Projects:ARRA:SlicerEM:AtlasCreator:Groupwise

Back to AtlasCreator..

Integration of Groupwise Registration in the AtlasCreator

Action Plan

• Step1:
  • Daniel will get the code from Jeremy and dump it into our atlascreator/commandline directory
  • Daniel will compile the code under slicer - should you run into problems Jeremy is going to work on figuring them out with / for Daniel . If the code needs changes, Jeremy is responsible for implementing them
• Step 2:
  • all of us agree on an API
    • To reduce the overhead, a wrapper application should be fine as the API instead of modifying the Congeal code directly. This wrapper should support the following:
      • create a config file based on the commandline args passed to the wrapper in "arg value" pairs
      • should include default settings for not specified arguments which get written to the config file by default
      • should support specification of a filepath to output the config file
      • should support specification of the congeal executable
      • calls congeal with the config file path
    • Jeremy will provide the wrapper and Daniel will access the wrapper in the AtlasCreator module.
    • To be decided:
      • should the wrapper be a simple bash script (downside might be no platform independency) or a executable
      • if an executable, should it be written using the Slicer Execution Model which generates a GUI automatically?
  • File formats:
    • Congeal supports NIfTI-1 file format
    • The AtlasCreator supports all 3D Slicer supported file formats but uses the NRRD file format to communicate with the registration and resampling tools
    • Daniel will investigate how to use the NIFTI file format in our Atlas Creator Module and will provide a converter
• Step 3:
  • Daniel modifies the atlas creator so that he can access Jeremy's command line
  • Jeremy modifies his command line interface
• Step 4:
  • Daniel creates an advanced tab in our tool that makes some of the key parameter visible to user and modify the docu accordingly
  • Jeremy will give us a link or modify our wiki page with respect to the meaning of specific parameters , ....
• Step 5:
  • Be happy

Questions

• For Kilian:
  • How does this effort coordinate with the integration of PCA? Which one has higher priority?
• For Jeremy:
• For Daniel: