EMSegmenter-CreateTask

Return to EMSegmenter Task Overview Page

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
./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1>
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_2>
[...]
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_i>
[...]
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_N>

• Create a new directory ./Slicer3/Modules/EMSegment/Tasks/Hello-World

• Copy the atlas files for air, GM, T1 into this directory.

• Start Slicer
• 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 ./Slicer3/Modules/EMSegment/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 ./Slicer3/Modules/EMSegment/Tasks/Hello-World/
  • generate mean and covariance values
  • specify node weights
• At step 9/9. click on 'Create Template File'
  • Save the file under ./Slicer3/Modules/EMSegment/Tasks/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 ./Slicer3/Modules/EMSegment/Tasks/Template.tcl to ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
• Adjust this tcl file to include your pre-processing pipeline.
• edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl to specify your own pre-processing
• edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml to use your own pre-processing
  • - <EMS TclTaskFilename="GenericTask.tcl" ></EMS>
  • + <EMS TclTaskFilename="Hello-World.tcl" ></EMS>
• 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.