1. Medical Image Analysis Medical Imaging Modalities: Magnetic Resonance Imaging Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

2. Magnetic Resonance Imaging Nuclear magnetic resonance ◦ The selected nuclei of the matter of the object ◦ Blood flow and oxygenation ◦ Different parameters: weighted, weighted, Spin-density ◦ Advance: MR Spectroscopy and Functional MRI ◦ Fast signal acquisition of the order of a fraction of a second Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

3. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

4. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure 4.12. MR images of a selected cross-section that are obtained simultaneously using a specific imaging technique. The images show (from left to right), respectively, the T1-weighted, T-2 weighted and the Spin-Density property of the hydrogen protons present in the brain.

5. Magnetic Resonance Imaging 1 H: high sensitivity and vast occurrence in organic compounds 13 C: the key component of all organic 15 N: a key component of proteins and DNA 19 F: high relative sensitivity 31 P: frequent occurrence in organic compounds and moderate relative sensitivity Adapted from the Wikipedia, www.wikipedia.org.www.wikipedia.org

6. MR Spectroscopy Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

7. MR Spectroscopy Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

8. Functional MRI Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

9. MRI Principles : spin-lattice relaxation time : spin-spin relaxation time : the spin density Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

10. MRI Principles 1. Great web sites 1.Simulations from BIGS - Lernhilfe für Physik und TechnikSimulations from BIGS - Lernhilfe für Physik und Technik 2.http://www.cis.rit.edu/class/schp730/bmri/b mri.htmhttp://www.cis.rit.edu/class/schp730/bmri/b mri.htm Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

11. MRI Principles Spin ◦ A fundamental property of nuclei with odd atomic weight and/or odd atomic numbers is the possession of angular moment Magnetic moment ◦ The charged protons create a magnetic field around them and thus act like tiny magnets Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

12. MRI Principles : the spin angular moment : the magnetic moment : a gyromagnetic ratio, MHz/T A hydrogen atom ◦ :42.58 MHz/T Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

13. N S J J Figure 4.13. Left: A tiny magnet representation of a charged proton with angular moment, J. Right: A symbolic representation of a charged proton with angular moment, J and a magnetic moment, μ.

14. MRI Principles Precession of a spinning proton ◦ The interaction between the magnetic moment of nuclei with the external magnetic field ◦ Spin quantum number of a spinning proton: ½ ◦ The energy level of nuclei aligning themselves along the external magnetic field is lower than the energy level of nuclei aligned against the external magnetic field Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

15. Figure 4.14 (a) A symbolic representation of a proton with precession that is experienced by the spinning proton when it is subjected to an external magnetic field. (b) The random orientation of protons in matter with the net zero vector in both longitudinal and transverse directions.

16. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. MRI Principles Equation of motion for isolated spin Solution:

17. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Longitudinal Vector OX at the transverse position X

18. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure 4.15 (a). Nuclei aligned under thermal equilibrium in the presence of an external magnetic field. (b). A non-zero net longitudinal vector and a zero transverse vector provided by the nuclei precessing in the presence of an external magnetic field.

19. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Non-zero Net Longitudinal Vector x y z x y z H0H0 Net Zero Transverse Vector

20. MRI Principles The precession frequency ◦ Depends on the type of nuclei with a specific gyromagnetic ratio and the intensity of the external magnetic field ◦ This is the frequency on which the nuclei can receive the Radio Frequency (RF) energy to change their states for exhibiting nuclear magnetic resonance ◦ The excited nuclei return to the thermal equilibrium through a process of relaxation emitting energy at the same precession frequency

21. MRI Principles 90-degree pulse ◦ Upon receiving the energy at the Larmor frequency, the transverse vector also changes as nuclei start to precess in phase ◦ Form a net non-zero transverse vector that rotates in the x-y plane perpendicular to the direction of the external magnetic field Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

22.  S N  S N x y z Figure 4.16. The 90-degree pulse causing nuclei to precess in phase with the longitudinal vector shifted clockwise by 90-degrees as a result of the absorption of RF energy at the Larmor frequency.

23. MRI Principles 180-degree pulse ◦ If enough energy is supplied, the longitudinal vector can be completely flipped over with a 180-degree clockwise shidf in the direction against the external magnetic field Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

24. S N  S N  x y z Figure 4.17. The 180-degree pulse causing nuclei to precess in phase with the longitudinal vector shifted clockwise by 180-degrees as a result of the absorption of RF energy at the Larmor frequency.

25. MRI Principles Relaxation ◦ The energy emitted during the relaxation process induces an electrical signal in a RF coil tuned at the Larmor frequency ◦ The free induction decay of the electromagnetic signal in the PF coil is the basic signal that is used to create MR images ◦ The nuclear excitation forces the net longitudinal and transverse magnetization vectors to move Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

26. MRI Principles A stationary magnetization vector The total response of the spin system Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

27. Figure 4.18. The transverse relaxation process of spinning nuclei.

28. MRI Principles The longitudinal and transverse magnetization vectors with respect to the relaxation times where Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

29. t t M x,y (t) M z (t) Figure 4.19. (a) Transverse and (b) longitudinal magnetization relaxation after the RF pulse.

30. MRI Principles The RF pulse causes nuclear excitation changing the longitudinal and transverse magnetization vectors After the RF pulse is turned off, the excited nuclei go through the relaxation phase emitting the absorbed energy at the same Larmor frequency that can be detected as an electrical signal, called the Free Induction Decay (FID) Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

31. MRI Principles The NMR spin-echo signal (FID signal) Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

32. MR Instrumentation The stationary external magnetic field ◦ Provided by a large superconducting magnet with a typical strength of 0.5 T to 1.5 T ◦ Housing of gradient coils ◦ Good field homogeneity, typically on the order of 10-50 parts per million ◦ A set of shim coils to compensate for the field inhomogeneity Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

33. Gradient Coils Magnet Gradient Coils RF Coils Patient Platform Monitor Data-Acquisition System Figure 4.20. A general schematic diagram of a MR imaging system.

34. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

35. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

36. MR Instrumentation An RF coil ◦ To transmit time-varying RF pulses ◦ To receive the radio frequency emissions during the nuclear relaxation phase ◦ Free Induction Decay (FID) in the RF coil Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

37. MR Pulse Sequences NMR signal ◦ The frequency and the phase Spatial encoding in MR imaging ◦ Frequency encoding and phase encoding Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

38. x z y y x x y z z Sagital Coronal Axial Figure 4.21 (a). Three-dimensional object coordinate system with axial, sagittal and coronal image views. (b): From top left to bottom right: Axial, coronal and sagittal MR images of a human brain.

39. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

40. MR Pulse Sequences Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Z Gradient 90 RF Pulse (Slice Selection) X Gradient Phase-Encoding (x-scan selection) Z Gradient 180 RF Pulse (Slice Echo Formation) Y Gradient Frequency Encoding (Read-Out Pulse) Figure 4.22. (a): Three-dimensional spatial encoding for spin-echo MR pulse sequence. (b): A linear gradient field for frequency encoding. (c). A step function based gradient field for phase encoding.

41. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Varying Spatially Dependent Larmor Frequency S N  S N  Linear Gradient Precessing Nuclei External Magnet Positive Phase Change Negative Phase Change Phase - Encoding Gradient Step

42. MR Pulse Sequences Frequency encoding ◦ A linear gradient is applied throughout the imaging space a long a selected direction ◦ The effective Larmor frequency of spinning nuclei is also spatially encloded along the direction of the gradient ◦ Slice selection for axial imaging Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

43. MR Pulse Sequences The phase-encoding gradient ◦ Applied in steps with repeated cycles ◦ If 256 steps are to be applied in the phase- encoding gradient, the readout cycle is repeated 256 times, each time with a specific amount of phase-encoding gradient Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

44. Spin Echo Imaging : ◦ Between the application of the 90 degree pulse and the formation of echo (rephasing of nuclei : ◦ Between the 90 degree pulse and 180 degree pulse Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

45. RF Energy: 90 Deg Pulse Zero Net Vector: Random Phase Relaxation Dephasing RF Energy: 180 Deg Pulse Echo - Formation RF Energy: 90 Deg Pulse Zero Net Vector: Random Phase In Phase Rephasing Echo - Formation In Phase Figure 4.23. The transverse relaxation and echo formation of the spin echo MR pulse sequence.

46. Spin Echo Imaging K-space ◦ The placement of raw frequency data collected through the pulse sequences in a multi-dimensional space ◦ By taking the inverse Fourier transform of the k-space data, an image about the object can be reconstructed in the spatial domain ◦ The NMR signals collected as frequency- encoded echoes can be placed as horizontal lines in the corresponding 2-D k-space Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

47. Spin Echo Imaging K-space ◦ As multiple frequency encoded echoes are collected with different phase-encoding gradients, they are placed as horizontal lines in the corresponding k-space with the vertical direction representing the phase-encoding gradient values Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

48. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

49. Spin Echo Imaging : the cycle repetition time weighted ◦ A long and a long weighted ◦ A short and a short Spin-density ◦ A long and a short Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

50. 90 deg RF pulse 180 deg RF pulse G z: Slice Selection Frequency Encoding Gradient G x: Phase Encoding Gradient G y: Readout Frequency Encoding Gradient T E /2 TETE RF pulse Transmitter NMR RF FID Signal Figure 4.24. A spin echo pulse sequence for MR imaging.

51. Spin Echo Imaging The effective transverse relaxation time from the field inhomogeneities Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

52. Spin Echo Imaging The effective transverse relaxation time from a spatial encoding gradient Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

53. Inversion Recovery Imaging IR imaging ◦ IR imaging pulse sequence allows relaxation of some or all of before spins are rephased through 90-degree pulse and therefore emphasizes the effect of longitudinal magnetization ◦ 180-degree pulse is first applied along with the slice selection frequency encoding gradient Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

54. Echo Planar Imaging A single-shot fast-scanning method Spiral Echo Planar Imaging (SEPI) ◦ where

55. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. 90 deg RF pulse 90 deg RF pulse G z: Slice Selection Frequency Encoding Gradient G x: Oscillating Gradient G y: Readout Gradient RF pulse Transmitter NMR RF FID Signal  Figure 4.25. A single shot EPI pulse sequence.

56. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. g y  gxgx xx yy Figure 4.26. The k-space representation of the EPI scan trajectory.

57. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. xx yy SEPI Trajectory Data Sampling Points Figure 4.27. The spiral scan trajectory of SEPI pulse sequence in the k-space.

58. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. 90 deg RF pulse 180 deg RF pulse G z: Slice Selection Frequency Encoding Gradient G x Gradient G y Gradient T E /2 TETE RF pulse Transmitter NMR RF FID Signal TDTD Figure 4.28. The SEPI pulse sequence

59. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure 4.29. MR images of a human brain acquired through SEPI pulse sequence.

60. Gradient Echo Imaging Fast low angle shot (FLASH) imaging ◦ Utilize low-flip angle RF pulses to create multiple echoes in repeated cycles to collect the data required for image reconstruction ◦ A low-flip angle (as low as 20 degrees) ◦ The readout gradient is inverted to re-phase nuclei leading to the gradient echo during the data acquisition ◦ The entire pulse sequence time is much shorter than the spin echo pulse sequence Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

61. Low Flip Angle RF pulse G z: Slice Selection Frequency Encoding Gradient RF pulse Transmitter G x: Phase Encoding Gradient G y: Readout Frequency Encoding Gradient TETE NMR RF FID Signal Figure 4.30. The FLASH pulse sequence for fast MR imaging.

62. Flow Imaging Tracking flow ◦ Diffusion (incoherent flow) and perfusion (partially coherent flow) ◦ The FID signal generated in the RF receiver coil by the moving nuclei and velocity- dependent factors MR angiography Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011.

63. 90 deg RF pulse 180 deg (selective) RF pulse G z: Slice Selection Frequency Encoding Gradient G x: Phase Encoding Gradient G y: Readout Frequency Encoding Gradient T E /2 TETE RF pulse Transmitter NMR RF FID Signal Figure 4.31. A flow imaging pulse sequence with spin echo.

64. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure 4.32: Left: A proton density image of a human brain. Right: The corresponding perfusion image.

65. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. 90 degree RF pulse G z: Slice Selection Frequency Encoding Gradient RF pulse Transmitter G x: Phase Encoding Gradient G y: Readout Frequency Encoding Gradient TETE NMR RF FID Signal Next 90 degree RF pulse TRTR Figure 4.33. Gradient echo based MR pulse sequence for 3-D MR volume angiography.

66. Figures come from the textbook: Medical Image Analysis, Second Edition, by Atam P. Dhawan, IEEE Press, 2011. Figure 4.34. An MR angiography image.

67. Flow Imaging Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org angiography image

68. FMRI fMRI imaging ◦ Measure blood oxygen level during sensory stimulation or any task that causes a specific neural activity ◦ Visual or auditory stimulation, finger movement, or a cognitive task ◦ Blood oxygenated level dependence (BOLD) ◦ Oxygenated hemoglobin ( ) is diamagnetic, while deoxygenated hemoglobin ( ) is paramagnetic

69. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org

70. FMRI fMRI imaging ◦ A reduction of the relative deoxy-hemoglobin concentration due to an increase of blood flow and hence increased supply of fresh oxy- hemoglobin during neural activity is measured as an increase in or weighted MR signals

71. Diffusion Imaging Diffusion process ◦ Water molecules spread out over time that is represented by Brownian motion ◦ An anisotropic Gaussian distribution along a given spatial axis such that the spread of the position of molecules after a time along a spatial axis can be represented with a variance of ◦ where is diffusion coefficient in the tissue

72. Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org DTI color image

73. Diffusion Imaging Diffusion process ◦ Anisotropic diffusion in the white matter ◦ Isotropic diffusion in the gray matter ◦ Motion probing gradients (MPG) to examine the motion of water molecules in the diffusion process in a specific direction ◦ The MR FID signal is decreased for healthy tissue, and increased with trapped-in water molecules

74. Diffusion Imaging Diffusion process ◦ where is the gyromagnetic ratio, is diffusion coefficient, and is the strength of two MPG gradients each with duration separated by applied in spatial directions

75. Diffusion Imaging Diffusion process

76. Diffusion Imaging Diffusion process ◦ Fractional anisotropy (FA) ◦ Multiple sclerosis, strokes, tumors, Parkinson’s and Alzheimer’s disease ◦ Attention deficit hyperactivity disorder (ADHS)

77. Contrast, Spatial Resolution, and SNR Spin-echo imaging pulse sequence Inversion recovery (180-90-180) imaging pulse sequence

78. Contrast, Spatial Resolution, and SNR Gradient echo imaging pulse sequence

79. Contrast, Spatial Resolution, and SNR Paramagnetic contrast agent ◦ gadolinium (Gd) to change the susceptibility of the net magnetization vector ◦ Reduces relaxation time and increases the signal intensity of -weighted images Noise and field inhomogeneities ◦ RF noise, field inhomogeneities, motion, chemical shift

80. Contrast, Spatial Resolution, and SNR Chemical shift ◦ The deviation of its effective resonance frequency in the presence of other nuclei from a standard reference without any other nuclei with their local magnetic fields present ◦ ppm

81. Contrast, Spatial Resolution, and SNR ◦ Induced magnetic field in alkenes ◦ Induced magnetic field in alkynes Figure comes from the Wikipedia, www.wikipedia.org.www.wikipedia.org