ShapeTools Applications

A list of ShapeTools applications

These applications are written and supported by the Shape Tools software group. Software written by others, that uses the ShapeTools Libraries, may be found here.

BooleanListsThreshold: Filters a group of text lists containing boolean values.

Compare Contours - A program to compare two sets of contours and output a measure of similarity.

ContourConcatenate - A program that concatenates one or more shapes containing contour lines into a single shape.

Convex Hull - A program to create convex hull of a given set of points.

DirTool : Provides cross platform directory utilities useful in creating application protocols.

DuffOffTranslator - A program that can convert between the Duff and Off formats.

ExtractAttributes - A program that extracts vertex data attributes from a Shape file.

ExtractContour - A program that extracts vertices from a Shape file and writes them as a contour file.

FDRShape - A program which calculates the FDR threshold of a Shape containing per-vertex attributes that are statistical p-values.

GeodesicPath - This program finds the shortest path on a surface connecting two vertices of that surface.

ImageToShape - A program to sample a 2d image from a 3D image volume, and creates a ShapeTools rectangular grid from the voxels so obtained, using an ImageJ plugin to read the image volume.

ImageToShapeAttribute - Maps image volume voxel values onto the vertices of a surface mesh.

ImageVoxelMap - Copies an image volume, changing the values of it's voxels according to a user specified mapping.

InterpolateContour - A program to interpolate the vertices and data attributes of contour files (obsoletes InterpolateUcf).

Jacobian : prints the Jacobian of a linear AIR transform file, or a MNC XFM transform file.

ListFilter : Selects lines from a text list.

MakeSceneFile - A program that simplfies creation of a ShapeViewer scene file.

Medial Distance Calculator - a Java application that computes and stores the distance between the vertices of a shape , defined as a group of contours, and a line passing through the centers of each of the contours.

ObjTranslation - A program to translate Minc Obj format files into OFF files.

Renamer : renames a set of files to new file names , based on a list of names, and a transformation pattern.

ReporterToMatrix: : reads princpal axis output from the ShapeReporter and translates it into matrix suitable for use by ShapeTransform

RigidAtlas - Computes an atlas from a group of shapes, using the RigidQuaternionTransform to align the shapes to the atlas.

Rigid Quaternion Transform - Calculates a rigid quaternion transform that maps one set of vertices onto another, given the correspondences between the two sets of vertices.

Shape Attribute - Adds scalar values to the vertices of a shape.

ShapeAverage - Averages a the coordinates and, optionally, per vertex attributes, of a population of shapes.

ShapeCurvature - A program that calculates and saves the curvature of a surface at its vertices (v1.1).

Shape Density - A Java application that computes various measures of surface parameterization regularity

ShapeDistance - A program to measure the distance between the vertices of two (homologous) shapes.

ShapeGroupDistance - Compares a reference shape and a group of other shapes. It's output may be analysed by ShapeTTest (will be replaced by ShapeGroupMeasure).

ShapeMeasurement - Calculates various shape properties at each vertex of the shape. These include local curvature, curvedness and the shape index.

ShapeReporter: - Reports many properties of a shape. These include surface area, and many diagnostic properties.

Shape Split - splits a shape into pieces (current version has very limited functionality).

Shape Statistics - calculate per-vertex statistics for a population of shapes.

ShapeToDX - A program which translates a variety of Shape files into an OpenDX general format data file.

ShapeToImage: A program that creates an binary valued image volume (mask) equivalent to the edges of a surface.

ShapeToObj : a Java application that triangulates an arbitrary surface and saves the triangulated surface as a Minc Obj polygon file.

ShapeTransform - A program that applies an AIR transform or a user specified transformation (translation + rotation) to the coordinates of a Shape's vertices.

ShapeTTest - calculate independent and dependent T-Test on two populations of values, read from ascii text tables.

Shape Viewer: An application program which uses Java3D to display shapes in a 3 dimensional viewer (v2.0). The ShapeViewer now supports user contributed 'plug-in' extensions. You can get some useful useful plug-ins here.

TransposeTable: transposes the elements of an ascii delimited table file.

TranslateTo: A Java application that translates a Shape data file into a different output file format.

UcfReorder - A program to correct common flaws in hippocampal contours stored as a Loni UCF.

Vertex Selector: selects vertices from a shape file and writes them to standard output.

Using Shape Tools applications

• A short note on Using ShapeTools applications
• Using Shape Tools applications in the LONI Pipeline

Non-Standard Applications that use the ShapeTools libraries

These applications use the shape tools libraries, but may not adhere to the standard shape tools application conventions, Please contact their authors for support.

ShapeTranslator: The Shape Translator allows conversion between many different shape formats

Color Surface: a java application that colors the vertices of a surface.

Shape Tools application collections

• A Collection of ShapeTools applications