M R I M R I Pulse SequencesPulse Sequences

Jerry Allison Ph.D.Jerry Allison Ph.D.

1017 pages 1017 pages ©2004 2

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OutlineOutlineI. Spin Echo ImagingI. Spin Echo Imaging

MultiplanarMultiplanarMultisliceMultisliceObliqueOblique

II. Inversion Recovery (IR)II. Inversion Recovery (IR)III. Gradient Recalled EchoIII. Gradient Recalled EchoIV. Three Dimensional (Volume) IV. Three Dimensional (Volume) TechniquesTechniquesV. Fast Imaging TechniquesV. Fast Imaging TechniquesVI. Echoplanar ImagingVI. Echoplanar Imaging

Image ContrastImage Contrast

Image contrast in radiography and CT is based upon a Image contrast in radiography and CT is based upon a few properties of the tissues or contrast agents few properties of the tissues or contrast agents involved:involved:

- physical density (g/cc)- physical density (g/cc) - electron density (electrons/cc)- electron density (electrons/cc) - atomic number- atomic number

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Image ContrastImage Contrast Contrast in MRI is more complex and depends Contrast in MRI is more complex and depends

on many properties/parameters, which can be on many properties/parameters, which can be classified into “intrinsic” properties and classified into “intrinsic” properties and “extrinsic” parameters. Intrinsic properties “extrinsic” parameters. Intrinsic properties relate directly to the tissue. Extrinsic relate directly to the tissue. Extrinsic parameters relate to the characteristics of the parameters relate to the characteristics of the MR imager and the details of the “MRI Pulse MR imager and the details of the “MRI Pulse sequence” used for imaging.sequence” used for imaging.

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Proton densityProton density TT1 1 relaxationrelaxation TT2 2 relaxationrelaxation TT22* relaxation* relaxation

- magnetic susceptibility- magnetic susceptibility

DiffusionDiffusion Magnetization transferMagnetization transfer

-cross relaxation-cross relaxation

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Intrinsic PropertiesIntrinsic Properties

Intrinsic PropertiesIntrinsic Properties

Chemical ShiftChemical Shift

TemperatureTemperature PerfusionPerfusion Changes in tissue composition (e.g. age)Changes in tissue composition (e.g. age) ViscosityViscosity Physiologic motion Physiologic motion Bulk flowBulk flow

BloodBlood

CSFCSF

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Extrinsic ParametersExtrinsic Parameters

Magnetic field strengthMagnetic field strength -static field-static field -gradient field-gradient field

Magnetic field homogeneityMagnetic field homogeneity

Hardware and software parametersHardware and software parameters -coil selection-coil selection -number of slices acquired-number of slices acquired -slice thickness and gap-slice thickness and gap

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Extrinsic ParametersExtrinsic Parameters Hardware and software parametersHardware and software parameters -slice location-slice location -slice orientation-slice orientation -number of averages or excitations-number of averages or excitations -RF pulse shape (#sinc lobes)-RF pulse shape (#sinc lobes) -RF transmitter bandwidth-RF transmitter bandwidth -RF receive bandwidth-RF receive bandwidth -pixel size-pixel size -matrix size-matrix size -field of view-field of view

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Extrinsic ParametersExtrinsic Parameters

-acquisition mode ( 2D / 3D )-acquisition mode ( 2D / 3D )

-artifact suppression-artifact suppression

-physiologic triggering / gating-physiologic triggering / gating

-orientation of phase and frequency -orientation of phase and frequency

encode gradientsencode gradients

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Extrinsic ParametersExtrinsic Parameters

RF pulse sequencesRF pulse sequences

-inversion recovery-inversion recovery

-spin echo-spin echo

-gradient recalled echo-gradient recalled echo

-fast scan sequences -fast scan sequences

-echoplanar (single shot techniques)-echoplanar (single shot techniques)

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Extrinsic ParametersExtrinsic Parameters

Pulse sequence parametersPulse sequence parameters

-repetition time (TR)-repetition time (TR)

-echo time (TE)-echo time (TE)

-inversion time (TI)-inversion time (TI)

-flip angle (-flip angle ())

-echo train length-echo train length

Contrast enhancing agentsContrast enhancing agents

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MRI Pulse SequencesMRI Pulse Sequences

An MRI pulse sequence dramatically An MRI pulse sequence dramatically impacts the appearance of an MRI image.impacts the appearance of an MRI image.

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Spin Echo Pulse SequencesSpin Echo Pulse Sequences

T2 weightedT2 weightedPD weightedPD weightedT1 weightedT1 weighted

TR 510TR 510

TE 14TE 14

2min 7sec for 17 slices2min 7sec for 17 slices

TR 4500TR 4500

TE 15eff (ETL7) TE 15eff (ETL7)

2min 39sec for 24 slices2min 39sec for 24 slices

TR 4500TR 4500

TE 105eff (ETL7) TE 105eff (ETL7)

2min 39sec for 24 slices2min 39sec for 24 slices

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Inversion Recovery Gradient Echo Pulse SequenceInversion Recovery Gradient Echo Pulse Sequence

TR 12.1TR 12.1

TE 5.4TE 5.4

3min 11sec for 160 slices3min 11sec for 160 slices

MRI Pulse SequencesMRI Pulse Sequences

More specifically, an MRI pulse sequence More specifically, an MRI pulse sequence is a “sequence” of temporal waveforms:is a “sequence” of temporal waveforms: Radiofrequency (RF) pulsesRadiofrequency (RF) pulses Gradient (magnetic field) pulsesGradient (magnetic field) pulses Data acquisiton intervalsData acquisiton intervals

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Here is a pulse-Here is a pulse-sequence diagram. sequence diagram. This shows a This shows a timeline for: 1) RF timeline for: 1) RF pulses; 2) gradient pulses; 2) gradient amplitudes for Gx, amplitudes for Gx, Gy, Gz; 3) the Gy, Gz; 3) the readout (i.e., A/D), readout (i.e., A/D), and 4) the signal of and 4) the signal of the excited nuclei.the excited nuclei.

Multiplanar ImagingMultiplanar Imaging Axial, sagittal, and coronal images can be acquired Axial, sagittal, and coronal images can be acquired

as follows: as follows:

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Notice that for each plane, the choice of axis for Notice that for each plane, the choice of axis for phase and frequency encoding can vary.phase and frequency encoding can vary.

MRI Image WeightingMRI Image Weighting

Many MRI images are described as:Many MRI images are described as: Proton density weightedProton density weighted T1 weightedT1 weighted T2 weightedT2 weighted (and T2* weighted)(and T2* weighted)

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Spin Echo ImagesSpin Echo Images

T2 weightedT2 weightedPD weightedPD weightedT1 weightedT1 weighted

TR 510TR 510

TE 14TE 14

2min 7sec for 17 slices2min 7sec for 17 slices

TR 4500TR 4500

TE 15eff (ETL7) TE 15eff (ETL7)

2min 39sec for 24 slices2min 39sec for 24 slices

TR 4500TR 4500

TE 105eff (ETL7) TE 105eff (ETL7)

2min 39sec for 24 slices2min 39sec for 24 slices

Proton Density WeightingProton Density Weighting

Images are (largely) weighted by the mobile Images are (largely) weighted by the mobile hydrogen content of the tissues (water and hydrogen content of the tissues (water and fat).fat).

PD: PD: FAT < WM < GM < CSF FAT < WM < GM < CSF

PD images: PD images: CSF > GM > WM > Fat CSF > GM > WM > Fat

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Proton Density WeightingProton Density Weighting Proton DensityProton Density -The nucleus of most hydrogen atoms is a single particle: the proton-The nucleus of most hydrogen atoms is a single particle: the proton -The number of “mobile” hydrogen nuclei per voxel directly affects the intensity -The number of “mobile” hydrogen nuclei per voxel directly affects the intensity

of the voxel in an MRI image (for all image weightings).of the voxel in an MRI image (for all image weightings). -Proton Density Weighting emphasizes proton density (as opposed to t1, t2 or -Proton Density Weighting emphasizes proton density (as opposed to t1, t2 or

T2*)T2*)

-Total proton densities-Total proton densities -CSF -CSF 0.112 g H/cc 0.112 g H/cc -Grey Matter -Grey Matter 0.1058 g H/cc 0.1058 g H/cc -White Matter -White Matter 0.1056 g H/cc 0.1056 g H/cc -Fat -Fat 0.1 g H/cc 0.1 g H/cc

- Protons in lung tissue volume ~ 0.01 g H/cc- Protons in lung tissue volume ~ 0.01 g H/cc

So, one of many problems with lung imaging is the low proton density per So, one of many problems with lung imaging is the low proton density per volume, leading to very low SNR.volume, leading to very low SNR.

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Proton Density WeightingProton Density Weighting

-Although white matter and grey matter have -Although white matter and grey matter have very similar proton density; they are very similar proton density; they are differentiated in MRI by their lipid and water differentiated in MRI by their lipid and water content.content.

Lipid (g H / cc) Water (g H / cc)Lipid (g H / cc) Water (g H / cc) Grey Matter 0.0072 0.0910Grey Matter 0.0072 0.0910 White Matter 0.0178 0.0796White Matter 0.0178 0.0796

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T1 WeightingT1 Weighting

Images demonstrate good contrast between Images demonstrate good contrast between soft tissue types (because different tissues soft tissue types (because different tissues have different “T1” values).have different “T1” values).

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T2 WeightingT2 Weighting

Images demonstrate good contrast between Images demonstrate good contrast between normal tissue and pathology (because many normal tissue and pathology (because many pathologies have elevated “T2” values due pathologies have elevated “T2” values due to increased free water content).to increased free water content).

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Approximate T1 and T2 Values for Human Tissue(37 oC)

TissueT1 at 1.5 T

(msec)T1 at 0.5 T

(msec)T2

(msec)

Skeletal Muscle 870 600 47Liver 490 323 43Kidney 650 449 58Spleen 780 554 62Fat 260 215 84Gray Matter 920 656 101White Matter 790 539 92Cerebrospinal Fluid >4,000 >4,000 >2,000

T1, T2 WeightingT1, T2 Weighting

In images of the headIn images of the head

T1: T1: FAT < WM < GM < CSF FAT < WM < GM < CSF T1 images: T1 images: FAT > WM > GM > CSFFAT > WM > GM > CSF T2: T2: FAT < WM < GM < CSF FAT < WM < GM < CSF T2 images: T2 images: CSF > GM > WM > FAT CSF > GM > WM > FAT

Careful: CSF or Fat can be suppressed Careful: CSF or Fat can be suppressed

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Pulse Sequence FamiliesPulse Sequence Families

Spin Echo: SESpin Echo: SE Gradient Echo:Gradient Echo:

• GEGE• Gradient Recalled Echo (GRE)Gradient Recalled Echo (GRE)• Field Echo (FE)Field Echo (FE)

Inversion Recovery: IRInversion Recovery: IR• STIR: short tau inversion recoverySTIR: short tau inversion recovery

• Fat suppressionFat suppression

• FLAIR: fluid attenuated inversion recoveryFLAIR: fluid attenuated inversion recovery• Fluid (CSF) suppressionFluid (CSF) suppression

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Spin Echo ImagingSpin Echo Imaging

Easy to control image weighting with SEEasy to control image weighting with SE• T1 weightedT1 weighted

• T2 weightedT2 weighted

• PD weightedPD weighted

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Spin Echo ImagingSpin Echo Imaging

The Spin Echo imaging technique has the The Spin Echo imaging technique has the advantage that it is not as sensitive to static advantage that it is not as sensitive to static inhomogeneity of the magnet and inhomogeneity of the magnet and inhomogeneity caused by magnetic inhomogeneity caused by magnetic susceptibility of patient tissue.susceptibility of patient tissue.

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Spin Echo ImagingSpin Echo Imaging

Spin Echo ImagingSpin Echo Imaging The pulse sequence must be repeated many times to produce an MRI The pulse sequence must be repeated many times to produce an MRI

image. The time interval between each execution of the pulse sequence image. The time interval between each execution of the pulse sequence is termed the is termed the Repetition Time (TR).Repetition Time (TR).

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Spin Echo ImagingSpin Echo Imaging

The value of the repetition time (TR) and the echo The value of the repetition time (TR) and the echo time (TE) can be varied to control contrast in spin time (TE) can be varied to control contrast in spin echo imaging. For example:echo imaging. For example:

TR = 2000 msec TE = 20 msec Proton Density WeightingTR = 2000 msec TE = 20 msec Proton Density Weighting

TR = 2000 msec TE = 80 msec TTR = 2000 msec TE = 80 msec T22 Weighting Weighting

TR = 600 msec TE = 20 msec TTR = 600 msec TE = 20 msec T11 Weighting Weighting

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Fast Spin Echo Pulse Sequence (FSE)Fast Spin Echo Pulse Sequence (FSE)

Turbo Spin Echo (TSE)Turbo Spin Echo (TSE)

Careful: Fat can be excessively Careful: Fat can be excessively bright on FSE images (j-coupling)bright on FSE images (j-coupling)

Gradient Recalled EchoGradient Recalled Echo Gradient recalled echo techniques have great Gradient recalled echo techniques have great

versatility. A variety of contrasts can be versatility. A variety of contrasts can be produced while imaging rapidly.produced while imaging rapidly.

GRE techniques include: GRE techniques include: GRASS, SPGR, FLASH, FISP, PSIF and many, GRASS, SPGR, FLASH, FISP, PSIF and many,

many others.many others.

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MIP MIP (Maximum Intensity Projection)(Maximum Intensity Projection)

Gradient Recalled Echo ImagesGradient Recalled Echo Images

2D-FLASH2D-FLASHTR 25msecTR 25msecTE 9msecTE 9mseca = 35a = 35oo

5.7sec per slice5.7sec per slice

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Multi Planar GRASS Multi Planar GRASS mixed T1/T2 weightingmixed T1/T2 weightingTR 500msec TE 13msec 2NEX a=60TR 500msec TE 13msec 2NEX a=60oo

3min 14 sec for 15 slices3min 14 sec for 15 slices

Gradient Recalled Echo ImageGradient Recalled Echo Image

Gradient Recalled EchoGradient Recalled Echo Exceptions are:Exceptions are: 1. The creation of the echo is accomplished solely by 1. The creation of the echo is accomplished solely by

gradient magnetic fields (no 180gradient magnetic fields (no 180oo RF pulse). RF pulse). 2. Deposition of RF energy in the patient is lower since 2. Deposition of RF energy in the patient is lower since

the 180the 180oo RF pulses are not used (less heating of patient RF pulses are not used (less heating of patient tissues).tissues).

3. Static inhomogeneity of the magnet and 3. Static inhomogeneity of the magnet and inhomogeneity caused by magnetic susceptibility of inhomogeneity caused by magnetic susceptibility of patient tissue are NOT corrected by gradient recalled patient tissue are NOT corrected by gradient recalled echo techniques.echo techniques.

4. T2 contrast becomes T2* contrast.4. T2 contrast becomes T2* contrast.

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Gradient Recalled EchoGradient Recalled Echo 4. The initial flip angle is frequently chosen to 4. The initial flip angle is frequently chosen to

be less than 90be less than 90oo . The flip angle in gradient . The flip angle in gradient recalled echo techniques is called recalled echo techniques is called . .

The optimum value of The optimum value of for a particular TR and for a particular TR and tissue having spin lattice relaxation Ttissue having spin lattice relaxation T11 is called is called the Ernst angle.the Ernst angle.

40ee

-TR-TRTT11

cos(cos(ee) =) =

Gradient Recalled EchoGradient Recalled Echo

5. 3D or volume imaging can be accomplished 5. 3D or volume imaging can be accomplished (resulting in thinner slices).(resulting in thinner slices).

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Vancouver, BC Vancouver, BC courtesy of Dr. Rawsoncourtesy of Dr. Rawson

Three Dimensional VolumeThree Dimensional Volume TechniquesTechniques

3D voxels are isotropic (or nearly isotropic). 3D voxels are isotropic (or nearly isotropic). The voxels are the same size in all 3 dimensions. The voxels are the same size in all 3 dimensions. The dimensions of a typical 3D voxel are The dimensions of a typical 3D voxel are

1 mm x 1 mm x 1 mm. The acquisition of 1 mm x 1 mm x 1 mm. The acquisition of isotropic voxels enables the data set to be isotropic voxels enables the data set to be reformatted into any oblique plane without reformatted into any oblique plane without significant loss of resolution using Post significant loss of resolution using Post Processing Techniques.Processing Techniques.

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MPRAGE: Magnetization Prepared Rapid Gradient EchoMPRAGE: Magnetization Prepared Rapid Gradient EchoTR 11.4msec TE 4.2msec a=12TR 11.4msec TE 4.2msec a=12oo 1.4mm 1.4mm6min 55sec for 120 slices (168mm slab)6min 55sec for 120 slices (168mm slab)Uses Inversion RecoveryUses Inversion Recovery

Three Dimensional VolumeThree Dimensional Volume ImageImage

Inversion Recovery (IR)Inversion Recovery (IR) Inversion recovery pulse sequences are useful for:Inversion recovery pulse sequences are useful for:

Suppression of selected tissues (e.g. orbital fat, liver Suppression of selected tissues (e.g. orbital fat, liver screening, fatty tumors, CSF) screening, fatty tumors, CSF)

Creation of heavily T1 weighted images without a Creation of heavily T1 weighted images without a dominant contribution from fat (e.g. brain, liver and dominant contribution from fat (e.g. brain, liver and musculoskeletal imaging).musculoskeletal imaging).

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Inversion Recovery (IR)Inversion Recovery (IR) A basic IR spin echo pulse sequence consists of A basic IR spin echo pulse sequence consists of

a 180a 180oo inversion pulse, followed by an inversion pulse, followed by an inversion inversion time TItime TI, then a 90, then a 90oo RF pulse. RF pulse.

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Consider two voxels, one of fat and one of H2O

This method of fat suppression is sometimes called “short TI” inversion recovery or STIR imaging.

Inversion Recovery (IR)Inversion Recovery (IR)

In spin echo inversion recovery imaging In spin echo inversion recovery imaging sequences, the 90sequences, the 90oo pulse is followed by a 180 pulse is followed by a 180oo pulse in order to produce a spin echo at time TE pulse in order to produce a spin echo at time TE following the 90following the 90oo pulse pulse

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FLAIR: fluid attenuated IR (T2 weighted spin echo)FLAIR: fluid attenuated IR (T2 weighted spin echo)Inversion time: 2.5sec (CSF is suppressed)Inversion time: 2.5sec (CSF is suppressed)TR 10sec TE 119msec (ETL7) TR 10sec TE 119msec (ETL7) 3min 49sec for 19 slices3min 49sec for 19 slices

IR ImageIR Image

vsvs

STD T2 weightingSTD T2 weighting

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GE MRI Image AnnotationGE MRI Image Annotation

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GE MRI Image AnnotationGE MRI Image Annotation

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GE MRI Image AnnotationGE MRI Image Annotation

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GE MRI Image AnnotationGE MRI Image Annotation

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GE MRI Image AnnotationGE MRI Image Annotation

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GE MRI Image AnnotationGE MRI Image Annotation