Glossary

Term	Meaning
3D surface model	See model.
aligning	Arranging two images so that the same structures in each overlap. Also called registration.
ambient	How much light some material is emitting. A value of 1 is a light source.
automatic registration	When a program, like Slicer automatically aligns two images so that the same structures in each overlap.
Biomedical Informatics Research Network	The Biomedical Informatics Research Network (BIRN) is a National Institutes of Health initiative that fosters distributed collaborations in biomedical science by utilizing information technology innovations. Currently BIRN involves a consortium of 15 universities and 22 research groups that participate in one or more of three test bed projects centered around brain imaging of human neurological disorders and associated animal models.
biopsy	A usually minor surgical procedure to extract tissue for testing.
BIRN	Biomedical Informatics Research Network
Brain shift	When tissue is resected from a brain during surgery, the remaining portions shift, causing a non-linear warping to be necessary to align the presurgical and intra-operative scans.
Brigham and Women's Hospital	A clinical and research hospital in Boston, Massachusetts, USA. SPL is part of Brigham and Women's Hospital.
BWH	Brigham and Women's Hospital
CIM	Class interaction matrix.
clinic	Medical setting where medical procedures and diagnoses are done.
craniotomies	A surgical operation that cuts the skull.
data sets	Groups of data that belong together, such as slices from an MRI.
developers	People who write computer programs.
development	The process of writing computer programs.
diagnostic	Used to diagnose illness.
diagnostic visualization	Enabling physicians to diagnose illness with images.
diffuse	How much light some material is reflecting in random directions.
distances	How far apart two structures are.
DTI	Diffusion tensor imaging: this tracks the diffusion of water molecules in the brain, resulting in vectors (or tensors) that describe the local direction of diffusion.
DTMRI	Performing diffusion tensor imaging in a magnetic resonance imaging device.
extracting	Removing or separating.
extracting structures	Separating structures of interest from surrounding material in an imaging.
FMRI	Functional magnetic resonance imaging: using MRI to detect the activation of brain areas, while the patient is doing motor/visual/auditory/memory tasks.
generation of 3D surface models	Using two-dimensional images of a structure from different points of view to create a 3D surface model of the structure.
glyph	A symbol, such as a stylized figure, that imparts information nonverbally. Each glyph is a small stick that shows the direction of maximal diffusion in a voxel. The glyphs are colored by their anisotropy (directionality) and their length is controlled by the magnitude of diffusion in the maximum diffusion direction (major eigenvalue).
Harvard Medical School	A medical school in Cambridge, Massachusetts, USA.
IJK coordinates	A coordinate system that gives the location in terms of which pixel on which slice.
image-guided medicine	Using images as part of medical diagnosis or treatment.
imaging	To obtain a visual image through some technology, such as CT, MR, x-ray, and so forth.
intra-operative imaging	Viewing images during a surgical procedure.
Johns Hopkins University	A university in Maryland, USA.
LCD monitor	A flat-screen monitor that creates displays using electronic diodes, rather than a CRT.
marching cubes	A smoothing algorithm.
MIT Artificial Intelligence Laboratory	The MIT Artificial Intelligence Laboratory is an interdisciplinary laboratory whose intellectual goal is to understand how the human mind works. We believe that vision, robotics, and language are the keys to understanding intelligence, and as such our laboratory is much more heavily biased in these directions than many other Artificial Intelligence laboratories. The MIT AI Lab has contributed algorithms and code to Slicer.
model	A model is a 3D surface. Model files have the suffix .vtk.
monitor	A display device attached to a computer or other electronic equipment.
motor cortex	A part of the brain responsible for controlling body motion.
MR	Magnetic resonance.
MR images	Images obtained using an MR scanner.
MR magnet	A magnet that is part of an MR scanner.
MR scan	A scan by a magnetic resonance device.
MR scanner	A device that scans bodies using magnetic resonance.
MRML	Medical Reality Modeling Language: a format for describing 3D scenes that consist of various types of medical data sets collected in various geometric locations. MRML files can have the extensions `.mrml` or `.xml`.
National Center for Research Resources	The National Center for Research Resources (NCRR) is a component of the National Institutes of Health that supports primary research to create and develop critical resources, models, and technologies. NCRR funding also provides biomedical researchers with access to diverse instrumentation, technologies, basic and clinical research facilities, animal models, genetic stocks, biomaterials, and more. These resources enable scientific advances in biomedicine that lead to the development of lifesaving drugs, devices, and therapies.
National Science Foundation	The National Science Foundation (NSF) is an independent agency of the U.S. Government to promote the progress of science; to advance the national health, prosperity, and welfare; and to secure the national defense.
neurosurgical cases	Medical cases that may require a surgical procedure on the brain or other parts of the nervous system.
open MR scanner	An MR scanner that has an opening that permits surgical procedures or other medical procedures during the MR scan.
Open Source development project	A project to develop software that will be made available to the public without charge, but possibly with certain restrictions in use or distribution.
operating room	A place, usually in a hospital, where surgical operations take place.
pitch	A rotation up (positive) or down (negative).
pre-operative data	Data that is available to patient and physicians before a surgical operation takes place.
pre-operative slices	Image slices obtained before a surgical operation takes place.
quantitative analysis	Measuring distances, angles, surface areas, and volumes of anatomical structures, often to determine their actual size or to compare their size to other measurements.
RAS coordinates	A coordinate system that gives the physical location in Right-left, Anterior-posterior, Superior-inferior form, in millimeters.
real-time scans	Scans where the image information is available immediately, such as during a surgical procedure.
registration	The process of lining up two different images so that matching anatomical structures overlap.
roll	A rotation around the direction of view, clockwise (positive) or counterclockwise (negative).
scanner	A device that scans bodies, such as an MR scanner or a CT scanner.
segmentation	The process of isolating an anatomical structure on an image from surrounding material.
segmented structures	On an image, an anatomical structure that has been isolated from surrounding material.
segmenting an anatomical MR scan	The process of isolating an anatomical structure on an image from surrounding material.
sets	A collection, usually of images or data.
slices	An image that is a two-dimensional section of a body, usually obtained from an MR or CT scanner.
source code	The original computer program, written in a human-understandable language like C++ or Tcl, from which the executable code, which actually runs on the computer, is compiled.
specular	How shiny some material is, from reflecting light like a mirror.
SPL	Surgical Planning Laboratory, part of Brigham and Women's Hospital.
structure	A portion of human anatomy. A single separate part of a body, such as the bone of a skull or the tissue of a brain.
surface area	The size of the two-dimensional exterior of a three-dimensional object. For example, the surface area of a solid cube consists of the six squares that make up the outside of the cube.
surface model	The reconstruction of the original surface of a three-dimensional object based on the two-dimensional slices of that object.
surgery	A medical operation that involves cutting part of a body.
surgical instruments	Instruments typically used during surgical procedures.
surgical planning	Planning the steps of a surgical procedure, including the best path to use to gain access to an anatomical structure.
Surgical Planning Laboratory	Part of Brigham and Women's Hospital, the Laboratory researches new techniques for carrying out surgical operations.
tumor	An undesired growth in a body.
vessels	The conduits in the body along which blood flows.
visualization	The process of seeing a representation of an anatomical structure that cannot be seen directly.
volume	A single image, or a collection of single images, such as a slice or label map.
volume	A volume is a 3-dimensional collection of voxels. A slice is an example of a volume.
voxel	A voxel is a 3-dimensional pixel.
www.slicer.org	The URL of the Slicer web site.
yaw	A rotation right (positive) or left (negative).