maribernardes / aineedletracking-3dslicer

3D Slicer module for AI-based needle tracking

AINeedleTracking-3DSlicer

Installation:

First, use the PyTorch Utils module to install the appropriate torch version in 3DSlicer: https://github.com/fepegar/SlicerPyTorch

Then, install the following python packages to 3D Slicer (use 3D Slicer Python Interactor):

slicer.util.pip_install('monai[all]')

Use:

BRPRobot Project:

• Setup
  • Input mode: magnitude/phase
  • Model: UNet_needle_segmentation
• Optional
  • Not in use for BRPRobot
• Tracking
  • Magnitude: input image
  • Phase: input image
  • Mask (optional): none or SegmentationNode
• Advanced:
  • Debug flag: off (less verbose)

OpenIGTLink Project:

• Setup
  • Input mode: magnitude/phase
  • Model: UNet_needle_segmentation
• Optional
  • Push to scanner: PLAN_0 (requires IGTLink Server, initializes with current slice in selected viewer)
  • Push to robot: target and current tip (requires IGTLink Client, ZFrame Transform, List of markups fiducials)
• Tracking
  • Magnitude: input image
  • Phase: input image
  • Mask (optional): none or SegmentationNode
• Advanced:
  • Debug flag: off (less verbose)