1. Surgical Planning Laboratory http://www.slicer.org -1- Brigham and Womens Hospital Slicer Tutorial 7 Saving Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.

2. Surgical Planning Laboratory http://www.slicer.org -2- Brigham and Womens 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 Womens 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 Womens Hospital Material QuestionsAnswers Exercises Slicer 2.6 http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started Sample Tutorial Data: tutorial-with-dicom.zip http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Womens Hospital Goal of this tutorial Guide you step-by-step through the process of saving data within Slicer.

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Womens Hospital Saving Data Slicer can save Volumes ………………….

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Womens Hospital Saving Data Slicer can save Volumes …………………. Models ………………………………..

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Womens Hospital Saving Data Slicer can save Volumes …………………. Models ……………………………….. Scenes ………………………………....

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Womens Hospital Scene A Scene in 3DSlicer can be composed of several volumes, fiducials and 3D models. It is represented by an.xml file written in Medical Reality Modeling Language (MRML), that lists the elements of the Scene and their attributes. Several views of the same Scene can be saved in 3DSlicer.

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Womens Hospital Tutorial 7: Overview Part 1: Loading a Scene Part 2: Saving Volumes Part 3: Saving Models Part 4: Saving Scenes Part 5: Saving Images of a Scene

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Womens Hospital Loading a Scene Select File OpenScene in the Main Menu. Load the file tutorial.xml in the directory Tutorial-with-dicom/tutorial

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Womens Hospital Loading a Scene Slicer loads the scene tutorial in the Viewer.

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Womens Hospital Loading a Scene The Scene tutorial.xml is composed of -a gray levels volume: SPGR

14. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Womens Hospital Loading a Scene The Scene tutorial.xml is composed of -a gray levels volume: SPGR -a segmented volume: all

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Womens 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

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Womens Hospital Tutorial 7: Overview Part 1: Loading a Scene Part 2: Saving Volumes Part 3: Saving Models Part 4: Saving Scenes Part 5: Saving Saving Images of a Scene

17. Surgical Planning Laboratory http://www.slicer.org -17- Brigham and Womens Hospital Saving Volumes Select the module Editor in the Main Menu Click on the button Save Select the Panel Volumes in the Editor Menu

18. Surgical Planning Laboratory http://www.slicer.org -18- Brigham and Womens Hospital Saving Volumes Left-click on the Volume to Save button and select the volume all Click on the button Save Enter the Filename Prefix SavedLabelmap

19. Surgical Planning Laboratory http://www.slicer.org -19- Brigham and Womens Hospital Saving Volumes Select the directory Tutorial_with_dicom/tutorial/labels to save the existing labelmap with the new name SavedLabelMap. Click on Save

20. Surgical Planning Laboratory http://www.slicer.org -20- Brigham and Womens Hospital Saving Volumes A message warns the user that the volume should not be saved, because it has not been changed since the last time it was saved. Click on Yes to save the volume with the new name

21. Surgical Planning Laboratory http://www.slicer.org -21- Brigham and Womens Hospital Saving Volumes Slicer writes the labelmap volume SavedLabelmap on the disk, and generates a MRML file SavedLabelmap.xml.

22. Surgical Planning Laboratory http://www.slicer.org -22- Brigham and Womens Hospital Tutorial 7: Overview Part 1: Loading a Scene Part 2: Saving Volumes Part 3: Saving Models Part 4: Saving Scenes Part 5: Saving Images of the Scene

23. Surgical Planning Laboratory http://www.slicer.org -23- Brigham and Womens Hospital Saving Models Select the module ModelMaker in the Main Menu Select the tab Save in the module ModelMaker

24. Surgical Planning Laboratory http://www.slicer.org -24- Brigham and Womens Hospital Saving Models Select the model Vessels as the Active Model to be saved Enter the new name SavedVessels Click on the button Save

25. Surgical Planning Laboratory http://www.slicer.org -25- Brigham and Womens Hospital Saving Models Save the model SavedVessels in the directory Tutorial_with_dicom/tutorial/models

26. Surgical Planning Laboratory http://www.slicer.org -26- Brigham and Womens Hospital Saving Models A message warns the user that the Model has not been changed since the last time it was saved. Click on OK to save the model with the new name.

27. Surgical Planning Laboratory http://www.slicer.org -27- Brigham and Womens Hospital Saving Models Slicer writes the file SavedVessels.vtk in the directory Tutorial_with_dicom/tutorial/models

28. Surgical Planning Laboratory http://www.slicer.org -28- Brigham and Womens Hospital Tutorial 7: Overview Part 1: Loading a Scene Part 2: Saving Volumes Part 3: Saving Models Part 4: Saving Scenes Part 5: Saving Images of the Scene

29. Surgical Planning Laboratory http://www.slicer.org -29- Brigham and Womens Hospital Saving a Scene A scene in Slicer can be composed of several volumes and several models.

30. Surgical Planning Laboratory http://www.slicer.org -30- Brigham and Womens Hospital Saving a Scene A scene in Slicer can be composed of several volumes and several models. All the volumes and all the models have to be saved separately before saving a Scene.

31. Surgical Planning Laboratory http://www.slicer.org -31- Brigham and Womens Hospital Saving a Scene Select Save Scene As Select the section File in the Main Menu

32. Surgical Planning Laboratory http://www.slicer.org -32- Brigham and Womens Hospital Saving a Scene The window Save As File for the scene name appears. Slicer sets the default name for the scene to data.

33. Surgical Planning Laboratory http://www.slicer.org -33- Brigham and Womens Hospital Saving a Scene Enter the name SavedScene, select the directory Tutorial_with_dicom/tutorial, and click on Apply.

34. Surgical Planning Laboratory http://www.slicer.org -34- Brigham and Womens Hospital Saving a Scene The file SavedScene.xml has been created in the directory Tutorial_with_dicom/tutorial

35. Surgical Planning Laboratory http://www.slicer.org -35- Brigham and Womens Hospital Saving a Scene Select Save Scene With Options The options of the Scene including the settings from the modules and the background color set are saved in the file SavedScene.xml.

36. Surgical Planning Laboratory http://www.slicer.org -36- Brigham and Womens Hospital Tutorial 7: Overview Part 1: Loading a Scene Part 2: Saving Volumes Part 3: Saving Models Part 4: Saving Scenes Part 5: Saving Images of a Scene

37. Surgical Planning Laboratory http://www.slicer.org -37- Brigham and Womens Hospital Saving Images of a Scene Manipulate the models and volumes within the Viewer, and choose a view of the data that you would like to save.

38. Surgical Planning Laboratory http://www.slicer.org -38- Brigham and Womens Hospital Saving Images of a Scene Select Set Save 3D View Parameters in File

39. Surgical Planning Laboratory http://www.slicer.org -39- Brigham and Womens Hospital Saving Images of a Scene Set the Save Mode to Single view Select the directory /tutorial to save the view Enter the File prefix SavedView

40. Surgical Planning Laboratory http://www.slicer.org -40- Brigham and Womens Hospital Saving Images of a Scene Set the File Type to PNG Check the option Include slice windows to save the anatomical views Click on Save View Now The Output zoom option provides a higher resolution image.

41. Surgical Planning Laboratory http://www.slicer.org -41- Brigham and Womens Hospital Saving Images of a Scene Slicer saves the image of the Viewer as the PNG file SavedView001.PNG

42. Surgical Planning Laboratory http://www.slicer.org -42- Brigham and Womens Hospital Saving Images of a Scene The resulting PNG file can be included in an article or a PowerPoint presentation.

43. Surgical Planning Laboratory http://www.slicer.org -43- Brigham and Womens Hospital Conclusion Saving data processed with Slicer MRML description of the Scene elements location Open-Source environment