How to Add a Python Script for Brain Extraction in a Custom 3D Slicer Template

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Hello everyone,

I want to integrate a Python script for brain extraction into a custom 3D Slicer template created using Kitware’s SlicerCAT framework. My goal is to add my own scripted module and make it functional within the custom application.

Could anyone guide me on how to:

  1. Properly add a Python-scripted module to the custom template?
  2. Ensure the script runs correctly within 3D Slicer?
  3. Build and test the changes effectively?

Additionally, I have two solution (.sln) files:

  • build/safe.sln
  • build/slicer_build/slicer.sln

Which one should I open in Visual Studio to see my changes and work on the project?

Any help, guidance, or references would be greatly appreciated. Thanks in advance!

2

Hey,

I’m still learning about creating modules, but I found a YouTube playlist that clarified many concepts and provides a great starting point. It covers topics like module templates and setting up/debugging with IDE:

YouTube Playlist
Start with tutorial 1

I recommend downloading the Python debugger extension first and then following along with the playlist. I also use vscode so i would recommend following the python debugger documentation instead because the vids uses pycharm.

From what I understand, a module generally consists of three parts:

  • GUI Component: The user interface.
  • Logic Component: Where your main script or functionality resides.
  • Test Component: For testing your module.

When you create the template using the extension wizard, it generates all the necessary template files and set up, allowing you to integrate your module directly into Slicer.

Hope this helps!
tas

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