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

Objective

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.

Progress

Strategy:
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

Action:
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

Problems:
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 ?

References

• 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