{"version":1,"kind":"Article","sha256":"","slug":"111","location":"","dependencies":[],"doi":"10.54294/q3fj21","frontmatter":{"title":"Implementing the Automatic Generation of 3D Statistical Shape Models with ITK","abstract":"Statistical Shape Models are a popular method for segmenting three-dimensional medical images. To\r\nobtain the required landmark correspondences, various automatic approaches have been proposed. In\r\nthis work, we present an improved version of minimizing the description length (MDL) of the model. To\r\ninitialize the algorithm, we describe a method to distribute landmarks on the training shapes using a conformal\r\nparameterization function. Then, we introduce a novel procedure to modify landmark positions\r\nlocally without disturbing established correspondences. We employ a gradient descent optimization to\r\nminimize the MDL cost function, speeding up automatic model building by several orders of magnitude\r\nwhen compared to the original MDL approach. The necessary gradient information is estimated from\r\na singular value decomposition, a more accurate technique to calculate the PCA than the commonly\r\nused eigendecomposition of the covariance matrix. In this work, we first present a basic version where\r\nspatial locations are used in the MDL cost function; next, we introduce an extended version where any\r\ncombination of features can be used as a metric. As an example application, we present results based on\r\nlocal curvature measurements. Finally, we present results for synthetic and real-world datasets demonstrating\r\nthe efficiency of our procedures and give details about the implementation using the Insight\r\nToolkit (ITK).","license":"You are licensing your work to Kitware Inc. under the\nCreative Commons Attribution License Version 3.0.\n\nKitware Inc. agrees to the following:\n\nKitware is free\n * to copy, distribute, display, and perform the work\n * to make derivative works\n * to make commercial use of the work\n\nUnder the following conditions:\n\\\"by Attribution\\\" - Kitware must attribute the work in the manner specified by the author or licensor.\n\n * For any reuse or distribution, they must make clear to others the license terms of this work.\n * Any of these conditions can be waived if they get permission from the copyright holder.\n\nYour fair use and other rights are in no way affected by the above.\n\nThis is a human-readable summary of the Legal Code (the full license) available at\nhttp://creativecommons.org/licenses/by/3.0/legalcode","keywords":["Correspondence","Statistical Shape Analysis"],"authors":[{"name":"Heimann, Tobias","email":"t.heimann@dkfz-heidelberg.de","affiliations":[]},{"name":"Oguz, Ipek","email":"ipek@cs.unc.edu","affiliations":["UNC"],"corresponding":true},{"name":"Wolf, Ivo","email":"i.wolf@dkfz.de","affiliations":[]},{"name":"Styner, Martin","email":"styner@cs.unc.edu","affiliations":[]},{"name":"Meinzer, Hans-Peter","affiliations":[]}],"date_submitted":"2006-07-11T02:10:48Z","external_publication_id":111,"revision_cids":["bafkreihveoat6bd4jji72i4jhygeh4lauilvakx5pkq3l54deucvuzx3fm"],"github":"https://github.com/midas-journal/midas-journal-111.git"},"mdast":{"type":"root"},"downloads":[{"url":"https://ipfs.desci.com/ipfs/bafkreiah722xw4punswh6zujvb6c524jrukduidziqen6v7hnmx7e262wq","title":"root/insight-journal-metadata.json","filename":"insight-journal-metadata.json","extra":{"size_bytes":18603,"type":"file"}},{"url":"https://ipfs.desci.com/ipfs/bafkreiexh2pj4lukq7scbinq5ufwiaffs2lljotxi5yzyycvmiecif7lma","title":"root/comments.md","filename":"comments.md","extra":{"size_bytes":557,"type":"file"}},{"url":"https://ipfs.desci.com/ipfs/bafkreidq7mbshyouiachkwalijlcpf6c5vrrqmskfjdpsa7lbmtyj5m6ya","title":"root/reviews.md","filename":"reviews.md","extra":{"size_bytes":10790,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidmwujrbc2s3h2bnwm32hyrbh3o4hprd7oiihud7cnypu5ldsqsmi","title":"root/code/itkCorrespondences/CMakeLists.txt","filename":"CMakeLists.txt","extra":{"size_bytes":3321,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihnuhpyciumpkotn6mmagispdixkwqn2z373odk5427nnlxxor7b4","title":"root/code/itkCorrespondences/CMakeTemplate.txt","filename":"CMakeTemplate.txt","extra":{"size_bytes":1966,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreigycembjx55zwfcjixsdcshzwttnfaxdjyg2bh7oxgnf7vznqzioa","title":"root/code/itkCorrespondences/IJMacros.txt","filename":"IJMacros.txt","extra":{"size_bytes":3278,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreicrdg7wvhiwuwt3bn3xscqe64vrwxwrz46akqubus2zepzxsohpxu","title":"root/code/itkCorrespondences/ImageCompare.cxx","filename":"ImageCompare.cxx","extra":{"size_bytes":8430,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreifrwqcc4r44t6afp7glqaezkp7ikondgbqmrvnpk3ce5rq5yfwcwi","title":"root/code/itkCorrespondences/Readme-license.txt","filename":"Readme-license.txt","extra":{"size_bytes":191,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreia7ivalhmnqttuspz3e2ybvlcxtlft4oeuqfngitt7sg22yix6sfa","title":"root/code/itkCorrespondences/itkConformalSphericalParameterizationFilter.h","filename":"itkConformalSphericalParameterizationFilter.h","extra":{"size_bytes":5686,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreie3pe56xa4yl3qjy7gjxdzoqrhsmmidouygyx2bmhuw4gjhatg2ji","title":"root/code/itkCorrespondences/itkConformalSphericalParameterizationFilter.txx","filename":"itkConformalSphericalParameterizationFilter.txx","extra":{"size_bytes":13894,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihz2wbohzfzjgr47beqdfhtcqcmgzeqqzwg5wixgdus3hwqoiny6e","title":"root/code/itkCorrespondences/itkConformalSphericalParameterizationFilter.txx.bak","filename":"itkConformalSphericalParameterizationFilter.txx.bak","extra":{"size_bytes":13899,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreifyrbvu35fj5fxzyk6tnzrdp4onuuhicunpoucwwswpryeegbxgfa","title":"root/code/itkCorrespondences/itkGaussianWarpSphericalParameterizationFilter.h","filename":"itkGaussianWarpSphericalParameterizationFilter.h","extra":{"size_bytes":4785,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiapbnfq3rtjvql5ta3ciygjosi3ioxryxqo5lcpk4dkdn37l5dkqq","title":"root/code/itkCorrespondences/itkGaussianWarpSphericalParameterizationFilter.txx","filename":"itkGaussianWarpSphericalParameterizationFilter.txx","extra":{"size_bytes":6332,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreiabr7bgxwyoe7upg4rdeqbwxfapot56j3b6qmbljkdoit66i7ssla","title":"root/code/itkCorrespondences/itkGaussianWarpSphericalParameterizationFilter.txx.bak","filename":"itkGaussianWarpSphericalParameterizationFilter.txx.bak","extra":{"size_bytes":6312,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreihtaexosi2i2f4yxfc5xvggkxae4lquy3kdotc34ur2maaloeirla","title":"root/code/itkCorrespondences/itkIndexedTriangleMesh.h","filename":"itkIndexedTriangleMesh.h","extra":{"size_bytes":9716,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibquzg4dcaoamndif2ic6tcqjm6s7ux2sdz6kknv36lss4oosx2sy","title":"root/code/itkCorrespondences/itkIndexedTriangleMesh.txx","filename":"itkIndexedTriangleMesh.txx","extra":{"size_bytes":12212,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreibelqllur52r3tiuesnbpru2ypbztpahvg7dqgkpttya4l7tbunwa","title":"root/code/itkCorrespondences/itkIndexedTriangleMesh.txx.bak","filename":"itkIndexedTriangleMesh.txx.bak","extra":{"size_bytes":12298,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidx4yxrnaquo4gwcirgy3gxwafnwefad3unielrfl7qcpouqbyhxi","title":"root/code/itkCorrespondences/itkMeshASCIIReader.h","filename":"itkMeshASCIIReader.h","extra":{"size_bytes":3296,"type":"file"}},{"url":"https://pub.desci.com/ipfs/bafkreidzoqchsyfsnbnjbjoe7yg57qc7bwmdbzz4fuzpnh6djdezzbsmpa","title":"root/code/itkCorrespondences/itkMeshASCIIReader.txx","filename":"itkMeshASCIIReader.txx","extra":{"size_bytes":3002,"type":"file"}},{"url":"https://pub.desc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