http://www.insight-journal.org The MIDAS journal Copyright www.insight-journal.org http://www.insight-journal.org/images/IJLogo2.gif http://www.insight-journal.org Fri, 13 Jan 2012 20:15:24 -0500 Fri, 13 Jan 2012 20:15:24 -0500 http://www.insight-journal.org//browse/publication/843 This document describes the implementation in ITK of the "point in circle" geometrical predicate. Based on Jonathan Shewchuk's work which implements an exact version of the predicate using standard floating point types and arithmetic, the implementation consist of an ITK wrapper around the public domain C routines made available by the author of the precedent paper. Wrapper using itk::PointSet, itk:CellInterface and itk:Mesh / itk:QuadEdgeMesh APIs are provided along with corresponding examples which should provide enough details for users to directly copy paste code in their application. The application in mind for us is an exact and robust implementation of a delaunay triangulation / voronoi tesselation in ITK, and will be presented in a separate paper. Mon, 28 Nov 2011 22:55:37 -0500 http://www.insight-journal.org//browse/publication/840 A contribution to the Insight Toolkit intended to support the process of statistical analysis in Computational Anatomy. The methods included here operate on open or closed triagulated surfaces (represented by a QuadEdgeMesh). The filter assigns basis function values as Point Data on each vertex of the Mesh. This paper is accompanied with the source code, input data, parameters and output data that we used for validating the algorithm described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results. Wed, 26 Oct 2011 15:43:54 -0400 http://www.insight-journal.org//browse/publication/836 This document presents a GUI application to manually select corresponding points in two data sets. The data sets can each be either an image or a point cloud. If both data sets are images, the functionality is equivalent to Matlab's 'cpselect' function. There are many uses of selecting correspondences. If both data sets are images, the correspondences can be used to compute the fundamental matrix, or to perform registration. If both data sets are point clouds, the correspondences can be used to compute a landmark transformation. If one data set is an image and the other is a point cloud, the camera matrix relating the two can be computed. Fri, 26 Aug 2011 08:32:14 -0400 http://www.insight-journal.org//browse/publication/835 This code provides an implementation of a simple technique to fill small holes in an image. We use a multi-pass method that fills pixels on the border of a hole with the average of its non-hole 8-connected neighbors. This process is repeated until all holes are filled. The code is available here: https://github.com/daviddoria/SmallHoleFiller Wed, 24 Aug 2011 15:09:29 -0400 http://www.insight-journal.org//browse/publication/839 The Hausdorff distance is a measure of the distance between sets of points. There are many advantages to using this metric compared to other similarity measures. This document describes a VTK class for computing the Hausdorff Distance between two sets of points. The main contribution, compared to other implementations, lies in the definition of the distance not only to the closest point but to the closest point in the represented surface, which yields an accurate measure even between undersampled surfaces. This is achieved by implementing a point-to-cell distance instead of a point-to-point. Furthermore, a plugin for ParaView was implemented, which is also available with the code. After introducing the interest of this distance, the VTK code is explained and illustrated with some examples. Thu, 22 Sep 2011 13:00:29 -0400 http://www.insight-journal.org//browse/publication/846 We have implemented filters for computing phase symmetry (PS) in ITK using steerable filters computed and applied in the Fourier domain. In some recent publications, phase symmetry has been shown to be a useful pre-processing measure for performing image registration and segmentation. Matlab implementations of the code are currently available, but may be slower than C++ versions and most importantly, do not work with volumetric (3D) data. In this paper we briefly provide background information and list some applications of PS filters from the literature. We then provide instructions and examples of how to use the classes and executables. Wed, 31 Dec 1969 19:00:00 -0500 http://www.insight-journal.org//browse/publication/845 In this document we present the implementation of three fuzzy clustering algorithms using the Insight Toolkit ITK. Firstly, we developed the conventional Fuzzy C-Means that will serve as the basis for the rest of the proposed algorithms. The next algorithms are the FCM with spatial constraints based on kernel-induced distance and the Modified Spatial Kernelized Fuzzy C-Means. Both of these introduce a Kernel function, replacing the Euclidean distance of the FCM, and spatial information into the membership function. These algorithms have been implemented in a threaded version to take advantage of the multicore processors. Moreover, providing an useful implementation make it possible that classes work with 2D/3D images, different kernels and spatial shapes. We included the source code as well as different 2D/3D examples, using several input parameters for the algorithms and obtaining the results generated on 2D/3D CT lung studies. Wed, 01 Feb 2012 00:00:00 -0500 http://www.insight-journal.org//browse/publication/111 Statistical Shape Models are a popular method for segmenting three-dimensional medical images. To obtain the required landmark correspondences, various automatic approaches have been proposed. In this work, we present an improved version of minimizing the description length (MDL) of the model. To initialize the algorithm, we describe a method to distribute landmarks on the training shapes using a conformal parameterization function. Then, we introduce a novel procedure to modify landmark positions locally without disturbing established correspondences. We employ a gradient descent optimization to minimize the MDL cost function, speeding up automatic model building by several orders of magnitude when compared to the original MDL approach. The necessary gradient information is estimated from a singular value decomposition, a more accurate technique to calculate the PCA than the commonly used eigendecomposition of the covariance matrix. In this work, we first present a basic version where spatial locations are used in the MDL cost function; next, we introduce an extended version where any combination of features can be used as a metric. As an example application, we present results based on local curvature measurements. Finally, we present results for synthetic and real-world datasets demonstrating the efficiency of our procedures and give details about the implementation using the Insight Toolkit (ITK). Mon, 12 Dec 2011 00:00:00 -0500 http://www.insight-journal.org//browse/publication/774 This document describes the implementation of a class for the Insight Toolkit (ITK) that takes an image with multi-component pixels and outputs a scalar image for each component. This can be useful when examining images of vectors, tensors, etc. This filter may be easier to use and require fewer pixel visitations than an itk::ImageAdaptor with a similar purpose, but it requires additional memory allocation. Wed, 12 Oct 2011 00:00:00 -0400 http://www.insight-journal.org//browse/publication/820 This document presents a VTK wrapper of an extracted portion of ‘3DTK - The 3D Toolkit’ (http://threedtk.de) to enable a developer to find planes in 3D point cloud data. Wed, 31 Dec 1969 19:00:00 -0500 http://www.insight-journal.org//browse/publication/820 This document presents a VTK wrapper of an extracted portion of ‘3DTK - The 3D Toolkit’ (http://threedtk.de) to enable a developer to find planes in 3D point cloud data. Wed, 31 Dec 1969 19:00:00 -0500