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Praful Agrawal
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README.md

Shapeworks Command Line Tools

The ShapeWorks software is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.
Table of Contents

Aknowledgements

If you use ShapeWorks in work that leads to published research, we humbly ask that you add the following to the 'Acknowledgments' section of your paper: "This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant number P41GM103545."

Relevant Papers

The following selected papers give background on the methods used in ShapeWorks and a sample of the areas ShapeWorks has been applied:

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

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

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.

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.

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.

Requirements

Setting up the source code

  • git clone https://github.com/SCIInstitute/shapeworks.git

  • git submodule init

  • git submodule update

  • cd ShapeWorks-Prep

  • git checkout master

  • git submodule init

  • git submodule update

  • cd Source/CommonLibraries/fim_v4

  • git checkout master

  • cd ../ShapeWorks-Post

  • git checkout master

  • cd ../ShapeWorks-Run

  • git checkout master

  • git submodule init

  • git submodule update

  • cd source/fim_v4

  • git checkout master

Building

  • Set ITK, VTK and VXL paths in CMakeLists.txt in shapeworks repo
  • Create a build directory for shapeworks,
  • cd shapeworks-build
  • ccmake path-to-shapeworks-repo
  • set CMake flags ON/OFF for the required tools
  • set CMAKE_INSTALL_PREFIX to install all binaries at one place (optional)
  • configure
  • generate
  • make -j4
  • make install (only if CMAKE_INSTALL_PREFIX is provided)

Contact and Bug Reports

Please email any questions to Shapeworks-users@sci.utah.edu . If there problems or bugs, please report them using the issue tracker on GitHub. This includes feature requests. Feel free to add improvements using git pull requests.