CCB !ArrayStatistics Project Components Documentation ArrayStatistics User's Guide v 1.0 Changes Log A list of Frequently Asked Questions. Feedback Project Bug List ...

CCB !ArrayToImage Project Components Documentation ArrayToImage User's Guide v 1.0 Changes Log A list of Frequently Asked Questions. Feedback Project Bug List (v1 ...

CCB !AttrStatistic Statistically analyze 4d attribute values of data files between one file and the other file. This analysis can also be done between one file and ...

CCB !AttributesStatistic Statistically analyze 4d attribute values of data files between one file and the other file. This analysis can also be done between one file ...

CCB !AverageUcf Calculates average values of coordinates and 4d attribute values of given data files. Project Components Documentation AverageUcf User's Guide v 1 ...

Blend Flatmap TOC{depth "2"} Description BlendFlatmap is an application which combines the flattened map of a surface and it's dual mapping into a single flattened ...

CCB !BooleanListsThreshold Project Components Documentation BooleanListsThreshold User's Guide v 1.0 Changes Log A list of Frequently Asked Questions. Feedback Project ...

Accessing the CCB CVS Tutorials CCB Wiki Homepage Back to CCB CVS Repository Pages CVS UNIX/Linux Tutorial 1 CVS UNIX/Linux Tutorial 2 CVS Tutorial 3 Eclipse CVS ...

NCBC All-Hands Meeting, Bethesda, MD, July 17-19, 2006 CCB/NCBC Wiki Resources Official Meeting Web page Official Dissemination Meeting Flier Meeting Goals (as of ...

ColorSurface Color Surface is a java application that colors the vertices of a surface. It (will) use the voxel intensities of an image volume to determine the colors ...

CompareContours Extracting three dimensional cortical surfaces from volumetric images such as MRI is becoming an important routine process for the medical image analysis ...

Contour Topology Checker version: 1.0.3 TOC{depth "2"} Overview This program examines a group of flattened contours (see MapContour to flatten the contours) to determine ...

Contour Topology Checker Frequently Asked Questions TOC{depth "2"} no questions yet

Public web page of ContourTopologyChecker !ContourTopoologyChecker Project Definition ( v1x01 ) TOC{depth "2"} Overview Restrictions, Exclusions, Limitations Only ...

CCB !ConvexHull Calculates the surface that wraps the set of points contained in a Shape. Interior points are not contained in the output surface. Project Components ...

CCB !DXJava library !OpenDX is a commonly used, public domain, visualization tool whose data model is able to represent a wide variety of data sets. It is difficult ...

DX Java Library Frequently Asked Questions (none yet asked)

ExtractAttributes Shape and other surface files often contain data attributes attached to the vertices of the shapes. These datum at times need to be manipulated ...

CCB !ExtractContour !ExtractContour is a !ShapeTools application program that will create a contour shape file from a subset of the vertices defined by a Shape file ...

A list of some commonly used shape file formats TOC{depth "2"} LONI TM NAME tm LONI triangle surface model format SYNOPSIS #include "/usr/local/lib/loni/geom.h" ...

!FlattenSurface TOC{depth "2"} Description This application takes a shape with a specific triangulation and maps its vertex and color data to a square regular grid ...

CCB !GeodesicPath This program finds the shortest path on a surface connecting two vertices of that surface. This path may be constrained to the vertices and edges ...

(None thus far) Revised: 07 Dec 2006

Image Coordinate Tools Library Version 1.0.0 This library provides methods that describes 3D image (volume) orientation and location in space. The library stores ...

CCB !ImageToShape Shape representation of image files are needed in order to display image and its multi tracer contour in the !ShapeViewer. The !ImageToShape application ...

CCB !ImageToShapeAttribute Project Components Documentation ImageToShapeAttribute User's Guide v 1.0 Examples using project version 1.0 A Glossary of terms version ...

ImageVoxelMap Overview: ImageVoxelMap is a !ShapeTools application program that will copy an image volume data file, applying a user specified mapping to the data ...

!InflateContour Maps a contour according to a transform defined by the corrospondences of the faces of two homologous shapes. TOC{depth "2"} Description The InflateContour ...

InflateSurface TOC{depth "2"} Description This application will generate a shape whose coordinates and colors are specified by data defined on a regular grid. In ...

!InterpolateContour TOC{depth "2"} Overview InterpolateContour uses spline interpolation to smoothly interpolate shape files containing contours. The number of interpolated ...

CCB !LONI Reader library Project Components Documentation User's Guide Examples using project version 1.0 Changes Log LONI Reader Programmers Guide. A list of Frequently ...

Landmark Warp Frequently Asked Questions TOC{depth "2} How do I choose a basis function? Some of the characteristics that differ between basis functions are number ...

Landmark Warp Tools This page describes a Java library and command-line toolkit that can be used to compute and apply warps that are guided by landmarks. Typically ...

mShape An interface to !ShapeTools from within Matlab TOC{depth "2"} Using !ShapeTools with Matlab Requirements Matlab 6, or greater (must support Java). Frequently ...

Using !ShapeTools from Matlab Frequently Asked Questions TOC{depth "2"} How do I install the !ShapeTools library so that Matlab can see it ? Tell your current matlab ...

MakeSceneFile Overview: This program allows creation of a ShapeViewer compatible scene file without having to start the ShapeViewer. Project Components Documentation ...

!MapContour Maps a contour according to a transform defined by the corrospondences of the faces of two homologous shapes. TOC{depth "2"} Description One approach ...

Medial Distance Calculator Various data analysis protocols use nonportable software to accomplish the computation described below. The details of this computation ...

Medial Distance Frequently Asked Questions TOC{depth "3"} Why does your medial distance differ from that calculated by Dr. Thompson's tools ? These differences arise ...

Previous week Agenda for 03 July 2007 Shape Tools meeting Review prior weeks to do items !BaeCheol first revision of !MapContour !BaeCheol improvements to !ShapeToImage ...

Previous week Meeting Purpose: Update status and plan the next week's work on the various CCB Shape Tools projects. Agenda for 03 May 2006 Shape Tools meeting Review ...

Previous week Meeting Purpose: Status review of last week, plans for next week Agenda for 06 September 2006 Shape Tools meeting (Week 36-37) Review prior weeks to ...

Previous week Meeting Purpose: Review Prior Development Cycle and assign general priorities for the next cycle Agenda for 07 June 2006 Shape Tools meeting discuss ...

Previous week Agenda for 10 July 2007 Shape Tools meeting Review prior weeks to do items !BaeCheol !ContourMap !BaeCheol, Craig, Ryan Define MapContour !BaeCheol ...

Previous week Meeting Purpose: Update status and plan the next week's work on the various CCB Shape Tools projects. Agenda for 10 May 2006 Shape Tools meeting Review ...

Previous week Agenda for 12 June 2007 Shape Tools meeting Review prior weeks to do items Craig plan for warp analysis alternative Craig improve point picking in ...

Previous week Meeting Purpose: Status review of last week, plans for next week Agenda for 13 September 2006 Shape Tools meeting (Week 37-38) Review prior weeks to ...

Previous week Meeting Purpose: Update status and plan the next week's work on the various CCB Shape Tools projects. Agenda for 17 May 2006 Shape Tools meeting Review ...

Previous week Meeting Purpose: Agenda for 19 April 2006 Shape Tools meeting Review prior weeks to do items X Ivo list of analysis script writers for various groups ...

Previous week Agenda for 19 June 2007 Shape Tools meeting Review prior weeks to do items X !BaeCheol finish ShapeToImage application program. !BaeCheol Write UifReader ...

Previous week Note: Meeting will not be held unless necessary. Meeting Purpose: Update status and plan the next week's work on the various CCB Shape Tools projects ...

Previous week Meeting Purpose: Update status and plan the next week's work on the various CCB Shape Tools projects. Agenda for 26 April 2006 Shape Tools meeting Review ...

Note: The following file format description is taken from this URL: http://www.bic.mni.mcgill.ca/~david/FAQ/lines format.txt This is a description of the polygons ...

Note: The following file format description is taken from this URL: http://www.bic.mni.mcgill.ca/~david/FAQ/polygons format.txt This is a description of the polygons ...

Regular Discrete Data Tools This package contains a Java library and several command-line tools that can be used to store and manipulate floating point data that ...

Renamer A tool that simplifies renaming files. Project Components Documentation Project User's Guide v 1.0 Changes since version 1.0 Frequently Asked Questions Feedback ...

RigidAtlas Overview Creates an atlas from a group of shapes whose vertices are homologous. Description File formats Any shape that may be read by the ShapeTools library ...

!RigidQuaternionTransform Table of Contents TOC{depth "2"} Overview Given two sets of homologous points, this program estimates the rigid transform that maps one ...

CCB !ShapeTools !ShapeAttribute TOC{depth "2"} Overview Adds a list of scalar values to a shape, as a per vertex attribute. This program may be used to associate ...

ShapeAverage ShapeAverage averages the coordinates, and optionally per-vertex attributes, of a population of shape files. Project Components Documentation User Guide ...

CCB Shape Curvature Project A common problem in analysis of shapes is to find the curvature of the surface (hull) defined by the shape. No tools exist for the data ...

!ShapeDistance TOC{depth "2} Documentation ShapeDistance Usage Guide Frequently Asked Questions

CCB !ShapeGroupDistance An application program that calculates various kinds of distance between a reference shape and other shapes. Project Components Documentation ...

CCB !ShapeGroupMeasure An application program that calculates various scalar measurements comparing a reference shape and a group of other shapes. Project Components ...

CCB !ShapeMeasurement The !ShapeMeasurement calculates various measurement of a surface mesh at each vertex, and write output with these computed values. These values ...

ShapeROI Overview: This is a tool kit that will provide classification of vertexes in a manifold mesh from region of interest which may be a set of points, open curve ...

CCB !ShapeReporter The ShapeReporter examines the properties of an input shape and reports it's results to the user. Examined characteristics include: Testing for ...

CCB !ShapeSplit Project Components Documentation ShapeSplit User's Guide v 1.0 Changes Log A list of Frequently Asked Questions. Feedback Project Bug List (v1.0) ...

ShapeStatistics ShapeStatistics Calculates various per-vertex scalar statistics describing a population of input shapes. Project Components Documentation User Guide ...

CCB !ShapeToDX A description of the problem solved by the project. A description of the project's purpose and expected result or contribution. A description of the ...

!ShapeToImage An application to create an image volume mask from the vertices in a Shape file. the current version of !ShapeToImage essentially traces the edges and ...

ShapeToObj This is an application which converts an arbitrary !ShapeTools-compatible surface file to a Minc Obj polygon file. Since not all shapes have an equivalent ...

CCB Shape Program Project Template A description of the problem or need motivating the project. A descriptiono the expected results of the project. A description ...

CCB !ShapeToolsData A java library for reading data from a variety of input sources and writing data to a variety of output sources. Project Components Documentation ...

ShapeToolsData Library TOC{depth "2"} Overview The !ShapeToolsData library provides a common I/O interface that allows java applications to read and write to a variety ...

ShapeTools Image Library TOC{depth "2"} Overview Provides a simple library that reads LONI specific 2D UIF image files. Documentation Java Doc v1.1.0 Changes since ...

K Ring Neighborhood This class finds all vertices which are reachable by crossing k or less edges from a given source vertex. The number of edges between two vertices ...

Shape Tools Library Version 1.2.0 ShapeTools Library A Definition of a Shape. Feature Wish List Documentation Shape Tools Libraries !JavaDoc Java Doc v1.2.0 Java ...

ConvexHull3D When n points in 3 dimensional space are given, sometime we would like to see only exterior of all the points. In another word, we would like to construct ...

Frequently Asked Questions #TableOfContentsAnchor TOC{depth "2"} Read a Shape File To read a file without knowing in advance the format of the shape data contained ...

FaceSetOrientationNormalizer A description of the problem or need motivating the project. Many surface mesh algorithms assume that the faces in a surface have a ...

False Discovery Rate This project will allow the users to identify active voxels in neuroimaging data. Project Components Feature Wish List Documentation False Discovery ...

Geodesic Distance A widely used definition of geodesic curve is a shortest path between two points on the surface. Geodesic curves are demanded in many areas of science ...

ImageJ Plugin Reader The project creates a shape that represent 2D section of an image. This project will enable the !ShapeTools library to create a shape that represents ...

QuadResampler A description of the problem or need motivating the project. Many algorithm requires triangle meshes. A description the expected results of the project ...

MeshTriangulation A description of the problem or need motivating the project. Many surface mesh algorithms assume triangulated surface, however, many mesh's are ...

NonConvexPolygonTriangulation A description of the problem or need motivating the project. The simple mesh triangulation algorithm assumes surface whose faces are ...

Shortest Path A widely used definition of geodesic curve is a shortest path between two points on the surface. Geodesic curves are demanded in many areas of science ...

Medial Distance This class computes the distance between the vertices of a shape, defined as a contours, and the centers of mass. Project Components Medial Distance ...

ShapeTransform Neurological image volumes are routinely mapped from one coordinate space into another. It is often necessary to apply this mapping to shapes (anatomical ...

ShapeViewer ( version 1.1.12) TOC{depth "3"} A simple 3-D viewer that displays Shape files read by the Loni ShapeTools library. Supported file formats include: LONI ...

CCB Special Interest Group on Automated Pipeline Workflows for Neuroimaging Data Analysis SIG Home CCB SIG Meeting Calendar CCB SIGFlow site Inside CCB (password ...

Surface Warping Protocol This page documents the Surface Warping Protocol. Given a collection of surfaces and anatomical contours on those surfaces, this process ...

A collection of questions and answers about the surface warp protocol workflows. TOC{depth "2"} How does the number of curves included affect the resulting surface ...

text of MapContour follows, in case testing proves destructive... 19 aug 08 !MapContour Maps a contour according to a transform defined by the corrospondences of the ...

CCB !UcfReorder Project The human Hippocampus is frequently represeted as a set of contours drawn in parallel planes that intersect the Hippocampus. Analyses of these ...

Virtual File System Browser It is common for data files to reside on computer file systems that are not connected to the computer on which the work is being performed ...

CCB Web Information Sharing Environment (WISE) CCB Wiki Homepage CCB Main Web Page CCB Shape Resources Individual Project Pages HCP iTools $ CCB Announcements: CCB ...

CCB Web Preferences The following settings are web preferences of the CCB web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...

Statistics for CCB Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 39584 153 15 ...

CCB !WorldCoordToVoxelValue This application reads an image volume and a surface that is create from the image volume, and creates output surface whose vertex attribute ...