Pulse Sequences

Types of Pulse Sequences: Spin Echo Gradient Echo Inversion Recovery Echo Planar Imaging

Functional Techniques Diffusion-weighted imaging Perfusion weighted imaging Spectroscopy fMRI

Pulse Sequences

Spin Echo (SE) (Conventional Spin Echo)

RF pulse sequence with a 90o excitation pulse followed by a 180o rephasing or refocusing pulse to eliminate field inhomogeneity and chemical shift effects.

• Main Points: 1) 90o excitation pulse

2)180o rephasing pulse

Pulse Sequences

Spin Echo (SE)

Pulse Sequences

Spin Echo (SE)

Pulse Sequences

Spin Echo – Multiple Echo

Pulse Sequences

Spin Echo – Multi-echo

Pulse Sequences

Spin Echo Pulse Sequence T1 weighted images

Short TR (300 ms – 700 ms) Short TE (10 ms – 30 ms)

T2 weighted Images Long TE ( > 80 ms) Long TR ( > 2000 ms)

Pulse Sequences

T1WI vs. T2WI____________________________________

*Short TR *Long TE

Short TE Long TR

T1WI T2WI

Pulse Sequences

Proton (Spin) Density Weighted

Density of Resonating spins in a given volume (e.g., tissue). The higher the concentration of spin density, the higher

(brighter) the received signal.

• Long TR (1000 ms – 2000 ms)• Short TE (10 ms – 30 ms)

Pulse Sequences

Spin Echo T1 – weighted image (short TR, short TE) Proton Density image (long TR, short TE) T2 – weighted image (long TE, long TR)

Pulse Sequences

Rapid Acquisition with Relaxation Enhancement Also known as RARE Fast Spin Echo (FSE) – GE, Picker, Toshiba &

Hitachi Turbo Spin Echo (TSE) – Siemens & Philips One advantage is speed without loss of S/N.

In CSE, if acquisition time is reduced by 50%, the S/N is reduced by 40%

Pulse Sequences

Fast Spin Echo

Pulse Sequences

RARE

Pulse Sequences

Fast (Turbo) Spin Echo Echo Train Length (ETL) or Turbo Factor (TF) Effective Echo Time (ETE) Echo Train Spacing (ETS)

Pulse Sequences

Rapid Acquisition with Relaxation Enhancement Acquires multiple echoes per excitation at

different phase encoding steps – echo train length (ETL)

The number of echos acquired per excitation pulse is referred to as echo train length

TE is referred to as “Effective TE” (ETE)

Pulse Sequences

Rapid Acquisition with Relaxation Enhancement Time between each echo (phase encoding

step) is referred to as echo train spacing (ETS)

TE is primarily responsible for image contrast. RARE reduces the amount of excitation

pulses. Scan Time – (TR x Gpe x NEX) / ETL

Pulse Sequences

Fast Spin Echo Scan Time = (TR x Gpe X NEX) / ETL

TR = 2000 ms (2000 x 256 x 4) / 8

Gpe = 256 2000 x 256 x 4 = 2048000

NEX = 4 2048000 / 1000 = 2048 secondsETL = 8 2048 / 60 (convert seconds to minutes) = 34.13

minutes

34.13 minutes / 8ETL = 4.26 minutes

Pulse Sequences

Fast Spin Echo Advantage

Reduced Scan Time Disadvantage

Possible flow and motion artifacts Fat may be brighter on FSE than CSE Image blur – Increased TF or ETL

Pulse Sequences

Gradient Echo (GE)

Generally uses an excitation flip angle (FA) of less than 90o degree and a gradient reversal to rephase the protons

• Main Points: 1) Variable Flip Angle (FA)

2) Gradient reversal

Pulse Sequences

Pulse Sequences

Gradient Echo

Pulse Sequences

Advantages: Gradient Echo Much shorter scan times than SE pulse

sequences Low FA allows for faster recovery of

longitudinal magnetization Gradients rephase faster than 180o RF pulses TR and TE values are shorter than spin echo

pulse sequences

Pulse Sequences

Disadvantages: Gradient Echo Susceptible to magnetic field inhomogeneities Contain magnetic susceptibility artifacts T2* weighting

Pulse Sequences

Fast Spin Echo (Advantage over GRE)

FSE uses a 180 degree pulse to eliminate susceptibility artifacts.

Heavy T2 – weighted images cannot be easily acquired with GRE

Pulse Sequences

Gradient Echo: Weighting T1 Weighting - 1o controlled by FA and TR T2* Weight – 1o controlled by TE

Pulse Sequences

Gradient Echo Pulse Sequence T1 – Weighted

Large Flip Angle Short TR Short TE

T2* - weighted Small Flip Angle Long TR Long TE

Proton Density Weighted Small Flip Angle Long TR Short TE

Pulse Sequences

Inversion Recovery

Sequence consisting of an initial 180o RF pulse to invert the magnetization, followed by a spin-echo (90o to 180o) or gradient sequence.

Pulse Sequences

Inversion Recovery

Pulse Sequences

Inversion Recovery FLAIR – Nulls CSF STIR – Nulls FAT

FLAIR STIR

Pulse Sequences

Dixon

Pulse Sequences

Null Point

Pulse Sequences

Echo Planar Imaging (EPI) Allows data to be collected and reconstructed

in less than a second Stronger and faster gradients (slew rate)

required Data collected along GFE (readout) direction

Pulse Sequences

Echo Planar Imaging

Functional Techniques

Diffusion-weighted image (DWI) Technique used to measure the motion of

water molecules Areas with increased diffusion within a tissue

show greater signal loss Terms such as – b-value, Apparent diffusion

coefficient (ADC) Clinical applications – acute cerebral infarcts

(ischemic areas) appear bright

Functional Techniques

Perfusion-weighted image (PWI) Technique used to measure the flow of blood

though the capillary region of an organ or tissue

Dynamic Susceptibility Contrast (DSC) uses gadolinum as a tracer

Arterial Spin Labeling (ASL) noninvasive Terms - Cerebral Blood Flow (CBF), Mean

transit Time (MTT) and Cerebral Blood Volume (CBV)

Functional Techniques

Spectroscopy (MRS) Technique that provides chemical information

about a tissue Nuclei such as 1H, 31P, 13C, 23Na, 39K, 19F Methods used:

Stimulated echo acquisition mode (STEAM) Point-resolved spectroscopy (PRESS) Image-selected in vivo Spectroscopy (ISIS) Chemical shift imaging (CSI) a.k.a. magnetic

resonance spectroscopic imaging (MRSI)

Functional Techniques

Functional MRI (fMRI) Term used to describe any technique that

evaluates brain physiology rather than anatomy

fMRI specifically used to map brain activity Areas of interest – motor cortex, visual cortex Blood oxygenation level-dependent (BOLD)

• BOLD: Blood Oxygen Level Dependence fMRI is the most common for research purposes• Measures the hemodynamic response (amount of

blood flow) related to neural activity in the brain• Increase in magnetic susceptibility when blood is

oxygenated• Direct correlation between brain activity and

cerebral blood flow has been observed, but unsure of exact underlying mechanisms

• Usually uses a T2* weighted contrast • TR: 2-4s• 2-4mm spatial resolution (better with 3-9T)

• Two common types of experimental design• Resting state: Participant has no task, just

lies still in the scanner• Experimental: Participants are presented

with tasks or stimuli at approximately 5s intervals• Or block design due to poor temporal

resolution

5s + 5s … to 2 min Repeat w Next Block of Images

• Although commonly thought of as a direct measure of brain activity, fMRI usually identifies relative differences in brain activity

• Correlation does NOT equal causality• Subtraction Technique• EX: Response to images of smoking

-

Smokers Nonsmokers

=

Difference

• fMRI is not currently used for diagnostic purposes• Used to identify functional maps of neural networks

& research relative deficiencies in brain function• New software allows for the quantification of

network activity via Independent Components Analysis

• Differences in network connectivity has been associated with certain disorders and fMRI should be capable of accurate diagnosis within the next decade• Allows early identification and treatment of

disordered individuals (e.g. Schizophrenia and Alzheimers)

Default Mode NetworkVisual Network

• Diffusion based fMRI• Contrast MR• Arterial Spin Labeling• Magnetic Resonance Spectroscopic

Imaging• Electroencephalography

• Although it has great spatial resolution, fMRI has poor temporal resolution of neuronal activity

• Combined EEG-fMRI may allow quantification of activity at sub-ms and sub-mm resolution