Allen W. Song, PhD Brain Imaging and Analysis Center Duke University

1. MRI: Contrast Mechanismsand Pulse Sequences Allen W. Song, PhD Brain Imaging and Analysis Center Duke University

2. Image Contrasts

3. The Concept of Contrast Contrast= difference in signals emitted by water protons between different tissues For example, gray-white contrast is possible because T1 is different between these two types of tissue

4. Two Types of Contrast Static Contrast: Image contrast is generated from the static properties of biological systems (e.g. density). Motion Contrast: Image contrast is generated from movement (e.g. blood flow, water diffusion).

5. MR Signal MR Signal T2 Decay transverse T1 Recovery longitudinal Static Contrast Imaging Methods time time 1 s 50 ms

6. Most Common Static Contrasts • Weighted by the Proton Density • Weighted by the Transverse Relaxation Times (T2 and T2*) • Weighted by the Longitudinal Relaxation Time (T1)

7. Proton Density Contrast Contrast solely dependent on proton density, without influence from relaxation times.

8. The Effect of TR and TE on Proton Density Contrast TE TR MR Signal MR Signal T1 Recovery T2 Decay t (s) t (ms)

9. Optimal 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

10. Proton Density Weighted Image

11. T2 and T2* Contrasts Contrast dominated by the difference in T2 and T2* (transverse relaxation times).

12. T2* Cars on different tracks Transverse Relaxation Times T2 Cars on the same track

13. To get pure T2 contrast, we need perfectly homogeneous magnetic field. This is difficult to achieve, as sometime even if the actual field is uniform, the presence of biological tissue will still change the homogeneity. So how do we then remove the influence of the magnetic field inhomogeneity?

14. Time Reversal Using 180o RF Pulse Fast Spin Fast Spin TE/2 t=0 180o turn t = TE/2 Fast Spin Fast Spin TE/2 t=TE Slow Spin Slow Spin TE/2 t=0 180o turn t = TE/2 Slow Spin TE/2 Slow Spin t=TE

15. The Effect of TR and TE on T2* and T2 Contrast TR TE T1 Recovery MR Signal MR Signal T2 Decay T1 Contrast T2 Contrast

16. Optimal 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]

17. T2 Weighted Image

18. T2* Weighted Image T2* Images PD Images

19. T1 Contrast Contrast dominated by the T1 (longitudinal relaxation time) differences.

20. TR TE T1 Recovery T2 Decay MR Signal MR Signal T1 contrast T2 contrast The Effect of TR and TE onT1 Contrast

21. Optimal 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

22. T1 Weighted Image

23. Inversion Recovery to Boost T1 Contrast S = So * (1 – 2 e –t/T1) So S = So * (1 – 2 e –t/T1’) -So

24. IR-Prepped T1 Contrast

25. 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.

26. Motion Contrast Imaging Methods Prepare magnetization to make signal sensitive to different motion properties • Flow weighting (bulk movement of blood) • Diffusion weighting (water molecule random motion) • Perfusion weighting (blood flow into capillaries)

27. Flow Weighting: MR Angiogram • Time-of-Flight Contrast • Phase Contrast

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

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

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

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

32. MR Angiogram

33. Random Motion: Water Diffusion

34. Diffusion Weighting Externally Applied Spatial Gradient -G Externally Applied Spatial Gradient G T 2T 0 Time

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

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

37. Diffusion Anisotropy

38. Determination of fMRI Using the Directionality of Diffusion Tensor

39. Advantages of DWI • The absolute magnitude of the diffusion • coefficient (ADC) can help determine proton pools • with different mobility • 2. The diffusion direction can indicate fiber tracks ADC Anisotropy

40. Fiber Tractography

41. D A B C DTI and fMRI

42. Perfusion The injection of fluid into a blood vessel in order to reach an organ or tissue, usually to supply nutrients and oxygen. In practice, we often mean capillary perfusion as most delivery/exchanges happen in the capillary beds.

43. Perfusion Weighting: Arterial Spin Labeling Imaging Plane Labeling Coil Transmission

44. Arterial Spin Labeling Can Also Be Achieved Without Additional Coils Pulsed Labeling Imaging Plane Alternating Inversion Alternating Inversion EPISTAR EPI Signal Targeting with Alternating Radiofrequency FAIR Flow-sensitive Alternating IR

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

46. Advantages of ASL Perfusion Imaging • It is non-invasive • Combined with proper diffusion weighting • to eliminate flow signal first, it can be used • to assess capillary perfusion

47. Perfusion Contrast

48. Perfusion Map Perfusion Diffusion

49. Some fundamental acquisition methods commonly used to generate static and motion contrasts, and their k-space views

50. k-Space Recap Equations that govern k-space trajectory: Kx = g/2p 0tGx(t) dt Ky = g/2p 0tGx(t) dt These equations mean that the k-space coordinates are determined by the area under the gradient waveform