EMSegmenter-CreateTask

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Task creation process - for developer

The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define

<DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and 
        for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)

After following the instructions below the new task will consist of following files:

<DIR>/Hello-World.mrml
<DIR>/Hello-World.tcl
<DIR>/Hello-World/<atlas_file_1>
[...]
<DIR>/Hello-World/<atlas_file_N>

• Create a new directory <DIR>/Hello-World

• Copy the atlas files for air, CSF, greymatter, whitematter, and T1 from <DIR>/MRI-Human-Brain into this directory.

• Start Slicer
• Set Scene of Slicer to <DIR> by saving scene in <DIR>. Afterwards remove resulting mrml file from <DIR> as it is not needed anymore

• Switch to the EMSegmenter module
• Create new task
  • Name: Hello World
  • Pre-processing: None
• Basically follow our EMSegmenter advanced tutorial, but create a simple tree
  • load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
  • Add a channel, call it T1, assign MRIHumanBrain_T1_aligned
  • Create a simple anatomical tree (air and GM)
  • Load atlas files only from <DIR>/Hello-World/
  • generate mean and covariance values
  • specify node weights
• At step 9/9. click on 'Create Template File'
  • Save the file under <DIR>/Hello-World.mrml
  • The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.
• Close Slicer
• Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl
• Adjust this tcl file to include your pre-processing pipeline.
• edit <DIR>/Hello-World.tcl to specify your own pre-processing
• edit <DIR>/Hello-World.mrml to use your own pre-processing
  • - <EMS TclTaskFilename="GenericTask.tcl" ></EMS>
  • + <EMS TclTaskFilename="Hello-World.tcl" ></EMS>
• For Slicer 3 only :

touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory

The result of the process above can also be downloaded here: After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.

EMSegmenter-Task Template

Please use this wiki page as a template for you task specific Wiki page.