1. -1- iGyne1.0 Tutorial Xiaojun Chen, Ph.D. and iGyne Team Surgical Planning Laboratory, Brigham and Women's Hospital, Harvard Medical School Surgical Planning Laboratory, Harvard Medical School

2. -2- Guide you step-by-step through the process of loading of applicator CAD models, performing registration, selecting virtual 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 Learning Objective Surgical Planning Laboratory, Harvard Medical School

3. -3- Prerequisites This tutorial assumes that you have completed the course Data Loading and Visualization. Tutorials for Slicer4 are available on the website: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Training Surgical Planning Laboratory, Harvard Medical School

4. -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 http://download.slicer.org/ Applicator CAD models download page https://github.com/xjchen/igyne/tree/master/scene%20for%20template%20a nd%20obturator Sample Image data download page https://github.com/xjchen/igyne/tree/master/Sample%20data 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. Surgical Planning Laboratory, Harvard Medical School

5. -5- Loading of Applicator CAD models and MR images 1.Click on Load(Scene/Template) Button 2.Choose the Template.mrml you have downloaded Surgical Planning Laboratory, Harvard Medical School

6. -6- 1.Click on AddVolume Button 2.Choose the Test.nrrd you have downloaded Loading of Applicator CAD models and MR images Surgical Planning Laboratory, Harvard Medical School

7. -7- Loading of Applicator CAD models and MR images Surgical Planning Laboratory, Harvard Medical School

8. -8- Initial registration 1.Switch to Annotation Module 2.Click Fiducial List_fixed 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) Surgical Planning Laboratory, Harvard Medical School

9. -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) Surgical Planning Laboratory, Harvard Medical School

10. -10- Initial registration Switch to Fiducial Registration Module, then perform the initial registration Surgical Planning Laboratory, Harvard Medical School

11. -11- Registration refinement Switch to Crop Volume Module, in order to crop the template region in the image volume Surgical Planning Laboratory, Harvard Medical School

12. -12- Registration refinement Surgical Planning Laboratory, Harvard Medical School

13. -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 Surgical Planning Laboratory, Harvard Medical School

14. -14- Registration refinement Use MakeModelEffect tool to build a 3D model of the template holes Surgical Planning Laboratory, Harvard Medical School

15. -15- Registration refinement Use GrowCut tool to segment the obturator in the image volume Surgical Planning Laboratory, Harvard Medical School

16. -16- Registration refinement Use MakeModelEffect tool to build a 3D model of the obturator Surgical Planning Laboratory, Harvard Medical School

17. -17- Registration refinement 1.Switch to Igyne Module 2. Click CADmodel2Image button to refine the registration Surgical Planning Laboratory, Harvard Medical School

18. -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 Surgical Planning Laboratory, Harvard Medical School