1. Contrast Mechanism and Pulse Sequences Allen W. Song Brain Imaging and Analysis Center Duke University

2. Part III.1 Image Contrast Mechanisms

3. The Concept of Contrast (or Weighting)  Contrast = difference in RF signals — emitted by water protons — between different tissues  T1 weighted example: gray-white contrast is possible because T1 is different between these two types of tissue

4. T2 Decay MR Signal T1 Recovery MR Signal 50 ms 1 s Static Contrast Imaging Methods

5. Optimal TR and TE for Proton Density Contrast T 2 Decay MR Signal t (ms)t (s) MR Signal TR TE T 1 Recovery

6. Proton Density Contrast   Technique: use very long time between RF shots (large TR) and very short delay between excitation and readout window (short TE)   Useful for anatomical reference scans   Several minutes to acquire 256  256  128 volume   ~1 mm resolution

7. Proton Density Weighted Image

8. Optimal TR and TE for T2* and T2 Contrast T 2 Decay MR Signal T 1 Recovery TR TE T1 Contrast T2 Contrast

9. T2* and T2 Contrast   Technique: use large TR and intermediate TE   Useful for functional (T2* contrast) and anatomical (T2 contrast to enhance fluid contrast) studies   Several minutes for 256  256  128 volumes, or second to acquire 64  64  20 volume   1mm resolution for anatomical scans or 4 mm resolution [better is possible with better gradient system, and a little longer time per volume]

10. T2T2* Cars on different tracks

11. 180 o turn t = TE/2 180 o turn t = TE/2 TE/2 t=0 t=TE t=0 t=TE Fast Spin Slow Spin Can we compensate the field term? … TE/2

12. T2 Weighted Image

13. Optimal TR and TE for T1 Contrast T1 contrastT2 contrast T 2 Decay MR Signal T 1 RecoveryTRTE

14. T1 Contrast   Technique: use intermediate timing between RF shots (intermediate TR) and very short TE, also use large flip angles   Useful for creating gray/white matter contrast for anatomical reference   Several minutes to acquire 256  256  128 volume   ~1 mm resolution

15. T1 Weighted Image

16. -S -S o SSoSSo S = S o * (1 – 2 e –t/T1 ) S = S o * (1 – 2 e –t/T1’ ) Inversion Recovery for Extra T1 Contrast

17. T2 Inversion Recovery (CSF Attenuated)

18. In summary, TR controls T1 weighting and TE controls T2 weighting. Short T2 tissues are dark on T2 images, but short T1 tissues are bright on T1 images.

19. Motion Contrast Imaging Methods  Can “prepare” magnetization to make readout signal sensitive to different motion properties  Flow weighting (bulk movement of blood)  Diffusion weighting (scalar or tensor)  Perfusion weighting (blood flow into capillaries)

20. MR Angiogram Time-of-Flight ContrastTime-of-Flight Contrast Phase ContrastPhase Contrast

21. Time-of-Flight Contrast No Flow Medium Flow High Flow No Signal Medium Signal High Signal Vessel Acquisition Saturation Excitation Vessel

22. 90 o Excitation Image Acquisition RF Gx Gy Gz 90 o Saturation Time to allow fresh flow enter the slice Pulse Sequence: Time-of-Flight Contrast

23. Phase Contrast (Velocity Encoding) Externally Applied Spatial Gradient G Externally Applied Spatial Gradient -G Blood Flow v Time T 2T 0

24. 90 o Excitation Phase Image Acquisition RF Gx Gy Gz G -G-G Pulse Sequence: Phase Contrast

25. MR Angiogram

26. Diffusion Weighted Imaging Sequences Externally Applied Spatial Gradient G Externally Applied Spatial Gradient -G Time T 2T 0

27. Pulse Sequence: Gradient-Echo Diffusion Weighting 90 o Excitation Image Acquisition RF Gx Gy Gz G -G-G

28. 90 o Excitation Image Acquisition RF Gx Gy Gz G 180 o G Pulse Sequence: Spin-Echo Diffusion Weighting

29. Advantages of DWI 1.The absolute magnitude of the diffusion coefficient can help determine proton pools coefficient can help determine proton pools with different mobility with different mobility 2. The diffusion direction can indicate fiber tracks

30. Diffusion Anisotropy

31. Determination of fMRI Using the Directionality of Diffusion Tensor

32. Display of Diffusion Tensor Using Ellipsoids

33. Diffusion Contrast

34. Perfusion/Flow Weighted Arterial Spin Labeling Transmission Imaging Plane Coil Tagging

35. AlternatingInversion Pulse Tagging AlternatingInversion Imaging Plane FAIR Flow-sensitive Alternating IR EPISTAR EPI Signal Targeting with Alternating Radiofrequency Perfusion/Flow Weighted Arterial Spin Labeling with Pulse Sequences

36. RF Gx Gy Gz Image 90 o 180 o Alternating opposite Distal Inversion Odd Scan Even Scan 180 o RF Gx Gy Gz Image 90 o 180 o Alternating Proximal Inversion Odd Scan Even Scan Pulse Sequence: Perfusion Imaging FAIR EPISTAR

37. Advantages of ASL Perfusion Imaging 1.It can non-invasively image and quantify blood delivery blood delivery 2.Combined with proper diffusion weighting, it can assess capillary perfusion it can assess capillary perfusion

38. Perfusion Contrast

39. Perfusion Diffusion Diffusion and Perfusion Contrast

40. Part III.3 Some fundamental acquisition methods And their k-space view

41. k-Space Recap Kx =  /2  0 t  Gx(t) dt Ky =  /2  0 t  Gx(t) dt Equations that govern k-space trajectory: These equations mean that the k-space coordinates are determined by the area under the gradient waveform

42. Gradient Echo Imaging  Signal is generated by magnetic field refocusing mechanism only (the use of negative and positive gradient)  It reflects the uniformity of the magnetic field  Signal intensity is governed by S = So e -TE/T2* where TE is the echo time (time from excitation to the center of k-space)  Can be used to measure T2* value of the tissue

43. MRI Pulse Sequence for Gradient Echo Imaging digitizer on Excitation Slice SliceSelection Frequency Encoding Encoding Phase Phase Encoding Encoding Readout

44. K-space view of the gradient echo imaging Kx Ky 123.......n123.......n

45. Multi-slice acquisition Total acquisition time = Number of views * Number of excitations * TR Number of views * Number of excitations * TR Is this the best we can do? Interleaved excitation method

46. readout Excitation Slice SliceSelection Frequency Encoding Encoding Phase Phase Encoding Encoding Readout readoutreadout …… …… …… TR

47. Spin Echo Imaging   Signal is generated by radiofrequency pulse refocusing mechanism (the use of 180 o pulse )   It doesn’t reflect the uniformity of the magnetic field   Signal intensity is governed by S = So e -TE/T2 where TE is the echo time (time from excitation to the center of k-space)   Can be used to measure T2 value of the tissue

48. MRI Pulse Sequence for Spin Echo Imaging digitizer on Excitation Slice SliceSelection Frequency Encoding Encoding Phase Phase Encoding Encoding Readout 90 180

49. K-space view of the spin echo imaging Kx Ky 123.......n123.......n

50. Fast Imaging How fast is “fast imaging”? In principle, any technique that can generate an entire image with sub-second temporal resolution can be called fast imaging. For fMRI, we need to have temporal resolution on the order of a few tens of ms to be considered “fast”. Echo-planar imaging, spiral imaging can be both achieve such speed.

51. Echo Planar Imaging (EPI)  Methods shown earlier take multiple RF shots to readout enough data to reconstruct a single image  Each RF shot gets data with one value of phase encoding  If gradient system (power supplies and gradient coil) are good enough, can read out all data required for one image after one RF shot  Total time signal is available is about 2  T2* [80 ms]  Must make gradients sweep back and forth, doing all frequency and phase encoding steps in quick succession  Can acquire 10-20 low resolution 2D images per second

52. ... Pulse Sequence K-space View

53. Why EPI?  Allows highest speed for dynamic contrast  Highly sensitive to the susceptibility-induced field changes --- important for fMRI  Efficient and regular k-space coverage and good signal-to-noise ratio  Applicable to most gradient hardware

54. Spiral Imaging t = TE RF Gx Gy Gz t = 0

55. K-Space Representation of Spiral Image Acquisition

56. Why Spiral? More efficient k-space trajectory to improveMore efficient k-space trajectory to improve throughput. throughput. Better immunity to flow artifacts (no gradient atBetter immunity to flow artifacts (no gradient at the center of k-space) the center of k-space) Allows more room for magnetization preparation,Allows more room for magnetization preparation, such as diffusion weighting. such as diffusion weighting.

57. Under very homogeneous magnetic field, images look good …

58. Gradient-Recalled EPI Images Under Homogeneous Field

59. Gradient Recalled Spiral Images Under Homogeneous Field

60. However, if we don’t have a homogeneous field … (That is why shimming is VERY important in fast imaging)

61. Distorted EPI Images with Imperfect x-Shim A B C D

62. Distorted Spiral Images with Imperfect x-Shim A B C D