Tutorial Part 2: Robot registration to the patient / phantom

Overview

In this portion of the tutorial, participants will learn how to register a robot to a phantom of patient anatomy.

Prerequisites: Complete Tutorial Part 1 first — this part continues from the navigation-ready scene built there, with 3D Slicer still running and the patient anatomy already registered to the optical tracker.

Part 4: Load the Micromate Robot

Step 44: Open a New Console

Open a new Konsole terminal, leaving Slicer running.

A new Konsole terminal open on the vast.ai desktop

Step 45: Launch the Micromate Driver

Type the following three commands to source the workspace and bring up the Micromate driver with mock hardware:

cd ../home/user/ros2_ws/
source install/setup.bash
ros2 launch micromate_ros2_driver micromate_with_custom_ros2_bringup.launch.py use_mock_hardware:=true

Konsole terminal showing the three commands used to launch the Micromate driver

Step 46: Confirm the Driver Starts

Wait for the launch output to settle. You should see the driver’s node and controller startup messages.

Terminal output showing the Micromate driver nodes starting successfully

Step 47: Open the SlicerROS2 Module

Switch back to Slicer, press Ctrl+F to open the Module Finder, and search for Slicer ROS. Select the ROS2 module and click OK.

Slicer Module Finder with Slicer ROS entered in the search field

Step 48: Add a New Robot

In the ROS2 module panel, select + Add New Robot to connect Slicer to the robot description published by the driver.

ROS2 module panel with the Add New Robot button

Step 49: Find the Robot in the 3D View

The Micromate model is now in the scene. You may have to navigate around in the 3D view to find it.

Slicer 3D view showing the loaded Micromate robot model

Step 50: Open the Data Module

Press the Data button in the top left.

Slicer toolbar with the Data module button highlighted

Step 51: Load the Robot Fiducials

Select the two .json files in the workshop data folder and press OK. These contain the robot-frame and tracker-frame fiducial positions used for the robot registration.

File dialog with the two JSON fiducial files selected

Step 52: Return to the Fiducial Registration Wizard

Go back to the Fiducial Registration Wizard tab.

Slicer showing the Fiducial Registration Wizard module panel

Step 53: Register the Robot

Select Robot Fiducials as the From list and OpticalTrackerFiducials_Robot as the To list, create a new transform called RobotToCT, and press Update.

Fiducial Registration Wizard configured with the robot fiducial lists and the RobotToCT output transform

Part 5: Visualize the Registered Robot

Step 54: Attach the Robot to the Registration Transform

Drag the robot onto the RobotToOpticalTracker transform. The robot model now sits in the same coordinate frame as the registered patient anatomy, completing the navigation-ready scene.

Step 55: Preview the Motion Control Module

With the scene assembled, the ROS2 Motion Control module can be used to plan and command robot motions relative to the registered anatomy.

Summary

In this session, you:

  • Launched 3D Slicer with the SlicerROS2 module from a ROS 2 workspace
  • Loaded a CT image of a spine phantom and segmented the bone using Grow from Seeds
  • Pivot-calibrated a tracked needle to produce a NeedleTipToNeedle transform
  • Collected four fiducial points on the gel block and computed a CTToOpticalTracker registration
  • Applied that registration to the CT image and segmentation to place the patient in tracker space
  • Launched the Micromate driver and loaded the robot into Slicer through SlicerROS2
  • Registered the robot to the patient using the Fiducial Registration Wizard
  • Visualized the fully registered robot and anatomy in a single navigation-ready scene

Back to Workshop Page

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