2009 Winter Project Week ShapePipeline

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Key Investigators

  • Univ Utah, SCI Institute: Manasi Datar, Josh Cates, Ross Whitaker
  • Kitware: Stephen Aylward
  • UNC: Martin Styner


We will investigate the use of BatchMake for automating and packaging our particle-based shape analysis pipeline. Major tasks include learning to use BatchMake, and designing compatible command-line interfaces for our existing software.

Approach, Plan

Our goal during project week is to spec out a design and API for a shape analysis pipeline that strings together a number of our existing software tools. If time allows, we will also construct a prototype system. Existing code that we hope to convert for use by BatchMake includes preprocessing routines, correspondence optimization routines, and visualization tools.


Create individual Batchmake scripts for the various components identified during discussions with the UNC group
String these (as required) into a master Batchmake script to run a customized pipeline
As a separate step, integrate these into Slicer3 as command line modules

Created a prototype Batchmake script which:
requires the user to set the data directory
dynamically creates the parameter file required for one of the pre-processing operations
runs the pre-processing operation on all images present in the data directory

1. The command appendFile(...) is used to create the parameter file dynamically - unable to print '(' and ')' to the file - e.g. appendFile('<path>/xyz.params','(inputs\n') does not work
2. What are the components that need to be bundled with this script when distributing it ?


  • J Cates, P T Fletcher, M Styner, H Hazlett, R Whitaker. Particle-Based Shape Analysis of Multi-Object Complexes. Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08), to appear.
  • J Cates, P T Fletcher, Z Warnock, R Whitaker. A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 512-516, 2008.
  • I Oguz, J Cates, P T Fletcher, R Whitaker, D Cool, S Aylward, M Styner. Entropy-Based Particle Systems and Local Features for Cortical Correspondence Optimization Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 1637-1641, 2008.
  • J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. Shape Modeling and Analysis with Entropy-Based Particle Systems. Information Processing in Medical Imaging IPMI 2007, LNCS 4584, pp. 333-345, 2007.
  • J Cates, P T Fletcher, R Whitaker. Entropy-Based Particle Systems for Shape Correspondence. Mathematical Foundations of Computational Anatomy Workshop, MICCAI 2006. pp. 90-99 Oct 2006. pdf