TractDesktop

Overview

TractDesktop is a 3D Slicer module developed for interactive tractography cleaning and manipulation in a conventional desktop environment. It is intended to support routine professional use outside virtual reality. The module relies on functionalities provided by the SlicerDMRI extension for tractography visualization and processing within 3D Slicer.

Repository context

This repository contains the operational desktop module intended for routine professional use. It is separate from the repositories developed specifically for the experimental user study.

Related repositories

• TractVR – operational VR module for routine professional use
• TractVRRandomisation – study planning and session randomization module
• TractVR_UserStudy – VR module used in the experimental study
• TractDesktop_UserStudy – desktop module used in the experimental study

Main features

• Desktop-based tractography visualization
• Interactive fiber bundle cleaning and editing
• ROI-based manipulation tools
• Integration within a 3D Slicer workflow
• Use of tractography-related functionalities available through SlicerDMRI

Intended users

This module is intended for trained professionals who perform tractography visualization and manual editing tasks using a standard desktop interface.

Dependencies

• 3D Slicer
• SlicerDMRI extension
• Python
• Other required Slicer libraries if applicable

Installation

1. Install 3D Slicer.
2. Install the SlicerDMRI extension.
3. Clone or download this repository.
4. Add the module to your 3D Slicer environment.
5. Restart 3D Slicer if needed.

Usage

1. Launch 3D Slicer.
2. Open the TractDesktop1 module.
3. Load the required tractography data.
4. Click on Start Tractography Display.
5. In the Tractography Display window:
   • Create a new ROI.
   • Check Disable ROI.
   • Close the Tractography Display window.
6. Resize the ROI in the 3D view to obtain a small cube that is easy to manipulate.
7. Click again on Start Tractography Display.
8. In the Tractography Display window:
   • Check Negative ROI.
9. Move the ROI cube with the mouse to the area where fibers need to be edited or removed.
10. Click on Update Bundle from ROI to save the current edit.
11. Repeat the ROI movement and update steps as needed until the fiber bundle is cleaned.
12. When the cleaning / editing task is completed:
    • Close the Tractography Display window.
    • Click on End in the TractDesktop module.

Notes

This module builds on functionalities provided by the SlicerDMRI extension. This repository contains the operational version of the desktop module. If you are looking for the version used specifically during the experimental study, please refer to the TractDesktop_UserStudy repository.

Funding

This work was developed as part of a project funded by the Canada Research Chair in Neuroinformatics for Multimodal Data.
Designated responsible investigator: Sylvain Bouix
Reference number: CRC-2022-00183

Acknowledgments

This module was adapted from templates and components from the 3D Slicer ecosystem. It also relies in part on functionalities provided by the SlicerDMRI extension.