EMSegmenter-CreateTask

From Slicer Wiki
Revision as of 21:34, 1 December 2010 by Belhachemi (talk | contribs) (Created page with '=Task creation process - for developer= The goal is to create a task with the name 'Hello World' After following the instructions below the new task will consist of following fi…')
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search
Home < EMSegmenter-CreateTask

Task creation process - for developer

The goal is to create a task with the name 'Hello World'

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

./Slicer3/Modules/EMSegment/Tasks/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'.