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

A short note on Using ShapeTools applications

InflateFlatmap - Maps a 2D, flattened surface, to either a sphere, or an icosahedron.

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

ShapeTools Applications

Shape Viewer : An application program which uses Java3D to display shapes in a 3 dimensional viewer (v1.2).

ContourTopologyChecker - Checks whether a contour is entirely contained on a surface manifold, or not.

ContourVolume: an application to calculate the volume outlined by a set of (Ucf) contours.

Blend Surfaces combines a flattened map of a surface and it's dual into a Shape.

FlatMapToolsLibrary: A Java library that simplifies maninpulation of shapes represented as a FlatMap.

TopologicalContourAverager: Averages contours, accounting for a complex surface connectivity

DecodeShape: Constructs a 3d shape surface from coordinates encocded as a pair of LONI UIF files.

EncodeShape: Encodes a 3d shape as pair of LONI UIF files.

Blend Surface: combines the flattened map of a surface and it's dual mapping into a single flattened two dimensional mapped surface.

InflateFlatmap - Maps a 2D, flattened surface, to either a sphere, or an icosahedron.

ShapeGroupMeasure - Compares a reference shape and a group of other shapes. It's output may be analysed by TTest _(obsoletes ShapeGroupDistance)_.

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

ArrayStatistics: calculates statistics for a set of numerical arrays.

ArrayToImage: creates an image from an array of numbers.

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

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

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

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

Extract4DucfAttributes - A program that extracts from a Ucf file it's data attribute column. (obsoleted by ExtractAttributes)

ExtractAttributes - A program that extracts from a Shape file it's data attribute column.

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 samples 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.

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

ListFilter : Selects lines from a text list.

Map Contour - Maps a contour according to a transform defined by the corrospondences of the faces of two homologous shapes.

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.

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 a 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).

ShapeGroupDistance - Calculate the distances between a reference shape and a group of other shapes. It's output may be analysed by TTest.

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

ShapeReporter: - Reports the properties of an input shape.

Shape Split - splits a shape into pieces.

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

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

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

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

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

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

Shape Viewer :

An application program which uses Java3D to display shapes in a 3 dimensional viewer (v1.1,v1.0).

Tiny Shape Viewer:

A minimal shape viewer, conforming to the Loni ViewerSpi interface, intended for use as a component of a LoniViewer.

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

Vertex Selector: selects vertices from a shape, based on user specified criteria.