ECEN 489 Lecture 08 Magnetic Resonance Imaging 2 (Wright)

2/17/2016
MRILecture#2for:
ECEN489:AttheInterfaceofEngineering
andLifeSciences
SteveWrightandStephenOgier
MagneticResonanceSystemsLab
smwright@tamu.edu
Magnetic Resonance Systems Lab 1
Outline
ReviewNMR
MRIscanner:Spatialfrequencydetector
T1andT2 weighting:Icanmakeanimage,how
doIencodediagnosticinformation?
HowdoIimagefaster?(WhywouldIwantto?)
Emergingtopics
Magnetic Resonance Systems Lab,

Texas A&M University 1
2/17/2016
Recalltheproblem:HowdowedetectAND
localizesmallmetabolicchangesinthebody?
ImagingExamples
Plum

2/17/2016
ReviewBasicNMR/MRI,thendelvedeeper:
NuclearMagneticResonance
Zeeman splitting of
nuclear energy
. states due to a
static magnetic
field
Manynucleiexhibitspin.
Wheninsideamagneticfield,thesenucleicanexistintwoormorespin
states.
Theenergydifferencebetweenthespinstates(andinteraction
frequency,orLarmor frequency)isproportionaltothemagneticfield.
TheLarmor frequencyisperturbedbythelocalmagneticfield,whichis
affectedbytemperature,pH,bloodflow,etc.,etc.
BasicsofNMR
NetMagnetizationandsignaldetection

z
M 0 M 0 a z
The net magnetization, in the spin up state,
is approximately 1 ppm in clinical MRI.
Mo y
At equilibrium, it lies along the magnetic field.
x Since it is static, and extremely weak, we
can not detect it with and RF coil.
By applying an RF pulse at the Larmor

frequency, we can tip the magnetization
vector away from the static magnetic field axis.
Like a top tipped over, It will spin about the

magnetic field axis- This creates a moving
magnetic field that can be detected by a
pickup coil.

2/17/2016
BasicsofNMR
Diagnosticinformation
A FID looks like a decaying
exponential.
The rates at which the

relaxation process occurs is
Specific to the tissue type and
can be altered by disease, etc.
Note that so far our signal is

from the entire sample.
NMR is the basic phenomenon.

MRI provides spatial localization.
In a chemistry magnet, localization may not be needed (bulk samples)

In a human, biomarkers are generally hidden in the huge water signal.
For those of us in ECE, the MRI system directly detects specific spatial
frequencies.
Larmorconstantsforcommonnuclei

2/17/2016
Summarysofar:
NMRgivesusinformationinbulkaboutthedifferent
chemicalenvironments,asachangeinfrequency
(shift),achangeinrelaxationrates(T1 andT2),anda
hostofothercontrastmechanismsaccessibleto
NMR.
MRIistheadditiontoNMRthatlocalizesthis
information criticalforsensitivityanddiagnosis.
i.e.,weneedtonotonlydetectaneedleinthe
haystack,butweneedtofindittoremoveit!
ImagingExamples
Onion

2/17/2016
Outline
ReviewNMR
doIimpressdiagnosticinformation?
Someemergingtopics
Spatiallocalization
In conventional MRI, spatial localization is done by creating magnetic field
gradients, referred to simply as gradients, in the static magnetic field.
For example, a z-directed gradient coil creates a linear taper along the z direction,
Illustration of three orthogonal Opposing currents in the two z coils A commercial gradient set about to
gradient coils to create linear (loops) create a linear taper along z. be loaded into a magnet.
gradients in B0 in the x, y and z Power supply for our gradients:
direction. Green coil produced Gz. 700 Amps/channel at 1400 Volts
(three channels)

2/17/2016
MRIcollectsspatialfrequencies
Inimageprocessingclasses,wethinkaboutanimage
andits2DFourierTransform.
TheFTcontainsthespatialfrequenciesoftheobject.
SomeproblemsarebestdoneintheFourierdomain.
SpatialFrequenciesareFouriercomponents
Youlearnedhowtobuildasquarewavefromsinusoidsin314.
Ifwearebuildingarepresentationofanobject,each
componentsinewaverepresentsaspatialfrequency.

2/17/2016
Spatialfrequenciesin2D
Herewehavethreedifferent
images(left).
Eachispredominantlyone
frequency.But:
ThereisaDCcomponent,(blackis
zero,whiteispositive).
Thefrequencyisambiguous:Could
bepositiveornegative,soboth
existhere.
And,thefrequencyhasa
direction.
Therighthandimages(theFourier
transforms)arespatialfrequency
mapsforeachimage.
SpatialfrequencymapsaretheFToftheimage
Some image processing/analysis functions are better in the spatial

frequency domain, such as many types of filtering.

2/17/2016
Exampleofusingspatialfrequencyfiltering.
NotethehatchintheimageshowsupasdotsintheFT.(thisis
notimmediatelyobvious).
http://www.cs.otago.ac.nz/cosc453/student_tutorials/fourier_analysis.pdf
Simplyzeroingthespatialfrequenciesgiving
thehatchingreducesthem.
http://www.cs.otago.ac.nz/cosc453/student_tutorials/fourier_analysis.pdf

2/17/2016
ImagingExamples
Banana
MRIcollectsspatialfrequencies
TheNMRsignalisaspatialfrequency.
WhenwecollectanMRimage,weobtaintheFourierTransform
oftheimage,NOTtheimage.
WecanusetheMRIscannertoselectivelycollectthespatial
frequenciesweneed.

2/17/2016
MRIcollectsspatialfrequencies(2)
Whenwecollect(digitize)
theMRsignal,wecollecta
setofspatialfrequencies.
Weneedtocollectenough
toobtaintheinformation
weneed.
Sensitizingtospatialfrequencies 2D
Considerasimpleobjectinthe
magnet,anditsspatial
frequencies.(Fouriertransform).
Notveryinteresting.Addmore
spatialfrequenciesbysaturating
thespinsinagridwithanRF
pulse.
14 cm By varying gradients in x and y
0.55cm
we can sample the spatial
2 rad/0.55 cm=
11.4 rad/cm spatial frequency
frequencies.
We may not need to sample

ALL of the spatial frequencies.
Here we may just want to follow
the gridlines.

2/17/2016
Spatiallocalization
In conventional MRI, spatial localization is done by creating magnetic field
gradients, referred to simply as gradients, in the static magnetic field.
For example, a z-directed gradient coil creates a linear taper along the z direction,
Illustration of three orthogonal Opposing currents in the two z coils A commercial gradient set about to
gradient coils to create linear (loops) create a linear taper along z. be loaded into a magnet.
gradients in B0 in the x, y and z Power supply for our gradients:
direction. Green coil produced Gz. 700 Amps/channel at 1400 Volts
(three channels)
Sensitizingtospatialfrequencies
SincetheMRfrequencyisproportionalthemagneticfield,
a gradientGx inthexdirectioncreatesafrequencyvariation
alongthexaxis:
Thefrequencychangeproducesaphasechangethatincrease
withtime:
Thistimeincreasingphaseoffset
modulatestheobjectwearetryingto
image,M(x,y).Eachpointalongxwill
returnasignalS(x,t):
Thegradienthasimpressedatime
varyingspatialfrequencyonourobject.
Oursignalisproportionaltothe
informationcontentatthatspatial
frequency.

2/17/2016
Sensitizingtospatialfrequencies
Thegradienthasimpressedaspatialfrequencyonour
object.
Thespatialfrequency,kx,istherateofphasechange
perdistance:
Ingeneral,wemayhavetimedependentgradients,so
thatourspatialfrequencycanvarynonlinearly:
Key:Usingourgradientcoils,wecansampleany
positioninkspace.(Wehavexandygradientsaswell).
Note:Movingthroughkspace
allowsustoencodeanentireobjectsFouriertransform
thespatialfrequencies.But,ittakestimeandcan
requirestronggradientamplifierstodosoquickly!
Sensitizingtospatialfrequencies 2D
Considerasimpleobjectinthe
magnet,anditsspatial
frequencies.(Fouriertransform).
Notveryinteresting.Addmore
spatialfrequenciesbysaturating
thespinsinagridwithanRF
pulse.
14 cm By varying gradients in x and y
0.55cm
we can sample the spatial
2 rad/0.55 cm=
11.4 rad/cm spatial frequency
frequencies.
We may not need to sample

ALL of the spatial frequencies.
Here we may just want to follow
the gridlines.

2/17/2016
BasicSpinEchoPulseSequence
BasicSpinEchoPulseSequence

2/17/2016
Outline
ReviewNMR
Someemergingtopics
Mostcommondiagnosticparameters:T1 andT2

2/17/2016
WecanoptimizetherepetitiontimeTRifwe
knowtheT1 valuesofthetissuesofinterest:
Aftera90degree
excitationpulse,the
magnetizationrelaxes
backtoequilibrium
accordingtotheT1 values
ofthetissues.
Wehavetorepeatthe
experiment(TR)to
sampleallofthespatial
frequencies(kspace).
WechooseTRtogiveusa
desiredcontrast.
SimilarlywithTE(echo
time)forT2 contrast.
SNRandContrastoptimization:
Tissuea:Graymatter,T1 =520ms,T2 =95ms
Tissueb:Whitematter,T1 =380ms,T2 =85ms

2/17/2016
T1 andT2 weightedimages.
Thebreadand
butterMRIstudyis
tocreatetwosetsof
images:
Inonesettheimage
intensityis
dominatedbyT1
Intheotherset,the
imageintensityis
dominatedbyT2.
CSF has a long T1 and long T2. CSF is dark in the T1

weighted image, bright in the T2 weighted image. Why?
ParametersselectionforT1,T2 andT2* contrast

forcommonsequences.

2/17/2016
ImagingExamples
Tomato
Outline
ReviewNMR
Someemergingtopics

2/17/2016
Speed:Howfastdoweneedtoimage?
FunctionalMRIusingtheboldeffectuses
periodicstimuli measurecorrelationofbrain
response.
Cardiacimagingisdoneovermultipleheart
beats.(5mstemporalresolutionover4
Courtesy Dan Sodickson,
minuteacquisition.) M.D.,Ph.D.
Harvard Medical School
Is there aperiodic (chaotic) functionality
that we would like to measure?
Flow in stenosis
Most brain patterns?
Tissue damage
Microfluidic lab-on-a-chip devices
AcceleratedImaging Scankspacefaster.
EchoPlanarImagingcanacquireanentiresetof
spatialfrequenciesinoneexcitation.
Requiresacarefullytunedsystemtopreventartifacts.
dB/dt mustbelimitedtoavoidnervestimulation.
phase encoding
loop
http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/zientara/fast/image95.gif

2/17/2016
AcceleratedImaging Scankspacefaster.
Therearemanywaystoscankspace.Spiralsarefast,butreconstruction
ismoredifficult.
ParallelimagingusesRFcoilphase(andamplitude)toreducesampling
densityinkspacebygradients.RFphaseisinstantlyencoded,butitis
notasflexibleasgradientsduetothetimeintegralofagradientpulse.
RFEncodingwithArraysofReceiveCoils
forFastMRI
Sourcesata,b,andc
producevoltagesineach
coilproportionaltothe
fieldproducedbythecoil
atthesourcepoint.
Thus,eachcoildetects
independentdatafrom
eachpoint.
Wecanusethis
informationforfast
imaging!

2/17/2016
RFEncodingwithArrays
Thedirectionoftheflux
linescorrespondtothe
phaseofthedetected
signal.
Wecanusethisto
providesomedegreeof
phaseencoding.
Phaseencodingbysurfacecoils
Hereweviewthefieldofacoil
inaplanecuttingthroughthe
coil(thebigblackdots).
Thefluxpatternofasurface
coilisnotuniform.
Theverticalcomponentand
horizontalcomponentare
detectedoutofphase.
Examine the region of

interest, above the coil,
more closely:

2/17/2016
Nearthecoil,wherethe
strongestsignalis
contributed,thecoil
impressesastrong
phaseshift.
Thisphaseshift
simulatestheeffectofa
gradientpulse.
Examine flux along the

green line:
XandYdirectedfluxdensities6cmabovea6cmdiametersurfacecoil.
This effective phase modulation closely simulates

the effects of the gradient pulse used to obtain the
first line of k-space.

2/17/2016
Phase Encoding:
Generate lines of k-space by applying different gradient pulses.
A linear gradient creates a progressive, linear phase shift- a harmonic
1st line of k-space
Signal x
Center line of k-space

Signal x 1
-1st line of k-space
Signal x
By adding the signals detected by different coils, we can synthesize

different lines of data- speeding up the imaging process.
UndersampledFourierData
N lines
DFT
Undersampling
by a factor of two
speeds up the image,
but causes aliasing. N/2 lines
DFT

2/17/2016
RFEncodingwithArrays:
SMASHImagingwithan8elementarray
The array, preamps and

decoupling networks are
housed in a sled which
inserts into a horizontally
polarized birdcage coil.
The elements were placed on

two separate layers, on either
side of a 1mm rigid substrate.
12cm
68mm
(including feeds)
RFEncodingwithArrays:
SMASHImagingwithan8elementarray
Images reconstructed with

partial k-space data show
excellent agreement with
full k-space images up to an
acceleration factor of 8
(1/8th of original data)
Images on left demonstrate

the aliasing due to
undersampling of k-space,
Images on right are
reconstructed using RF
encoding (SMASH) by Dan
Sodickson and Mark
Griswold.

2/17/2016
ImagingExamples
Potato
SingleEchoAcquisition(SEA)MRI
Phaseencodingisentirelyeliminatedandreplacedbythe
spatiallocalizationoflongandverynarrowcoils
z
DCBlockingCap
2xVaractorDiode
fortune
x
Tunablecapacitor
formatch
10kresistor
underneath
McDougall,M.P.andWright,S.M.,Magn.Reson.Med.,Aug,2005

2/17/2016
SingleEchoAcquisition(SEA)MRI (64x256resolution)
64 element array coil and Step #1: Simultaneously digitize and

64 channel receiver demodulate 1 echo with 64 coils.
Total time ~ 1 TR or 1 echo.
Step #2: 64 1-D FFTs
Step #3: Stack in video memory

and display.
Achieved 1000 frames per second.
Motionimaging
Test phantom
Spin Echo, 256x256
resolution
0 RPM, 100 percent
speed
Test phantom
SEAImagingisremarkably
Gradient Echo, 64 x 128
insensitivetomotionartifacts. resolution
Eachimageiscreatedfroma TR/TE = 8/4 msec.
singleecho. 60 RPM, 80 percent display
Nomotionartifactsduetomotion speed.
inphaseencodinggradients

2/17/2016
Applications:UltraFastImaging
Evolution of transverse Motion imaging Flow Measurement

magnetization
Gradient echo SEA imaging Rotating water dish. Dividing channel.
sequence 60 rotations/second, 200 frames/second
RF Tip angle 3 degrees 125 frames/second
TE = 4 msec, TR = 8 msec Flow rates stepped from
125 frames/sec 0 cm/sec to 112 m/sec in entry
Total movie time = 1 second. tube.
SNRimprovementwithsurfacecoilarrays.
Arrayscanovercomesmallfieldofview:
MicrocoilsMicroFOV
Arraysoflongcoils
+
ParallelImaging
www.brockwaybiomedical.com SNRofsmallcoil
FOVoflargecoil
Notimeexpense

2/17/2016
SNRimprovementwithsurfacecoilarrays.
Example:WideFieldMicroscopy
TR/TE=500/40 msec
Volume Coil Array Coil

2048x2048 acquisition, Nav = 16 256x2048 (by 64) acquisition
2048x2048 reconstruction Nav = 1
Imaging time = 4.5 hrs Imaging time = 2.13 mins
FOV=130x130mm FOV=16.25mm x 130mm

res = 63x63 microns res = 63x63 microns
SNR = 13 SNR = 12.3
McDougall and Wright, MRM 68(3), 2012
WideFOVMicroscopyResults:2DImaging
2048x2048 image
(63 microns in-plane)

2/17/2016
ImagingExamples
Cupcake
Outline
ReviewNMR
Someemergingtopics
MRElastography palpationwithanMRIScanner
MagneticParticleImaging Theperfectmodality?

2/17/2016
MagneticResonanceElastography
TheMRimagecanbemadeextremelysensitivetomotion.
Sosensitive,infact,thatwecanmeasuresoundwaves
passingthroughabody.
Soundwavestravelatdifferentspeedsthroughtissuewith
differentstiffness sousingMRIphasecontrast,wecan
measurethestiffnessofatissue.
Remember,palpationwascertainlyoneoftheearliest
diagnostictools,andisstilltheearliestformofdetection
ofmanytumors.
Ultrasoundcannotbeusedtodetecttumorsinabrain,for
example.MRIcan,usingthistechnique,calledMR
Elastography.(Ultrasounddoesnotpassthroughbone
hardtouseinthelungs,brain,behindribs.)
(McCracken,etal.,MRM,2005)
Inessence,wegenerateasoundwaveinthe
objectbeingstudied.
Wefreezethewavebygatingtothe
vibration,muchlikecardiacmotion.
Wecansensitizebysynchonizing our
gradientstothevibration(HarmonicMRE)
HarmonicMREisveryslow wehavetoform
animageforeverypointinthewaveform.
WeareinvestigatingtransientMRI
(McCracken,etal.,MRM,2005)

2/17/2016
Allowsquantitative
assessmentoftissuestiffness
Comparabletoinformation
gainedbypalpation
Mayo Clinic Animation of

shear waves in the liver
during MRE
http://discoverysedge.mayo.edu
/de071biotechehman/
(Muthupillai,etal.,Science,1995)
(Muthupillai,etal.,MRM,1996)
SEAMRElastography
Using Single Echo Imaging each echo visualizes one time point in the propagation of
the wave.
Eliminates the need to choose an excitation frequency.
Eliminates the need to encode the image (allows transients).
Gel Phantom
Speaker
outside magnet room
64 element array
Wright, Yallapragada, Bosshard, McDougall, ISMRM 2007

2/17/2016
MRE ActuatorandPhantomSetup
Direction
Direction
ofOscillation
ofshearwave
64Channel propagation
SEACoil
Volumecoilfor Vibrating
RFtransmit Wedge
HalogenBulb
(Heatsource)
0.7g/Lagaroseconcentration
200Hzexcitationfrequency
Bosshardet.al.,ISMRM,2008
SEAMREmovieofagarosegelheating
Phase contrast images

obtained by subtracting
the +ve and ve motion
encoded phase images
TR = 2.5s
TE = 22s
1 image per echo.
Collected 950 frames

while the
temperature was varied
from 20oC to 72oC
Displaying every 20th

frame

2/17/2016
ISMRM2013 BothHighResandHighSpeed
fromoneprobe.(thatsnoteasyinMRI).
Movie herehas156x126micronresolution.
ImagingExamples
Graduate
Student

2/17/2016
MRSL:MagneticResonanceSystemsLab
Established>15yearsagoinECEN
dept.
4.7T
33m Faculty:
SteveWright(ECEN/BMEN)
JimJi(ECEN)
MaryMcDougall(ECEN/BMEN)
Threeprimarymagnets
4.7T/33cm
Development.
4.7T/40cm
Translation.
1.0T/20cm
HumanExtremity
Training/EducationinMRIintheMRSL
ECEN 411 Intro to MRI/MRS

Students use our 4.7T MRI
systems to learn spectroscopy and imaging.
ECEN 463/763: Each student assembles,

codes and tests their own desktop MRI.
ECEN 648: Principles of MRI


ECEN 489 Lecture 08 Magnetic Resonance Imaging 2 (Wright)

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2/17/2016

Magnetic Resonance Systems Lab 1

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

By applying an RF pulse at the Larmor

Like a top tipped over, It will spin about the

Magnetic Resonance Systems Lab,

The rates at which the

Note that so far our signal is

NMR is the basic phenomenon.

In a chemistry magnet, localization may not be needed (bulk samples)

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Some image processing/analysis functions are better in the spatial

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

We may not need to sample

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

We may not need to sample

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

CSF has a long T1 and long T2. CSF is dark in the T1

ParametersselectionforT1,T2 andT2* contrast

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Examine the region of

Magnetic Resonance Systems Lab,

Examine flux along the

This effective phase modulation closely simulates

Magnetic Resonance Systems Lab,

1st line of k-space

Center line of k-space

-1st line of k-space

By adding the signals detected by different coils, we can synthesize

Magnetic Resonance Systems Lab,

The array, preamps and

The elements were placed on

Images reconstructed with

Images on left demonstrate

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

64 element array coil and Step #1: Simultaneously digitize and

Step #2: 64 1-D FFTs

Step #3: Stack in video memory

Magnetic Resonance Systems Lab,

Evolution of transverse Motion imaging Flow Measurement

Magnetic Resonance Systems Lab,

Volume Coil Array Coil

FOV=130x130mm FOV=16.25mm x 130mm

SNR = 13 SNR = 12.3

McDougall and Wright, MRM 68(3), 2012

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Magnetic Resonance Systems Lab,

Mayo Clinic Animation of