Basic & Detailed Tutorial in CT & MRI for Biomedical Beginners

A extensive tutorial in CT & MRI which will cover all the aspect required by an engineer who has just entered Biomedical Imaging field and wants to explore new avenues of the field

This tutorial will help you in getting familiarized with the operation of CT & MRI

In the first, the terms “CT” (computed tomography) and “CAT” (computer axial tomography; also used: computer assisted tomography) are the usual way to refer to the method involved when x-rays are used to generate the means by which the “target” is examined. (Also in common use is a process connotation: “CATscan“.) When other forms of radiation or waves are involved, specialized terms such as “PET” or “SPECT“, two techniques in emission topography, are applied (some of these are defined by the nature of the signal carrier). Thus, there are many other specialized uses of tomographic techniques, such as in Magnetic Resonance Imaging (MRI), optical tomography, acoustical tomography, and processing of Synthetic Aperture Radar (SAR). As an aside, we now show one example of a geophysical tomography application – specifically, seismic tomography – in which the surface of the subduction zone running south of Japan into the Kurile Islands has been reconstructed from seismic refraction data.

Important to an in-depth understanding of tomography are underlying physics and mathematical operations, which are pertinent to the methods of Signal Processing. This complex subject will not be treated here (an extensive search of the Internet failed to find a good review); intrinsic to some types of tomography are such concepts as image formation, wave transformation, interferometry, and Fast Fourier Transforms.

Three Internet Sites that cover some general aspects of CAT are at: (1), (2), and (3).

We will explain the operating principles by reviewing how a typical CATscan is conducted. As a general statement, the advantage of this and other medical tomographic methods is an improved delineation and differentiation of the various soft tissue organs in humans and other mammals. Thus, x-rays in this mode are usually able to separate these organs discretely, especially when absorbing chemicals (e.g., barium compounds) or dyes are used. We begin by showing a typical CAT Scanner in an examining room:


The modus operandi by which a CAT Scanner functions is shown in this diagram:

The patient is placed between an x-ray source and an array of detectors arranged in an arc of the circle. The x-rays are collimated (narrowed to a beam of some specific angular width) through a long slit which focuses them into a planar beam spread over a particular angle. At any moment when the x-ray source is in some position, it produces a “slice” (analogous to a cross-section) image representing a sweep of the signals in the detector array. The x-ray tube and the detectors move as a unit through a complete 360° rotation around the patient, thus providing a succession of images, each consisting of a view of the body at some angle. This multiple viewing provides additional information that improves the image contrasts among the organ(s) being examined and hence better defines them. Upon completion of the scan for that slice, the unit can move forwards or backwards parallel to the length of the body (or part(s) thereof), hence the designation of “axial”, when the person is placed on a horizontal table. The result of this combined axial and rotational motion is a scan trace described by close-spaced spiral loops. A computer is programmed to handle the scanning operation, digitize the signals, and assemble the successive slices to produce a 3-D composite image.

Because the CAT Scanner is still the prime diagnostic tool for imaging a body’s interior, and it illustrates the basic configuration of tomographic scanners, we show a cutaway diagram that depicts the main components of the system in more detail:

As an introduction to the appearance of a single slice image, here is a view of a transaxial section through the human brain.

The gray levels in the image can be assigned colors – this usually heightens the differences in contrast in the image which can help to recognize anomalies:

The next three images are taken from a group of 102 slices made of the human head in sagittal (side) view. All such slices can be integrated into a three-dimensional depiction of the head.

Here are two transaxial slices through the head. The right image shows a normal brain at this level; the left has differences that are interpreted as indication of Alzheimer’s disease:

This next image shows slices through the chest in which the lungs appear dark, with a lighter blotch in the right lung (left side of the image, with backbone at the bottom) that discloses a carcinoma (lung cancer):

Moving further down the body, this slice shows some of the organs between the heart and the upper intestine. The backbone is at the bottom center. A tumor has developed on the pancreas.

Now, let’s show a colorized 3-D image of the human kidneys made by combining many slices through that part of the body (other organs were blocked out during computer processing to isolate the kidneys).

One of the most remarkable images found by the writer (NMS) during his perusal of the Internet seeking inputs to these medical imaging pages was generated by Imatron’s ultrafast Electron Beam CT Scanner (EBCT). In this variant, 4 tungsten targets arranged as arcs extending over 270° are swept by a high intensity beam of electrons which produces the x-rays; thus the ring or “donut” around the patient does not move. This configuration allows a much faster rate of whole body scanning, thus reducing the extent of exposure to the x-rays. Here is a view of the scanner without its covering sheath:

Below is the above-mentioned colorized 3-D image made by this Scanner showing the internal organs from the neck to the pelvis of a human patient.

This image is an example of a slice made by the EBCT of a diseased heart (the white blotches are calcified arterial vessels) of a 68 year old woman

The image (second above) of the human torso is an example of a rapidly developing, but quite controversial, approach known as Full Body CT Scanning (or Whole Body CT Screening). An overview of this approach, which looks at large segments of the body at one time, is reviewed in the Body Scan MD. Here is a figure that shows different results using different methods.

This approach tends to pick up unsuspected abnormalities in internal organs or bones. However, the large dosage of radiation needed to encompass much of the body is considered by critics to be excessive and dangerous. A general rule of the moment: Do not do this to healthy body but weigh the potential risks for scanning a person whose malady has not been detected by local scanning.

CAT scans have been used in archaeological studies, in particular of mummies whose wrappings are ordinarily not removed. 3-D images of whole bodies have been created. Here is a CAT image of an Inca child found preserved in Peru:

Examination of mummies or otherwise preserved ancient individuals by CAT scanning can reveal unusual things, such as the contents of the stomach (in the “Iceman”) or evidence of cause of death. This image of the skull of an Egyptian mummy shows a blow to the head as a possible forensic indicator:

CT Scanners are coming into widespread use at entry points to airport concourses. They are proving adept at examining baggage for possible items that would be security risks. Here is a typical scanning station, familiar to air travelers:

We turn now to the other major imaging technique that many of the larger hospitals and diagnostic centers are using routinely: Magnetic Resonance Imaging (MRI). Generally, MRI provides more details in the resulting imagery but the costs to operate tend to be higher (and caution must be taken to protect the surroundings from intense magnetic fields).

The theory behind Nuclear Magnetic Resonance (NMR) which is the basis for MRI is rather esoteric and complex. For the interested reader, we provide these Internet links to Tutorials: Lawrence Berkeley Laboratory; HowStuff Works; and MRI Tutor. A more extensive and technical review is given by Dr. Joseph Hornack of the Rochester Institute of Technology. The first three were used as information sources to prepare this brief synopsis of how MRI works.

The basis for this method is the behavior of atomic nuclei of certain elements when subjected to a strong constant magnetic field plus superimposed variable magnetic fields and then further modified by radio waves of frequencies that induce these nuclei into resonant states. Hydrogen is the usual element investigated by MRI but Carbon, Phosphorus and some other elements are also capable of being responsive to the process. In such elements, the nucleus of each atom is spinning around an axis of rotation. Atoms of Hydrogen (which makes up about 60% of the body’s soft materials) in their normal state have their individual axes (spin vector) spatially oriented at random. But, when subjected to an intense external magnetic field (B0) that is held constant (static), the hydrogen-bearing material (e.g., human tissue) is said to be itself magnetized to some degree. The hydrogen nucleus (single unpaired proton) behaves as a “tiny magnet” in which its axis tends to align parallel to the magnetic lines of force produced by the magnet that is a key part of an MRI instrument; its spin axis will also precess (wobble) around the direction of the external field. Like a compass needle, this hydrogen “magnet” can also be considered to be dipolar, with a “north” (parallel to the external field) and a “south” (antiparallel) end to the magnetic moment. Statistically, when hydrogen protons are thus aligned there are about as many oriented in one direction as the opposite one (in terms of polarity) and therefore the assemblage will almost cancel out in terms of net magnetization. There will not be an exact balance, so that a few atoms (of the billions of billions in, say, the human body’s soft tissue) thus unmatched will remain in a free magnetic state that allows manipulation by small varying magnetic fields and by radio waves.

So, when alternating magnetic fields from auxiliary gradient magnets (of much weaker magnetic strength compared with the main magnet) are superimposed on the hydrogen assemblage, those remaining (unbalanced) hydrogen protons will reach a new magnetic field state (B1) and they experience new spin vector orientations, a change in precession angle (nutation), and oscillations that include a characteristic resonance frequency whose value lies in the Megahertz range (within the radio wave segment of the electromagnetic spectrum). A separate unit, coils that develop radio waves as pulses/second that can be tuned to the appropriate resonance frequency, produces a condition in which the protons absorb a specific amount of energy (resonance energy) and are therefore excited to a higher energy state as they acquire a new spin state and magnetic field strength B1. When the alternating magnetic field is turned off, the protons revert to their lower energy state(s) (referred to as relaxation), giving off signals in the radio wave region of the EM spectrum that are detectable by radio receivers in the MRI unit. Since the B1 field is repeatedly turned off and on, it produces a time varying magnetic field functioning as an electromagnetic wave. If the B1 wave frequency is adjusted to match the proton precession frequency in the B0 state (imposed by the master magnet), the hydrogen system as now influenced by the gradient magnet(s) is said to be in resonance. (Several factors govern the specific resonance frequency value, including the magnitude of the static field strength B0.) Through electronic and computer processing (with sophisticated control programs, including construction of tomographic slices), these varying (in intensity) signals are used to construct images of the various spatially distinct organs and tissue that were subjected to magnetic resonance.

Below is a photo of an MRI Scanner, which in its exterior resembles some CAT Scanners:

This schematic diagram depicts the functional configuration of an MRI unit:

The outer (near surface) part of the chamber, into which the patient is moved by progressive insertion to produce tomographic [3-D] scans of a body segment, contains the main magnet. Today, most such magnets are supercooled (to about 6°K) and superconducting, producing very strong B0 fields; both permanent and resistive magnets can also be used but these have more limited field strengths. Those strengths range from about 0.8 to 4.0 T (Tesla; 1 T = 10000 Gauss [for comparison, the Earth’s {much weaker} magnetic field is ~0.5 Gauss]). The lines of force for the main magnet are configured to pass parallel to the chamber axis (and thus follow the length of the patient’s body). In the chamber cylinder are also the Gradient Magnets and the Radio Frequency Signal Generator. This signal is sent to the body and a return signal is collected and processed to form black and white images (to which colors can be assigned to gray level intervals), seen on a monitor and/or stored digitally for analysis and hardcopy.

Compared to most CAT Scan images, those made by MRI tend to be more detailed and often with more contrast; they are especially suited to displaying soft tissue organs and maladies thereof but also can image bone. Let us examine some representative examples. First a view of a person’s head, showing some brain structure:

This next image set is each a slice through a patient’s brain, comparing a young individual (left) with an athletic male in his 80’s (center) and with a person of similar age having Alzheimer’s Disease (right), all imaged at the same level:

Next, note the tumor growth in a female’s brain, sliced here in lateral view:

Dyes and chemicals are often introduced into the patient’s system to help accentuate contrasts. A compound containing the element Gadolinium is commonly used. Here is a view of veining in the head after allowing a chemical tracer to work its way into the brain:

Similar contrast enhancement using a dye is evident of this view of the heart and arteries and veins emanating therefrom:

This MRI image shows some of the internal organs in the upper torso:

Now, we present another image of the upper torso in side view in which the bones of the spine are the objective of this MRI scan:

Since this page was prepared, the writer (NMS) has undergone a spinal MRI in which a condition called spinal stenosis was revealed from image analysis. I cannot resist the desire to add two examples from the series of images produced from my tests. One shows the lumbar (lowermost) segment of my spine; the other is a cross-sectional view of one of the vertebrae in which narrowing of the spinal canal is evident, causing the nerves to be pressed upon. This stenosis appears responsible for the leg pains and weakness that afflicts my mobility today.

Speaking of bones, note the shattered fragments in this MRI of human wrist broken from a fall:

We close our consideration of Magnetic Resonance Imaging by showing a figure which simply points out (without our comment) that it is possible to do MR spectroscopy; the various compounds in the brain were not identified in the Internet source.

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