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

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

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

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%20and%20obturator • Sample Image data download page https://github.com/xjchen/igyne/tree/master/Sample%20data 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.

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

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

Loading of Applicator CAD models and MR images

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

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)

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

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

Registration refinement

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

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

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

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

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

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