1. M R I Pulse Sequences
Jerry Allison Ph.D.

2. 1017 pages ©2004 2

3. Outline I. Spin Echo Imaging Multiplanar Multislice Oblique
II. Inversion Recovery (IR)
III. Gradient Recalled Echo
IV. Three Dimensional (Volume)
Techniques
V. Fast Imaging Techniques
VI. Echoplanar Imaging

4. Image Contrast
Image contrast in radiography and CT is based upon a few properties of the tissues or contrast agents involved:
- physical density (g/cc)
- electron density (electrons/cc)
- atomic number 4

5. Image Contrast
Contrast in MRI is more complex and depends on many properties/parameters, which can be classified into “intrinsic” properties and “extrinsic” parameters. Intrinsic properties relate directly to the tissue. Extrinsic parameters relate to the characteristics of the MR imager and the details of the “MRI Pulse sequence” used for imaging. 5

6. Intrinsic Properties Proton density T1 relaxation T2 relaxation
- magnetic susceptibility
Diffusion
Magnetization transfer
-cross relaxation 6

7. Intrinsic Properties Chemical Shift Temperature Perfusion
Changes in tissue composition (e.g. age)
Viscosity
Physiologic motion
Bulk flow
Blood
CSF 7

8. Extrinsic Parameters Magnetic field strength
-static field
-gradient field
Magnetic field homogeneity
Hardware and software parameters
-coil selection
-number of slices acquired
-slice thickness and gap 8

9. Extrinsic Parameters Hardware and software parameters -slice location
-slice orientation
-number of averages or excitations
-RF pulse shape (#sinc lobes)
-RF transmitter bandwidth
-RF receive bandwidth
-pixel size
-matrix size
-field of view 9

10. Extrinsic Parameters -acquisition mode ( 2D / 3D )
-artifact suppression
-physiologic triggering / gating
-orientation of phase and frequency
encode gradients 10

11. Extrinsic Parameters RF pulse sequences -inversion recovery -spin echo
-gradient recalled echo
-fast scan sequences
-echoplanar (single shot techniques) 11

12. Extrinsic Parameters Pulse sequence parameters -repetition time (TR)
-echo time (TE)
-inversion time (TI)
-flip angle ()
-echo train length
Contrast enhancing agents 12

13. MRI Pulse Sequences
An MRI pulse sequence dramatically impacts the appearance of an MRI image. 13

14. Spin Echo Pulse Sequences
T1 weighted
PD weighted
T2 weighted
TR 510
TE 14
2min 7sec for 17 slices
TR 4500
TE 15eff (ETL7)
2min 39sec for 24 slices
TR 4500
TE 105eff (ETL7)
2min 39sec for 24 slices 14

15. Inversion Recovery Gradient Echo Pulse Sequence
TR 12.1
TE 5.4
3min 11sec for 160 slices 15

16. MRI Pulse Sequences
More specifically, an MRI pulse sequence is a “sequence” of temporal waveforms:
Radiofrequency (RF) pulses
Gradient (magnetic field) pulses
Data acquisiton intervals 16

17. Here is a pulse-sequence diagram
Here is a pulse-sequence diagram. This shows a timeline for: 1) RF pulses; 2) gradient amplitudes for Gx, Gy, Gz; 3) the readout (i.e., A/D), and 4) the signal of the excited nuclei. 17

18. Multiplanar Imaging
Axial, sagittal, and coronal images can be acquired as follows:
Notice that for each plane, the choice of axis for phase and frequency encoding can vary. 18

19. MRI Image Weighting Many MRI images are described as:
Proton density weighted
T1 weighted
T2 weighted
(and T2* weighted) 19

20. Spin Echo Images T1 weighted PD weighted T2 weighted TR 510 TE 14
2min 7sec for 17 slices
TR 4500
TE 15eff (ETL7)
2min 39sec for 24 slices
TR 4500
TE 105eff (ETL7)
2min 39sec for 24 slices 20

21. Proton Density Weighting
Images are (largely) weighted by the mobile hydrogen content of the tissues (water and fat).
PD: FAT < WM < GM < CSF
PD images: CSF > GM > WM > Fat 21

22. Proton Density Weighting
-The nucleus of most hydrogen atoms is a single particle: the proton
-The number of “mobile” hydrogen nuclei per voxel directly affects the intensity of the voxel in an MRI image (for all image weightings).
-Proton Density Weighting emphasizes proton density (as opposed to t1, t2 or T2*)
-Total proton densities
-CSF g H/cc
-Grey Matter g H/cc
-White Matter g H/cc
-Fat g H/cc
- Protons in lung tissue volume ~ 0.01 g H/cc
So, one of many problems with lung imaging is the low proton density per volume, leading to very low SNR. 22

23. Proton Density Weighting
-Although white matter and grey matter have very similar proton density; they are differentiated in MRI by their lipid and water content.
Lipid (g H / cc) Water (g H / cc)
Grey Matter
White Matter 23

24. T1 Weighting
Images demonstrate good contrast between soft tissue types (because different tissues have different “T1” values). 24

25. T2 Weighting
Images demonstrate good contrast between normal tissue and pathology (because many pathologies have elevated “T2” values due to increased free water content). 25

27. T1, T2 Weighting In images of the head
T1: FAT < WM < GM < CSF
T1 images: FAT > WM > GM > CSF
T2: FAT < WM < GM < CSF
T2 images: CSF > GM > WM > FAT
Careful: CSF or Fat can be suppressed 27

28. Pulse Sequence Families
Spin Echo: SE
Gradient Echo: GE
Gradient Recalled Echo (GRE)
Field Echo (FE)
Inversion Recovery: IR
STIR: short tau inversion recovery
Fat suppression
FLAIR: fluid attenuated inversion recovery
Fluid (CSF) suppression 28

29. Spin Echo Imaging Easy to control image weighting with SE T1 weighted
PD weighted 29

30. Spin Echo Imaging
The Spin Echo imaging technique has the advantage that it is not as sensitive to static inhomogeneity of the magnet and inhomogeneity caused by magnetic susceptibility of patient tissue. 30

31. Spin Echo Imaging 31

32. Spin Echo Imaging
The pulse sequence must be repeated many times to produce an MRI image. The time interval between each execution of the pulse sequence is termed the Repetition Time (TR). 32

33. Spin Echo Imaging
The value of the repetition time (TR) and the echo time (TE) can be varied to control contrast in spin echo imaging. For example:
TR = 2000 msec TE = 20 msec Proton Density Weighting
TR = 2000 msec TE = 80 msec T2 Weighting
TR = 600 msec TE = 20 msec T1 Weighting 33

34. Fast Spin Echo Pulse Sequence (FSE) Turbo Spin Echo (TSE)
Careful: Fat can be excessively bright on FSE images (j-coupling) 34

35. Gradient Recalled Echo
Gradient recalled echo techniques have great versatility. A variety of contrasts can be produced while imaging rapidly.
GRE techniques include:
GRASS, SPGR, FLASH, FISP, PSIF and many, many others. 35

36. 36

37. Gradient Recalled Echo Images
2D-FLASH
TR 25msec
TE 9msec
a = 35o
5.7sec per slice
MIP
(Maximum Intensity Projection) 37

38. Gradient Recalled Echo Image
Multi Planar GRASS
mixed T1/T2 weighting
TR 500msec TE 13msec 2NEX a=60o
3min 14 sec for 15 slices 38

39. Gradient Recalled Echo
Exceptions are:
1. The creation of the echo is accomplished solely by gradient magnetic fields (no 180o RF pulse).
2. Deposition of RF energy in the patient is lower since the 180o RF pulses are not used (less heating of patient tissues).
3. Static inhomogeneity of the magnet and inhomogeneity caused by magnetic susceptibility of patient tissue are NOT corrected by gradient recalled echo techniques.
4. T2 contrast becomes T2* contrast. 39

40. Gradient Recalled Echo
4. The initial flip angle is frequently chosen to be less than 90o . The flip angle in gradient recalled echo techniques is called a .
The optimum value of a for a particular TR and tissue having spin lattice relaxation T1 is called the Ernst angle. e
-TR T1
cos(ae) = 40

41. Gradient Recalled Echo
5. 3D or volume imaging can be accomplished (resulting in thinner slices).
Vancouver, BC courtesy of Dr. Rawson 41

42. Three Dimensional Volume Techniques
3D voxels are isotropic (or nearly isotropic). The voxels are the same size in all 3 dimensions. The dimensions of a typical 3D voxel are
1 mm x 1 mm x 1 mm. The acquisition of isotropic voxels enables the data set to be reformatted into any oblique plane without significant loss of resolution using Post Processing Techniques. 42

43. Three Dimensional Volume Image
MPRAGE: Magnetization Prepared Rapid Gradient Echo
TR 11.4msec TE 4.2msec a=12o 1.4mm
6min 55sec for 120 slices (168mm slab)
Uses Inversion Recovery 43

44. Inversion Recovery (IR)
Inversion recovery pulse sequences are useful for:
Suppression of selected tissues (e.g. orbital fat, liver screening, fatty tumors, CSF)
Creation of heavily T1 weighted images without a dominant contribution from fat (e.g. brain, liver and musculoskeletal imaging). 44

45. Inversion Recovery (IR)
A basic IR spin echo pulse sequence consists of a 180o inversion pulse, followed by an inversion time TI, then a 90o RF pulse. 45

46. Consider two voxels, one of fat and one of H2O
This method of fat suppression is sometimes called “short TI”
inversion recovery or STIR imaging. 46

47. Inversion Recovery (IR)
In spin echo inversion recovery imaging sequences, the 90o pulse is followed by a 180o pulse in order to produce a spin echo at time TE following the 90o pulse 47

48. 48

49. IR Image vs FLAIR: fluid attenuated IR (T2 weighted spin echo)
STD T2 weighting vs
FLAIR: fluid attenuated IR (T2 weighted spin echo)
Inversion time: 2.5sec (CSF is suppressed)
TR 10sec TE 119msec (ETL7)
3min 49sec for 19 slices 49

50. GE MRI Image Annotation50

51. GE MRI Image Annotation51

52. GE MRI Image Annotation52

53. GE MRI Image Annotation53

54. GE MRI Image Annotation54

55. GE MRI Image Annotation55