Pulse Sequence Design Made Easier

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Pulse SequenceDesign MadeEasier Gregory L. Wheeler, BSRT(R)(MR)MRI Consultantgurumri@gmail.com1 2A pulse sequence is a timing diagramdesigned with a series of RF pulses,gradients switching, and signal readoutused in MR image formation. Pulse Sequences generallyhave the followingcharacteristics: An RF line characterizingRF Pulse applications Gradients switching toencode the volume forspatial localization Signal reception used tocreate MR imagePulse sequence componentsPulse Sequence Design Made Easier 3 There are four processes inpulse sequence design: 4 This is a timing diagram. All linesare read left to right and top tobottom simultaneously.Excitation Above line is positive direction.Below line is negative direction.Encoding The RF line characterizes RF pulseapplications. The height and width ofthe pulse determines how much(watts) and how long the pulse isapplied. Gradients are switched on and off tospatially localize the volume or theslice for image reconstruction. Gradients are switched on and offfor: Slice Selection Phase Encoding Frequency Encoding or Readout RF pulse(s) is/are applied Phase encoding is performed todetermine how K-space is filled Refocusing Refocusing Net Magnetizationback into transverse plane Readout Signal is encoded and recordedPulse sequence processesPulse Sequence Guidelines56Page 1

The gradient on while theRF is applied is the SliceSelect Gradient. The gradient on while thesignal is received orrecorded is the FrequencyEncoding or ReadoutGradient. The gradient that changesamplitude per TR and onprior to refocusing is thePhase Encoding Gradient. Which gradient is theslice select gradient? ?Pulse Sequence GuidelinesPulse Sequence Quiz7 8Which gradient is theslice select gradient? Which gradient is theslice select gradient? Gz Gz Which gradient is thephase encodinggradient? ?Pulse Sequence QuizPulse Sequence Quiz9 10Which gradient is theslice select gradient?Which gradient is theslice select gradient? Gz Which gradient is thephase encodinggradient? Gy Which gradient is thefrequency encodinggradient? ? Gz Which gradient is thephase encodinggradient? GyPulse Sequence QuizPulse Sequence Quiz1112Page 2

Which gradient is theslice select gradient? Gz Which gradient is thephase encodinggradient? Gy Which gradient is thefrequency encodinggradient? GxPulse Sequence Quiz1314What slice orientation will the images createdfrom this pulse sequence have?What slice orientation will the images created fromthis pulse sequence have? AXIALS(Gz - is the slice select gradient)1516More on Phase Encoding Phase encoding isperformed to providespatial localizationand to guide k-spacefilling. What do you noticeabout the phaseencoding gradient?Phase amplitude changes every TR1718Page 3

19Each amplitude designates another line in k-space What do you notice about the signal as gradient changes? 20Signal gets strongerwith low amplitudegradients (shallow).The signal getsweaker with highamplitude gradients(steeper). Outer lines of K-space,use high amplitudegradients which yield lowsignal return. Center lines of K-spaceuse low amplitudegradients which yield highsignal return. Outer lines reconstructedyield spatial resolution. Center lines reconstructedyield signal (S/N) andcontrast.21222324High Spatial ResolutionHigh S/N and ContrastHigh Spatial ResolutionFrequency EncodingK-Space FillingPage 4

There are three conventional pulsesequence designs. Spin Echo Gradient Recalled Echo Inversion Recovery Spin Echo pulse sequences begin with a90 RF pulse followed by at least one 180 RF pulse. Produces T1-, T2-, and PD-wt. type tissuecontrastSpin Echo Pulse Sequence (SE)Conventional Pulse Sequences2526 Image parametersShort TR - contrastShort TE - signal Image ParametersLong TR - signalShort TE - signal Image ContrastBright Fat - short T1Dark CSF - long T1 Image ContrastBright or Gray FatGray CSF Contrast based onproton concentrationSE T1-weightedSE Double Echo Proton Density Image ParametersLong TR - signalLong TE - contrast180 180 90 echoRFImage ContrastDark Fat – short T2Bright CSF – Long T2echo90 GssGpeGroTE1SE Double Echo T2-weightedTRTE2Conventional Spin Echo Diagram30Page 5

Which two processes are repeated in a DualSE Sequence?Which two processes are repeated in a DualSE Sequence? Refocusing and ReadoutTau Time3334Spin EchoParametersEffects of the 1800 PulseT1 is TRDependent eliminates signal loss due to fieldinhomogeneitieseliminates signal loss due tosusceptibility effectseliminates signal loss due towater/fat dephasingall signal decay is caused by T2relaxation onlyPD is TR andTE DependentT2 is TEDependentSpin Echo Parameters that manipulateTissue Characteristics3536Page 6

Multi Echo Spin Echo only 1 phaseencodeper TRRFsliceST TR(msec) x Npe x NEX /60,000(msec)phaseST: Scan time in minutesNpe: Number of phase stepsNEX: Number of acquisitions, NAQ, NEX, NSAreadoutsignal2DFT Scan Time Formulaecho 13790 180 echo180 echo192 4321 4321Frequency EncodingFrequency Encoding38 First developed as the RARE (RapidAcquisition with Relaxation Enhancement)method. A 90 pulse initiates the sequence,followed by multiple 180 pulses togenerate multiple echoes. However separate phase encodes areused prior to each echo to fill k-spacemore rapidly.RF192echo 238Fast Spin Echo39404142Fast Spin Echo Pulse DiagramPage 7

Parameter Acronyms ETE ETL or Turbo Factor Terminology Effective TE Selectable and determines TE in center of kspace. Therefore determines image contrast. The TE placed inportion of k-spacewith greatest impacton signal. ETS ETL Selectable and determines number of echoesacquired per TR. Determines how fast sequence is run; higherthe ETL the shorter the scan time. Higher ETL reduce time for slices.Echo Train Length Number of Echoesacquired per TR ETEEcho Train Spacing Time (msec) betweenechoes in Echo Train ETS Not selectable; higher spacing leads toblurriness.Fast Imaging ParametersFast Imaging Parameters43 44Optimal TR is 2000 – 4000msec or longer so magnetization fully recovers. Longer TR’s allow more signal and slices. Shorter TR ( 2000msec) image not T2weighted even though CSF is bright. Single shot FSE or TSE acquires 53% of kspace and reconstructs in Half-Fourieralgorithm to achieve final resolution. Allows T2-wt studies with reduced motionartifacts and low susceptibility. Adaptable for breath hold exams anduncooperative patients. Too much T1 contrast added to the image. ETE time is long 80msec. Longer ETE’s are allowed due to longer TR (signal)Fast or Turbo SE GuidelinesSingle Shot FSE concept46SE & FSE ContrastParameterGuidelinesTEshortlongshortScan Time TR(msec) x Npe x NEX(Minutes)60,000(msec) x ETLTRshortlonglongWEIGHTINGT1T2Proton densityFast Imaging Scan Time Formula4748Page 8

Spin EchoAll vendors use SpinEcho designation Fast Imaging T2Siemens:Turbo Spin EchoGE:Fast Spin EchoHitachi:Fast Spin EchoPhilips:Turbo Spin EchoPicker:Fast Spin EchoToshiba:Fast Spin Echo ot SEHASTESSFSESSFSESSTSEEXPRESSFASE FSE w/90 Flip-BackSiemens:RESTOREGE:FRFSEHitachi: Driven EquilibriumPhilips:DRIVEToshiba:FSE T2 pulsVendor Terminology4950Inversion Recovery SequenceInversion Spin Echo Diagram51 52Inversion Recovery pulse sequences arehighly sensitive to differences in T1 valuesof tissues. Especially useful where T1 values aresimilar. The primary contrast control mechanism isTI. TI, Time of Inversion, is the length of timenet magnetization is allowed to recover beforestarting the 90 RF pulse (Spin Echo). STIR, Short TI or Tau Inversion Recovery,sequences are created by shortening the TItime to 69% of T1 relaxation of fat for fatsuppression. FLAIR, Fluid Attenuated InversionRecovery, sequences are created bylengthening the TI time to 69% of T1 relaxationof water for water suppression.Inversion Recovery5354Page 9

The effect of inverting the magnetizationvector by the 180 RF pulse allows for thetissues dynamic range to be increased. The magnitude of magnetization M is afunction of time after a 180 pulse. Magnetization starts negative (-Z), passesthrough zero at t .69 T1 and recoverscompletely by t 5T1. Suppression occurs at the tissue’s NULLPOINT. Null point is the point at which netmagnetization crosses the transverseplane. The Null point is approximately 69% ofthe T1 of the tissue to be suppressed.Inversion RecoveryNull Point – Suppression Point5556Desired Contrast Inversion Time (TI)Null PointsHeavily T1-wtTI is approx. ¼ TRSTIR(Fat Suppressed)85 – 250msecFLAIR(Water Suppressed)1900 - 2500msecIR Parameter Guidelines5758T2 FSE and T2 STIR TE long50 - 80msec TR long4000 – 10,000msec ETL16 – 20 TInull point of fatSTIR Parameter Guidelines5960Page 10

STIR should not be used with contrastbecause STIR will suppress both the fatand the contrast. Useful in MSK imaging – normal bone isfatty marrow – bone bruises and fracturesare clearly seen.STIR Imaging GuidelinesSTIR Images - MSK6162 Long TE, Long TR, Long ETL Helps visualize stroke. Helps in determining Multiple Sclerosis TI/TAU time of 1700 ‐ 3200msec(depending on magnetic field strength) Achieves suppression of CSF. Fluid Attenuated IRUsed in brain and cord imaging – seeperiventricular and cord lesions more clearlyFluid Attenuated IR Parameters63646566FLAIR Axial BrainPage 11

Gradient Recalled Echo Diagram(Static) Gradient Recalled Echo Diagram(Dynamic)6768In Gradient Recalled Echo, a reversedgradient technique refocuses the spinphases.Flip angles less than 90 are optimized toenhance T1 or T2 tissue-like contrast(T2*).Flip angles less than 90 , flip somecomponent of longitudinal magnetizationvector into the transverse plane, whileportions remain.GradientGradient Echo sequences show a widerange of variations compared to theSpin Echo and Inversion Recoverysequences.Recalled Echo (GRE)69 70The major benefit is the use of thegradients to refocus the net magnetizationinstead of an RF pulse.A gradient reversal in the readout directionis used to create the echo.Spins will either speed up or slow downpending the gradient influence.This is different from the 180 RF pulsewhich flips the spins for refocusing.The spins are refocused by reversingthe speed of the spins rather thanflipping them over to the other side ofthe x-y plane as occurs with the spinecho sequence.Magnetic susceptibility artifacts aremore pronounced on gradient echosequences.Gradient Reversal7172Page 12

Magnetic Susceptibility Magnetic susceptibility, caused byprotons of one tissue precessingfaster than the protons of anadjacent tissue, is exaggerateddue to the affect the spins haveon each other while under theinfluence of the reversedgradient. The MR signal returned is due primarily toT1 longitudinal magnetization.The MR signal returned is also due tofaster T2 relaxation rates due to fieldinhomogeneities.The information is therefore T2*information, which is T2 relaxation due tomagnetic field inhomogeneities as well astissue characteristics.Gradient Recalled Echo (GRE)7374short FAT2*-weightedmedium FAPD-weightedFlip AngleShortT1-weightedMedium36 - 59 PDLong60 - 90 T1long FADegree Range1 - 35 ContrastT2*Flip Angles control GRE ContrastFlip Angles75 Spoiled GRE76Incoherent aka SPGR, FLASH, T1-FFE Uses gradients or RF to spoil or destroyaccumulated transverse coherence maximizes T1 contrastRefocused GRECoherent Aka FISP, GRASS, FFE, Rephased SARGE Uses RF or gradients to refocus accumulatedtransverse magnetization Maximizes T2 ContrastGradient Recalled EchoGradient Recalled Echo7778Page 13

A Fast GRE sequence generates gradient echoesvery rapidly using similar fast imagingtechniques to fill k-space. Image contrast cannot be controlled with the flipangle, TR, and TE. Rather, a preparation pulse (TI) creates thedesired contrast. echoRFGssGro GpeSpoilerPulsesTEThe sequence is initiated with the 180 preparation pulse followed by a waiting period(the inversion time).TR1 phase encode/TRInversion times of 200 to 1000msec are used.Conventional GRE w/ SpoilersFast Gradient Echo79180 echo echo80 180 RFRFGssInversion Time 200 - 1000 msGroTR 9 - 13 msTE 3 - 6 ms180 GpeRFInversionTimeData AcquisitionWindowFast GRE Pulse DiagramFast GRE Pulse Diagram8182Field Strength(T)W-F Offset(Hz)inoutinoutinoutinoutinoutinoutinMore on GRE. MR signal is a composite of fatand water in the imaging voxel. Water and fat resonate atslightly different frequencies. TE time will determine whetherfat and water will appear inphase or 22.3724.6026.8484Page 14

Field Strength(T)W-F 9511.1813.4215.6717.8920.1322.3724.6026.84 Frequency difference in ppm Fat frequency minus water frequency dividedby the water frequency equals the frequencydifference. This difference is about 3.3 - 3.5ppm. Frequency difference in hertz Multiply 3.5ppm by the imaging system’soperating frequency.SIFatfrequency85Quiz water86Fat/Water difference in hertzDetermine the frequency differencebetween fat and water at 3.0T?Answer:1st: Larmor Equation: ώ γ x βώ 42.58mHz x 3.0Tώ 127.74 mHzHints: To find the operating frequency you must usethe Larmor equation ώ γ x β Multiply 3.5ppm by the imaging system’soperating frequency to find the frequencydifference.2nd: 3.5ppm x operating frequency3.5ppm x 127.74mHz 447 Hz @3.0T0.35T1.5T14.90 mHz x 3.5ppm63.86 mHz x 3.5ppm 52.1 Hz 223 Hz8788Gradient Echo Vendor AcronymsOut of PhaseSequenceSiemens GE Philips Hitachi Toshiba PickerSpoiled GEFLASHCoherent ASSFFETrueFISPFIESTATurboFLASHFastSPGR3D MPRAGE3D FastSPGRT2-FFETFE3DTFERSSGFERe-SARGEFET1 FastSARGETrue SSFPCE FastRGEFast GERF FastMPRAGE90Page 15

Thanks for sharing your time with me!9192Page 16

Pulse Sequence Design Made Easier A pulse sequence is a timing diagram designed with a series of RF pulses, gradients switching, and signal readout used in MR image formation. 3 Pulse sequence components Pulse Sequences generally have the following characteristics: An RF line characterizing RF

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