Projects:ARRA:SlicerEM:AtlasCreator:Groupwise

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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
      • Daniel waits for the GIT repository from Jeremy
        • Run some tests
    • If Congeal doesn't compile cross platform then we could use the Slicer extension system as a backup
  • 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.
    • File formats:
      • Congeal supports NIfTI-1 file format
      • Slicer does too :)
      • 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 all:
    • should the wrapper in Step 2/3 be a simple bash script (downside might be no platform independency) or an executable (Daniel)
      • If an executable, should it be written using the Slicer Execution Model which generates a GUI automatically? This GUI would be separate from our AtlasCreator module and would list all parameters.
  • For Kilian:
    • How does this effort coordinate with the integration of PCA? Which one has higher priority? (Daniel)
      • PCA will sit on top of this. This effort is an alternative to the registration stage. (Daniel after talking to Kilian)
  • For Jeremy:
    • Please send the code after you are done cleaning up (Daniel)
  • For Daniel: