1. Workflow based Slicer IGT Module : Tutorial Andinet Enquobahrie, PhD Kitware Inc December, 2008

2. Purpose of the module Provide a generic workflow based wizard to be used as a framework for IGT applications development. Identify the major steps in IGT procedure and translate these steps into wizard interfaces.

3. Download and Build Instructions 1.Download the module source code – http://www.na-mic.org/Wiki/index.php/Image:SlicerIGTModule.tgz http://www.na-mic.org/Wiki/index.php/Image:SlicerIGTModule.tgz 2.Specify your Slicer3 build directory during CMake configuration 3.Build the module If you have successfully build the module, then in the module subdirectory of your build, you should get a shared library for SlicerIGT module ( "IGT.dll" for windows or "libIGT.so" for Unix build.

4. How to load SlicerIGTModule to Slicer 1.Start slicer 2.Click on "Application Settings" in View menu and then click on "Module settings" 3.Add the path to your SlicerIGTModule plugin 4.Restart slicer and verify “Image Guided Therapy Module” exists in the modules list

5. Load required Data for the IGT application Three types of data can be loaded 1.Preoperative Image Data 2.Model Data for Surgical Tools 3.Calibration Data

6. Preoperative Image Data – Using Volumes Module

7. Use Fiducials Module – Generate fiducials image coordinates for registration

8. SlicerIGT Module Interface

9. Interface Design Five major steps 1.Initialization 2.Loading preoperative data 3.Calibration 4.Registration 5.Intrapoperative procedure Designed using KWWidgets wizard

10. Step 1/5 Initialization Initialization step includes establishing communication with Navigation system and/or tracking device Endoscope External tracking software – For example, setup communication with IGSTK using OpenIGT link Robot control computer if a robot is used in the surgical procedure.

11. Initialization Interface

12. Step 2/5 Loading Preoperative Data Preoperative data includes Images ( such as CT, MRI data ) Models Surgical planning ( developed preoperatively )

13. Preoperative Data Loading Interface Select Image Data loaded using Volumes Module

14. Step 3/5 Calibration This step includes – Calibration of camera (Endoscope) and probe – Calibration of tracker tools For example, Pivot calibrations – Calibration of robot tools Two options are available – Load precomputed calibration data – Run calibration algorithm

15. Calibration Interface

16. Step 4/5 Registration In this step, transformations between different coordinate systems are established Register preoperative image with the navigation system’s reference frame ( i.e. Patient-Image registration ) If robot is available, register robot coordinate system with the navigation system reference frame.

17. Registration Interface Select fiducial coordinates from the list of fiducials marked in Fiducals module

18. Step 5/5 Intraoperative procedure During the procedure – Start Tracking – If robot is available, transmit commands to robot to get it to the right mode – Gather pose information of tracker/surgical tools and update the display

19. Intraoperative Procedure Interface

20. Summary Workflow based design streamlines application development IGT application developers fill in the SlicerIGT module steps with implementations specific to their application