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Chapter 3 Principles of nuclear magnetic resonance and MRI Review.

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1 Chapter 3 Principles of nuclear magnetic resonance and MRI Review

2 Basic Physics of MRI Nuclei line up with magnetic moments either in a parallel or anti- parallel configuration. In body tissues more line up in parallel creating a small additional magnetization M in the direction of B 0. Nuclear magnetic moments precess about B 0. Nuclei spin axis not parallel to B 0 field direction.

3 Basic Physics of MRI Frequency of precession of magnetic moments given by Larmor relationship   ~ 43 mHz/Tesla Larmor frequencies of RICs MRIs 3T ~ 130 mHZ 7T ~ 300 mHz 11.7T ~ 500 mHz f =  x B 0 f = Larmor frequency (mHz)   = Gyromagnetic ratio (mHz/Tesla) B 0 = Magnetic field strength (Tesla)

4 NMRable Nuclei Basic Physics of MRI  Body 1 H content is high due to water (>67%)  Hydrogen protons in mobile water are primary source of signals in fMRI and aMRI

5 M is parallel to B 0 since transverse components of magnetic moments are randomly oriented. The difference between the numbers of protons in the parallel (up here) and anti- parallel states leads to the net magnetization (M). Proton density relates to the number of parallel states per unit volume. Signal producing capability depends on proton density. Basic Physics of MRI B0B0

6 RF pulse duration and strength determine flip angle duration strength RF Pulse Frequency of rotation of M about B 1 determined by the magnitude (strength) of B 1. Basic RF Pulse Concepts

7 Basic Physics of MRI FID magnitude decays in an exponential manner with a time constant T2. Decay due to spin-spin relaxation. 90° RF pulse rotates M into transverse (x-y) plane Rotation of M within transverse plane induces signal in receiver coil at Larmor frequency. Magnitude signal dependent on proton density and M xy. FID = Free Induction Decay

8 Need for 180° Pulse - Spin Echo 90 ° 180 ° 0 TE TE/2 - time TE/2 + FID also diminishes due to local static magnetic field inhomogeneityFID also diminishes due to local static magnetic field inhomogeneity Some spins precess faster and some slower than those due to B 0Some spins precess faster and some slower than those due to B RF pulse reverses dephasing at TE (echo time)180 ° RF pulse reverses dephasing at TE (echo time) Residual decay due to T2Residual decay due to T2 Spin Echo Signal

9 Nuclear Magnetic Resonance (NMR) Signal: Spin Echo (SE) TE/2 90 o TR (repetition time) = time between RF excitation pulses 90 o 180 o FIDSpin Echo TE = time from 90 o pulse to center of spin echo

10 Developing Contrast Using Weighting Contrast = difference in image values between different tissues T1 weighted example: gray-white contrast is possible because T1 differs between these two types of tissue

11 T1 and T2 T1-Relaxation: Recovery –Recovery of longitudinal orientation of M along z-axis. –‘T1 time’ refers to time interval for 63% recovery of longitudinal magnetization. –Spin-Lattice interactions. T2-Relaxation: Dephasing –Loss of transverse magnetization M xy. –‘T2 time’ refers to time interval for 37% loss of original transverse magnetization. –Spin-spin interactions,and more.

12 Properties of Body Tissues TissueT1 (ms)T2 (ms) Grey Matter (GM) White Matter (WM)60080 Muscle90050 Cerebrospinal Fluid (CSF) Fat25060 Blood T1 values for B 0 ~ 1Tesla. T2 ~ 1/10 th T1 for soft tissues

13 Basic Physics of MRI: T1 and T2 T1 is shorter in fat (large molecules) and longer in CSF (small molecules). T1 contrast is higher for lower TRs. T2 is shorter in fat and longer in CSF. Signal contrast increased with TE. TR determines T1 contrast TE determines T2 contrast.

14 Contrast, Imaging Parameters  - proton density SE – spin echo imaging GRE – gradient echo imaging Short TEs reduce T2W Long TRs reduce T1W T1W T2W

15 Making an Image k-space (frequency domain) Making an Image k-space (frequency domain) A k-space domain image is formed using frequency and phase encoding

16 Two Spaces FT FT -1 k-space kxkxkxkx kykykyky Acquired Data Image space x y Final Image MRI task is to acquire k-space image then transform to a spatial-domain image. kx is sampled (read out) in real time to give N samples. ky is adjusted before each readout. MR image is the magnitude of the Fourier transform of the k-space image

17 The k-space Trajectory kx =  0 t  G x (t) dt ky =  0 t’  G y (t) dt if G y is constant ky =  G y t’ Equations that govern 2D k-space trajectory The kx, ky frequency coordinates are established by durations (t) and strength of gradients (G). if G x is constant kx =  G x t

18 Simple MRI Frequency Encoding: digitizer on RF Excitation Slice Slice Selection (G z ) Frequency Encoding (G x ) Encoding (G x ) Readout Exercise drawing k-space manipulation

19 The k-space Trajectory Frequency Encoding Gradient (G x ) kx ky (0,0) Digitizer records N samples along kx where ky = 0 Move to left side of k-space.

20 Simple MRI Frequency Encoding: Spin Echo digitizer on Excitation Slice SliceSelection Frequency Encoding (G x ) Encoding (G x ) Readout Exercise drawing k-space representation

21 The K-space Trajectory 180 pulse Digitizer records N samples of kx where ky = 0

22 Frequency and Phase Encoding for 2D Spin Echo Imaging digitizer on Excite SliceSelect FrequencyEncode PhaseEncode Readout kx ky

23 The 2D K-space Trajectory 180 pulse Digitizer records N samples of kx and N samples of ky

24 Gradient Echo Imaging Signal is generated by magnetic field refocusing mechanism only (the use of negative and positive gradient) Signal intensity is governed by S = S o e -TE/T2* Can be used to measure T2* value of the tissue R2* = R2 + R2 ih +R2 ph (R2=1/T2) Used in 3D and BOLD fMRI

25 MRI Pulse Sequence for Gradient Echo Imaging digitizer on Excitation Slice SliceSelection Frequency Encoding Encoding Phase Phase Encoding Encoding Readout Ernst angle (  E ) for optimum SNR. E.E.

26 crusher B1B1 GzGz GxGx GyGy B1B1 GzGz GxGx GyGy TR 1 TR 2 TR N/2 TR N TR 1 TR 2 TR N/2 TR N Fig Courtesy of Peter Jezzard. refocus acquire FLASH Pulse Sequence 2D Gradient Echo RF (10-15 degrees) Short TR (10-50 msec) N= 256 ( sec per slice)

27 3D Sequence (Gradient Echo) GxGx GyGy GzGz B1B1 acq kxkx kyky kzkz Scan time = N y N z TR Good for high resolution T1W images of brain Select & phase phase read RF

28 3D T1W brain image 0.8mm spacing Time = 25 min

29 B1B1 GzGz GxGx GyGy Fig Courtesy of Peter Jezzard. refocus acquire a) b) 2D Echo Planar Imaging (EPI) 2d Gradient Echo Entire 2D slice within one TR 64x64 or 128x128 Time per slice (30-50 msec) Whole volume (2-4 sec) Good for fMRI studies

30 Fig courtesy of Peter Jezzard. FLASH Image T2* Weighted TE = 30 msec CSF is bright Signal loss and distortions due to local differences in magnetic field Sources of Contrast in Brain - Endogenous - BOLD - Exogenous - could be contrast agent (Gd based) - Other - Susceptibility R2* = net T2 relaxation rate = 1/T2* R2* = R2 tis + R2 ih + R2 BOLD + R2 suc

31 Chapter 8 Quantitative Measurements Using fMRI Review

32 T2* fMRI Signal

33 From Neural Activity to fMRI Signal Neural activitySignallingVascular response Vascular tone (reactivity) Autoregulation Metabolic signalling BOLD signal glia arteriole venule B 0 field Synaptic signalling Blood flow, oxygenation and volume Complex relationship between change in neural activity and change in blood flow (CBF), oxygen consumption (CMRO 2 ) and volume (CBV). dendrite End bouton

34 fMRI Bold Response Model time BOLD response, % initial dip positive BOLD response post stimulus undershoot overshoot stimulus Figure 8.1. from textbook. Initial dip0.5-1sec Overshootpeak 5-8 sec + BOLD response2-3% Final undershootvariable Deoxyhemoglobin BOLD signal

35 Graded BOLD Response Figure 8.2. from textbook. N=12 subjects. Graded change in signal for a) BOLD and b) perfusion (CBF). 3 minute visual pattern stimulation with different luminance levels. Note max BOLD change of 2-3 % and max CBF change of %.

36 Perfusion vs. Volume Change Figure 8.4. from textbook. 30 second stimulation 3-second intervals  CBF rapid  CBV slow Mandeville et al., 1999 In rat experiments TC for  CBV similar to that for BOLD overshoot. BOLD volume assessed using exogenous tracer that remains in blood.

37 Measurement of Cerebral Blood Flow with PET or MRI (Arterial Spin Labeling - ASL) Uses magnetically labeled arterial blood water as an endogenous flow tracer Potentially provide quantifiable CBF in classical units (mL/min per 100 gm of tissue) Detre et al., 1992 ++ 511 keV PET Method O-15 H 2 0

38 Arterial Spin Labelling ASL is an example of a motion contrast IMAGE perfusion = IMAGE uninverted – IMAGE inverted Perfusion is useful for clinical studies: how much blood is getting to a region, how long does it take to get there? inversion slab imaging plane excitation inversion x y z (=B 0 ) blood white matter = low perfusion Gray matter = high perfusion

39 Chapter 5 Hardware for MRI Review

40 3T Siemens Trio 60 cm patient bore60 cm patient bore 40 mT/m max gradient amplitude per axis40 mT/m max gradient amplitude per axis 200 T/m/sec slew rate200 T/m/sec slew rate 2 nd order active shimming2 nd order active shimming ~0.30 ppm B 0 homogeneity over 40 cm sphere~0.30 ppm B 0 homogeneity over 40 cm sphere self shieldedself shielded Shielding Shims Field Strength

41 MRI Scanner Anatomy A helium-cooled superconducting magnet generates the static field. –Always on: only quench field in emergency. –niobium titanium wire. Coils allow us to –Make static field homogenous (shims: solenoid coils) –Briefly adjust magnetic field (gradients: solenoid coils) –Transmit, record RF signal (RF coils: antennas)

42 Superconductor Magnet

43 Necessary Equipment Magnet Gradient Coils RF Coil 3T magnet gradient coils (inside)

44 Figure 5.2 from textbook. Magnet Shielding and Shimming Iron Shielding Shims superconducting static room temperature Magnet Shim coil Gradient coil RF coil Subject

45 Gradient Coils Sounds generated during imaging due to mechanical stress within gradient coils.

46 Current and Gradient Pulse Shape a. gradient current supplied (short rise time induces eddy currents) a. gradient current supplied (short rise time induces eddy currents) b. eddy currents oppose changing field w/o compensation b. eddy currents oppose changing field w/o compensation c. gradient current supplied with eddy current compensation c. gradient current supplied with eddy current compensation d. potential field vs time with eddy current compensation d. potential field vs time with eddy current compensation a d c b Jerry Allison.

47 dB/dt Effect (more eddy currents) Peripheral Nerve Stimulation dB/dt -- dE/dt dt is gradient ramp time dB/dt largest near ends of gradient coils spatial gradient of dE/dt also important dBdB dt

48 dB/dt / E-Field Characteristics of Stimulation Not dependent on B 0 Gradients - 40mT/m (larger Bmax for longer coil) Gradient Coil Differences - strength (increases dB) and length (head vs. body determines site) Rise Time - shorter rise time means larger shorter dt and therefore larger dB/dt Other –Disruption of nearby medical electronic devices –Subject Instructions Don’t clasp hands - closed circuit, lower threshold Report tingling, muscle twitching, painful sensations

49 MRI Scanner Components

50 Figure 5.1b from textbook. Exciter Synthesizer XMTR T/R switch RF Coil Preamp RCVR A/PRAM Host Pulse programmer Synthesizer, A/P XMTR, RCVR, T/R Shim driver Shim coils Gradient coils Amps Gx, Gy, Gz Network Schematic of MRI System A/P - Array Processor RF, Shim, Gradient Coils inside magnet All but Host, RAM, and A/P in equipment room Same or different transmit and receive coil.

51 RF Coil RF Coils can transmit and receive RF signals (i.e. apply B 1 and monitor M xy ) A typical coil is a tuned LC circuit and may be considered a near-field antenna

52 NSM-P035 Permanent Magnet MRI Comprehensive Receiving coils  7 standard configuration : QD head coil QD Neck Coil QD Body Coil QD Extremity CoilFlat Spine CoilBreast Coil

53 Surface Coils

54 Figure 5.7 from textbook. SNR Surface coil/head coil comparison cm spherical phantom distance, mm b SNRSNR (1) two surface coils on opposite sides in phase. (2) two surface coils out of phase. (3) single surface coil on right side. (largest SNR) (4) head coil. (most uniform SNR) RF Coil Uniformity and SNR (1)(2) (3)(4) B 1 directions indicated by color arrows.

55 Stimulus Presentation / Monitoring

56 Additional Equipment Software Time-Line –Control Stimulus –Monitor Response –Synchronize timing with MRI E-Prime

57 fMRI Study Time New Design Scanning –Setup –Scans –Take down Preprocessing Statistical Analysis hr/subject 4+ hr (one instance) variable <2 hr/ subject min 45 min to 1 hr 15 min 

58 fMRI Study – All Data Raw Data ~200 mBytes Motion Correction ~180 mBytes Other Corrections ~180 mBytes each possibly Spatial Normalization ~ 30 mBytes Statistical Analysis Statistical Parametric Image (128x128x20)< 1 MByte Statistical Parametric Map (2x SPI)> 1 MByte Total Data per subject can be gBytes

59 Chapter 7 Spatial and temporal resolution in fMRI Review

60 Typical Paradigm Instruction Presentation –stimulation –timing Processing –sensing –decision Response –plan –motor fMRI responses time (s) Trial #1 Trial #2 Presentation Response Behaviour time (s) Figure 7.4 from textbook. BOLD signal time course presentation (black) processing (light grey) response (dark grey) Task Behavior Onset and Width of BOLD response as temporal measures Not time to peak ----

61 Estimating Neural Processing Time From BOLD Response Onset V1 SMA M1 time fMRI response ampitude   (a) Figure 7.5 from textbook. Task – use joystick to move cursor from start box to target box as rapidly and accurately as possible (10 trials in multiple subjects). BOLD response – V1 (primary visual cortex), SMA (supplementary motor area), M1 (primary motor area) Analysis –  but not  increases with increasing reaction time (RT). Conclusion – Delay in reaction time from planning rather than execution of movement.

62 Estimating Neural Processing Time From from BOLD Response Width fMRI signal change from SPL Time after presentation (s) fMRI (b) Trial A Trial B RT(A) RT(B) Task (a) (c) Normalized width of BOLD response (s) Reaction Time (s) Figure 7.6 from textbook. Task – determine if one object could be rotated to match a second. Rotation angle varied by design. Press button yes or no. BOLD response – Superior Parietal Lobule (SPL) Analysis – Normalized width of BOLD response correlated with reaction time (RT). Conclusion – SPL intimately involved in mental rotation of object.

63 Chapter 6 Selection of optimal pulse sequences for fMRI Review

64 AdvantagesDisadvantages BOLDHighest activation contrast 2x-4x over perfusion complicated non-quantitative signal easiest to implementno baseline information multislice trivialsusceptibility artifacts can use very short TR Perfusionunique and quantitative informationlow activation contrast baseline informationlonger TR required easy control over observed vasculaturemultislice is difficult non-invasiveslow mapping of baseline information no susceptibility artifacts Table 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook)

65 Venous outflow Perfusion No Velocity Nulling Velocity Nulling ASL TI Time/secs12403 Venous outflow Figure 6.1a Signal is detected from water spins in the arterial-capillary region of the vasculature and from water in tissues surrounding the capillaries. Relative sensitivity controlled by adjusting TI and by incorporating velocity nulling gradients (also known as diffusion weighting). Nulling and TI~1 sec makes ASL sensitive to capillaries and surrounds. ArteriesArteriolesCapillariesVenulesVeins

66 GE-BOLD No Velocity Nulling Velocity Nulling Figure 6.1b Gradient Echo BOLD is sensitive to susceptibility perturbers of all sizes, and are therefore sensitive to all intravasculature and extravascular effects in the capillary- venous portions of the vasculature. If a very short TR is used may show signal from arterial inflow, which can be removed by using a longer TR and/or outer volume saturation. ArteriesArteriolesCapillariesVenulesVeins Arterial inflow (BOLD TR < 500 ms) Time/secs12403

67 SE-BOLD No Velocity Nulling Velocity Nulling Figure 6.1c Spin Echo BOLD is sensitive to susceptibility perturbers about the size of a red blood cell or capillary, making it predominantly sensitive to intravascular water spins in vessels of all sizes and to extravascular (tissue) water surrounding capillaries. Velocity nulling reduces the signals from larger vessesl. ArteriesArteriolesCapillariesVenulesVeins Arterial inflow (BOLD TR < 500 ms) Time/secs12403

68 Figure 6.2 Pulse sequence diagrams of (a) gradient echo, (b) spin echo, and (c) asymmetric spin echo EPI. The TE is shown at the center of 9-line k-space (typically 64 or more lines).  is the offset from center of k-space to echo. Additional pulses needed for ASL are indicated schematically. Gradient-echo RF Gx Gz Gy 90° TE ASL pulse TI spin-echo 180° TE RF Gx Gz Gy   

69 Chapter 4 Ultrafast fMRI Review

70 Effects of Field Homogeneity R2* = R2 + R2 mi +R2 ma R2 = transverse relaxation rate due to spin-spin interactions and diffusion through microscopic gradients R2 mi = transverse relaxation rate due to microscopic changes, i.e. deoxyhemoglobin R2 ma = transverse relaxation rate due to macroscopic field inhomogeneity R2* a is relaxation rate during activation R2* r is relaxation rate at rest

71 Fig. 4.3 EPI obtained with TE= 60 and TR=3000 msec and 63 and 95 ky lines. Note recovery of signal loss in d vs c and ghosting in c. Spin Echo 4x4x4 mm 3 Gradient Echo EPI 2x2x2 mm 3

72 Fig. 4.5 Gradient echo (GE) echo forms at center of readout window where area under rephasing gradient = area of dephasing gradient. Unlike spin echo dephasing is due to spatial difference in Larmor frequencies during application of gradients. First half of readout window is rephasing and second half is dephasing again. This process repeats at the center of readout window for each ky line in k-space for EPI. gradient echo readout window r.f. read gradient TE dephase rephasedephase For EPI where is the readout signal largest?

73 Fig. 4.7 GE EPI pulse sequence and k-space organization of samples. RF Slice Read Phase a) Read Phase b) 1 2 n n n What flip angle is used for EPI?

74 Effect of system parameters on EPI images for fixed field of view. ParameterEcho Spacing ResolutionSNRGeometric distortion Increase gradient slew rateReduced--- Reduced Increase sampling bandwidth (kx) Reduced---Reduced Increase number of shots (interleaving ky) Reduced---IncreasedReduced Use of ramp sampling (similar to slew rate effect) Reduced--- Reduced Increase read matrix (kx)Increased ReducedIncreased Increase phase matrix (ky)---Increased * Reduced--- Increase field strength--- Increased Table 4.1 from text. * actual resolution increase less than expected due to smoothing effect of signal decay.

75 fMRI methods for reduced k-space coverage Keyhole –acquire full k-space as reference –acquire reduced low-frequency k-space fMRI study –fill in missing k-space from reference Half-Fourier –acquire 50-60% of k-space starting at highest ky –theoretical symmetry used to fill in missing ky

76 fMRI methods for reduced k-space coverage Sensitivity encoding (SENSE) –Multiple RF coils with independent signal for each (parallel imaging) –Calibration maps from full k-space –each coil part of k-space –2X improvement EPI, 4X for GE UNFOLD –Acquire k-space in sequential time segments time 1 acquire lines 1, 5, 9, time 2 acquire lines 2, 6, 10, time 3 acquire lines 3, 7, 11, time 4 acquire lines 4, 8, 12, reorder into k-space 4x faster per segment reduces inter echo distortions

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