Transcript Chapter 3
Chapter 3 Principles of nuclear magnetic resonance and MRI Review Basic Physics of MRI • Nuclei line up with magnetic moments either in a parallel or antiparallel configuration. • In body tissues more line up in parallel creating a small additional magnetization M in the direction of B0. Nuclei spin axis not parallel to B0 field direction. Nuclear magnetic moments precess about B0. Basic Physics of MRI • Frequency of precession of magnetic moments given by Larmor relationship f = g x B0 f = Larmor frequency (mHz) g = Gyromagnetic ratio (mHz/Tesla) B0 = Magnetic field strength (Tesla) g ~ 43 mHz/Tesla Larmor frequencies of RICs MRIs 3T ~ 130 mHZ 7T ~ 300 mHz 11.7T ~ 500 mHz Basic Physics of MRI NMRable Nuclei Body 1H content is high due to water (>67%) Hydrogen protons in mobile water are primary source of signals in fMRI and aMRI Basic Physics of MRI • M is parallel to B0 since transverse components of magnetic moments are randomly oriented. • The difference between the numbers of protons in the parallel (up here) and antiparallel 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. B0 Basic Physics of MRI Frequency of rotation of M about B1 determined by the magnitude (strength) of B1. Basic RF Pulse Concepts RF Pulse strength duration RF pulse duration and strength determine flip angle Basic Physics of MRI FID = Free Induction Decay • 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 Mxy. FID magnitude decays in an exponential manner with a time constant T2. Decay due to spin-spin relaxation. t T2 S (t ) S0e sin(2ft ) Need for 180° Pulse - Spin Echo • FID also diminishes due to local static magnetic field inhomogeneity • Some spins precess faster and some slower than those due to B0 90 ° 180° • 180 ° RF pulse reverses dephasing at TE (echo time) • Residual decay due to T2 Spin Echo Signal Nuclear Magnetic Resonance (NMR) Signal: Spin Echo (SE) TR (repetition time) = time between RF excitation pulses 90o 90o 180o FID TE/2 Spin Echo TE/2 TE = time from 90o pulse to center of spin echo 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 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 Mxy. – ‘T2 time’ refers to time interval for 37% loss of original transverse magnetization. – Spin-spin interactions,and more. Properties of Body Tissues Tissue T1 (ms) T2 (ms) Grey Matter (GM) 950 100 White Matter (WM) 600 80 Muscle 900 50 Cerebrospinal Fluid (CSF) 4500 2200 Fat 250 60 Blood 1200 100-200 T1 values for B0 ~ 1Tesla. T2 ~ 1/10th T1 for soft tissues 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. Contrast, Imaging Parameters T1W T2W S(TR,TE) r1 eTR /T1 eTE /T2 orr1 e TR /T1 e TE /T2* SE GRE r - proton density SE – spin echo imaging GRE – gradient echo imaging Short TEs reduce T2W Long TRs reduce T1W Making an Image k-space (frequency domain) A k-space domain image is formed using frequency and phase encoding Two Spaces Image space y k-space ky FT-1 kx x FT Acquired Data 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. Final Image MR image is the magnitude of the Fourier transform of the k-space image The k-space Trajectory Equations that govern 2D k-space trajectory kx = g 0t Gx(t) dt if Gx is constant kx = gGxt ky = g 0t’ Gy(t) dt if Gy is constant ky = gGyt’ The kx, ky frequency coordinates are established by durations (t) and strength of gradients (G). Simple MRI Frequency Encoding: RF Excitation Slice Selection (Gz) Frequency Encoding (Gx) digitizer on Readout Exercise drawing k-space manipulation The k-space Trajectory Frequency Encoding Gradient (Gx) Move to left side of k-space. (0,0) ky Digitizer records N samples along kx where ky = 0 kx Simple MRI Frequency Encoding: Spin Echo Excitation Slice Selection Frequency Encoding (Gx) digitizer on Readout Exercise drawing k-space representation The K-space Trajectory 180 pulse Digitizer records N samples of kx where ky = 0 Frequency and Phase Encoding for 2D Spin Echo Imaging 90 180 Excite Slice Select kx ky Frequency Encode Phase Encode digitizer on Readout The 2D K-space Trajectory 180 pulse Digitizer records N samples of kx and N samples of ky 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 = So e-TE/T2* • Can be used to measure T2* value of the tissue • R2* = R2 + R2ih +R2ph (R2=1/T2) • Used in 3D and BOLD fMRI MRI Pulse Sequence for Gradient Echo Imaging E. Excitation Slice Selection Frequency Encoding Phase Encoding digitizer on Readout Ernst angle (E) for optimum SNR . TR T1 cos(E ) e FLASH Pulse Sequence Gz refocus TR2 crusher TR1 crusher B1 Gy Gx acquire Gy Gx Fig. 3.19. Courtesy of Peter Jezzard. crusher Gz TRN/2 TRN TRN/2 crusher B1 TRN TR2 TR1 2D Gradient Echo RF (10-15 degrees) Short TR (10-50 msec) N= 256 (2.5-13 sec per slice) 3D Sequence (Gradient Echo) read acq Gx phase Gy Select & phase Gz RF B1 kz kx Scan time = NyNzTR Good for high resolution T1W images of brain ky 3D T1W brain image 0.8mm spacing Time = 25 min 2D Echo Planar Imaging (EPI) a) b) B1 Gz refocus Gy Gx acquire Fig. 3.20. Courtesy of Peter Jezzard. 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 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* Fig. 3.23 courtesy of Peter Jezzard. R2* = R2tis + R2ih + R2BOLD + R2suc Chapter 8 Quantitative Measurements Using fMRI Review T2* fMRI Signal From Neural Activity to fMRI Signal Neural activity Signalling Vascular response Vascular tone (reactivity) Autoregulation Synaptic signalling BOLD signal Blood flow, oxygenation and volume arteriole B0 field glia Metabolic signalling End bouton dendrite venule Complex relationship between change in neural activity and change in blood flow (CBF), oxygen consumption (CMRO2) and volume (CBV). fMRI Bold Response Model positive BOLD response • • • • Initial dip 0.5-1sec Overshoot peak 5-8 sec + BOLD response 2-3% Final undershoot variable 3 BOLD response, % 2 initial dip overshoot post stimulus undershoot 1 Deoxyhemoglobin BOLD signal 0 time stimulus Figure 8.1. from textbook. Graded BOLD Response • 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 40-50 %. Figure 8.2. from textbook. N=12 subjects. Perfusion vs. Volume Change • • • • 30 second stimulation 3-second intervals DCBF rapid DCBV slow BOLD volume assessed using exogenous tracer that remains in blood. In rat experiments TC for DCBV similar to that for BOLD overshoot. Figure 8.4. from textbook. Mandeville et al., 1999 Measurement of Cerebral Blood Flow with PET or MRI (Arterial Spin Labeling - ASL) PET orPET SPECT MRI PERFUSION Ste ady State M ethod Ste ady State M ethod Method keV 511 decay arterial labeling imaging slice control labeling T1 relaxation + 511 keV arterial spin labeling 15 O infusion O-15 H 0 2 or inhalation • 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 Arterial Spin Labelling z (=B0) excitation y inversion slab blood x inversion imaging plane • ASL is an example of a motion contrast white matter = low perfusion Gray matter = high perfusion • IMAGEperfusion = IMAGEuninverted – IMAGEinverted • Perfusion is useful for clinical studies: how much blood is getting to a region, how long does it take to get there? www.fmrib.ox.ac.uk/~karla/ Chapter 5 Hardware for MRI Review 3T Siemens Trio • • • • • • 60 cm patient bore 40 mT/m max gradient amplitude per axis 200 T/m/sec slew rate 2nd order active shimming ~0.30 ppm B0 homogeneity over 40 cm sphere self shielded • Shielding • Shims • Field Strength • 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) MRI Scanner Anatomy Superconductor Magnet Necessary Equipment 3T magnet Magnet RF Coil gradient coils (inside) Gradient Coils RF Coil Magnet Shielding and Shimming Iron Shielding Magnet Shim coil Subject Gradient coil RF coil Figure 5.2 from textbook. Shims superconducting static room temperature Gradient Coils Sounds generated during imaging due to mechanical stress within gradient coils. Current and Gradient Pulse Shape a c d b Jerry Allison. a. gradient current supplied (short rise time induces eddy currents) b. eddy currents oppose changing field w/o compensation c. gradient current supplied with eddy current compensation d. potential field vs time with eddy current compensation 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 dB dt dB/dt / E-Field Characteristics of Stimulation • Not dependent on B0 • 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 MRI Scanner Components Schematic of MRI System Exciter XMTR T/R switch Synthesizer RCVR RF Coil Same or different transmit and receive coil. Preamp Network A/P Host RAM Shim coils Pulse programmer Synthesizer, A/P XMTR, RCVR, T/R Gx, Gy, Gz Figure 5.1b from textbook. Amps Shim driver Gradient coils A/P - Array Processor RF, Shim, Gradient Coils inside magnet All but Host, RAM, and A/P in equipment room RF Coil • RF Coils can transmit and receive RF signals (i.e. apply B1 and monitor Mxy) • A typical coil is a tuned LC circuit and may be considered a near-field antenna NSM-P035 Permanent Magnet MRI Comprehensive Receiving coils 7 standard configuration： QD head coil QD Extremity Coil QD Neck Coil Flat Spine Coil QD Body Coil Breast Coil Surface Coils RF Coil Uniformity and SNR Surface coil/head coil comparison 1400 17 cm spherical phantom b S N R (1) SNR 1200 1000 2 800 600 (2) 1 400 4 3 200 0 (3) 0 50 100 150 200 250 distance, mm (4) B1 directions indicated by color arrows. (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) Figure 5.7 from textbook. Stimulus Presentation / Monitoring Additional Equipment E-Prime • Software • Time-Line – Control Stimulus – Monitor Response – Synchronize timing with MRI fMRI Study Time • New Design • Scanning – Setup – Scans – Take down • Preprocessing • Statistical Analysis 4+ hr (one instance) 1-1.5 hr/subject 15-20 min 45 min to 1 hr 15 min <2 hr/ subject variable fMRI Study – All Data • • • • • Raw Data Motion Correction Other Corrections Spatial Normalization Statistical Analysis • • ~200 mBytes ~180 mBytes ~180 mBytes each possibly ~ 30 mBytes Statistical Parametric Image (128x128x20) Statistical Parametric Map (2x SPI) < 1 MByte > 1 MByte Total Data per subject can be 0.5-1.0 gBytes Chapter 7 Spatial and temporal resolution in fMRI Review Typical Paradigm Behaviour • • Task • Behavior • Instruction Presentation – stimulation – timing Processing – sensing – decision Response – plan – motor Presentation Response Trial #1 Trial #2 Onset and Width of BOLD response as temporal measures. ---- Not time to peak ---Figure 7.4 from textbook. fMRI responses 0 time (s) 5 0 5 time (s) • BOLD signal time course • presentation (black) • processing (light grey) • response (dark grey) Estimating Neural Processing Time From BOLD Response Onset (b) M1 SMA V1 D Figure 7.5 from textbook. 300 BOLD onset difference (ms) fMRI response ampitude (a) time 250 D 200 150 100 50 0 -50 150 200 250 300 kinematic RT (ms) 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 – D but not increases with increasing reaction time (RT). Conclusion – Delay in reaction time from planning rather than execution of movement. 350 Estimating Neural Processing Time From from BOLD Response Width (b) fMRI (a) Task fMRI signal change from SPL 1. 03 1. 02 Trial B 1. 01 Trial A 1. 00 RT(A) RT(B) 0. 99 0. 9 8 5 10 15 Time after presentation (s) 0 (c) Normalized width of BOLD response (s) 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. 20 16 12 8 4 00 4 8 12 Reaction Time(s) 16 Figure 7.6 from textbook. Chapter 6 Selection of optimal pulse sequences for fMRI Review Advantages BOLD Disadvantages Highest activation contrast 2x-4x over perfusion complicated non-quantitative signal easiest to implement no baseline information multislice trivial susceptibility artifacts can use very short TR Perfusion unique and quantitative information low activation contrast baseline information longer TR required easy control over observed vasculature multislice is difficult non-invasive slow mapping of baseline information no susceptibility artifacts Table 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook) Time/secs 0 1 2 3 4 Perfusion Venous outflow No Velocity Nulling Velocity Nulling Arteries Arterioles Capillaries Venules Veins TI ASL 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. Time/secs Arterial inflow (BOLD TR < 500 ms) 0 1 2 3 4 GE-BOLD No Velocity Nulling Velocity Nulling Arteries Arterioles Capillaries Venules Veins 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 capillaryvenous 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. Time/secs Arterial inflow (BOLD TR < 500 ms) 0 1 2 3 4 SE-BOLD No Velocity Nulling Velocity Nulling Arteries Arterioles Capillaries Venules Veins 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. TI TI ASL pulse Gradient-echo TE 90° ASL pulse Spin-echo 180° TE 90° RF RF Gx Gx Gy Gy Gz Gz spin-echo 180° 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. 90° RF Gx Gy Gz /2 TE Chapter 4 Ultrafast fMRI Review Effects of Field Homogeneity R2* = R2 + R2mi +R2ma • R2 = transverse relaxation rate due to spin-spin interactions and diffusion through microscopic gradients • R2mi = transverse relaxation rate due to microscopic changes, i.e. deoxyhemoglobin • R2ma = transverse relaxation rate due to macroscopic field inhomogeneity R2*a is relaxation rate during activation R2*r is relaxation rate at rest DR 2* ( R 2 *a R 2 *r ) ( R 2 R 2 mi R 2 ma ) a ( R 2 R 2 mi R 2 ma ) r DR 2* ( R 2 R 2 mi ) a ( R 2 R 2 mi ) r ( R 2 a R 2 r ) ( R 2 mi a R 2 mi r ) DR 2* DR 2 DR 2 mi 4x4x4 mm3 2x2x2 mm3 Spin Echo Gradient Echo EPI 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. r.f. TE readout window read gradient rephase dephase gradient echo dephase 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. For EPI where is the readout signal largest? a) b) n Phase n-1 RF Slice n-1 1 Read 2 n 2 Phase 1 Read Fig. 4.7 GE EPI pulse sequence and k-space organization of samples. What flip angle is used for EPI? Effect of system parameters on EPI images for fixed field of view. Parameter Echo Spacing Resolution SNR Geometric distortion Increase gradient slew rate Reduced --- --- Reduced Increase sampling bandwidth (kx) Reduced --- Reduced Reduced Increase number of shots (interleaving ky) Reduced --- Increased Reduced Use of ramp sampling (similar to slew rate effect) Reduced --- --- Reduced Increase read matrix (kx) Increased Increased Reduced Increased Increase phase matrix (ky) --- Increased* Reduced --- Increase field strength --- --- Increased Increased Table 4.1 from text. * actual resolution increase less than expected due to smoothing effect of signal decay. 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 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, 13 ... • time 2 acquire lines 2, 6, 10, 14 ... • time 3 acquire lines 3, 7, 11, 15 ... • time 4 acquire lines 4, 8, 12, 16 ... • reorder into k-space • 4x faster per segment reduces inter echo distortions