2012 Project Week:BatchProcessing

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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.


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.


  • 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