Difference between revisions of "Projects:ARRA:SlicerEM:AtlasCreator:Groupwise"

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== Action Plan ==
 
== Action Plan ==
−
* Step1:
+
* Step1 (until 04/01/11):
 
** Daniel will get the code from Jeremy and dump it into our atlascreator/commandline directory
 
** 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 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
 
*** Daniel waits for the GIT repository from Jeremy
−
**** Run some tests
+
**** 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
 
** If Congeal doesn't compile cross platform then we could use the Slicer extension system as a backup
−
* Step 2:
+
* Step 2 (until 04/01/11):
−
** all of us agree on an API
+
** Daniel will write a wrapper to create Congeal config files by specifying command line arguments  
−
***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
 
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**** calls congeal with the config file path
 
−
***Jeremy will provide the wrapper and Daniel will access the wrapper in the AtlasCreator module.
 
 
** File formats:
 
** File formats:
 
*** Congeal supports NIfTI-1 file format
 
*** Congeal supports NIfTI-1 file format
 
*** Slicer does too :)
 
*** 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:
 
* Step 3:
 
** Daniel modifies the atlas creator so that he can access Jeremy's command line
 
** Daniel modifies the atlas creator so that he can access Jeremy's command line

Revision as of 03:01, 26 March 2011

Home < Projects:ARRA:SlicerEM:AtlasCreator:Groupwise

Back to AtlasCreator..

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
    • File formats:
      • Congeal supports NIfTI-1 file format
      • Slicer does too :)
  • 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:
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