• FsTutorial
• Glossary

top

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).

hypointensities (wm)

• Dark white matter on a T1-weighted image.

hypointensities (non-wm)

• Dark gray matter on a T1-weighted image.

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 SNR signal 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.