Kenneth Johnson - Confidence Connected HW
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Kenneth Johnson's submission for the Open Source Software Practice course homework. Includes an implementation of Confidence Connected. Brain data, Normal007-T2.mha from MIDAS - Kitware is not included, as I don't have permission to redistribute it.

Reader/Writer for Analyze Object Maps for ITK
This document describes an addition to the Image IO Library of the Insight Toolkit (ITK). ITK has been able to read in Analyze image files but not the Analyze Object Maps that correspond to the images. Analyze Object maps define regions of interest that are [...]

Introduction to ITK Resample In-Place Image Filter
In this document we present an ITK image filter that outputs a new image with identical voxel contents but with modified physical space representation. The physical space representation of an image is modified to reflect the physical space transform on the [...]

Image Calculator
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ImageCalculator is a command line program for doing simple mathematical operations to a series of images and generating an new output image and basic statistics about the output image. The program uses the Insight Toolkit ( for file IO and [...]

BRAINSDemonWarp: An Applicaton to Perform  Demons Registration
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In this paper, a software application is introduced for image registration. BrainDemonsWarp is a com- mand line program using Thirion and diffeomorphic demons algorithms. The program takes in a template image and a target image along with other optional [...]

Diffeomorphic demons registration was widely used for medical image registration. This document describes the addition of mask processing mode with spatial objects for itkDiffeomorphicemonsRegistrationFilter when just considering the deformation field at the [...]

Affine Transformation for Landmark Based Registration Initializer in ITK
This document describes an affine transformation algorithm as an additional feature for landmark based registration in ITK The algorithm is based on the paper by Spath, H [1]. The author derives a set of linear equations from paired landmarks and [...]

ITK in Biomedical Research and Commercial Applications
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The Insight Segmentation and Registration Toolkit ( has become a standard in academia and industry for medical image analysis. In recent years, the ITK developers' community has focused on providing programming interfaces to ITK from Python, Java, [...]

BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit
The University of Iowa’s Psychiatric Iowa Neuroimaging Consortium (PINC) has developed a program for mutual information registration of 3D brain imaging data using ITK classes, called BRAINSFit. We have written a helper class, [...]

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