Conceptual Overview of Magnetic Resonance Image Formation
In the above discussion of MRI signal formation, precession frequencies of proton spins were discussed. In the gradient magnetic fields produced in an MR scanner, the precession frequency of any given proton depends on the strength of the magnetic field around it (recall: gradient fields don’t change the direction of the static field, which is always longitudinal, only the strength along the z-axis). As such, the difference in precession from one area to the next is what allows the conversion of a collected MR signal to a viewable image. The process by which this occurs consists of three steps: 1) slice selection, 2) frequency encoding, and 3) phase encoding.
Slice selection is necessary because the simultaneous extraction of a full three-dimensional image via MR requires extraordinary amounts of computing power. A more accessible approach is to take a series of two-dimensional slices and then stitch them together into a full 3D image after acquisition. To do this, one must ensure that only the desired slice to be imaged contains proton spins precessing at the same frequency as the energy of the radiofrequency coils. This is accomplished via the gradient magnetic field, the control of which allows adequate determination of the field strength (and thus the resonant frequency) at any point along the longitudinal field (z-axis). In this way, the frequency of the radiofrequency energy output can be matched to the range found in the desired slice to be imaged. This process is very rapid--a single slice can be imaged within a few milliseconds
Once the radiofrequency coil is set for a particular slice and the proton spins in that slice are excited, the precession rates of individual protons in the x and y-axes of that slice must be differentiated in order to create a useable image. Without such differentiation, it would be like looking into a dark room and having to tell whether there are one or two chairs in it. A sort of flashlight into the room would be helpful, and for MRI such a process is known as frequency encoding, and is done by creating yet another magnetic gradient within the selected slice so that the protons on one side precess at a higher frequency than those on the other side, allowing for a one-dimensional discrimination of individual precession points in the slice.
In order to visualize the full x-y axis of the slice, phase encoding must also be completed with each collection of slice images. Phase encoding employs a series of other gradient magnetic fields on top of the frequency encoding field, in the same direction on the same x-y axis but sequentially spaced in time around the frequency encoding gradient so as to allow the various points of precession in one axis (say, the x-axis) without much affecting the other axis (the y-axis). By retrieving images at multiple points throughout this timespan, one can combine the many one-dimensional images to form a usable, final two-dimensional one. The primary drawback to this approach is that higher resolution images require more time to produce, as each point of precession to be visualized will require an entirely independent set of frequency and phase encodings within each slice.
Finally, the construction of an image from collected MR data requires complex mathematics in which a Fourier transformation is used to fill something called k-space, an inverse sampling of image space. The transition from a point in image space to one in k-space is not 1:1, however, and the full details of this process are not necessary to understand the theoretical underpinnings of MR data acquisition.
Reference: Huettel, S. A., Song, A. W., & McCarthy, G. (2008). Functional magnetic resonance imaging (2nd ed.). Sunderland, Mass.: Sinauer Associates.