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Introduction and Acknowledgements

Authors: Andinet Enquobahrie Kitware, Guillaume Sala, Kitware, Rahul Khare, ChildrensNational, Julien Finet Kitware, Dženan Zukić Kitware
Acknowledgements: This work is supported by NIH grants 2R42CA153488-02A1, R41CA153488-01 and 3R42CA153488-03S1 "Improving liver lesion biopsy in the CT suite through fusion with PET images"
Contact: Andinet Enquobahrie, Dženan Zukić

Module Description

The GuidedInterventionPETCT is a workflow-based module that guides the user in a step-by-step interface to realize a guided biopsy after fusing respiratory-compensated PET/CT with images in the interventional CT suite.
In each step of the workflow we prepare the necessary requirements to fulfill the end goal, following a given pipeline: Registration of the different volumes acquired, establishing the connection between the tracking device and Slicer, registration of the coordinate system of the tracking system and the registered volume and live tracking of the needle in Slicer.
This module uses existing modules to accomplish some of the steps:

Use Cases


Loading Step

The loading step is the first step of the workflow. The user selects the data that is going to be used for the guided biopsy.
Read here the instructions to load data into Slicer.

  • MC PET Volume: This combobox allows selecting the motion-compensated PET scans.
  • MC CT Volume: This combobox allows selecting the motion-compensated CT scans.
  • CBCT Volume: This combobox allows selecting the interventional CT Scan.

The volumes in these comboboxes will be used to compute the image registration, between the pre-operative PET/CT acquisition and the interventional CT. The fused PET and interventional CT images will guide the biopsy procedure.

Loading data panel

Volume Registration Step

In this step we compute the image registration of the motion-compensated PET/CT and interventional CT.
The user can tweak initial position and orientation - in case that the automatic registration fail or to make it converge faster.

  • Sampling percent: Percentage of voxels which are sampled to calculate registration metric
  • Precise rigid phase: Should a higher-resolution rigid registration be conducted in addition to low resolution rigid registration?
  • BSpline: Should a BSpline registration be conducted in addition to rigid registration?
  • Grid Size: Number of divisions for BSpline registration. Bigger number mean more degrees of freedom, implying slower registration with a potential for higher precision.
  • Start Registration: Push Button to start the registration with the volumes selected in the previous step.
Volume Registration panel

OpenIGTLinkIF Step

In this step of the workflow we establish the link between Slicer and the tracking system.
To establish this connection we import the OpenIGTLinkIF module of Slicer. For more information about the use of this module please see the OpenIGTLinkIF documentation.
One method to establish the connection is using IGSTK:

OpenIGTLinkIF panel

Pivot Calibration Step

This section allows the user to run a pivot calibration algorithm on the tracker device (whose connection was establish on the previous step). To accomplish this, we import the existing PivotCalibration module.
For more information about the use of this module please see the Pivot Calibration documentation.

Pivot calibration panel

Hardware Registration Step

This step allows the user to run a fiducial registration to transform the tracker coordinate system to the registered volume (PET/CT scans with the interventional CT scans) coordinate system.
To run the fiducial registration we need to create two fiducial lists (TrackerMarkers and CTMarkers) containing respective points in the different coordinate system.

For more information about the fiducial registration, please see the documentation here.

  • Acquire 1 tracker fiducial: This button allows the user, by clicking on it, to create a new fiducial at the current position of the tracking device, and adding it to the "TrackerMarkers" list.
  • Place 1 image fiducial: The user needs to place the fiducials on the CT volume (in a position corresponding to TrackerMarkers) to be able to run the registration.
  • Register: This button allows the user to call the fiducial registration CLI module with two fiducial lists previously filled.
Hardware registration panel

Path Planner

In this step the guidance path can be planned. "Place target" and "Place entry point" buttons allow the user to choose those points in the PET/CT fused image using mouse. "Entry from needle tip" allow entry point to be taken from the current needle tip position (usually after the interventional radiologist has placed it on the skin of the patient). Clicking on positions in the "RAS" row jumps all the slices to that position (target or entry point).

Path planner panel


This is the last step of the workflow. It displays 4 slice views: axial, sagittal, a slice through the needle, and a slice perpendicular to the needle, all according to the position of the tracker device. The panel allows control over size and opacity of target sphere and guidance line thickness.

Guidance panel