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, 10 May 2012 14:22:23 -0400 Thu, 10 May 2012 14:22:23 -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/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/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/852 Unlike the measure of the area in 2D or of the volume in 3D, the perimeter and the surface are not easily measurable in a discretized image. In this article we describe a method based on the Crofton formula to measure those two parameters in a discritized image. The accuracy of the method is discussed and tested on several known objects. An algorithm based on the run-length encoding of binary objects is presented and compared to other approaches. An implementation is provided and integrated in the LabelObject/LabelMap framework contributed earlier by the authors. Tue, 21 Feb 2012 10:35:12 -0500 http://www.insight-journal.org//browse/publication/860 This document describes the workflow for unwarping structural MR images, in particular T1-weighted SPGR and MP-RAGE scans, using reference scans of the Magphan(R) EMR051 Quantitative Imaging Phantom (a.k.a. ADNI Phantom) and the tools of the Computational Morphometry Toolkit (CMTK). Fri, 05 Oct 2012 00:00:00 -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. Thu, 05 Jan 2012 00:00:00 -0500