http://www.insight-journal.org The Insight Journal Copyright www.insight-journal.org http://www.insight-journal.org/images/IJLogo2.gif http://www.insight-journal.org Sun, 21 Dec 2008 21:26:30 -0500 Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/310 This technical note presents an alternative threading model for the Insight Toolkit. The existing ITK threading model is based on a "scatter / gather" model and divides work evenly amongst all threads. Though suitable for many filters, considerations such as memory allocation per thread are important in some classes of filters. We propose to use the ZThread (http://sourceforge.net/projects/zthread/) library to explore a threading model based on an execution pool. The ZThread library is a cross platform, open source thread abstraction library loosely based on Java's threading model. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/228 Morphological erosion and dilation filters employ a structuring function, with flat structuring functions being the most common example. This article will use the term ``parabolic'', but much of the literature uses ``quadratic'' structuring functions are less well known but theoretically very important and practically very useful. This paper briefly introduces morphology using parabolic structuring functions, describes the ITK classes used to implement them and includes a number of sample applications. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/309 In a surgical environment, there are many tools and objects (including the patient) being used. In a computer-aided surgery, the position of each of these tools in the operating room is very critical and generally will be tracked in their own coordinate systems. To show the surgeon a real time picture of the operating environment on a computer monitor, we need to know the position of each object with respect to one common coordinate system, which in turn can be achieved by knowing each coordinate system and the transforms between them. Image-Guided Surgical Toolkit is a software toolkit designed to enable biomedical researchers to rapidly prototype and create new applications for image-guided surgery. In IGSTK, in which the coordinate systems and the transforms are being successfully used, there is no central data structure or repository, which will hold all the coordinate systems and the transforms between them. Such a data structure could help the IGSTK software developers to have more confidence in the code they have written. This project develops a tool, which will create such a data structure and dynamically show the changes to it, to help such software developers to write better code. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/285 Although greyscale intensity values are primarily used in image data visualization oftentimes, due to the requirements of aesthetics (whether they be self-imposed or collaborator-suggested), mapping the greyscale image to a user-defined colormap is desired. In this paper, we propose a framework for inclusion in the ITK library for converting intensity-valued images to user-defined RGB colormap images. We also include several colormaps that can be readily applied for visualization of images in such programs as ITK-SNAP or can be used as examples for creating new colormaps. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/285 Although greyscale intensity values are primarily used in image data visualization oftentimes, due to the requirements of aesthetics (whether they be self-imposed or collaborator-suggested), mapping the greyscale image to a user-defined colormap is desired. In this paper, we propose a framework for inclusion in the ITK library for converting intensity-valued images to user-defined RGB colormap images. We also include several colormaps that can be readily applied for visualization of images in such programs as ITK-SNAP or can be used as examples for creating new colormaps. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/308 An implementation of the minimum error thresholding algorithm is presented. In this implementation, two versions of the minimum error thresholding algorithm are made available, one utilizing a Gaussian- and the other utilizing a Poisson- mixture model. Two ITK classes are created: The first one (MinErrorThresholdImageCalculator) is used to compute the threshold; the second (MinErrorThresholdImageFilter) is used as an image-thresholding filter. The results indicate code correctness and are comparable to those of Otsu’s thresholding algorithm. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/154 This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion's demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver framework. We show that this framework can be extended to handle diffeomorphic transformations. The source code is composed of a set of reusable ITK filters and classes. In addition to an overview of our implementation, we provide a small example program that allows the user to compare the different variants of the demons algorithm. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/154 This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion's demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver framework. We show that this framework can be extended to handle diffeomorphic transformations. The source code is composed of a set of reusable ITK filters and classes. In addition to an overview of our implementation, we provide a small example program that allows the user to compare the different variants of the demons algorithm. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/154 This article provides an implementation of our non-parametric diffeomorphic image registration algorithm generalizing Thirion's demons algorithm. Within the Insight Toolkit (ITK), the demons algorithm is implemented as part of the finite difference solver framework. We show that this framework can be extended to handle diffeomorphic transformations. The source code is composed of a set of reusable ITK filters and classes. In addition to an overview of our implementation, we provide a small example program that allows the user to compare the different variants of the demons algorithm. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/307 This document describes a new class for the Insight Toolkit~(ITK www.itk.org) for reading images across a network. Network access is handled by CURL (http://curl.haxx.se/libcurl/), an Open Source library for client-side URL transfer. CURL supports the FTP, FTPS, HTTP, HTTPS, SCP, SFTP, TFTP, TELNET, DICT, LDAP, LDAPS and FILE protocols. This paper is accompanied with source code and a test to load a NRRD file across the network and verify that is is read properly. Sun, 21 Dec 2008 21:26:30 -0500 http://www.insight-journal.org//browse/publication/307 This document describes a new class for the Insight Toolkit~(ITK www.itk.org) for reading images across a network. Network access is handled by CURL (http://curl.haxx.se/libcurl/), an Open Source library for client-side URL transfer. CURL supports the FTP, FTPS, HTTP, HTTPS, SCP, SFTP, TFTP, TELNET, DICT, LDAP, LDAPS and FILE protocols. This paper is accompanied with source code and a test to load a NRRD file across the network and verify that is is read properly. Sun, 21 Dec 2008 21:26:30 -0500