{"title":"The Image-based Vascular Analysis Toolkit (IvanTk)","authors":"I. Macía","doi":"10.54294/lyqifg","DOIUrl":"https://doi.org/10.54294/lyqifg","url":null,"abstract":"This document describes the Image-based Vascular Analysis Toolkit (IvanTk), a set of cross-platform C++ open source software libraries for the detection, extraction and modeling of vessels in 2D/3D medical images based on the Insight Toolkit. We provide an overview of the libraries and their purpose and describe their functional modules and future directions of the toolkit.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71188277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data.","authors":"Michael Bowers, L. Younes","doi":"10.54294/loekqj","DOIUrl":"https://doi.org/10.54294/loekqj","url":null,"abstract":"This document describes a contribution to the Insight Toolkit intended to support the analysis of the principal components of data sets, optionally point data associated with the vertices of a mesh. This paper is accompanied with the source code, input data, parameters and output data that we used for validating the implementation described in this paper. This adheres to the fundamental principle that scientific publications must facilitate reproducibility of the reported results.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"2012 1","pages":"878"},"PeriodicalIF":0.0,"publicationDate":"2013-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71188099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
I. Vidal-Migallón, O. Commowick, X. Pennec, J. Dauguet, T. Vercauteren
{"title":"GPU and CPU implementation of Young - Van Vliet's Recursive Gaussian Smoothing Filter","authors":"I. Vidal-Migallón, O. Commowick, X. Pennec, J. Dauguet, T. Vercauteren","doi":"10.54294/cpyaig","DOIUrl":"https://doi.org/10.54294/cpyaig","url":null,"abstract":"This document describes an implementation for GPU and CPU of Young and Van Vliet’s recursive Gaussian smoothing as an external module for the Insight Toolkit ITK, version 4.* www.itk.org. In the absence of an OpenCL-capable platform, the code will run the CPU implementation as an alternative to the existing Deriche recursive Gaussian smoothing filter in ITK.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71184216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Laplacian Mesh Deformation","authors":"A. Gelas","doi":"10.54294/s91axg","DOIUrl":"https://doi.org/10.54294/s91axg","url":null,"abstract":"Deforming a 3D surface mesh while preserving its local detail is useful for editing anatomical atlases or for mesh based segmentation. This contribution introduces new classes for performing hard and soft constraints deformation in a flexible design which allows user to switch easily in between Laplacian discretization operators, area weighing and solvers. The usage of these new classes is demonstrated on a sphere.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71191457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Structural MRI Unwarping Using CMTK","authors":"T. Rohlfing","doi":"10.54294/d0pwqi","DOIUrl":"https://doi.org/10.54294/d0pwqi","url":null,"abstract":"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).","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71184452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Label Geometry Image Filter for Multiple Object Measurement","authors":"D. Padfield, James Miller","doi":"10.54294/saa3nn","DOIUrl":"https://doi.org/10.54294/saa3nn","url":null,"abstract":"The itkLabelGeometryImageFilter is a new ITK filter that enables the measurement of geometric features of labeled objects. It calculates features similar to the “regionprops” command of Matlab. It is related to the itkLabelStatisticsImageFilter in that both filters measure features of labeled masks. It differs, however, in that it measures geometric features of the objects themselves rather than statistics of image intensities under the masks defined by the objects. This document describes the mathematical background of the geometric features measured by this filter and describes the framework of the code, which is structured to enable easy expandability as new object features are desired.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71191495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Importing Contours from DICOM-RT Structure Sets with ITK4","authors":"J. Dowling","doi":"10.54294/5fj4z4","DOIUrl":"https://doi.org/10.54294/5fj4z4","url":null,"abstract":"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.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71180015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Parallel algorithms for erosion and dilation of label images.","authors":"R. Beare, P. Jackway","doi":"10.54294/3akpoz","DOIUrl":"https://doi.org/10.54294/3akpoz","url":null,"abstract":"It is sometimes useful to be able to apply binary morphological operations, such as erosions and dilations, to labelled images in a fashion that preserves the labels. This article introduces a specialised class implementing parallel methods described in beare et al [2011] that provide very fast dilations by circles and spheres of arbitary size. Comparisons with other implementations using currently available building blocks are also made.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71179596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Tubular Geodesics using Oriented Flux: An ITK Implementation","authors":"Fethallah Benmansour, Engin Türetken, P. Fua","doi":"10.54294/jdl70j","DOIUrl":"https://doi.org/10.54294/jdl70j","url":null,"abstract":"This document describes an ITK implementation of an interactive method for tracing curvilinear structures. The basic tools provided in this framework are an oriented flux-based tubularity measure and a geodesic path tracer that uses the fast marching algorithm. The framework is efficient and requires minimal user interaction to trace curvilinear structures such as vessels and neurites in 2D images and 3D image stacks.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71187460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Skull-Stripping Filter for ITK","authors":"S. Bauer, Thomas Fejes, M. Reyes","doi":"10.7892/BORIS.39690","DOIUrl":"https://doi.org/10.7892/BORIS.39690","url":null,"abstract":"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.","PeriodicalId":89491,"journal":{"name":"The insight journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71357402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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