Section: Application Domains

Diffusion MRI

In biological tissues, water is abundant and magnetic resonance imaging (MRI) exploits the magnetic property of the nucleus of the water proton. The imaging contrast (the variations in the grayscale in an image) in standard MRI can be from either proton density, T1 (spin-lattice) relaxation, or T2 (spin-spin) relaxation and the contrast in the image gives some information on the physiological properties of the biological tissue at different physical locations of the sample. The resolution of MRI is on the order of millimeters: the greyscale value shown in the imaging pixel represents the volume-averaged value taken over all the physical locations contained that pixel.

In diffusion MRI, the image contrast comes from a measure of the average distance the water molecules have moved (diffused) during a certain amount of time. The Pulsed Gradient Spin Echo (PGSE) sequence is a commonly used sequence of applied magnetic fields to encode the diffusion of water protons. The term 'pulsed' means that the magnetic fields are short in duration, an the term gradient means that the magnetic fields vary linearly in space along a particular direction. First, the water protons in tissue are labelled with nuclear spin at a precession frequency that varies as a function of the physical positions of the water molecules via the application of a pulsed (short in duration, lasting on the order of ten milliseconds) magnetic field. Because the precessing frequencies of the water molecules vary, the signal, which measures the aggregate phase of the water molecules, will be reduced due to phase cancellations. Some time (usually tens of milliseconds) after the first pulsed magnetic field, another pulsed magnetic field is applied to reverse the spins of the water molecules. The time between the applications of two pulsed magnetic fields is called the 'diffusion time'. If the water molecules have not moved during the diffusion time, the phase dispersion will be reversed, hence the signal loss will also be reversed, the signal is called refocused. However, if the molecules have moved during the diffusion time, the refocusing will be incomplete and the signal detected by the MRI scanner if weaker than if the water molecules have not moved. This lack of complete refocusing is called the signal attenuation and is the basis of the image contrast in DMRI. the pixels showning more signal attenuation is associated with further water displacement during the diffusion time, which may be linked to physiological factors, such as higher cell membrane permeability, larger cell sizes, higher extra-cellular volume fraction.

We model the nuclear magnetization of water protons in a sample due to diffusion-encoding magnetic fields by a multiple compartment Bloch-Torrey partial differential equation, which is a diffusive-type time-dependent PDE. The DMRI signal is the integral of the solution of the Bloch-Torrey PDE. In a homogeneous medium, the intrinsic diffusion coeffcient D will appear as the slope of the semi-log plot of the signal (in approporiate units). However, because during typical scanning times, 50-100ms, water molecules have had time to travel a diffusion distance which is long compared to the average size of the cells, the slope of the semi-log plot of the signal is in fact a measure of an 'effective' diffusion coefficient. In DMRI applications, this measured quantity is called the 'apparent diffusion coefficient' (ADC) and provides the most commonly used form the image contrast for DMRI. This ADC is closely related to the effective diffusion coefficient obtainable from mathematical homogenization theory.