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
+
** <strike>Daniel will get the code from Jeremy and dump it into our atlascreator/commandline directory</strike>
−
** 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
+
** <strike>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</strike>
−
*** Daniel waits for the GIT repository from Jeremy
+
*** <strike>Daniel waits for the GIT repository from Jeremy</strike>
−
**** 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
+
** <strike>Daniel will write a wrapper to create Congeal config files by specifying command line arguments </strike>
−
***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:
+
*** <strike>Jeremy and Daniel will communicate if the "wrapper" fits Congeal's config needs and test the config files</strike>
−
**** 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:
 
** 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
+
* Step 3 (until 04/06/11):
−
*** Daniel will investigate how to use the NIFTI file format in our Atlas Creator Module and will provide a converter
+
** Daniel will modify the atlas creator so that he can access the wrapper
−
* Step 3:
+
* Step 4 (until 08/04/11):
−
** 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
 
** 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 , ....
 
** Jeremy will give us a link or modify our wiki page with respect to the meaning of specific parameters , ....
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== Questions ==
 
== Questions ==
 
* For all:
 
* 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:
 
* For Kilian:
 
** How does this effort coordinate with the integration of PCA? Which one has higher priority? (Daniel)
 
** 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)
 
*** PCA will sit on top of this. This effort is an alternative to the registration stage. (Daniel after talking to Kilian)
 
* For Jeremy:
 
* For Jeremy:
−
** Please send the code after you are done cleaning up (Daniel)
+
** <strike>Please send the code after you are done cleaning up (Daniel)</strike>
 
* For Daniel:
 
* For Daniel:

Latest revision as of 20:58, 13 April 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
      • 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 (until 04/06/11):
    • Daniel will modify the atlas creator so that he can access the wrapper
  • Step 4 (until 08/04/11):
    • 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:
  • 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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