2012 Project Week:BatchProcessing

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  Projects List

Key Investigators

• 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.

Objective

Batch processing with Slicer and Nipype

Approach, Plan

• 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.

Progress

• 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)

Delivery Mechanism

• Possibly nipype as an extension.
  • Need to resolve dependencies
  • Optionally require users to install independent version of scipy