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Glossary
anatomically derived defect: A topological defect in the cortical surface that arises from a feature of normal neuroanatomy to be distinguished from defects arising entirely from segmentation errors. See topological defect.
artifact: A feature that appears in an image but is not actually present in the imaged object.
average convexity: The signed distance that a vertex moves during the inflation process.
brain volume: The T1 volume after the skull and other non-brain structures have been removed. This volume can be viewed using tkmedit.
canonical surface: Surface-based atlas constructed from the cortical surfaces of 40 normal individuals (used for inter-subject averaging).
conversion/averaging: Process of converting and averaging multiple structural acquisitions from the native magnet format into the native FreeSurfer format (see COR files).
COR files: The native file format used by FreeSurfer to store 3D structural image data.
Euler number: After Leonhard Euler (1707-83). A topological invariant of a surface that can be computed from the number of edges, vertices and faces in a polygonal tessellation (command mris_euler_number). The Euler number of a sphere will equal 2; the Euler number of a surface with n handles is 2 2n.
filled volume: The wm volume after separation of the left and right hemispheres and filling of each hemisphere. This volume can be viewed using tkmedit.
flattening: Producing a planar (flat) representation of a patch of the cortical surface that has minimal metric distortion.
gyrus: A fold or convolution of brain tissue (an outward folded region).
inflated surface: The smoothwm surface after inflation. This surface can be viewed using surfer.
inflation: The process of smoothing the cortex while minimizing metric distortion, so that all sulci are fully visible and surface distances are apparent to visual inspection.
intensity: Measured amount of magnetic field at a given spatial location, represented by a voxel (higher SNRsignal to noise ratio means voxels will have a higher intensity relative to the background noise, and appear brighter).
label: A particular region of interest. e.g. in tksurfer the label would be a region of interest in the surface. In tkmedit a label is a region of interest in the volume.
morphing: Computer graphics technique whereby a mapping is computed that smoothly transforms one image or surface into another.
morphometrics: The study of geometric properties of the human brain.
motion correction: Processing multiple structural volumes so that the effects of subject movement are minimized. This is typically done by aligning multiple images/volume to an initial image/volume (see conversion/averaging).
MRI volume: The three dimensional volumetric data set collected from a MRI scanner.
orig volume: The original MRI volume. This volume can be viewed using tkmedit.
orig surface: The first surface constructed by covering the labeled voxels in the filled volume. This surface can be viewed using surfer.
pial: Pertaining to the delicate pia mater which envelops the brain (gray matter). Also, the model of the pial surface (?h.pial).
pial surface: The refined estimate of the gray/CSF boundary (pial surface). This surface can be viewed using surfer.
region growing process: An algorithm that groups voxels or sub-regions into larger regions.
RF-field inhomogeneities: Spatial variations in the Radio Frequency (RF) excitation pulse. These variations result in changes in the measured intensity for a given tissue class that are related to the spatial location of the voxel.
segmentation: Labeling of tissue classes from MRI data (e.g. white matter).
smoothing: Process of producing a relatively even and regular cortical surface.
smoothwm surface: The orig surface after smoothing. This surface can be viewed using surfer.
sulcus: A groove or furrow in brain tissue (an inward folded region).
supertessellated icosahedron: Polygonal approximation to a sphere.
T1: Longitudinal relaxation constant.
T1 volume: The MRI volume after intensity normalization. This volume can be viewed using tkmedit.
T1 Weighted Image: A magnetic resonance image where the contrast is predominantly dependent on T1.
T2 Weighted Image: A magnetic resonance image where the contrast is predominantly dependent on T2.
T2: Transverse relaxation constant.
Talairach coordinate: The corresponding location in the Talairach atlas for a given point in a brain that has been coregistered with the atlas (Talairach et al, 1967).
tessellation: Covering of a surface by repeated use of a single shape.
topology: The properties of a surface related to its connectivity that are unaffected by geometric (i.e. rubber sheet) transformations.
topological defect: A portion of a surface that results in the surface topology differing from that of a sphere.
volume: A 3-D data set that typically contains either intensity information derived from the original MRI, or the results of segmenting this data into tissue classes.
voxel: The basic element of an MRI volume (analogous to a pixel in a 2-D image). The volume of a structural voxel is approximately 1 mm3.
white surface: The refined estimate of the gray/white boundary. This surface can be viewed using surfer.
wm volume: The brain volume after white matter segmentation. This is also the volume that is manually edited. This volume can be viewed using tkmedit.