond to this slice the t e and the TR for

each slice will be exactly the same and they are filling different K spaces remember k space encodes for a specific

slice in our patients so let's look at what that looks like we again filling two separate K spaces in multi-eco

imaging those two k spaces represent a different weighting in multi-slice spin Echo we are representing the same

weighting here we've got the same te per slice and the same TR per slice but these two k spaces are encoding four

different slices now in multi-eco imaging with different waiting for the same slice in multi-slice spin Echo

Imaging we've got different slices with the same weighting there's a subtle difference between the two

now we don't want to excite slices that are exactly next to each other because when we looked at that RF bandwidth

remember there was a range of frequencies in that RF bandwidth and there's some overlap between slices here

so what we can do is as we're looking at our patient we can select slices that are further apart from one another and

as we select slices that are further apart from one another when we repeat the cycle again we can choose slices

that lie between those slices and afterwards we can combine those signals this is what's known as interleaving of

our signals we take all those separate case based data points and put them in their correct positions corresponding to

the correct slices in our patient you can see how this is going to drastically reduce the amount of time it takes to

acquire our MRI signal and the number of slices that we can put into a single TR is going to correspond to the total

reduction within our scan time so multi-slice Imaging allows us to use that downtime to then image other slices

within our patient but before combining all of that to generate our whole MRI image that we can scroll through from

slice to slice now the last spin Echo sequence that we're going to look at is what's known as fast spin echoimaging

now again we've started all these sequences the same apply the 90 degree rfas allow them to defaze flip them 180

degrees allowing them to reface creating an echo and that Echo is then sampled and placed in k space

we've now created sample that's going to correspond to this region in k space that corresponds to this specific phase

encoding gradients we can then apply another 180 degree RF pulse like we did in our multi-eco Imaging but we can see

that something different is happening here in our phase encode ingredients we've applied an equal and opposite

phase encoding gradient to the initial phase encoding gradient that we used prior to the 180 degree RF pulse

remember when we apply a phase encoding gradient that phase encoding has memory throughout the sequence once we've

de-phased them we turn off the phase encoding gradient and those spins have the same frequency because it's exposed

to the main magnetic field they have the Llama frequency in fact defacing has had memory in our

slice if we apply an equal and opposite phase encoding gradient that is going to re-phase that phase encoding gradient

cancel out the effect of this initial facing coding gradients we can then use a different phase encoding gradients and

the echo that we generate here is going to be a different line of K space we haven't selected another slice we've

just created another Echo they defased flipped the 180 rephased then after that 180 they've again started to defaze at

T2 star flip them 180 re-phase getting this Echo here this Echo and when we measure out the

signal here is going to correspond to a different phase encoding gradient a different part of K space we can then

repeat this again in equivalent opposite phase encoding gradients a new phase including gradient to give us another

Echo at te that's going to correspond to a different part of K space you can see now that these Echoes are

filling different lines of K space obviously the signal is going to decrease over time because of that T2

relaxation and the contrast throughout k space is not going to be identical now remember contrast predominantly comes

from the middle of K space so we can start filling k space initially with small phase encoding gradients allowing

us to get good contrast within our image before then filling out k space with higher and higher phase encoding

gradients to give us that detail in our image now why would we do this we're obviously

going to lose some of that classical contrast that we want and we're going to lose signal the more and more tees we

cram in between our first 90 degree rfos and the TR well it drastically reduces the amount

of time it takes to fill k-space here and the number of Echoes that we have within our pulse sequence between the

first RF pulse and TR is what's known as the echo train length the ETL the number of Echoes here

and here I've just included three Echoes if we had an echo train length of three that would reduce our total scan Time by

a factor of three this can lead to a drastic reduction in total scan time when we use hundreds of

Echoes between the first RF files and the TR and that's what we can do in fast spin Echo that's why it's fast I've got

multiple Echoes within one single TR that's filling one slice one k space here now of course this is going to come

with some consequences we are going to get a reduction in signal to noise ratio and we are going to get a change of

contrast as we are getting this T2 relaxation with Time Each Echo is only going to represent the degree of T2

relaxation at that period of time for that specific tissue so The Echoes at the end of our sequence nearing the TR

here are going to have very little signal very little transverse magnetization left now there are certain

tissues that keep their transverse magnetization for quite a long time like fluid and when we are creating images

like an MRCP where we're only interested in water these can be really useful because that water around pains its

signal for such a long period of time because of its long T2 relaxation times now we can go one step further and make

this even quicker when we looked at k space before we saw that k-space had what's known as conjugate symmetry we

can separate k space flip one half of K space and we see that they're exactly symmetrical here this tells us that we

could probably get away with only filling half of K space so we can create an image where we only fill half of K

space and the order in which we fill that case space will also have consequences for the contrast that we're

going to get in our image we've reduced the time it takes to create that single slice by another factor of two and we

can get really quick images even though we're using spin Echo sequences now spin Echo sequences can't be used

for every single application when we try and create T1 weighted images we want really short te times to negate that T2

differences in tissue and really short te times are often quite difficult within a spin Echo sequence because we

need time to apply the 90 degree RF pulse and apply the 180 degree rfos there are other sequences that allow us

to flip spins at smaller flip angles not using that full 90 degree flip angle and allow us to retain that longitudinal

magnetization that then gets flipped into the transverse plane and give us better T1 weighted images and that's

what we're going to cover when we look at gradient Echo signals we're then going to round this off by looking at

inversion recovery seeing how we can null signal coming from a specific tissue because we know that T1 and T2

relaxation rates now this is a complicated and long talk I would encourage you to go over these Concepts

to make sure that you have them in your head I hope I haven't lost you here let me know if you found this useful in the

comments below let me know if you've learned anything today and as always I will have a question bank with curated

questions Linked In the description you can go and test your knowledge on these Concepts so until next time goodbye

everybody