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
- Daniel waits for the GIT repository from Jeremy
- 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.
- 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:
- 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
- all of us agree on an API
- 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
- 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.
- should the wrapper in Step 2/3 be a simple bash script (downside might be no platform independency) or an executable (Daniel)
- 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)
- How does this effort coordinate with the integration of PCA? Which one has higher priority? (Daniel)
- For Jeremy:
- Please send the code after you are done cleaning up (Daniel)
- For Daniel:
