Translational Imaging Glossary

Term Definition
AFNI AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.
Cerebral Blood Volume The amount of contrast agent flowing in and out of a voxel.
Cerebral Spinal Fluid This is a clear watery substance that baths the brain and spine. It acts as a watery cushion for the brain. Abnormal accumulations of CSF in the brain due increase in fluid or blockage of drainage can lead to hydrocephalus.
DEMRI Dynamic contrast-enhanced magnetic resonance imaging is a technique used by radiologist to evaluate the grade or aggressivness of a tumor. This technique looks at how rapidly a contrast agent is sequestered in or around a tumor.
Diffusion The tendency of a substance to move from an area of high concentration to an area of low concentration. For example Oxygen diffuses from the lungs to the blood during respiration.
Dosimetry Measuring the dose of radiation emitted by a radioactive source.
DTI Diffusion tensor imaging is an MRI based technique which allows us to map major white matter pathways in the brain.
Fast Light Toolkit (FLTK) FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX®/Linux® (X11), Microsoft® Windows®, and MacOS® X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL® and its built-in GLUT emulation.
fMRI Functional magnetic resonance imaging allows us to detect areas of brain activity associated with a stimulus or task of interest.
FreeSurfer FreeSurfer is a set of semi-automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
FSL FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data.
Gray Matter Gray matter is a category of nervous tissue with many nerve cell bodies and few myelianted axons.

Gray matter looks reddish gray on a freshly removed brain. It forms the superficial parts of the brain and the deep parts of the spinal cord. It is composed of the bodies of the nerve cells (neuron) and the initial parts of its processes (axons and dendrites) just emerging from the neurons. Grey matter is the major part of the nervous system in which the nerve impulses for all kinds of mental functions are produced and then sent away to be carried to their target organs by white matter.

The cerebrum and the subcortical nuclei, such as the putamen and the caudate nucleus, are composed of grey matter. Generally, grey matter can be understood as the parts of the brain responsible for information processing; whereas, white matter is responsible for information transmission.
Homogeneity Magnetic field homogeneity simply describes the consistency or uniformity of the main magnetic field. Main field homogeneity is very important. As an analogy, envision a calm, smooth pond with no ripples flowing across the water's surface. In this scenario, one could easily see a mirror-like reflection from the pond water. The quality of the pond's reflective ability can be severely affected by a few dropped pebbles. Likewise, MRI systems must be able accurately "reflect" the RF signal that eminates from the pulse sequence energy transmitted into the patient. Any ripples, or inhomogeneities present in the main magnetic field can cause our imaging to be blurred.
Image Registration

Image registration is the process of determining a mapping between the coordinates in one image space and those in another, to achieve biological, anatomical or functional correspondence.

Image registration adds value to medical images:

  • to allow monitoring of change in the individual
  • to fuse information from multiple sources in a clinically meaningful way
  • to compare one subject with another

Transformations - also referred to as Degrees of Freedom (DOF) - are described by a number of parameters.

Rigid Transformation includes global translation and rotation thereby preserving distances, planarity of surfaces and non-zero angles. It is typically used to compensate for global patient repositioning.

If the objects are the same size and shape, then you should be able to register any two images of the objects.

Affine Transformation includes and global scaling and sheering in addition to rigid transformation. It preserves planarity of surfaces and parallelism but not the angle. It compensates for additional global size changes and shears. It is typically used to account for the scale and size differences in inter-subject brain registration.

Non-Rigid Transformation includes local transforms in addition to the global affine transform. It does not preserve distance, planarity, parallelism or the angle. It is typically used to compensate for longitudinal tissue changes and deformation.

Transformation Matrix Representation

More examples:

In Vivo In vivo (Latin for (with)in the living) means within a living organism (a cell). For example, biochemical reactions can take place in vivo. The opposite is in vitro, something that is or happens in an artificial environment (for example, in vitro fertilization). As many experiments that deal with molecular biology are conducted outside of cells, and the conditions do not necessarily represent the conditions inside the cell, results are often annotated with in vivo or in vitro.

MATrix LABoratory) A programming language for technical computing from The MathWorks, Natick, MA (

Used for a wide variety of scientific and engineering calculations, especially for automatic control and signal processing, MATLAB runs on Windows, Mac and a variety of Unix-based systems. Developed by Cleve Moler in the late 1970s and based on the original LINPACK and EISPACK FORTRAN libraries, it was initially used for factoring matrices and solving linear equations. Moler commercialized the product with two colleagues in 1984. MATLAB is also noted for its extensive graphics capabilities.

Mean Transit Time The amount of time taken by contrast agent to travel through a voxel.

The term neurotoxic is used to describe a substance, condition or state that damages the nervous system and / or brain, usually by killing neurons.

The name implies the role of a neurotoxin although the term 'neurotoxic' may be used more loosely to describe states that are known to cause physical brain damage but where no obvious neurotoxin has been identified.

Spatial Voluming Partial voluming Is when a pixel represents more than one kind of tissue type. Partial Voluming blurs the distinction between tissue classes at the border of two tissues.
Perfusion Supplying an organ or tissue with oxygen and or nutrients via an artery. In the context of our work, perfusion is determined by using a ‘spin labeling’ MRI technique.
ROI Regions of interest are the segments of an image that are being evaluated or calculated.
Segmentation Brain segmentation in magnetic resonance images is the delineation of neuroanatomical structures. Outlines of brain structures can be drawn on images to indicate the extents of those structures.
Statistical Parameter

Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM.

The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT and similar modalities.

VBM Voxel-based morphometry shows local differences in gross anatomy of the brain.
Voxel (VOlume piXEL)A three-dimensional pixel. A voxel represents a quantity of 3D data just as a pixel represents a point or cluster of points in 2D data. It is used in scientific and medical applications that process 3D images.
White Matter

White matter is one of two categories of tissue in the nervous system. It forms the deep parts of the brain and the superficial parts of the spinal cord. It is composed of nerve cells processes (axons and dendrites) that connect various parts of the brain to each other and carry nerve impulses to or from the bodies of nerve cells (neuron).

White matter is distinguished in that it is composed of nerve fibers often covered with myelin. This is as opposed to grey matter, which is composed primarily of nerve cell bodies. Generally, white matter can be understood as the parts of the brain responsible for information transmission; whereas, grey matter is responsible for information processing.