Presentation on theme: "Principles of nuclear magnetic resonance and MRI Review"— Presentation transcript:
1 Principles of nuclear magnetic resonance and MRI Review Chapter 3Principles of nuclear magnetic resonance and MRIReview
2 Basic Physics of MRINuclei 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 B0.Nuclei spin axis not parallel to B0 field direction.Nuclear magnetic moments precess about B0.
3 Larmor frequencies of RICs MRIs Basic Physics of MRIFrequency of precession of magnetic moments given by Larmor relationshipf = g x B0f = Larmor frequency (mHz)g = Gyromagnetic ratio (mHz/Tesla)B0 = Magnetic field strength (Tesla)g ~ 43 mHz/TeslaLarmor frequencies of RICs MRIs3T ~ 130 mHZ7T ~ 300 mHz11.7T ~ 500 mHz
4 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
5 Basic Physics of MRIM 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 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.B0
6 RF pulse duration and strength determine flip angle Basic Physics of MRIFrequency of rotation of M about B1 determined by the magnitude (strength) of B1.RF pulse duration and strength determine flip angleBasic RF Pulse ConceptsRF Pulsestrengthduration
7 Basic Physics of MRIFID = Free Induction Decay90° RF pulse rotates M into transverse (x-y) planeRotation 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.
8 Need for 180° Pulse - Spin Echo FID also diminishes due to local static magnetic field inhomogeneitySome spins precess faster and some slower than those due to B090°Blue one is fast precessing spins.Question: What is the time between 90 and 180 pulse?Note: to use vector concept to explain a common question concerning the180 flipping of both blue and red spins.180°timeTE/2-TE/2+180 ° RF pulse reverses dephasing at TE (echo time)Residual decay due to T2Spin Echo SignalTE
9 Nuclear Magnetic Resonance (NMR) Signal: Spin Echo (SE) TR (repetition time) = time between RF excitation pulses90o180o90oFIDSpin Echo90 itself is capable of generate a FID signalpair used to obtain a spin-echo (SE) signal.Definition of TR TE.TE/2TE/2TE = time from 90o pulse to center of spin echo
10 Developing Contrast Using Weighting Contrast = difference in image values between different tissuesT1 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: DephasingLoss of transverse magnetization Mxy.‘T2 time’ refers to time interval for 37% loss of original transverse magnetization.Spin-spin interactions,and more.
12 Properties of Body Tissues T1 (ms)T2 (ms)Grey Matter (GM)950100White Matter (WM)60080Muscle90050Cerebrospinal Fluid (CSF)45002200Fat25060Blood1200T1 values for B0 ~ 1Tesla.T2 ~ 1/10th 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 contrastTE determines T2 contrast.
15 Making an Image k-space (frequency domain) A k-space domain image is formed using frequency and phase encoding
16 Two Spaces k-space Image space ky y FT-1 x kx FT Final Image Acquired DataImage spacexyFinal ImageFT-1FTMRI 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 Equations that govern 2D k-space trajectorykx = g 0t Gx(t) dtif Gx is constant kx = gGxtky = g 0t’ Gy(t) dtif Gy is constant ky = gGyt’The kx, ky frequency coordinates are established by durations (t) and strength of gradients (G).
21 The K-space Trajectory 180 pulseDigitizer records N samples of kx where ky = 0
22 Frequency and Phase Encoding for 2D Spin Echo Imaging digitizer onExciteSliceSelectFrequencyEncodePhaseReadout90180kxky
23 The 2D K-space Trajectory 180 pulseDigitizer records N samples of kx and N samples of ky
24 Gradient Echo ImagingSignal is generated by magnetic field refocusing mechanism only (the use of negative and positive gradient)Signal intensity is governed byS = So e-TE/T2*Can be used to measure T2* value of the tissueR2* = R2 + R2ih +R2ph (R2=1/T2)Used in 3D and BOLD fMRI
25 MRI Pulse Sequence for Gradient Echo Imaging ExcitationSliceSelectionFrequencyEncodingPhaseEncodingdigitizer onReadoutErnst angle (E) for optimum SNR .
26 FLASH Pulse Sequence TR1 TR2 TRN crusher crusher TRN/2 TRN/2 TRN B1TR1TR2refocusGzTRNGycrushercrusherGxacquireTRN/2B1TRN/2TRNGzGycrushercrusherTR2GxTR12D Gradient EchoRF (10-15 degrees)Short TR (10-50 msec)N= 256 ( sec per slice)Fig Courtesy of Peter Jezzard.
27 3D Sequence (Gradient Echo) acqkzGxreadGyphaseSelect& phaseGzkyB1kxRFScan time = NyNzTRGood for high resolution T1W images of brain
29 2D Echo Planar Imaging (EPI) b)B1refocusGzGyGxacquire2d Gradient EchoEntire 2D slice within one TR64x64 or 128x128Time per slice (30-50 msec)Whole volume (2-4 sec)Good for fMRI studiesFig Courtesy of Peter Jezzard.
30 FLASH Image T2* Weighted TE = 30 msecCSF is brightSignal loss and distortions due to local differences in magnetic fieldSources of Contrast in Brain- Endogenous - BOLD- Exogenous - could be contrast agent (Gd based)- Other - SusceptibilityR2* = net T2 relaxation rate = 1/T2*R2* = R2tis + R2ih + R2BOLD + R2sucFig courtesy of Peter Jezzard.
31 Quantitative Measurements Using fMRI Review Chapter 8Quantitative Measurements Using fMRIReview
33 From Neural Activity to fMRI Signal SignallingVascular responseVascular tone (reactivity)AutoregulationMetabolic signallingBOLD signalgliaarteriolevenuleB0 fieldSynaptic signallingBlood flow,oxygenationand volumeEnd boutondendriteComplex relationship between change in neural activity and change in blood flow (CBF), oxygen consumption (CMRO2) and volume (CBV).
35 Graded BOLD ResponseGraded 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 %.Figure 8.2. from textbook. N=12 subjects.
36 Perfusion vs. Volume Change 30 second stimulation3-second intervalsDCBF rapidDCBV slowBOLD 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
37 Measurement of Cerebral Blood Flow with PET or MRI (Arterial Spin Labeling - ASL) +511 keVPETMethodO-15 H20Uses magnetically labeled arterial blood water as an endogenous flow tracerPotentially provide quantifiable CBF in classical units (mL/min per 100 gm of tissue)Detre et al., 1992
38 Arterial Spin Labelling z (=B0)inversionslabimagingplaneexcitationbloodyxinversionwhite matter = low perfusionGray matter = high perfusionASL is an example of a motion contrastIMAGEperfusion = IMAGEuninverted – IMAGEinvertedPerfusion is useful for clinical studies: how much blood is getting to a region, how long does it take to get there?
39 Hardware for MRI Review Chapter 5Hardware for MRIReview
40 3T Siemens Trio 60 cm patient bore 40 mT/m max gradient amplitude per axis200 T/m/sec slew rate2nd order active shimming~0.30 ppm B0 homogeneity over 40 cm sphereself shieldedShieldingShimsField Strength
41 A helium-cooled superconducting magnet generates the static field. Always on: only quench field in emergency.niobium titanium wire.Coils allow us toMake static field homogenous (shims: solenoid coils)Briefly adjust magnetic field (gradients: solenoid coils)Transmit, record RF signal (RF coils: antennas)MRI Scanner Anatomy
44 Magnet Shielding and Shimming Iron ShieldingMagnetShim coilGradient coilRF coilSubjectShimssuperconductingstaticroom temperatureFigure 5.2 from textbook.
45 Gradient CoilsSounds generated during imaging due to mechanical stress within gradient coils.
46 Current and Gradient Pulse Shape ba. gradient current supplied (short rise time induces eddy currents)b. eddy currents oppose changing field w/o compensationc. gradient current supplied with eddy current compensationd. potential field vs time with eddy current compensationJerry Allison.
47 dB/dt Effect (more eddy currents) Peripheral Nerve Stimulation dB/dt -- dE/dtdt is gradient ramp timedB/dt largest near ends of gradient coilsspatial gradient of dE/dt also importantdBdt
48 dB/dt / E-Field Characteristics of Stimulation Not dependent on B0Gradients - 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/dtOtherDisruption of nearby medical electronic devicesSubject InstructionsDon’t clasp hands - closed circuit, lower thresholdReport tingling, muscle twitching, painful sensations
50 Same or different transmit and receive coil. Schematic of MRI SystemExciterSynthesizerXMTRT/RswitchRFCoilPreampRCVRA/PRAMHostPulseprogrammerSynthesizer, A/PXMTR, RCVR, T/RShimdrivercoilsGradientAmpsGx, Gy, GzNetworkSame or different transmit and receive coil.A/P - Array ProcessorRF, Shim, Gradient Coils inside magnetAll but Host, RAM, and A/P in equipment roomFigure 5.1b from textbook.
51 RF CoilRF 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
52 Comprehensive Receiving coils 7 standard configuration：QD head coilQD Neck CoilQD Body CoilNSM-P035 Permanent Magnet MRIQD Extremity CoilFlat Spine CoilBreast Coil
54 RF Coil Uniformity and SNR 50100150200250400600800100012001400Surface coil/head coil comparison123417 cm spherical phantomdistance, mmb(1)(2)(3)(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.
56 Additional Equipment Software Time-Line Control Stimulus E-PrimeSoftwareTime-LineControl StimulusMonitor ResponseSynchronize timing with MRI
57 fMRI Study Time New Design Scanning Preprocessing Statistical Analysis 4+ hr (one instance)New DesignScanningSetupScansTake downPreprocessingStatistical Analysis1-1.5 hr/subject15-20 min45 min to 1 hr15 min<2 hr/ subjectvariable
58 fMRI Study – All Data Total Data per subject can be 0.5-1.0 gBytes Raw Data ~200 mBytesMotion Correction ~180 mBytesOther Corrections ~180 mBytes each possiblySpatial Normalization ~ 30 mBytesStatistical AnalysisStatistical Parametric Image (128x128x20) < 1 MByteStatistical Parametric Map (2x SPI) > 1 MByteTotal Data per subject can be gBytes
59 Spatial and temporal resolution in fMRI Review Chapter 7Spatial and temporal resolution in fMRIReview
60 Typical Paradigm Instruction Presentation stimulation timing fMRI responsestime (s)Trial #1Trial #2PresentationResponseBehaviour5InstructionPresentationstimulationtimingProcessingsensingdecisionResponseplanmotorTaskBehaviorBOLD signal time coursepresentation (black)processing (light grey)response (dark grey)Onset and Width of BOLD response as temporal measures.---- Not time to peak ----Figure 7.4 from textbook.
61 Estimating Neural Processing Time From BOLD Response Onset 350300250200150-5050100kinematic RT (ms)BOLD onset difference (ms)(b)V1SMAM1timefMRI 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 – D but not t 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 SPLTime after presentation (s).98123fMRI(b)5Trial ATrial BRT(A) RT(B)Task(a)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.(c)16284Normalized width of BOLD response (s)ReactionTm(s)Figure 7.6 from textbook.
63 Selection of optimal pulse sequences for fMRI Review Chapter 6Selection of optimal pulse sequences for fMRIReview
64 AdvantagesDisadvantagesBOLDHighest activation contrast 2x-4x over perfusioncomplicated non-quantitative signaleasiest to implementno baseline informationmultislice trivialsusceptibility artifactscan use very short TRPerfusionunique and quantitative informationlow activation contrastbaseline informationlonger TR requiredeasy control over observed vasculaturemultislice is difficultnon-invasiveslow mapping of baseline informationno susceptibility artifactsTable 6.1a. Summary of practical advantages and disadvantages of pulse sequences (derived from textbook)
65 Time/secs 1 2 4 3 Perfusion TI ASL 3PerfusionVenous outflowVenous outflowNoVelocityNullingVelocityNullingArteriesArteriolesCapillariesVenulesVeinsTIASLFigure 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.
66 Time/secs1243Arterial inflow(BOLD TR < 500 ms)GE-BOLDNoVelocityNullingVelocityNullingArteriesArteriolesCapillariesVenulesVeinsFigure 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.
67 Time/secs1243Arterial inflow(BOLD TR < 500 ms)SE-BOLDNoVelocityNullingVelocityNullingArteriesArteriolesCapillariesVenulesVeinsFigure 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.
68 Gradient-echoRFGxGzGy90°TEASLpulseTISpin-echo180°TERFGxGzGyASLpulseTI90°spin-echo180°TERFGxGzGy90°tt/2Figure 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.
70 Effects of Field Homogeneity R2* = R2 + R2mi +R2maR2 = transverse relaxation rate due to spin-spin interactions and diffusion through microscopic gradientsR2mi = transverse relaxation rate due to microscopic changes, i.e. deoxyhemoglobinR2ma = transverse relaxation rate due to macroscopic field inhomogeneityR2*a is relaxation rate during activationR2*r is relaxation rate at rest
71 4x4x4 mm32x2x2 mm3Spin EchoGradient Echo EPIFig. 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.
72 For EPI where is the readout signal largest? gradientechoreadout windowr.f.read gradientTEdephaserephaseFig. 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?
73 RFSliceReadPhasea)ReadPhaseb)nn-11n-12n21Fig GE EPI pulse sequence and k-space organization of samples.What flip angle is used for EPI?
74 Effect of system parameters on EPI images for fixed field of view. Echo SpacingResolutionSNRGeometric distortionIncrease gradient slew rateReduced---Increase sampling bandwidth (kx)Increase number of shots (interleaving ky)IncreasedUse of ramp sampling (similar to slew rate effect)Increase read matrix (kx)Increase phase matrix (ky)Increased*Increase field strengthTable 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 Keyholeacquire full k-space as referenceacquire reduced low-frequency k-space fMRI studyfill in missing k-space from referenceHalf-Fourieracquire 50-60% of k-space starting at highest kytheoretical 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-spaceeach coil part of k-space2X improvement EPI, 4X for GEUNFOLDAcquire k-space in sequential time segmentstime 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-space4x faster per segment reduces inter echo distortions