Difference between revisions of "2009 Winter Project Week ShapePipeline"
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===Key Investigators=== | ===Key Investigators=== | ||
* Univ Utah, SCI Institute: Manasi Datar, Josh Cates, Ross Whitaker | * Univ Utah, SCI Institute: Manasi Datar, Josh Cates, Ross Whitaker | ||
| − | + | * Kitware: Stephen Aylward | |
| + | * UNC: Martin Styner | ||
<div style="margin: 20px;"> | <div style="margin: 20px;"> | ||
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<h1>Progress</h1> | <h1>Progress</h1> | ||
| + | Strategy:<br> | ||
| + | Create individual Batchmake scripts for the various components identified during discussions with the UNC group <br> | ||
| + | String these (as required) into a master Batchmake script to run a customized pipeline <br> | ||
| + | As a separate step, integrate these into Slicer3 as command line modules <br> | ||
| + | |||
| + | Action: <br> | ||
| + | Created a prototype Batchmake script which: <br> | ||
| + | requires the user to set the data directory <br> | ||
| + | dynamically creates the parameter file required for one of the pre-processing operations <br> | ||
| + | runs the pre-processing operation on all images present in the data directory <br> | ||
| + | |||
| + | Problems: <br> | ||
| + | 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 <br> | ||
| + | 2. What are the components that need to be bundled with this script when distributing it ? <br> | ||
</div> | </div> | ||
Latest revision as of 15:25, 9 January 2009
Home < 2009 Winter Project Week ShapePipeline Return to Project Week Main Page |
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
