Projects:ARRA:SlicerEM:AtlasCreator:Groupwise

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Integration of Groupwise Registration in the AtlasCreator

Action Plan

  • Step1 (until 04/01/11):
    • 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
        • Then, run some tests provided by Jeremy
    • If Congeal doesn't compile cross platform then we could use the Slicer extension system as a backup
  • Step 2 (until 04/01/11):
    • Daniel will write a wrapper to create Congeal config files by specifying command line arguments
      • Jeremy and Daniel will communicate if the "wrapper" fits Congeal's config needs and test the config files
    • File formats:
      • Congeal supports NIfTI-1 file format
      • Slicer does too :)
  • Step 3:
    • Daniel will modify the atlas creator so that he can access the wrapper
    • 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: