# Relevant Papers

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The following selected papers give background on the methods used in ShapeWorks, and a sample of the areas ShapeWorks has been applied:
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M. Jacxsens, S. Elhabian, S. Brady, P. Chalmers, R. Tashjian, and H. Henninger. "Coracoacromial morphology: a contributor to recurrent traumatic anterior glenohumeral instability," Journal of Shoulder and Elbow Surgery, 1:1316-1325, 2019.
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P. R. Atkins, Y. Shin, P. Agrawal, S. Y. Elhabian, R. T. Whitaker, J. A. Weiss, S. K. Aoki, C. L. Peters ,and A. E.  Anderson. "Which Two-dimensional Radiographic Measurements of Cam Femoroacetabular Impingement Best Describe the Three-dimensional Shape of the Proximal Femur?," Clinical Orthopaedics and Related Research, 477(1):242–253, 2019.
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T. Sodergren, R. Bhalodia, R. Whitaker, J. Cates, N. Marrouche, and S. Elhabian. "Mixture modeling of global shape priors and autoencoding local intensity priors for left atrium segmentation," In STACOM- MICCAI: Statistical Atlases and Computational Modeling of the Heart workshop, page in press. Springer, 2018.
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A. Goparaju, I. Csecs, A. Morris, E. Kholmovski, N. Marrouche, R. Whitaker, and S. Elhabian. "On the Evaluation and Validation of Off-the-Shelf Statistical Shape Modeling Tools: A Clinical Application," In International Workshop on Shape in Medical Imaging, pages 14–27. Springer, 2018.
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E. T. Bieging, A. Morris, B. D. Wilson, C. J. McGann, N. F. Marrouche, and J. Cates. "Left atrial shape predicts recurrence after atrial fibrillation catheter ablation," Journal of Cardiovascular Electrophysiology, 2018.
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P. R. Atkins, S. Y. Elhabian, P. Agrawal, M. D. Harris, R. T. Whitaker, J. A. Weiss, C. L. Peters, and A. E. Anderson. "Quantitative comparison of cortical bone thickness using correspondence-based shape modeling in patients with cam femoroacetabular impingement," Journal of Orthopaedic Research, 35(8):1743–1753, 2017.
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J. Cates, L. Nevell, S. I. Prajapati, L. D. Nelon, J. Y. Chang, M. E. Randolph, B. Wood, C. Keller, and R. T. Whitaker. "Shape analysis of the basioccipital bone in Pax7-deficient mice," Scientific Reports, 7(1):17955, 2017.
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J. Cates, S. Elhabian, and R. Whitaker. "ShapeWorks: particle-based shape correspondence and visualization software," In G. Zheng, S. Li, and G. Szekely, editors, Statistical Shape and Deformation Analysis: Methods, Implementation and Applications, 1st Edition, chapter 10. Academic Press, 2017.
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P. Agrawal, S.Y. Elhabian, R.T. Whitaker, "Learning Deep Features for Automated Placement of Correspondence Points on Ensembles of Complex Shapes," In International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 185-193. Springer, Cham, 2017.
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S. Sultana, P. Agrawal, S. Elhabian, R. Whitaker, T. Rashid, J. Blatt, J. Cetas, and M. Audette. "Towards a statistical shape-aware deformable contour model for cranial nerve identification," In Workshop on Clinical Image-Based Procedures, pages 68–76. Springer, 2016.
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J. Cates, E. Bieging, A. Morris, G. Gardner, N. Akoum, E. Kholmovski, N. Marrouche, C. McGann, and R. S. MacLeod. "Computational shape models characterize shape change of the left atrium in atrial fibrillation," Clinical Medicine Insights. Cardiology, 8(Suppl 1):99, 2015.
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Ken Museth. "VDB: High-resolution sparse volumes with dynamic topology" ACM Transactions on Graphics, July 2013, Article No.: 27
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M. Datar, I. Lyu, S. Kim, J. Cates, M. Styner, R. Whitaker. "Geodesic distances to landmarks for dense correspondence on ensembles of complex shapes," In International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer, Berlin, Heidelberg, pp. 19-26, 2013.
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M.D. Harris, M. Datar, R.T. Whitaker, E.R. Jurrus, C.L. Peters, A.E. Anderson. 
"Statistical Shape Modeling of Cam Femoroacetabular Impingement," In Journal of Orthopaedic Research, 
Vol. 31, No. 10, pp. 1620--1626. 2013.
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K.B. Jones, M. Datar, S. Ravichandran, H. Jin, E. Jurrus, R.T. Whitaker, M.R. Capecchi. 
"Toward an Understanding of the Short Bone Phenotype Associated with Multiple Osteochondromas," 
In Journal of Orthopaedic Research, Vol. 31, No. 4, pp. 651--657. 2013.
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J. Cates, P.T. Fletcher, Z. Warnock, R.T. Whitaker. 
"A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with 
a Targeted Disruption of Hoxd11," In Proceedings of the 5th IEEE International Symposium 
on Biomedical Imaging (ISBI '08), pp. 512--516. 2008. DOI: 10.1109/ISBI.2008.4541045
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J. Cates, P.T. Fletcher, M. Styner, H. Hazlett, R.T. Whitaker. 
"Particle-Based Shape Analysis of Multi-Object Complexes," 
In Proceedings of the 11th International Conference on Medical Image Computing and 
Computer Assisted Intervention (MICCAI '08), Lecture Notes In Computer Science (LCNS), 
pp. 477--485. 2008. ISBN: 978-3-540-85987-1
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J. Cates, P. T. Fletcher, M. Styner, M. Shenton, and R. Whitaker. "Shape modeling and analysis with entropy-based particle systems," In Information Processing in Medical Imaging, pages 333–345. Springer, 2007.
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