1. Surgical Planning Laboratory http://www.slicer.org -1- Brigham and Women’s Hospital 3DSlicer Hands-on session Sonia Pujol, Ph.D.

2. Surgical Planning Laboratory http://www.slicer.org -2- Brigham and Women’s Hospital Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218

3. Surgical Planning Laboratory http://www.slicer.org -3- Brigham and Women’s Hospital Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules.

4. Surgical Planning Laboratory http://www.slicer.org -4- Brigham and Women’s Hospital Material 3DSlicer: version 2.5 http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.5_Getting_Started Tutorial-with-Dicom dataset –MRI brain acquisition –3D models of the skin, cerebral vasculature and ventricles. http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Women’s Hospital Goal of this tutorial Guide you step-by-step through the process of using 3D Slicer for the visualization of imaging volumes and 3D reconstruction of the anatomy.

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Women’s Hospital Overview Part 1: Loading Data Part 2: Interacting with 3D Models Part 3: Interacting with 2D Images

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Women’s Hospital Slicer Interface Viewer Menu Tk window

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Women’s Hospital Loading Data Slicer can load Volumes ………………….. Models ……………………. Scenes ……………………. Scene = Volume + Model

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Women’s Hospital Loading a Scene Select File  OpenScene in the Main Menu. Load the file tutorial.xml in the directory Tutorial-with-dicom

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Women’s Hospital Loading a Scene Slicer loads the scene tutorial.

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Women’s Hospital Loading a Scene The Scene tutorial.xml is composed of -a gray levels volume: SPGR -a segmented volume: all -three models: Skin, Ventricles, Vessels

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Women’s Hospital Loading a Scene The model appears in the 3D Viewer. The anatomical slices appear in the 2D Viewer

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Women’s Hospital Overview Part 1: Loading Data Part 2: Interacting with 3D Models Part 3: Interacting with 2D Images

14. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Women’s Hospital Manipulating a Model Position the mouse on the model inside the Viewer Left-click and move the mouse to the left Rotation The model moves to the left

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Women’s Hospital Manipulating a Model Right-click and move the mouse down Zoom The viewer gets closer to the model

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Women’s Hospital Manipulating a Model Right-click and move the mouse up The viewer moves away from the model Zoom

17. Surgical Planning Laboratory http://www.slicer.org -17- Brigham and Women’s Hospital Manipulating a Model Position the mouse on the 3D Slicer icon

18. Surgical Planning Laboratory http://www.slicer.org -18- Brigham and Women’s Hospital Manipulating a Model The Control Window appears

19. Surgical Planning Laboratory http://www.slicer.org -19- Brigham and Women’s Hospital Manipulating a Model The six letters correspond to the anatomical orientations of the patient R: Right L: Left A: Anterior P: Posterior S: Superior I:Inferior

20. Surgical Planning Laboratory http://www.slicer.org -20- Brigham and Women’s Hospital Manipulating a Model Position the mouse on the R letter (Right) inside the window

21. Surgical Planning Laboratory http://www.slicer.org -21- Brigham and Women’s Hospital Manipulating a Model The View Panel shows the model from the right side of the patient

22. Surgical Planning Laboratory http://www.slicer.org -22- Brigham and Women’s Hospital Model Opacity Click on Models in the Main Menu Set the opacity of the Skin model to 0.5 Select the Display tab

23. Surgical Planning Laboratory http://www.slicer.org -23- Brigham and Women’s Hospital Model Opacity Skin model Opacity = 0.5

24. Surgical Planning Laboratory http://www.slicer.org -24- Brigham and Women’s Hospital Model Visibility Left Click on the Vessels Button in the list of models

25. Surgical Planning Laboratory http://www.slicer.org -25- Brigham and Women’s Hospital Model Visibility The Vessels model disappears from the 3DViewer.

26. Surgical Planning Laboratory http://www.slicer.org -26- Brigham and Women’s Hospital Global Visibility Click Show None to display none of the models in the 3D Viewer

27. Surgical Planning Laboratory http://www.slicer.org -27- Brigham and Women’s Hospital Viewing 3D Models The models have disappeared.

28. Surgical Planning Laboratory http://www.slicer.org -28- Brigham and Women’s Hospital Overview Part 1: Loading Data Part 2: Interacting with 3D Models Part 3: Interacting with 2D Images

29. Surgical Planning Laboratory http://www.slicer.org -29- Brigham and Women’s Hospital 2D Viewer Axial View Sagittal View Coronal View Sliders

30. Surgical Planning Laboratory http://www.slicer.org -30- Brigham and Women’s Hospital Viewing Volumes Select the 3D View The View Menu contains different options to visualize the data

31. Surgical Planning Laboratory http://www.slicer.org -31- Brigham and Women’s Hospital Viewing Volumes 3D View focuses on 3D

32. Surgical Planning Laboratory http://www.slicer.org -32- Brigham and Women’s Hospital Viewing Volumes 4x512 view: larger image views to see details

33. Surgical Planning Laboratory http://www.slicer.org -33- Brigham and Women’s Hospital Viewing Volumes 1x512 view: one large, three small images

34. Surgical Planning Laboratory http://www.slicer.org -34- Brigham and Women’s Hospital Viewing Volumes 4x256 view: smaller equal- sized images Come back to Normal View

35. Surgical Planning Laboratory http://www.slicer.org -35- Brigham and Women’s Hospital Viewing Volumes V toggle button controls whether slice is visible in 3D Viewer Click on the V buttons to display the Axial and Sagittal images inside the Viewer.

36. Surgical Planning Laboratory http://www.slicer.org -36- Brigham and Women’s Hospital Viewing Volumes The Axial and Sagittal images appear in the Viewer Left-click on the images inside the Viewer to orient the slices.

37. Surgical Planning Laboratory http://www.slicer.org -37- Brigham and Women’s Hospital Viewing Models and Volumes Left-click on Show All to display the models in the 3D Viewer.

38. Surgical Planning Laboratory http://www.slicer.org -38- Brigham and Women’s Hospital Viewing Models and Volumes Slicer superimposes the models on the anatomical images.

39. Surgical Planning Laboratory http://www.slicer.org -39- Brigham and Women’s Hospital Conclusion Open-Source environment Fusion of volumes and models Intuitive Graphical User Interface