Introduction to Biomedical Imaging - Unitat de ...afrangi/ibi/MagneticResonanceImaging.pdf ·...
Transcript of Introduction to Biomedical Imaging - Unitat de ...afrangi/ibi/MagneticResonanceImaging.pdf ·...
Introduction to Biomedical Imaging
Alejandro Frangi, PhDComputational Imaging Lab
Department of Information & Communication TechnologyPompeu Fabra University
www.cilab.upf.edu
Introduction to Biomedical Imaging
Magnetic Resonance Imaging
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMRI advantages
Superior soft-tissue contrast
– Depends on among others proton density, relaxation times
3D acquisitions possible
Free orientation of tomographic scan planes
No ionizing radiation
No iodinated contrast agent
Non-invasive
Imaging of anatomy/pathology and function
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMRI Principle
Based upon: nuclear magnetic resonance
Resonance phenomenon of nuclear spins (magnetic moments of atomic nuclei) in a
strong external magnetic field
A rotating charge has an electromechanical momentum (μ) which has a direction
coincident with the rotation axis and a magnitude proportional to the angular
momentum of electrons and protons by the expression
The electromechanical momentum is known as nuclear spin
In the presence of an external magnetic field (B) all spins line up with it yielding a
net macroscopic moment (M); otherwise they are randomly distributed with no net
macroscopic momentum
Not all atoms have a zero spin. The spin is non-zero when the atom has an odd
number of protons or nucleons (p is odd or p+n is odd)
Practically speaking a spin can be seen as a kind of elemental magnet
Most important proton in the human body is Hydrogen
Introduction to Biomedical Imaging
Magnetic Resonance ImagingPrecession
Spins presses around the direction of the external field (Bo) at a frequency (Larmorfrequency) proportional to Bo
The proportionality constant is known as gyro magnetic constant
For hydrogen, γ = 42.58 MHz / T
From quantum mechanics it seems that only a limited number of spin states are possible (each with their own energy). E.g.: for H only ± 1/2
oBω = γ
Introduction to Biomedical Imaging
Magnetic Resonance ImagingNet magnetization
The spins altogether form a net magnetization vector M
M depends on the external field and the temperature
Introduction to Biomedical Imaging
Magnetic Resonance ImagingResonance phenomenon
Magnetization can be flipped toward the xy-plane by adding energy to the system by applying an RF pulse at the Larmor frequency
M-vector rotates toward the xy-plane over an angle θ (flip angle)
1B dtθ = γ∫
Introduction to Biomedical Imaging
Magnetic Resonance ImagingSituation before RF pulse
Longitudinal vs. transverse magnetization
After RF pulse only longitudinal magnetization (Mz)
Mz is static and, hence, cannot produce induction signal
Introduction to Biomedical Imaging
Magnetic Resonance ImagingSituation after RF pulse
RF perturbs the magnetization vector
Both longitudinal (Mz) and transverse (Mxy) components exist
Mxy component rotates at Larmor frequency
M is now time-varying and an induction signal can be measured with a receive coil (Free Induction Decay – FID)
Introduction to Biomedical Imaging
Magnetic Resonance ImagingRelaxation processes
The perturbation of the magnetization has a limited life-time
Relaxation returns M to its original (lower energy) state (exponentially)
Longitudinal relaxation increases Mz to M → T1 relaxation constant
Transverse relaxation reduces Mxy to zero → T2 relaxation constant
The increase of Mz can be slower than the decrease of Mxy
The nature of T1 and T2 relaxations is different!
T1 is related to spin-lattice interactions (between H protons and its surroundings)
T2 is related to spin-spin interactions (between protons themselves)
They depend on molecular structure, physical state (solid or liquid), temperature, external field strength, etc.
1/( ) (1 )t Tz oM t M e−= −
2/( ) t Txy oM t M e−=
@1.5T T1 [ms] T2 [ms]
Fat 260 84
WM 920 101
GM 790 92
Introduction to Biomedical Imaging
Magnetic Resonance ImagingWhy is MR becoming so important?
Provides nice contrast between soft tissues (vs. hard/soft tissue contrast in CT)
Each tissue has characteristic MR properties
T1, relaxation time for Mz
T2, relaxation time for Mxy
Proton density
This allows to obtain application-specific tissue-contrast by designing appropriate RF pulse sequences
Provides additional possibilities through flow-dependent phenomena or using saturation pulses
Introduction to Biomedical Imaging
Magnetic Resonance ImagingFree Induction Decay (FID)
RF pulse creates transverse magnetisation Mxy
Precession of transverse magnetisation at Larmor frequency
Amplitude of Mxy is initially dependent on proton density
Signal decays exponentially with time constant T2*
Signal can be measured using receive coil: Free Induction Decay (FID)
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMeasurement Strategy
Free induction decay
Hard to measure (directly after the RF pulse)
Fast decay (T2*)
For imaging: echo techniques
Signal is recalled after some time (echo)
Two methods:
Spin echo techniques
Gradient (recalled) echo techniques
Introduction to Biomedical Imaging
Magnetic Resonance Imaging
Spin Echo
Magnetization is flipped to transverse plane
through a RF pulse
Dephasing due to local field inhomogeneities
Inversion pulse (180º) for spin refocusing at TE/2
TE = echo time
Spin rephasing
First echo is recalled thus reconstructing the FID
TE
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMR image formation
Main scanner components
Magnet: constant main magnetic field Bo
Gradient coils: fields that vary in space
RF coils: for transmitting and receiving RF signals
Introduction to Biomedical Imaging
Magnetic Resonance ImagingImage formation
Static field gives a net magnetization
RF pulse excites nuclei and creates transverse magnetization
Spatial encoding of the signal using gradient fields
Echo read-out (using receive coil)
Reconstruction of image from measured echoes (mostly Fourier reconstruction)
Pulse sequence
Series of events in time: sequence
Pulse sequence contains components necessary to produce an MR image
Components: RF pulses, gradients, echo sampling
Nature and order of components determines kind of scan: sequence design
Spatial encoding
Slice selection
Frequency encoding
Phase encoding
Localization if based upon the fact that spins presses at the Larmor frequency, which depends on the local value of the magnetic field B
Introduction to Biomedical Imaging
Magnetic Resonance Imaging
Spatial encoding: slice selection
The excitation pulse can be selective or non selective
S: Only spins in a given slice are excited
NS: All spins covered by the transmit coil are excited
Thickness and location of slice are determined by the bandwidth of the RF pulse and gradient in direction of slice selection
Slice selection
Gradient field encodes space in frequency
Larmor frequency depends on local strength of magnetic field B: f ~ B
RF excitation pulse has finite bandwidth
Spins within a limited range of frequencies are excited: selective excitation
Slice thickness: determined by the shape of the pulse (bandwidth) and the gradient strength
Introduction to Biomedical Imaging
Magnetic Resonance ImagingSpatial encoding: slice selection
Gradient field causes dephasing within the slice
An inversion pulse is applied to achieve rephasing and thus yield maximal signal
Selection and rephasing lobes
Introduction to Biomedical Imaging
Magnetic Resonance ImagingSpatial encoding: frequency encoding (also read-out gradient)
By applying a gradient Gx along the x-direction, every position along the x-axis is associated with its own unique Larmor frequency: frequency encoding
The Fourier transform of the detected signal is a projection onto the x-axis
The amplitude of each frequency component is proportional to the summed signal in the y-direction for that x position
By repeated rotation and application of the read-out gradient, spatial information in more than one direction can be obtained
Lauterbur used this technique in combination with backprojection reconstruction to generate the first MR images
Introduction to Biomedical Imaging
Magnetic Resonance ImagingSpatial encoding: frequency encoding
Signal has now been encoded in slice (z) en frequency (x) directions
A third gradient is needed for full localization
Phase encoding gradient is kept on for a certain duration
Precession at different frequencies during that period of time gives different phases along the gradient direction: phase encoding
Introduction to Biomedical Imaging
Magnetic Resonance ImagingSpatial encoding: phase encoding
Combination of frequency and phase encoding gives spatial signal encoding in 2D plane
First step: phase encoding (y gradient)
– Between excitation and echo read-out
Second step: frequency encoding (x gradient)
– Gradient switched on during echo read out (a.k.a. read out gradient)
Image formation using Fourier transform on all acquired echo data
Data collection: sampling
With the frequency encoding gradient switched on (here: x-direction) Nx data points are sampled (digitized echo read-out)
Read out is performed for all Ny phase encoding steps:
– Ny phase encoding steps give Ny echos
Result Nx×Ny data points per slice: MATRIX
This signal matrix exists in so-called k-space
2D Fourier transform used to reconstruct an image from k-space
Introduction to Biomedical Imaging
All spins have same precessional frequency
Magnetic Resonance Imaging
Spatial encoding
Introduction to Biomedical Imaging
Apply Phase Encoding Gradient
Slower Unchanged Faster
Magnetic Resonance Imaging
Spatial encoding
Introduction to Biomedical Imaging
After Phase Encoding Gradient is turned offAll spins have same frequency again, but different phase
+90° 0° -90°
Magnetic Resonance Imaging
Spatial encoding
Introduction to Biomedical Imaging
App
ly F
requ
ency
Enc
odin
g G
radi
ent Faster
Unchanged
Slower
Magnetic Resonance Imaging
Spatial encoding
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space
k-space contains raw scan data (sampled data points)
In 2D x-direction in k-space is frequency encoding: measured echoes
y-direction is phase encoding direction (gradient strength during phase encoding)
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space: interpretation
K-space is the Fourier domain of the target image
Trivial reconstruction: Inverse Fourier Transform
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space: interpretation
Duality between image and k space
Field of View (FOV)
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space: interpretation
K-space allows to think in terms of frequency content
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space: interpretation
Low frequencies = image contrast
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space: interpretation
High frequencies = image details and edges
Introduction to Biomedical Imaging
Magnetic Resonance ImagingK-space filling strategies
By thinking in terms of frequency content one can devise non linear filling strategies which can have advantages in certain applications
Warning! These strategies may impose hardware constrains as the field gradients may need to switch very fast (slew rate limitations)
Standard Echo planar imaging (EPI)
Interleaved EPI Spiral Scanning
Introduction to Biomedical Imaging
Magnetic Resonance Imaging3D Imaging
Concept of spatial localization can be expanded to 3D by adding an extra phase encoding in the slice direction
Thick slab volume excitation is used
Introduction to Biomedical Imaging
Magnetic Resonance ImagingAngiographgy
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMR Scanners
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMR Coils
Brain coil Split head coilGeneral purposeflex coil
Torso coil Extremity coil
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMR Scanner Console
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMR Images
Introduction to Biomedical Imaging
Magnetic Resonance ImagingMR Images
Introduction to Biomedical Imaging
References & AcknowledgementsReferences
Amersham Health http://www.amershamhealth.com
Basics of MRI - Joseph P. Hornak http://www.cis.rit.edu/htbooks/mri/
Basic Principles of MR Imaging – Philips Medical Systems
Medical Imaging – D. Liley http://marr.bsee.swin.edu.au/~dtl/het408.html
Acknowledgements for some material used in these lectures
ImPACT http://www.impactscan.org
Magnetic Resonance Imaging – W. Bartels http://www.isi.uu.nl/Education/MBT-MTI