[[FsTutorial|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 [[http://surfer.nmr.mgh.harvard.edu/fswiki/mris_euler_number|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 mm^3^. == 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.