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Lecture 1Explain common medical imaging formats, modalities and their basic principles. Explain the
applications of the modalities and how the modalities differ from each other. Explain the basic
principles of X-ray imaging and understand the various use cases.
The evolution of medical imaging:
- “Old” = 2D: X-ray radiography, nuclear
- “Recent” = 3D: CT, MRI, PET
- “New” = 4D: dynamic CT, MRI, US
- “Horizon” = 4D+ function
The major advances in medical imaging are that it’s faster, that of 4D protocols, farther (3D
anatomy), whole body imaging in less than 20 seconds, functional (physiology), PET, SPECT, Optical
and MRS, fusion (anatomy and function) and combinations (PET/CT, PET/MRI, …).
There are different modalities in medical imaging
Modality Physical Agent Strength Weakness Comment
Plain film X-ray Global view of Does not reveal fine detail Least expensive
anatomy of organs
Ultrasound Sound waves Good organ Operator-dependent; air No radiation, no
detail, and/or bone may prevent sedation, less
anatomical visualization of organs invasive,
relatively cheap
CT X-ray Good organ May need sedation and/or Moderately
detail, quick, contrast expensive,
anatomical radiation
MR Electromagnetic Great tissue Relatively slow, needs Most expensive,
waves contrast, sedation in younger no radiation
multiple planes, children, may need contrast
anatomical,
new inroads to
functional
imaging
Nuclear Gamma rays Physiological Organ-specific; poor on Moderately
(function) anatomic detail expensive
MRI= magnets + radio waves, CT are X-rays and PET are radiation traces with CT scan.
Coronal plane: front side. Transaxial plane: upside. Sagittal plane: side.
Advanced image processing used in medical image applications are: enhancement, rendering,
segmentation, modelling, and fusion. Volume rendering represents a collection of methods used in
computer graphics and scientific visualization to create a 2D projection from a discretely sampled 3D
dataset. An example of a 3D data set is a collection of MRI/CT/MicroCT scanner 2D slice images. For
instance, a series of 2D slice images of a human brain can be assembled to render 3D volume
rendered images using a volume rendering algorithm. Volume image registration/fusion is for
example MRI & CT.
Medical image components
- Pixel depth: the number of bits used to encode the information of each pixel.
, - Photometric interpretation: specifies how the pixel data should be interpreted for the
correct image display as monochrome or color image. Clinical radiological images, like x-ray
computed tomography (CT) and magnetic resonance (MR) images have a gray scale
photometric interpretation. Nuclear medicine images, like positron emission tomography
and single photon emission tomography (SPECT) are typically displayed with a color map or
color palette.
- Metadata: the information that describe the image. In any file format, there is always
information associated with the image beyond the pixel data. Metadata is typically stored at
the beginning of the file as a header and contains at least the image matrix dimensions,
spatial resolution, pixel depth and photometric interpretation.
- Pixel data: numerical values of the pixel. Pixel data are stored as integers or floating-point
numbers, using the minimum number of bytes required to represent the values.
Medical imaging formats:
1. DICOM (Digital Imaging and Communications in Medicine). International standard for
medical imaging and related information. Consensus standard: adherence is voluntary.
Managed by the medical imaging and technology alliance (MITA), a division of the national
electrical manufacturers association (NEMA). NEMA oversees meetings of competitors to
avoid anti-trust problems. DICOM has a preamble and prefix as header, followed by data
elements (data set). Header contains information such as patient ID/Name/modality and
other information. DICOM patient coordinate system: frame of reference is a right-handed
coordinate system defined by one or more image series. The identified by a frame of
reference UID: objects with the same frame of reference UID (unique identification device)
share the same coordinate system.
2. NIFTI (neuroimaging informatics technology initiative): originally created for neuroimaging.
Format was envisioned by neuroimaging informatics technology initiative as a replacement
for ANALYZE 7.5 format. It has its origin in the field of neuro-imaging but can be used in
other fields as well. A major feature is that the format contains 2 affine coordinate
definitions which relates each voxel index (I, j, k) to a spatial location (x, y, z).
3. PAR/REC (Philips MRI scanner formats)
4. ANALYZE (Mayo Medical Imaging)
5. NRRD (nearly raw raster data): flexible format includes a single heard file and image file(s)
that can be separated or combined. A nrrd header accurately represents N-dimensional
raster information for scientific visualization and medical image processing. National Alliance
for Medical Image Computing (NA-MIC) has developed a way of using the nrrd format to
represent Diffusion Weighted Images volumes and Diffusion Tensor Images.
6. MNIC: Medical Imaging NetCDF Toolkit. MINC2 switched to HDF5, supporting an unlimited
variety of datatypes.
, X-ray Imaging
X-rays are the oldest and most used medical imaging technique. X-rays are an integral part of
contemporary hospitals and medical centres. This is their most common application, with doctor’s
using machines to take photographs of a patient’s body. Photographic film is placed behind the body,
with the x-ray turned on. The rays easily pass through the skin, but take a little longer to travel
through the bone. This is why bones appear much lighter in color. Using the results, doctors can
develop effective treatment plans.
X-ray imaging relies on the principles of X-ray physics and the interaction of X-ray photons with the
electronic energy levels of atoms within the body. X-rays are on the right of light (after UV, waves)
1. X-ray Production: X-rays are produced when high-energy electrons are accelerated and then
suddenly decelerated or stopped. In medical X-ray machines, a stream of electrons is
generated and accelerated towards a metal target, typically tungsten. When these high-
speed electrons collide with the metal atoms in the target, they interact with the innermost
electron shells of the metal atoms, causing the removal of inner-shell electrons.
2. Electronic Energy Levels: Electrons in an atom occupy specific energy levels or electron
shells. The innermost shell, closest to the nucleus, has the lowest energy, while the outer
shells have progressively higher energies. Electrons can move between these energy levels
by absorbing or emitting energy in discrete packets called photons.
3. Binding Energies: Each electron in an atom is bound to its nucleus by a certain amount of
energy, known as the binding energy. When an incoming high-energy electron from the X-ray
tube collides with an inner-shell electron of a target atom, it can impart enough energy to
the inner-shell electron to overcome its binding energy, causing the electron to be ejected
from the atom. This results in an ionized atom with an electron vacancy in the inner shell.
4. X-ray Emission: When an inner-shell electron is ejected from an atom, an electron from a
higher energy shell may transition to the lower energy shell to fill the vacancy. During this
process, energy is released in the form of X-ray photons. These emitted X-ray photons have
energies that correspond to the difference in energy levels between the two electron shells
involved in the transition. These characteristic X-rays are specific to the type of target
material used, such as tungsten, and are used for diagnostic imaging.
5. Interaction with Tissues: X-rays emitted from the tube pass through the body and interact
with the atoms in the tissues. Different types of tissues have varying atomic compositions,
and X-rays are attenuated or absorbed differently as they pass through these tissues. Dense
materials like bones absorb more X-rays and appear white on the X-ray image (radiopaque),
while soft tissues like muscles and organs allow more X-rays to pass through and appear
darker (radiolucent).
In summary, X-ray imaging relies on the generation of X-rays through the interaction of high-energy
electrons with the inner-shell electrons of target atoms. The differences in X-ray absorption by
various tissues in the body allow for the creation of detailed images that help diagnose medical
conditions and visualize internal structures.
Alpha, proton, electron, positron, neutron.
Sources of radiation
- Electrons: beta decay, internal conversion, Auger electrons
- Heavy particles: alpha decay (charged), spontaneous fission
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