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.
      • Link to the Slicer Execution Model: http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation
      • If not, there will be only limited parameters exposed in the AtlasCreator GUI's advanced panel
• 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: