Pulse Sequences

Field trip: Tuesday, Feb 5th

Hardware tour of VUIIIS Philips 3T Meet here at regular class time (11.15) Complete MRI screening form!

Chuck Nockowski Philips Service Engineer

Reminder: Project/Presentation Pick a special topic of interest to you:

Clinical (e.g., cancer, stroke, Alzheimers disease) Technical (e.g., parallel imaging, k-space, novel acquisition) Hardware (e.g., coils, gradients, radiofrequency transmission)

NOTE: if you are actively working on an imaging research project (Ph.D., etc.) you must choose something different from your thesis topic! I must approve all topics: just email or talk to me.

Prepare written report 10-20 pgs; double-spaced; font=12 pt; margins=1

Present summary to class 15 min (~10 slides)

What do we know so far about how MR imaging works?

When we place a brain, body, etc. in MRI scanner, spins of protons on water molecules will align, on average, with the main magnetic field Main field is in z-direction This occurs due to Zeeman effect

Lower energy state for alignment of spins with, vs. against, B0 z

What do we know so far about how MR imaging works?

After magnetization (M) reaches equilibrium with main magnetic field B0 (few seconds), we can apply a rotating field B1 to cause M to move into the transverse (x-y) plane Frequency of pulse given by ( B ) The duration of the pulse determines the flip

angle e.g., if 5 ms pulse gives 45 degree flip angle 10 ms pulse gives 90 degree flip angle

What do we know so far about how MR imaging works?

If we turn off the B1 pulse, M will revert to its equilibrium orientation because of relaxation Longitudinal component (Mz) re-aligns with z

according to time constant T1 Transverse component (Mxy) decays to zero with

time constant T2(*)

T1 and T2 are (i) independent and (ii) unique for different tissue types. Sources of two different contrasts in MRI!

What do we know so far about how MR imaging works?

We detect oscillations from M by using a coil Oscillating magnetic field will induce current in a coil Faraday induction

We discern spatial information from sample by: Applying a gradient during signal acquisition

This generates a spatially varying phase for the M vectors (i.e., the gradient encodes spatial information)

Perform Fourier transform of acquired signal to obtain estimate of spin density function (i.e., image) Generally, we do this in 2-D and consider spatial frequencies.

Signal Detection

Changing magnetic field introduces a current in a wire Precessing magnetization detected with a coil tuned to the

appropriate frequency Important: can only detect components in transverse (x-y)

plane

B0

Movie courtesy of William Overall

Going further We know basics of MRI physics, slice selection,

and image formation

How do we use this information to generate contrast?

How do we obtain T1, T2, T2*, diffusion, flow, etc. weightings?

Need to understand pulse sequence variants and parameters

How do we represent pulse sequences?

Gradient strength (mT / meter)

When we turn on receiver i.e., detect signal

Our B1 pulses RF = radiofrequency (T) Time ( ~ ms )

Pulse sequence timing What is a pulse sequence?

Time description of RF, gradients and data acquisition Or, a sequence of RF, gradient and acquisition timings

Important sequence timing parameters TE: echo time, or the time between B1 excitation and the

center of k-space TR: repetition time, or the time between repeated

excitations of the same slice TI: inversion time, or the time between inversion and

excitation

Complete description of what the scanner is doing, sufficient info to predict what images will look like!

Most important parameters of MRI pulse sequence

Excita'on

Echo 'me (TE)

Acquire

Repe''on 'me (TR)

Introduction to pulse sequences

What influences signal level? Proton density, T1, T2, T2*

Simple pulse sequences Gradient echo, spin echo and inversion

recovery

Readout trajectory and considerations Bandwidth, SNR, artifacts, and time

Excitation

Tip magnetization vector from being aligned with the magnetic field (B0) so that it is in the x-y (transverse) plane Do this with radiofrequency (RF) excitation

pulse

The flip angle of the RF excitation can be more or less than 90 degrees So long as some magnetization is in

transverse plane

Excitation Pulse

Laboratory reference frame (e.g., sitting at the scanner console)

Movie courtesy of William Overall

Excitation Pulse

Rotating reference frame of B1 (e.g., riding on B1) Rotating at angular frequency ( = -0)

Movie courtesy of William Overall

Turn off the RF pulse

Excitation pulse moves some component of the magnetization vector into the transverse plane

After this, we turn off the RF pulse The excited magnetization will relax back

to its original state The speed of this relaxation is determined by two

time constants: Transverse plane: T2 Longitudinal plane: T1 T2 and T1 are completely independent!

What happens after we turn off the RF excitation pulse?

Mz returns to alignment with main magnetic field T1 describes this relaxation time

Movie courtesy of William Overall

What happens after we turn off the RF excitation pulse?

Now look at just the transverse (Mx,y) component Dephasing! T2 / T2* describes this time

Movie courtesy of William Overall

Transverse magnetization

T2 = 25 ms T2 = 50 ms T2 = 100 ms

Mx,y = e-TE/T2

Longitudinal magnetization

T1 = 800 ms T1 = 1200 ms T1 = 4300 ms

Mz = 1-e-TR/T1

We can add pulses before the excitation pulse too!

Excita'on

Echo 'me (TE)

Acquire

Inversion 'me (TI)

Longitudinal magnetization in inversion recovery experiment

T1 = 800 ms T1 = 1200 ms T1 = 4300 ms

Mz = 1-(2e-TI/T1-e-TR/T1)

Inversion Mme (TI; ms)

MRI signal

T1 = 800 ms T1 = 1200 ms T1 = 4300 ms

T2 = 25 ms T2 = 50 ms T2 = 100 ms

Signal ~ C Mx,y(TE) Mz(TR,TI)

Water density Specific to tissue We dont change this

Transverse magnetization Manipulate magnitude by varying TE

Longitudinal magnetization Manipulate magnitude by varying TR

What are T1 and T2 values? Depends on field strength. T1 increases with field strength whereas

T2 decreases with field strength

T2 times at 3 Tesla White matter ~ 110 ms Gray matter ~ 80 ms Cerebrospinal fluid ~ 600 ms

T1 times at 3 Tesla White matter ~ 800 ms Gray matter ~ 1200 ms Cerebrospinal fluid ~ 4300 ms

Unique T1/T2 for other tissue types as well (e.g., tumor, blood, edema, etc.) Unique T1/T2 provides contrast between tissues More to come on this next week!

One additional relaxation time: T2*

Dephasing of spins in transverse plane causes magnetization vectors to oppose each other. Net signal is lower due to dephasing Leads to apparent decrease in T2.

This is called effective T2, or T2* T2 = relaxation due to field inhomogeneity

1T2*

=1T2'

+1T2

Relaxation times thus far

T1: relaxation time in longitudinal plane T2*: effective relaxation time in transverse

plane. Includes dephasing from controllable

inhomogeneities (e.g., imperfect scanner shielding, magnetic objects/implants, etc.)

Also includes dephasing from uncontrollable interactions (e.g., local interactions of molecules in voxel)

T2: Relaxation time in transverse plane only from uncontrollable spin-spin effects

How can we obtain T2 and/or T2* contrast?

Gradient echo (GRE): Fundamentally T2*-weighted

Spin echo (SE): Fundamentally T2-weighted

Note: we can vary pulse sequence parameters to make these sequences T1-weighted instead (more to come on this next time)

Fundamentals of gradient echo (GRE)

What does signal look like after the excitation?

RF

Signal

Free induction decay (FID) Well-defined frequency (Modulated by decaying exponential)

Gradient echo (GRE) pulse sequence

Vendor-speak

Philips: Fast Field Echo (FFE) Siemens: Fast Low Angle Shot (FLASH) GE: SPoiled Gradient Recall (SPGR)

Gradient echo can be used with different k-space trajectories e.g., GRE spinwarp, GRE spiral, GRE radial

Many structural, fMRI, susceptibility scans utilize GRE contrast

Fundamentals of gradient echo (GRE)

Apply Gx gradient with half the area sequentially with slice-select gradient Causes an echo: spins within the slice will

be in-phase at time TE

RF

Gz

Signal TE

Gx

Fundamentals of gradient echo (GRE) BUT: We can choose TE to be anything we

want This may reduce absolute signal However may increase T2* contrast

TE-choose

RF

Gz

Signal TE

Gx

Fundamentals of gradient echo (GRE) Optimum TE has most signal TE-choose has most contrast! Best choice may depend on application BOLD fMRI: choose TE to maximize contrast in

and around venous blood water

TE-choose

RF

Gz

Signal TE

Gx

Problem: dephasing of spins quite short, especially at high field

At 7 Tesla, venous blood water T2* < 5 ms

At 7 Tesla, tissue water T2* ~ 25 ms

At 3 Tesla, these numbers are longer (15 40 ms)

Difficult to fill our k-space when the signal decays so quickly. Can we do better?

Can we do anything to lengthen the time it takes for spins to dephase?

Yes, apply an RF pulse to transverse magnetization

Movie courtesy of William Overall

Spin echo (SE) signal

SE can refocus only part of the signal decay T2 refers to part that can be refocused

(1/T2*=1/T2+1/T2) Without refocusing, signal will have T2* contrast

Even spin echo signal experiences some decay T2 refers to signal decay that cannot be refocused With refocusing, signal will have T2 contrast

T2* < T2

Gradient vs. spin echo sequences

Gradient echo (GRE) T2* decay Fast!

Spin echo (SE) T2 decay T2 > T2*

Gradient and spin echo sequences can have different k-space readout trajectories

Cartesian Spiral

Examples of different MRI sequences

Gradient echo (T2*-weighted depending on TE) Blood oxygenation level-dependent (BOLD)

functional MRI (fMRI) Susceptibility weighted imaging

Spin echo (T2-weighted depending on TE) Fluid attenuated inversion recovery (FLAIR) Diffusion weighted imaging

Inversion recovery (inversion prepulse followed by GRE or SE) FLAIR Arterial spin labeling (ASL) Vascular space occupancy (VASO)

Introduction to pulse sequences

Basic image contrast Proton density, T1, T2, T2*

Simple pulse sequences Gradient echo and spin echo

Readout trajectory and considerations Bandwidth Signal-to-noise ratio (SNR)

Gradient and spin echo sequences can have different k-space readout trajectories

Cartesian Radial Spiral

Remember:

Low frequencies describe basic object structure High frequencies contain ne structure informa'on Best readout choice oOen depends on applica'on

Objects and frequencies

Object

Frequency = 0

Low frequency High frequency

Remember:

Low frequencies describe basic object structure High frequencies contain ne structure informa'on Best readout choice oOen depends on applica'on

Object

Object Object

Frequencies in images

High frequency Low frequency

Low frequency

High frequency

Cornelius Vanderbilt 1794-1877

Signal to noise ratio (SNR) Image quality frequency evaluated in terms of signal-

to-noise ratio (SNR) SNR: signal / noise () Signal is easy to characterize: just the net signal we

detect Noise is more difficult, with multiple contributions:

Thermal noise: noise due to hardware, outside RF interference, etc.

Physiological noise: fluctuations secondary to biological changes (e.g., cardiac fluctuations, respiratory fluctuations, spontaneous brain activity

Should keep track of which noise you are interested in

Thinking about thermal and physiological noise

In simplest cases (single coil, absence of parallel imaging), the thermal noise can be quan'ed from the signal outside the brain

Time

Physiological noise can be thought of as varia'on in signal over 'me

More to come on these later

What influences SNR? Voxel size

1 x 1 x 1 mm Volume = 1 mm3

2 x 2 x 1 mm Volume = 4 mm3

Larger voxels have signal contribution from more spins Signal proportional to voxel

volume

Note: reducing voxel size by n along each m dimensions costs nm in signal

For example, changing from 1x1x1 mm to 2x2x1 mm increases signal by four-fold

What influences SNR? Bandwidth

Bandwidth: the range of frequencies sampled Determined by strength of gradient field

Frequencies of Object Noise

Bandwidth

What influences SNR? Bandwidth

High bandwidth = high noise Low bandwidth = low noise

Frequencies of Object Noise

Bandwidth

Bandwidth and the readout Tshot

Tshot

Gradient Strength

Increasing the readout bandwidth reduces total time required to obtain signal (Tshot ~ 1/Gx)

Gx

Gx

What influences SNR? Multiple acquisitions

Each time additional measurement is acquired, signal adds but random noise does not Each line in multi-line readout Every plane in 3D acquisition Any repetition or averaging of acquisition

Longer acquisitions generally lead to higher SNR There are diminishing returns however.

Increases scale with square root.

Nshot

Noise Nshot = NPE x N3D x Nave

1/ ~ Nshot

What influences SNR? Multiple acquisitions

Good rule of thumb: SNR is higher for longer scan times For multi-shot acquisitions, where multiple

excitations and readouts are used to acquire a single slice of data, the total time time (Ttot) is the product of the number of shots (Nshot) and the time of each shot (Tshot):

Ttot = Nshot x Tshot

1/ ~ [Nshot x Tshot] = TTot

What influences SNR? Imaging time

Noise in images

1. Smaller voxel sizes 2. Fewer averages 3. Lower Mxy 4. Lower Mz 5. Higher bandwidth 6. Lower B0

Pulse sequence summary Pulse sequence variants:

Gradient echo (GRE) Spin echo (SE)

Gradient echo refocuses signal decay with bipolar gradient (negative refocusing component with half the area of slice-select positive component) Fundamentally T2*-weighted Fast signal decay

Spin echo refocuses signal decay with 180-degree refocusing RF pulse Fundamentally T2-weighted Slower signal decay

Pulse sequence summary

Excita'on

Echo 'me (TE)

Acquire

Repe''on 'me (TR)

Noise in images

1. Smaller voxel sizes 2. Fewer averages 3. Lower Mxy 4. Lower Mz 5. Higher bandwidth 6. Lower B0

Coming up Thursday: Contrast manipulation + example

problems Tuesday: Jay Moore: RF pulses / hardware Thursday: Jay Moore: RF pulses / hardware Tuesday: Chuck Nockowski: Hardware tour

Mid-term exam: 19 Feb (not 14 Feb)