2012 Project Week:BatchProcessing
- MIT: Satra Ghosh
- Iowa: Hans Johnson
- Kitware: Jean-Christophe Fillion-Robin
- BWH: Andrey Fedorov
- Isomics: Steve Pieper
Various DBP projects and other users have requested the ability to automate large tasks and interoperate with other image analysis tools. Nipype is a solution that is proving useful in this domain so we would like to further refine it as an option to the na-mic community.
Batch processing with Slicer and Nipype
- Work on HD use cases to improve batch processing framework
- Develop example workflows as templates for other projects
- Identify and if possible fix any issues that prevent smooth integration of slicer modules into batch workflows.
- Satra and Hans resolved a number of issues and are now processing multi-hundred dataset studies (building on fixes from Chris)
- HD Processing scripts can be example for others integrating slicer modules with other neuroimaging tools with data in XNAT
- This project drove a wide discussion about further leveraging python code in slicer (ipython, ScipPy, PyXNAT, etc)
- Possibly nipype as an extension.
- Need to resolve dependencies
- Optionally require users to install independent version of scipy