Terms - Githubissues

i put mindboggle turtle terms in a wiki, but all of the indentation disappeared, so i am including mbterms.ttl here. in addition to some basic terms at the beginning, i include all of the (cortical) features and shape measures at the bottom. the rdfs label for each term is used in mindboggle's current output shape tables, but the tables include extra words. for example, one column of label_shapes.csv includes the label 'position in standard space': "mean position in standard space", and another column in the same table includes the labels 'label' and 'mean curvature': "label: mean curvature: median (weighted)"

@prefix rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# . @prefix owl: http://www.w3.org/2002/07/owl# . @prefix skos: http://www.w3.org/2004/02/skos/core# . @prefix rdfs: http://www.w3.org/2000/01/rdf-schema# . @prefix mbterms: http://mindboggle.info/terms/ . @prefix dcam: http://mindboggle.info/dc/dcam/ .

http://mindboggle.info/terms/ mbterms:modified "2013-07-14"^^http://www.w3.org/2001/XMLSchema#date ; mbterms:publisher http://mindboggle.info/ ; mbterms:title "Mindboggle Metadata Terms"@en .

mbterms:StandardSpace mbterms:description "A standard space is most often accompanied by a template used for image registration purposes. The preeminent standard space used in brain imaging is the 'MNI space', also called 'Talairach space' for historical reasons."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A conventional ('common') space consisting of fiducial markers defining a coordinate frame, used for comparing, presenting, or reporting brain image data."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "standard space"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:Template mbterms:description "A template is often used for image registration purposes. Examples include any of the Mindboggle-101 templates on http://mindboggle.info/data/"@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A canonical or reference brain image."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "template"@en . rdfs:seeAlso http://mindboggle.info/data/ .

mbterms:AverageTemplate mbterms:description "The preeminent example of an average template is the MNI152 template, the result of co-registering 152 brain images."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Intensity average of multiple, co-registered individual brain images. This average may be accompanied by a corresponding set of probability values."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "average template"@en . rdfs:seeAlso http://mindboggle.info/data/ . rdfs:subClassOf mbterms:Template .

mbterms:OptimalAverageTemplate mbterms:description "Examples include any of the Mindboggle-101 optimal average templates on http://mindboggle.info/data/."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "An average template constructed by multiple iterative co-registration steps."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "average template"@en . rdfs:seeAlso http://mindboggle.info/data/ . rdfs:subClassOf mbterms:AverageTemplate .

mbterms:Atlas mbterms:description "Examples include any of the Mindboggle-101 manually labeled brain images on http://mindboggle.info/data/"@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Annotations of a template."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "atlas"@en . rdfs:seeAlso http://mindboggle.info/data/ .

mbterms:IndividualAtlas mbterms:description "Examples include any of the Mindboggle-101 manually labeled brain images on http://mindboggle.info/data/"@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Manual annotations of a single individual’s brain image."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "individual atlas"@en . rdfs:seeAlso http://mindboggle.info/data/ . rdfs:subClassOf mbterms:Atlas .

mbterms:ProbabilisticAtlas mbterms:description "Probability values are usually assigned to each vertex or voxel of a probabilistic atlas after registering a set of individual atlases to a template. An example is a maximum probability atlas accompanied by an image volume of probability values. See the Mindboggle-101 probabilistic atlases on http://mindboggle.info/data/"@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Aggregate of multiple atlases, with multiple labels assigned to each vertex or voxel, or the probabilistic assignment of labels to a template."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "probabilistic atlas"@en . rdfs:seeAlso http://mindboggle.info/data/ . rdfs:subClassOf mbterms:Atlas .

mbterms:MaximumProbabilityAtlas mbterms:description "Examples include any of the Mindboggle-101 maximum probability atlases on http://mindboggle.info/data/"@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Aggregate of multiple atlases, with a single label assigned to each vertex or voxel."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "maximum probability atlas"@en . rdfs:seeAlso http://mindboggle.info/data/ . rdfs:subClassOf mbterms:ProbabilisticAtlas .

mbterms:Voxel mbterms:description "A voxel may be isometric (e.g., a 1x1x1mm cube) or anisometric."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Voxels ('volume elements) are volumetric pixels - that is, they are values in a regular grid in three dimensional space."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "voxel"@en .

mbterms:Vertex mbterms:description "Conceptually, a vertex in a mesh is equivalent to a node in a graph."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A point/node of a surface mesh."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "vertex"@en .

mbterms:Label mbterms:description "Labeling is distinct from "segmentation", which usually refers to breaking up dissimilar or clustering similar, contiguous points, for example tissue class segmentation into gray matter."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "An annotation of a region of the brain, such as when delineating the anatomical boundaries of a gyrus or sulcus. This process is often called "parcellation" when labeling a surface such as the cortical surface."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "voxel"@en . rdfs:seeAlso http://en.wikipedia.org/wiki/Voxel .

mbterms:CorticalSurface mbterms:description "Pial surface."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "The outer surface of the cerebrum, sometimes referred to as the "pial surface" or "cerebral exterior."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "cortical surface"@en .

mbterms:CorticalFeature mbterms:description "Examples of cortical features, or simply 'features', include a gyrus, sulcus, and cortical fold."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Any feature or structure derived from a brain's cortical surface."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "cortical feature"@en .

mbterms:Fold mbterms:description "A fold is sometimes loosely referred to as, but should be distinguished from, a 'sulcus'."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A crease, infolding, fissure, crevice, or intrusion of the cortical surface."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "fold"@en . rdfs:subClassOf mbterms:CorticalFeature .

mbterms:Sulcus mbterms:description "A sulcus is sometimes loosely referred to as, but should be distinguished from, a cortical 'fold'. It is defined by a labeling protocol and is based on the folding pattern (topography) of the cortical surface."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A sulcus (pl.: sulci; adj.: sulcal) is a whole or a portion of one or more cortical folds."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "sulcus"@en . rdfs:subClassOf mbterms:CorticalFeature .

mbterms:Gyrus mbterms:description "Examples include the superior, middle, and inferior frontal and temporal gyri."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A gyrus (pl: gyri; adj.: gyral) is the exterior portion of a fold of the cortical surface. The outermost protrusions are sometimes referred to as a 'gyral crest' or 'gyral crown'. rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "gyrus"@en . rdfs:subClassOf mbterms:CorticalFeature .

mbterms:Fundus mbterms:description "A fundus is delimited by the extent of the sulcus it runs through, even if the curve continues along a fold."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A fundus (pl: fundi; adj.: fundal) is a curve traversing the bottom of a sulcus."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "fundus"@en . rdfs:subClassOf mbterms:CorticalFeature .

mbterms:Pit mbterms:description "A sulcal pit is closely related to the 'sulcal root', and may arise during cortical development from a buried or annectant gyrus (a 'plis de passage')."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Local, deep, pit-like intrusion in a fold."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "pit"@en . rdfs:subClassOf mbterms:CorticalFeature .

mbterms:MedialSurface mbterms:description "The medial surface for a sulcus fold lies between the banks of the sulcus without intersecting the cortical surface."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A surface running midway between two structures."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "medial surface"@en . rdfs:subClassOf mbterms:CorticalFeature .

mbterms:ShapeMeasure mbterms:description "A shape measure can be computed at a single vertex/voxel, or for a cortical feature."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A measure of shape."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "shape measure"@en .

mbterms:Area mbterms:description "The surface area for a patch of a triangular surface mesh is the sum of the areas of triangles within the patch. For a single vertex, area is measured based on the vertex's contribution to the area of each of the faces containing it."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Surface area."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "area"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:MeanCurvature mbterms:description "A neighborhood size is applied to the Laplacian filtering."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "The mean curvature based on the direction of the displacement vectors during a Laplacian filtering."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "mean curvature"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:TravelDepth mbterms:description "Travel depth was developed by Joachim Giard as part of his doctoral dissertation, and was first applied to protein molecules. It was adapted for use with cortical surfaces as part of the Mindboggle software."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "A measure of depth from an outer surface or hull that combines Euclidean distances (straight line-of-sight) and geodesic distances (along the surface)."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "travel depth"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:GeodesicDepth mbterms:description "Approximations to geodesic depth run along edges of a surface mesh."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "Distance between two points along a surface."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "geodesic depth"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:Convexity mbterms:description "FreeSurfer's convexity measure is used as a proxy for depth, and is a function of the distance traveled by a vertex as the surface containing it is inflated."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "FreeSurfer convexity measure."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "convexity"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:Thickness mbterms:description "FreeSurfer's thickness measure is computed within a segmented gray matter volume ('cortical ribbon')."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "FreeSurfer cortical thickness measure."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "thickness"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:LaplaceBeltramiSpectra mbterms:description "Martin Reuter first applied Laplace-Beltrami spectra to study the 'shape-DNA' of whole cortical surfaces [Reuter, 2006]."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "The first coefficients of the Laplace-Beltrami spectra."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "Laplace-Beltrami spectra"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:Position mbterms:description "[x,y,z] coordinates."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "3-D coordinates."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "position"@en . rdfs:subClassOf mbterms:ShapeMeasure .

mbterms:StandardPosition mbterms:description "[x,y,z] coordinates in standard (MNI152) space."@en ; mbterms:issued "2013-07-04"^^http://www.w3.org/2001/XMLSchema#date ; a mbterms:AgentClass, rdfs:Class ; rdfs:comment "3-D coordinates in standard space."@en ; rdfs:isDefinedBy http://mindboggle.info/terms/ ; rdfs:label "position in standard space"@en . rdfs:subClassOf mbterms:ShapeMeasure .

nipy / mindboggle

Terms #20