TractDesktop_UserStudy

Overview

TractDesktop_UserStudy is a 3D Slicer module developed for the desktop condition of the experimental study. It provides the conventional desktop interaction workflow used by participants during the experiment. The module relies on functionalities provided by the SlicerDMRI extension for tractography visualization and interaction

Repository context

This repository was developed specifically for the experimental study and is separate from the operational TractDesktop module intended for routine professional use

Related repositories

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

Main features

• Desktop-based tractography interaction for experimental sessions
• Standardized workflow for study participants
• Logging of user actions and study-related data
• Integration with the study protocol
• Use of tractography-related functionalities available through SlicerDMRI

Intended users

This module is intended exclusively for use in the experimental study.

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 TractDesktop_UserStudy module
3. Click on Load Study and enter the participant ID created with the TractVRRandomization module to load the corresponding study data and participant configuration
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 for one case, click on Next to load the next case, and redo step 4 to 11
13. When all the cases are completed
    • Close the Tractography Display window
    • Click on End in the TractDesktop module to save data

Notes

This module builds on functionalities provided by the SlicerDMRI extension. This repository was developed specifically for the experimental study and should not be confused with the operational TractDesktop repository intended for routine professional use.

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.