1. Principles of MRI Physics and Engineering Allen W. Song Brain Imaging and Analysis Center Duke University

2. Part III.1 Some fundamental acquisition methods And their k-space view

3. 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

4. A 2x2 Matrix I(1,1) I(1,2) I(2,1) I(2,2) S(1,1) S(1,2) S(2,1) S(2,2) Image Space k-Space (data space) S(1,1)S(1,2) S(2,1)S(2,2)

5. 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

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

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

8. 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

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

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

11. Inversion Recovery Imaging Inversion Recovery Imaging

12. Time History of MR Signal -S -S o SSoSSo S = S o * (1 – 2 e –t/T1 ) S = S o * (1 – 2 e –t/T1’ )

13. Pulse Sequence for Inversion Recovery RF Gz GRE or SE Readout 180 o

14. Part III.2 Image Contrast Mechanisms

15. 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

16. T2 Decay MR Signal T1 Recovery MR Signal 50 ms 1 s

17. 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

18. T2 Decay MR Signal T1 Recovery MR Signal 50 ms 1 s Proton Density Contrast

19. Proton Density Weighted Image

20. T2* and T2 Contrast   Technique: use large TR and intermediate TE   Useful for anatomical and functional studies   Several minutes for 256x256X128 volumes, or ~several seconds 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]

21. T2 Decay MR Signal T1 Recovery MR Signal 50 ms 1 s T2* and T2 Contrast

22. T2 Weighted Image

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

24. T2 Decay MR Signal T1 Recovery MR Signal 50 ms 1 s T1 Contrast

25. T1 Weighted Image

26. -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

27. T2 Inversion Recovery (CSF Attenuated)

28. 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.

29. Other Imaging Methods  Can “prepare” magnetization to make readout signal sensitive to different physical properties of tissue  Flow weighting (bulk movement of blood)  Diffusion weighting (scalar or tensor)  Perfusion weighting (blood flow into capillaries)  Magnetization transfer (sensitive to proteins in voxel)  Temperature

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

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

32. 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

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

34. 90 o Excitation Phase Image Acquisition RF Gx Gy Gz G -G-G Pulse Sequence: Phase Contrast

35. MR Angiogram

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

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

38. 90 o Excitation Image Acquisition RF Gx Gy Gz G 180 o G Pulse Sequence: Spin-Echo Diffusion Weighting

39. 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

40. Diffusion Anisotropy

41. Determination of fMRI Using the Directionality of Diffusion Tensor

42. Display of Diffusion Tensor Using Ellipsoids

43. Diffusion Contrast

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

45. 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

46. 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

47. 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

48. Perfusion Contrast

49. Perfusion Diffusion Diffusion and Perfusion Contrast

50. Other Interesting Types of Contrast  Perfusion weighting: sensitive to capillary flow  Diffusion weighting: sensitive to diffusivity of H 2 O  Very useful in detecting stroke damage  Directional sensitivity can be used to map white matter tracts  Also useful in functional MRI to determine the signal origin  Flow weighting: used to image blood vessels (MR angiography)  Magnetization transfer: provides indirect information about H nuclei that aren’t in H 2 O (mostly proteins)

51. Part III.3 Introduction to Fast Imaging Very useful techniques for fMRI, Diffusion, Perfusion, etc. when brain functions are being investigated

52. 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.

53. 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

54. GE-EPI Pulse Sequence Actually have 64 (or more) freq. encodes in one readout (each one < 1 ms) [only 13 freq. encodes shown here]

55. K-space view of the echo-planar imaging ….. Kx Ky

56. 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

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

58. K-Space Representation of Spiral Image Acquisition

59. 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.

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

61. Gradient-Recalled EPI Images Under Homogeneous Field

62. Gradient Recalled Spiral Images Under Homogeneous Field

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

64. Magnetic Field Inhomogeneity Introduced by x-Shim Coil

65. Distorted EPI Images with Imperfect x-Shim

66. Distorted Spiral Images with Imperfect x-Shim

67. Magnetic Field Inhomogeneity Introduced by y-Shim Coil

68. Distorted EPI Images with Imperfect y-Shim

69. Distorted Spiral Images with Imperfect y-Shim

70. Magnetic Field Inhomogeneity Introduced by z-Shim Coil

71. Distorted EPI Images with Imperfect z-Shim

72. Distorted Spiral Images with Imperfect z-Shim