AINeedleTracking-3DSlicer

Installation:

First, install the appropriate torch version in 3DSlicer.

Use the PyTorch Utils module (https://github.com/fepegar/SlicerPyTorch)

OR

install it manually using 3D Slicer Python Interactor (and adjusting the url for the appropriate version):

slicer.util.pip_install("torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu")

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

slicer.util.pip_install('monai')
slicer.util.pip_install('nibabel')
slicer.util.pip_install('scikit-image')

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)