1. Igyne Tutorial Xiaojun Chen, Ph.D.1 Jan Egger, Ph.D., Ph.D.1
Tina Kapur, Ph.D1
Akila N. Viswanathan, M.D., M.P.H2
1 Surgical Planning Laboratory
Harvard Medical School
2 Brigham and Women's Hospital, Dana-Farber Cancer Institute

2. Learning Objective
Guide you step-by-step through the process of loading of applicator CAD models, performing registration, and selecting virtural needle and viewing the results within Slicer4. This module features include:
Loading of Applicator CAD models and MR images
Initial registration of CAD model of the Template to MR images
Registration Refinement
Visualization of Registration
Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation

3. Prerequisites
This tutorial assumes that you have completed the course Data Loading and Visualization.
Tutorials for Slicer4 are available on the website:

4. Materials
This tutorial requires the installation of the Slicer4 software and the tutorial dataset. These materials are available at the following locations:
• Slicer4 download page
• Applicator CAD models download page
• Sample Image data download page
Note that the training tutorial website has not been updated yet with this particular dataset.
Disclaimer: It is the responsibility of the user of Slicer to comply with both the terms of the license and with the applicable laws, regulations, and rules.

5. Loading of Applicator CAD models and MR images
1.Click on Load(Scene/Template) Button
2.Choose the Template.mrml you have downloaded

6. Loading of Applicator CAD models and MR images
1.Click on AddVolume Button
2.Choose the Test.nrrd you have downloaded

7. Loading of Applicator CAD models and MR images

8. Initial registration
3. Click 3 Fiducials of the center points of the long holes in the template on the axial images(First: Top point(shown in the picture), Second: Left point, Third:Right point)
1.Switch to Annotation Module
2.Click Fiducial List_fixed

9. Initial registration
The other 2 Fiducials of the center points of the long holes in the template on the axial images(Left and Right point, point, shown in the picture)

10. Initial registration
Switch to Fiducial Registration Module, then perform the initial registration

11. Registration refinement
Switch to Crop Volume Module, in order to crop the template region in the image volume

12. Registration refinement

13. Registration refinement
1.Switch to Editor Module, in order to segment the template and obturator in the image volume
2. Use Threshold tool to segment the template holes

14. Registration refinement
Use MakeModelEffect tool to build a 3D model of the template holes

15. Registration refinement
Use GrowCut tool to segment the obturator in the image volume

16. Registration refinement
Use MakeModelEffect tool to build a 3D model of the obturator

17. Registration refinement
1.Switch to Igyne Module
2. Click CADmodel2Image button to refine the registration

18. Needle selection and visualization
Click the hole label on the template sheet to show/hide the corresponding needle, and its insertion depth can also be adjusted