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 Thu, 16 May 2013 14:39:33 -0400 Thu, 16 May 2013 14:39:33 -0400 http://www.insight-journal.org//browse/publication/859 Skull-stripping (or brain extraction) is an important pre-processing step in neuroimage analysis. This document describes a skull-stripping filter implemented using the Insight Toolkit ITK, which we named itk::StripTsImageFilter. It is a composite filter based on existing ITK classes. The filter has been implemented with usability, robustness, speed and versatility in mind, rather than accuracy. This makes it useful for many pre-processing tasks in neuroimage analysis. This paper is accompanied by the source code, input data and a testing environment. Mon, 30 Apr 2012 12:06:59 -0400 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/854 This paper documents on-going work to facilitate ITK-based processing and 3D Slicer scene management in ParaView. We believe this will broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView. In this paper, we present KWScene, an open source cross-platform library that is being developed to support implementation of these types of plugins. We describe the overall design of the library and provide implementation details and conclude by presenting a concrete example that demonstrates the use of the KWScene library in computational anatomy research at Johns Hopkins Center for Imaging Science. Tue, 28 Feb 2012 13:23:47 -0500 http://www.insight-journal.org//browse/publication/858 Open interfaces/frameworks increase the pace of research and discovery by promoting collaborations within and between clinicians, biomedical engineers, and software developers. These systems usually employ modular architectures to model the complexity involved in surgical assistance systems. Hence, standards are critical to allow for cross-framework interoperability of systems, and modules. SACAI workshop aims to establish a forum for discussing systems and architectures for computer assisted discussing intervention (CAI) applications. Continuing the success of the series, the workshop will focus on open interfaces, interoperability, and standards. In addition, this year, we will discuss clinical applications and future directions of CAI systems and frameworks. The workshop will continue to include the robust discussion between industry and academia. Fri, 27 Apr 2012 16:39:05 -0400 http://www.insight-journal.org//browse/publication/857 In this document, we report our activities on the subcontract with Kitware where we carefully study the upcoming ITK v4 pipeline design to help the ITK v4 development team to add support of modern dataflow architectures to ITK. Fri, 27 Apr 2012 01:36:27 -0400 http://www.insight-journal.org//browse/publication/887 This paper presents code for reading contours from DICOM RT structure set files into binary labels. This is a common requirement for transferring expert manual segmentations from radiotherapy treatment planning software into external image analysis environments (such as ITK). An implementation of RT structure set importing is provided with sample data from a prostate cancer radiotherapy planning volume. This is an update to the 2009 Insight Journal paper "Importing Contours from DICOM-RT Structure Sets" which worked with ITK 3.x and a local GDCM2 install. Updates: Mar 2013 Now correctly handles holes within structures. Thanks to Sebastian Steger for the code fix. Tue, 26 Feb 2013 19:07:03 -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/870 This document describes the implementation in ITK of the Incremental Delaunay Triangulation algorithm. Using the Straight Walk in Triangulation function, the exact discrete geometrical orientation predicate, and the itk::QuadEdgeMesh API of ITK , we propose a geometrically exact and robust implementation that, from a given 2-dimensional itk::PointSet, incrementally constructs the corresponding 2-dimensional Delaunay Triangulation as an itk::QuadEdgeMesh. Thu, 26 Jul 2012 04:45:34 -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/871 This paper describes the Statismo framework, which is a framework for PCA based statistical models.Statistical models are used to describe the variability of an object within a population, learned from a set of training samples. Originally developed to model shapes, statistical models are now increasingly used to model the variation in different kind of data, such as for example images, volumetric meshes or deformation fields. Statismo has been developed with the following main goals in mind: 1) To provide generic tools for learning different kinds of PCA based statistical models, such as shape, appearance or deformations models. 2) To make the exchange of such models easier among different research groups and to improve the reproducibility of the models. 3) To allow for easy integration of new methods for model building into the framework. To achieve the first goal, we have abstracted all the aspects that are specific to a given model and data representation, into a user defined class. This does not only make it possible to use Statismo to create different kinds of PCA models, but also allows Statismo to be used with any toolkit and data format. To facilitate data exchange, Statismo defines a storage format based on HDF5, which includes all the information necessary to use the model, as well as meta-data about the model creation, which helps to make model building reproducible. The last goal is achieved by providing a clear separation between data management, model building and model representation. In addition to the standard method for building PCA models, Statismo already includes two recently proposed algorithms for building conditional models, as well as convenience tools for facilitating cross-validation studies. Although Statismo has been designed to be independent of a particular toolkit, special efforts have been made to make it directly useful for VTK and ITK. Besides supporting model building for most data representations used by VTK and ITK, it also provides an ITK transform class, which allows for the integration of Statismo with the ITK registration framework. This leverages the efforts from the ITK project to readily access powerful methods for model fitting. Tue, 24 Jul 2012 08:47:23 -0400