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>

Step 1: Create Template without Preprocessing

• 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
• Now follow up to Step 9 our [EMSegmenter advanced tutorial EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf ] with the following modifcations:
  • 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, GM, ... )
  • Load atlas files only from <DIR>/Hello-World/
  • for Slicer 3 only: generate mean and covariance values
• At step 9/9. click on 'Create Template File' and save the file under <DIR>/Hello-World.mrml. Hello-World.mrml now only consists of nodes needed to parameterize the EMSegmenter.
• Close Slicer

Step 2: Include Preprocessing (Optional)

For templates that do not include atlas files the following instructions are optional

• Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl
• Edit <DIR>/Hello-World.tcl to customize/modify the pre-processing pipeline
• Edit <DIR>/Hello-World.mrml to use your own pre-processing by replacing <EMSGlobalParameters ... TclTaskFilename="GenericTask.tcl" ... > with <EMSGlobalParameters ... TclTaskFilename="Hello-World.tcl" ...>

Step 3: Update Slicer Build (only for Slicer 3)

touch <DIR>/../CMakeLists.txt and do a 'make' to copy the new files into the binary directory

When you start Slicer again 'Hello World' should appear in the task list of the EMSegmenter.

EMSegmenter-Task Template

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