Magnetic Resonance Imaging (MRI)

Basic principle
Magnetic resonance imaging (MRI) has seen enormous development over the last 25 years. MRI is noninvasive and does not use ionizing radiation. MRI exploits the magnetic behavior of water protons to portray tissue structure. MRI offers a huge variety of tissue parameters as measures that then become contrast mechanisms.

MRI images

Brain Tumor

Multiple Sclerosis

Image Acknowledgement: Foothills Medical Centre

MRI magnet

Brain anatomy

A Brief History of MRI

1935: Rabi uses the magnetic resonance phenomenon to measure spin quantum numbers in the nuclei of particle beams. Wins the 1944 Nobel Prize. 1946: Measurement by Bloch et al. & Purcell et al. in condensed (solid) matter. Wins 1952 Nobel Prize. 1950: E.L. Hahn proposes the use of the spin-echo sequence for T2 determination. 1954: Carr & Purcell. Spin-echo train. 1960: Development of computerized Fourier Transform methods. 1970: Damadian suggests that magnetic resonance can be used to image the body, and that MR can be used to visualize tumors; development of high-field superconducting magnets. 1973: Lauterbur, Mansfield & Grannell. Utilization of resonant frequency shift by magnetic field gradient. 1977: Damadian et al. First whole body image.

MRI scanner

Motion within an atom

The classical interpretation of the quantum mechanical property of a particles spin leads to a number of analogies of spinning motions present in an atom, amongst which are: Electrons spinning on their own axis Electrons orbiting the nucleus The nucleus itself spinning about its own axis.

NMR phenomenon
MRI interprets the collective behavior of an ensemble of a large number of nuclei MRI signals are generated at the nuclear level well known by the phenomenon: nuclear magnetic resonance (NMR). A water proton has odd atomic number and odd atomic weight. According to the fundamental property of nuclei, a water proton possesses an angular momentum known as spin. Having non-zero spin, a water proton creates a magnetic field, known as magnetic moment , analogous to a bar magnet. The magnetic moment of a water proton is depicted in Figure 1; the black arrow defines the direction of proton spin and the grey arrow defines the direction of the generated magnetic field. All the water protons generate individual magnetic moments under any condition, but these magnetic moment vectors are randomly oriented due to thermal random motion. The vector sum of all the magnetic moments approaches zero as the number of vectors increase. An ensemble of proton spins in the absence of an external magnetic field is displayed in Figure 1. The spheres represent the protons and the grey arrows define the magnetic moment directions (direction of ).

NMR Phenomenon

Figure 1: Magnetic moment of a proton with non-zero spin (A). Randomly oriented magnetic moments in the absence of an external magnetic field (B). Protons are indicated by blue spheres and their magnetic moment vectors are shown by grey arrows.

NMR Phenomenon
If these magnetic moments are exposed to a strong static magnetic field, each magnetic moment can take one of the two possible orientations: parallel and anti-parallel as depicted in Figure 2. In Figure 2, B0 is the external static magnetic field applied along the z direction; spin orientation is quantized along the external magnetic field while spin transverse components remain random. The parallel spins are at a lower energy state with higher stability. It results in an uneven spin distribution between the two spin states with higher number of spins in parallel. The population difference between the two spin states generate an observable macroscopic magnetization, along the direction of the external magnetic field, as depicted in Figure 2. By convention, the bulk magnetization is defined by M and its orientation defines the z-axis of the imaging object.

NMR Phenomenon

Figure 2: Nuclear magnetic moment vectors aligned along the direction of the external magnetic field B0 (A). Macroscopic magnetization M generated by magnetic moment vectors along B0 (B).

Resonance condition
Under the influence of an external static magnetic field, the angular frequency 0 of a spin system is defined by the Larmor equation: 0 = B0 where of B0 is the strength of the static magnetic field and is a physical constant known as the gyromagnetic ratio with a nucleus dependent value. The angular frequency 0 is known as the Larmor frequency; it is the normal resonance frequency of a spin system. The Larmor frequency is linearly dependent on both the external magnetic field B0 and the nucleus based constant . Multiple spin systems are expected to co-exist in a biological environment and nuclei of different elements will resonate at different frequencies. This difference is the physical basis for achieving nucleus specificity.

Resonance condition
Under the influence of B0, the magnetic moments rotate with specific longitudinal orientations, resulting in the longitudinal magnetization, Mz. The magnetic moments precess with random phases and the combined transverse magnetization remains null. RF pulses are applied at the Larmor frequency to establish phase coherence among these randomly precessing spins. RF pulses are signals in the radio frequency range; RF field vectors are orthogonal to the static magnetic field and stationary relative to the rotating spin distribution. The phase coherence among spin phases results in the transverse magnetization, Mxy. Mz and Mxy are modified further by additional RF pulses and magnetic fields for signal relaxation analysis.

Frame of reference
For conceptual simplicity in describing RF pulses and signal measurements, a rotating frame of reference is used. A rotating frame is a three dimensional co-ordinate system, with the transverse plane rotating clock-wise at the Larmor frequency, 0. Three orthogonal axes of this frame are denoted by x, y , and z and the associated unit vectors are denoted by i, j, and k. This rotating frame of reference will be used in describing MR imaging principles.

Radio frequency (RF) excitation

An additional magnetic field B1 is applied on the magnetized spin system for RF excitation. B1 is a temporary magnetic field generated by an RF pulse; it is short-lived and oscillates in the radio-frequency range. The time-dependent behavior of bulk magnetization M in response to B1 is described by the Bloch equation. The Bloch equation can be expressed in the following form for an MR system:

Radio frequency (RF) excitation

Mz0 is the thermal equilibrium value for M in the presence of B0 only. T1 and T2 are time constants characterizing the relaxation process of a spin system after the system has been perturbed by the magnetic field B1. For simplification, the behavior of M is analyzed in two steps: excitation during the RF pulse and relaxation after the RF pulse is over.

RF excitation
As the duration of an RF pulse is very short compared to T1 and T2, the Bloch equation takes the following form during an RF excitation period:

Ideally, B1 is applied with an angular frequency rf , which equates to the resonance frequency of the spin system. rf = 0 = B0

RF excitation
In an RF excitation process, B1 is applied along the x or the y axis. If B1 points along the x, the magnetization of a spin system with single isochromat can be described by:

These equations demonstrate that M is moved from its original position and it precesses about the x axis. As M is tipped away from the z axis, a measurable transverse magnetization component Mxy is created. The smaller angle between M and the z-axis is known as the flip angle .

RF Excitation
The value of depends on the strength of B1 field and exposure time:

An RF pulse is named after its value. The concept of flip angle is very important for pulse sequence designing.

Relaxation
After a magnetized spin system has been perturbed by an RF pulse, if no other external forces are applied, the spin system will return back to its thermal equilibrium state by magnetization relaxation. Given that B0 is always present, the relaxation process is characterized by the precession of M about the B0 field, which is known as the free induction decay (FID). The longitudinal and transverse magnetization components observed in the rotating frame are as follows:

Relaxation

where Mz (0+) and Mxy (0+) are the magnetization components along the z-axis and on the transverse plane immediately after the RF pulse and Mz0 is the longitudinal magnetization at thermal equilibrium. As time progresses, the longitudinal magnetization Mz is recovered and the transverse magnetization Mxy is diminished by the relaxation process. Measuring from a stationary co-ordinate system, an oscillating decay is observed for the transverse magnetization:

Relaxation

Figure 3: Time evolution of the bulk magnetization M according to Bloch equation. A constant external magnetic field is applied along the z-axis. The three dimensional behavior of M over time is depicted in black line in A. M rotates around the z-axis at the Larmor frequency and returns to equilibrium, its vector behavior along the x, y, and z axes are shown in B, C, and D. Longitudinal magnetization Mz grows along the z-axis and transverse magnetization Mxy decays as time progresses.

Free Induction Decay (FID)

One sequence for measuring T1 is represented by 90 TR 90. TR specifies the delay time between successive 90 RF excitations. Signal intensity is now dependent on the magnitude of the Mz recovery. If we have a long T1, then recovery is slow, and we can see this with decreased FID amplitude.

Spin echo sequence

After a 90 RF pulse, a single FID signal has an exponential envelope on it. The decay of this signal represents a loss of magnetization from the xy plane due to Loss of net signal (T1 recovery - usually long). Loss of phase coherence due to spin-spin interactions with a decay constant of T2. Very slight inhomogeneties in B0 - This causes slight changes in 0 over the volume in which we have the ensemble - leads to a decay constant of T2.

Spin echo sequence

After the application of the 90 pulse, the spins are initially all in phase and the moments lie in the xy plane. Once the pulse is off, the spins begin to dephase, because they will have slightly different Larmor frequencies. This dephasing leads to a loss of signal in the xy plane. The time between (b) where the FID magnitude is strongest and (e), where it has decayed to zero, is characterised by T2.

Spin echo sequence

Before the application of the 180 pulse, the differing precessional frequencies are acting to dephase the spins (a). This is due to spatial field inhomogeneities. If we flip the spins by 180, (b) the different precessional frequencies now act to bring the nuclei back into phase again. An echo forms, peaking when all spins are back into phase. Any dephasing at this point is due to spin-spin interactions (c).

Spin echo sequence

Multiple 180 pulses yield multiple echoes, with decaying amplitudes.

Contrast: PD, T1, and T2

In most cases, the contrast between tissue types in an image will be due to variations of both T1 and T2 in the image tissues, and also to differences in proton density (PD). Let us consider 2 tissues types a and b, of equal hydrogen density. Let us study the relationship between the contrast mechanism and the values of TE and TR.

Proton density (PD)

TR >>T1 TE <<T2 PD weighting. Neither the T1 nor T2 relaxation curves show great differences at the points of sampling. Image intensity is more strongly weighted to the plateau levels (for Mz) or maximum transverse magnetisation Mxy . These are affected by proton density. Differences in image intensity (contrast) are said to be protondensity weighted.

T1 Weighting

TR T1 TE <<T2 T1 weighting. Any contrast is strongly weighted towards any differences in the Mz decay. This is, therefore, a T1 weighted measurement.

T2 weighting

TR >>T1 TE T2 T2 weighting. Any contrast is strongly weighted towards any differences in the Mxy decay. This is effectively, therefore, a T2 weighted measurement.

Signal localization
The basic principles of NMR are applied for the MRI. Spatial localization of NMR signal is necessary to differentiate measured signals from different parts of an imaging object. The gradient coil system, typically made up of three orthogonal coils, produces time varying magnetic fields of controlled spatial non-uniformity for signal localization.

Slice selective gradient

The volumetric MR image of a three-dimensional object is created by assembling multiple planar images of that object. These imaging planes are defined by slice-selective gradients using selective excitation method Figure 4 shows a slice-selective pulse sequence that selects a slice orthogonal to the z-axis. According to the Larmor equation, an RF pulse can only be frequency selective. If both the magnetic field B0 and the imaging object are homogeneous, the entire volume of the imaging object shown will oscillate at the Larmor frequency, 0. By applying gradient magnetic fields, the resonance frequency is made position-dependent that allows spatially selectivity of an RF pulse. In the pulse sequence depicted in Figure 4, the gradient field Gz is applied along the z-axis; the RF pulse and the gradient pulse are applied concurrently for slice selection.

Slice selective gradient

The linear gradient field Gz will linearly vary the resonance frequency along the z-axis. While the gradient field is on, the magnetic field experienced by the imaging object is

The resonance frequency will also change as the magnetic field B changes.

Slice selective gradient

Figure 4A: A pulse sequence for selecting a slice orthogonal to the z-axis. A linear gradient magnetic field Gz is applied along the z-axis.

Figure 4B: An illustration of slice selection by the slice selection pulse sequence. A homogeneous imaging object volume with B0 defining the z-direction (A). A slice is selected between z0 and z1 using a gradient Gz with a 90 RF pulse (B).

Slice selective gradient

Tuning an RF pulse to the frequency will permit selective manipulation of spins resonating at the same frequency. The 90 RF pulse applied with the Gz pulse will select a slice between z0 and z1 as shown in Figure 4B. Different slices can be chosen by gradients of different strengths along the z-axis. The bandwidths of the transmitting and receiving RF coils determine the slice width to be selected around a focused plane. However, the repetition time (TR) would have to be long enough to allow adequate signal recovery from T1 relaxation between slice excitations.

Frequency encoding
After an imaging plane has been selected by the slice selective gradient Gz, the spatial information about the imaging plane is encoded into the signal during the free precision period. A frequency encoding pulse sequence is given in Figure 5. The MR signal is frequency encoded along the x-axis by the gradient vector Gx. This pulse sequence is built on the slice-selection pulse in Figure 4. Frequency encoding makes the resonance frequency of an MR signal linearly dependent on its spatial origin. If a linear gradient field Gx is applied along the x-axis, the imaging object will experience the homogeneous B0 field plus the linear gradient field Gxx.

Frequency encoding
For an ideal one dimensional object, the Larmor frequency at position x is Correspondingly, the FID signal generated locally from spins, with the omission of the transverse relaxation effect is (x) is the spin distribution in imaging object. The oscillation frequency of the FID signal is linearly related to the spatial origin of spins. In a two-dimensional imaging plane, frequency encoding defines a family of isofrequency lines, all perpendicular to the frequency gradient vector. Only one-dimensional spatial localization is achieved by frequency encoding along one axis; multi-dimensional localization can be achieved by frequency encoding along multiple axes.

Figure 5A: frequency encoding pulse sequence. Slice selective gradient is applied along z-axis, a linear gradient magnetic field Gx is applied along the x-axis. Figure 5B: An illustration of frequency encoding of a two-dimensional imaging plane by the pulse sequence above. A linear gradient field Gx is applied along the x-axis (A). The imaging object has uniform spin distribution . Frequency encoding defines three isofrequency line volumes with frequencies 0, 1, and 2, perpendicular to the xaxis (B).

Phase encoding
Phase encoding localizes MR signals based on the phases of the MR signals. It allows a two-dimensional imaging volume to be measured using a series of sequential line acquisitions. Based on the principles of frequency encoding, phase encoding makes the phase of an MR signal linearly dependent on its spatial origin. A phase encoding pulse sequence is shown in Figure 6.; MR signal is phase encoded along the y-axis by the gradient vector Gy during the free precision period.

Phase encoding
After an RF pulse, a linear gradient field is applied for a short interval Tpe. The signal under the influence of this gradient is

Gy frequency encodes the local signal during the interval 0 t Tpe. Signals from different y-positions accumulate different phase angles after the time interval Tpe. The signal measured after Tpe will bear an initial phase angle along the y-direction; (y) is linearly dependent on the y-position of the measured signal.

Figure 6A: A phase encoding pulse sequence built on pulse sequence in Figure 5A. A linear gradient magnetic field Gy is applied for time Tpe along the y-axis.

Figure 6B: An illustration of phase encoding of a two-dimensional imaging plane by the pulse sequence above. A linear gradient field Gy is applied along the y-axis for time Tpe (A). Phase encoding defines three isophase line volumes with phases 0, 1, and 2 (B).

Signal localization

Figure 7: Spatially encoded imaging plane by the pulse sequence in Figure 6A. A slice is selected between z0 and z1 by slice selective gradient. Voxels in the slice are frequency encoded along the x-axis and phase encoded along the y-axis.

K-space acquisition
The k-space is an extension of the concept of Fourier space; it is a temporary memory that holds the raw MR data during the data acquisition period. The mapping of a k-space is directly related to the spatial encoding gradients applied to the imaging object. By changing the gradients over time, the k-space data are collected in trajectories. A uniform coverage of the k-space is required to preserve all the information about the imaging object. After the k-space is full, the data are mathematically processed to produce the final MR image. A two-dimensional k-space is generated for each two-dimensional imaging plane. A spin-echo sequence designed for uniform coverage of a two-dimensional k-space is depicted in Figure 8.

K-space acquisition

Figure 8: A spin-echo pulse sequence with slice selective gradient applied along the z-axis, phase encoding along the y-axis, and frequency encoding along the x-axis (A). Following the slice selection pulse, and assuming Gy positive, Gx and Gy gradients cause the vector k to move diagonally in k-space position (a), as shown in (B). The 180 pulse flips k to (b), about the origin. The second frequency encoding gradient reads k-space values horizontally from (b). Three different phase encoding gradients (Gy < 0, Gy = 0, Gy > 0) allow three lines of kspace to be collected (C).

K-space acquisition
In a spin-echo sequence, a 180 RF pulse is applied following the initial 90 RF pulse. A slice-selective pulse is applied along the z-axis, phase-encoding gradient is applied along the y-axis, and frequency encoding gradient is applied along the x-axis as depicted. Two frequency encoding pulses are applied; the first pulse allows symmetric coverage of k-space about the ky axis and the second pulse is used as a read gradient. The MR signal is collected while the read gradient is on; this gradient is used to encode spatial positions of the collected signals by frequency encoding. Prior to the 180 pulse, Gx and Gy act as phase encoding gradients, bringing the k-space vector, k, to position (a) before the pulses are turned off. The 180 pulse rotates k about the origin, to position (b). The read gradient reads (second Gx pulse) the k-space line at a constant ky value, as depicted by the lower arrow in Figure 8B.

Image reconstruction
The k-space data generated by a pulse sequence is the frequency domain representation of an MR image. For visual interpretation and analysis, the k-space data is converted into a time domain image; this process is commonly known as image reconstruction. The image reconstruction techniques vary considerably for different spatial encoding methods used for imaging. For rectilinear k-space sampling as described in this section, the mathematical algorithm Fourier transform is used for image reconstruction. The Fourier transform defines the relationship between a continuous signal in the time domain and its representation in the frequency domain. In practice, only a finite number of k-space points are sampled at regular intervals. Inverse fast Fourier transform (iFFT) is applied for such k-spaces to reconstruct digital MR images.

Image reconstruction

Figure 9: The k-space representation of a T2 MR image of a normal human brain at 3T (A). The magnitude Fourier transform pair of (A) after image reconstruction (B).