tel. 04-8295361/364 ediths@tx.technion.ac · 2015. 10. 29. · tel. 04-8295361/364...

Tel. 04-8295361/364 ediths@tx.technion.ac.il


• Introduction to Aspect M2™ MRI• MR safety• Possible applications and examples• MR Basics• “Recipe” for MR Imaging• Useful notes• Scan protocols• Custom MRI Analysis Tool• K‐Pacs Basic Instructions• How to begin

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Permanentmagnet vs. Standard superconducting coil based

(*illustrative photos)3


Mouse/rat head coil

Mouse/rat body coil

Anastasia

Cradle Heating system 4


• Compact • A new level in MR safety• Virtuallymaintenance‐free• Simple to install• Magnet is always ON, always ready to image

• Located in the SPF at Rappaport : enables follow‐up scanning

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• Frommouse (or rat) to man• Easy to Learn• 1 Tesla field strength: most suitable for Gadolinium based contrast agent imaging

• Easy to Use• High‐performance: Superior (100µm) resolution, 2D and 3D imaging

• Fast

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• Scanned size: rat and mouse only, up to 60mm in diameter• Field strength of 1 Tesla: “costs” longer durations or lower resolution• No option for functional imaging or DTI• No option for cardiac gating

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• No external fringe field: metal objects can be in the proximity of the system.

• Safe for PCs or mobile phones• Aspect system is safer to operate

** CAUTION: Metal objects cannot be placed or inserted directly inside Aspect Imaging magnets.Aspect system is still a powerful magnet and placing metal objects inside the bore can create irreparable damage to the system.Metal objects must be kept outside of the magnet’s 5 gauss line.

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• The Power of 1.5 Tesla (GE)

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• Welding tank

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• Cancer• Cardiovascular• Contrast‐based Molecular Imaging• Diabetes and Obesity• Embryology / Developmental Biology• Nephrology• Neurobiology• Stem Cell / Cell Tracking• Histology (PM / Ex‐vivo)

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1. Gadolinium (Gd) – Paramagnetic:Increases T1 signal– Extracellular fluid agents– Blood pool agents– Organ‐specific agents2. Iron oxide – Superparamagnetic:Reduces T2 signals3. Iron Platinum – Superparamagnetic:Reduces T2 signals4. Manganese – Paramagnetic:Increases T1 signal

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FSE, TR/TE=1918/76 ms, 1 mm slice, NEX=2, 176X176, FOV=64 mm

Movie: Photo:

T2W T2W

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Control (T1w+C): CHF: T1W+C

Zaid Aba

ssi’s

Lab

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Pathology: Control:


FSE, TR/TE=1705/80 ms, 1.3 mm slice, NEX=4, 256X256, FOV=64 mm

T2W T2W

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Yuval Sha

ked’sL

ab


FSE, TR/TE=3000/80 ms, 0.8 mm slice, NEX=4, 200X200, FOV=40 mm

T2W

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T2W

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SE‐DWI, TR/TE=500000/19 ms, 1.5 mm slice, NEX=1, 128X128, FOV=64 mm, BIGDELTA = 10, DIFFMAG = 961, b=1 and b=300

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T2WDWI


IR‐SE, TR/TE=500/9 ms, TI=100 ms, 1 mm slice, NEX=1, 128X128, FOV=100 mm

Water

Fat

T1W

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FSE, TR/TE=1700/102, ST=0.7mm, NEX=22, 176X176, FOV=40 mm

Ovary

Kidney

OvaryKidney

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Pre‐injection Post injection

GRE‐SP, TR/TE=12/3, ST=0.9mm, NEX=6, 128X128, FOV=45 mm

GRE‐SP, TR/TE=12/3, ST=1mm, NEX=4, 128X128, FOV=40 mm

Yuval Sha

ked’sL

ab

Pre‐injection Post injection

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GRE‐SP, TR/TE=12/3, ST=0.9mm, NEX=5, 160X160, FOV=64 mm 25


Lung tumor:

T2W

FSE, TR/TE=2080/60 ms, 0.9 mm slice, NEX=2, Ext. Ave=3, 256X256, FOV=50 mm

Control:

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Vlodavsky’s Lab

Tumor imaging

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FSE, TR/TE=2080/60 ms, 0.9 mm slice, NEX=2, Ext. Ave=3, 256X256, FOV=50 mm


Magnetic

Resonance

Imaging

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Tel. 04-8295361/364 ediths@tx.technion.ac.il 29

• Proton has magnetic moment – behaves like a little magnet

• There are a lot of protons in the body - ~70% water , x% fat

• They create ‘net magnetization’

• Largest Gyro Magnetic Ratio 1T 42.57 MHz


B0 = Big Magnetic Field Produced by Main Magnet(1.5 Tesla ~ 30,000 times earth magnetic field)

Aligns ‘net magnetization’ in the direction of the field

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• Small B0 produces small net magnetization (M)

• Thermal motions “try” to randomize alignment of proton magnets

• Larger B0 produces larger net magnetization M, lined up with B0

(Reality check: 0.0003% of protons are perfectly aligned per Tesla)

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Excitation: Relaxation:


RF energy Excitation

Relaxation

Energy

Energy

Applying RF Energy

Only protons that spin with the same resonance frequency as the RF pulse will respond

The result: A shift of the net magnetization vector away from the direction of the static B0 field in a flip angle

Note: The RF signal intensity/duration determines the flip angle of M.


RF energy Excitation

Relaxation

Energy

Energy

The return of net magnetization to the direction of the static B0 field

Accompanied by energy release

Note: Left alone, net magnetization will align itself with B0 in about 2–3 sec


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Spin‐ lattice relaxation:•Microscopically, the spins exchange energy with the environment (the “lattice"). The time constant of this relaxation type is called T1.

•It is related to Mz recovery.

Spin‐spin relaxation•The spins in the high and low energy state exchange energy but do not loose energy to the surrounding lattice. The time constant of this relaxation type is called T2.

•It is related to Mxy decay.Note: T2 decay is faster than T1 recovery


T1: Recovery of Mz– Usually 500-1000 ms in the brain

T2: Disappearance of Mxy only due to molecular interactions– Usually 50-100 ms in the brain

T2*: Disappearance of Mxy due to molecular interactions and variations in B0– Measured in practice

Note: Drugs containing magnetic impurities can alter T1, T2, and T2* — contrast agents

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1) Put subject in big magnetic field (leave him there)

2) Excitation: transmit radio waves into subject [about 3 ms]

3) Turn off radio wave transmitter

4) Relaxation: receive radio waves re-transmitted by subject

– Readout interval :10-100 ms - MRI is not a snapshot!

5) Store measured radio wave data vs. time

– Repeat (2) to obtain more data and average

6) Process raw data to reconstruct images

7) Allow subject to leave scanner (optional)37


After the excitation the protons remains with energy in the form of a flip angle.

During relaxation, an oscillating voltage is generated and received by a coil of wires placed around the subject.

This voltage is the RF signal, whose measurements form the raw data for MRI.

– At each instant in time, it is possible to measure only one combined voltage V(t), that includes the sum RF signals.

Must find a way to separate signals from different regions38


• 3D encoding:– Z‐dir: frequency encoding for slice selection– X‐dir: phase encoding– Y‐dir: frequency encoding with readout

• K‐Space ‐ Fourier Transform

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Extra static Gradient Magnetic Fields (in addition to B0) that linearly vary in intensity across the subject

This allows frequency encoding : the excitation frequency changes with location

x-axis

f

60 KHz

Left = –7 cm Right = +7 cm

Central frequency(63 MHz at 1.5 T)

(* scan noise: turning the gradient fields ON/OFF)

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z

RF freq. bandwidth

Excited location

Slice profile

Frequency

Applying a gradient field Simultaneous RF excitation corresponding to a narrow range of resonance

frequencies

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The phase of the signal depend on location This is done by applying a gradient field in the 2nd

direction The phase encoding gradient (GPE) intervenes for a

limited time period. While it is applied, it modifies the spin resonance

frequencies. When turning the gradient off, the spin resonance

frequencies return to the original one, but now with a phase change.

The process has to be for each column of the image (time consuming).

This phase difference lasts until the signal is recorded.

Applying gradient field in the 3rd direction. Simultaneous with acquisition (readout) of re-transmitted signals. Signal is sampled about once every microsecond, digitized, and stored in a

computer. 42


Input signal: Output signal:

44Phase encoding

Freq

uency en

coding

X [mm]

Y [m

m]


Echo time, TE, is the time from the RF excitation to the center of the echo being received. Shorter echo times allow less T2signal decay.

Repetition time, TR, is the time between one acquisition and the next. Short TR values do not allow the spins to recover Mz, so the net magnetization available is reduced, allowing T1 weighted imaging.

Short TE and long TR give strong signals.

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)1(),( 21 //0 TTETTR eeMTETRS

TE TR Image WeightingShort Long Proton Density Short Short T1 Long Long T2

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T1 ContrastTE = 14 msTR = 400 ms

T2 ContrastTE = 100 msTR = 1500 ms

Proton DensityTE = 14 msTR = 1500 ms

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T1w images T2w imagesDark: ‐ Increased water: edema, tumor,

infarction, inflammation, infection, hemorrhage

‐ Low proton density‐ Calcification‐ Flow void

‐ Low proton density‐ Calcification‐ Fibrous tissue‐ Paramagnetic substances ‐ Protein‐rich fluid‐ Flow void

Bright: ‐ Fat‐ Subacute hemorrhage‐ Melanin‐ Protein‐rich fluid‐ Slowly flowing blood‐ Paramagnetic substances (gadolinium)

‐ Laminar necrosis of cerebral infarction

‐ Increased water: edema, tumor, infarction, inflammation, infection, hemorrhage , subdural collection

‐ Methemoglobin (extracellular) in subacute hemorrhage


MRI has high contrast for different tissue types!

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

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T1 and T2 relaxation time of tissue depend on three factors: a. The inherent energy of the tissueb. How closely packed the molecules arec. How well the molecular tumbling (“self‐movement”) rate matches the Lamar frequency of

hydrogen. The molecule tumbling rate is determined by: Molecular weight, temperature, shape of the molecule


• Higher Signal to Noise Ratio (SNR) results in a better image

–K – constant (related among others to TR,TE, T1,T2…)–FOVx , FOVy - the field-of-view in the x and y directions–Nx , Ny - the number of frequency and phase encoding steps–∆z - the slice thickness–NEX (or NA) - the number of signal averages–BW - the receive bandwidth

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• Total scan time is given by:

Npe - the number of phase encoding stepsS – number of slices

∝ · · ·

51


• Spin Echo Based Sequences– SE– Fast Spin Echo (FSE)– Inversion Recovery Spin Echo (IR‐SE)– Spin Echo Diffusion Weighted Imaging (SE‐DWI)

• Gradient Echo Based Sequences– Gradient Echo Spoiled (GRE‐SP)– Gradient Echo Spoiled External Averaging (GRE‐EXT)– Gradient Echo Steady State; ESS/FESS (GRE‐SS)

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Rephase spins with a 180° pulse: Prevents Spins from rotating at different rates in different

locations Overcomes spins dephasing with time

Most sensitive if TE average T2 In Diffusion: refocusing will not be perfect for protons that

have moved

Used for measuring T2:

53

time

e-t/T2*

e-t/T2

MR

sig

nal

Fast Spin Echo:

TETE/2


1. Equilibrium 2. 90 Pulset=0

3. Spin Dephasing

4. 180 Pulset=TE/2

5. Spin echot=TE 54


55


Changing the polarity of the Gradient: Dephase and rephase the

spins Shorter TR/TE decreases

scan time

Most sensitive if TE average T2* time

e-t/T2*

MR sig

nalUsed for measuring T2*

56

TEGradientON


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Tool features:‐ ROI measurements‐ Volume measurements‐ Series synchronization & comparison‐ T1, T2, T2* and Diffusion mapping‐ Noise filtering

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GRE, TR/TE [ms]=40/5, 40/8, 40/10, 40/12, 40/15, 1 mm slice, NEX=1, 200X200, FOV=64 mm

T2*W

MATLAB MRI analysis tool for T2* mapping:T2*=18.5689 ms

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IR‐SE, TR/TE=800/8 ms, TI=400, 300, 200 ms, 1.5 mm slice, NEX=2, 128X128, FOV=64 mm

200 250 300 350 40016

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20

22

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TE [msec]

T1 m

agni

tude

T1 mapping

Real DataMAP T1=254.9848

MATLAB MRI analysis tool for T1 mapping:T1=254.98 ms

T1W

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Installation: • Copy the K‐PACS software from the Tech‐MED ‐MRI server (Aspect folder K‐PACS folder) to your computer and install.

Loading your DICOM files: • Double‐click on the software icon and press accept.• Press Filesystem and select the preferred folder.

• The selected data will be saved in the software database for future viewing.• Mark the folder or scan you would like to view:

• Press viewer 61


Once the viewer is opened, select the scan you would like to see from the scans presented in the upper part of the page:•• Tools: • All tools are presented once you stand on the bottom part of the image or in the upper icon roller.

• Available options: Measure ROI, Zoom, rotate, magnifier, print, export to tiff, Avi etc. 62


• Set a meeting with Edith to discuss the application• Prepare a literature review on other’s MR protocols for similar application• Begin feasibility test (small pilot) with Aspect M2™ – easy to operate• Analyze the results with our MRI tool – continuously developed according to researchers needs

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• Evert J Blink, “MRI: Physics”• http://www.revisemri.com/questions/basicphysics/• http://www.imaios.com/en/e‐Courses/e‐MRI/• http://www.simplyphysics.com/flying_objects.html• http://quizlet.com/14282869/mri‐physics‐chapter‐2‐flash‐cards/• http://www.tele.ucl.ac.be/PEOPLE/OC/these/node100.html• http://en.wikipedia.org/wiki/Shim_(magnetism)• http://saturn.med.nyu.edu/research/sb/turnbulllab/PDFS/JohnsonMRM99.pdf

• http://www.med.harvard.edu/aanlib/basicsMR.html

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tel. 04-8295361/364 ediths@tx.technion.ac · 2015. 10. 29. · tel. 04-8295361/364...

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