1. Pulse Sequences Types of Pulse Sequences: Functional Techniques
Spin Echo
Gradient Echo
Inversion Recovery
Echo Planar Imaging
Functional Techniques
Diffusion-weighted imaging
Perfusion weighted imaging
Spectroscopy
fMRI

2. 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

3. Pulse Sequences
Spin Echo (SE)

4. Pulse Sequences
Spin Echo (SE)

5. Pulse Sequences
Spin Echo – Multiple Echo

6. Pulse Sequences
Spin Echo – Multi-echo

7. 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)

8. Pulse Sequences T1WI vs. T2WI ____________________________________
*Short TR *Long TE
Short TE Long TR
T1WI T2WI

9. 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)

10. 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)

11. 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%

12. Pulse Sequences
Fast Spin Echo

13. Pulse Sequences
RARE

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

15. 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)

16. 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

17. Pulse Sequences Fast Spin Echo Scan Time = (TR x Gpe X NEX) / ETL
TR = 2000 ms (2000 x 256 x 4) / 8
Gpe = x 256 x 4 =
NEX = / 1000 = 2048 seconds
ETL = / 60 (convert seconds to minutes) = minutes
34.13 minutes / 8ETL = 4.26 minutes

18. Pulse Sequences Fast Spin Echo Advantage Disadvantage
Reduced Scan Time
Disadvantage
Possible flow and motion artifacts
Fat may be brighter on FSE than CSE
Image blur – Increased TF or ETL

19. 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

20. Pulse Sequences

21. Pulse Sequences
Gradient Echo

22. 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

23. Pulse Sequences Disadvantages: Gradient Echo
Susceptible to magnetic field inhomogeneities
Contain magnetic susceptibility artifacts
T2* weighting

24. 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

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

26. 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

27. 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.

28. Pulse Sequences
Inversion Recovery

29. Pulse Sequences Inversion Recovery FLAIR – Nulls CSF STIR – Nulls FAT

30. Pulse Sequences
Dixon

31. Pulse Sequences
Null Point

32. 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

33. Pulse Sequences
Echo Planar Imaging

34. 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

35. 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)

36. 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)

37. 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)

38. Functional Magnetic Resonance Imaging fMRI
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)

39. Methods 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 s … to 2 min Repeat w Next Block of Images

40. Methods- cont’d
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 - =

41. Clinical Utility 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)
Visual Network
Default Mode Network

42. Other Functional Techniques
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