Data Saving-3767
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Slicer can save volumes, models, scenes, and images of scenes. The tutorial guides the user through saving each element separately: volumes are saved using the Editor module, models using ModelMaker, scenes using File > Save Scene As, and images using File > Set Save 3D View Parameters. All elements must be saved individually before saving the overall scene. The tutorial demonstrates how to name and locate saved files.
Data Saving-3767
- 1. Slicer Tutorial 7 Saving Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
- 2. Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218
- 3. 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. Material 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 Questions Answers Exercises
- 5. Goal of this tutorial Guide you step-by-step through the process of saving data within Slicer.
- 6. Saving Data Slicer can save Volumes ………………….
- 7. Saving Data Slicer can save Volumes …………………. Models ………………………………..
- 8. Saving Data Slicer can save Volumes …………………. Models ……………………………….. Scenes ………………………………....
- 9. 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. 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. Loading a Scene Select File OpenScene in the Main Menu. Load the file tutorial.xml in the directory Tutorial-with-dicom/tutorial
- 12. Loading a Scene Slicer loads the scene tutorial in the Viewer .
- 13. Loading a Scene The Scene tutorial.xml is composed of a gray levels volume: SPGR
- 14. Loading a Scene The Scene tutorial.xml is composed of a gray levels volume: SPGR a segmented volume: all
- 15. 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. 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. Saving Volumes Select the module Editor in the Main Menu Click on the button Save Select the Panel Volumes in the Editor Menu
- 18. 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. Saving Volumes Select the directory Tutorial_with_dicom/tutorial/labels to save the existing labelmap with the new name SavedLabelMap. Click on Save
- 20. 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. Saving Volumes Slicer writes the labelmap volume SavedLabelmap on the disk, and generates a MRML file SavedLabelmap.xml.
- 22. 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. Saving Models Select the module ModelMaker in the Main Menu Select the tab Save in the module ModelMaker
- 24. Saving Models Click on the button Save Select the model Vessels as the Active Model to be saved Enter the new name SavedVessels
- 25. Saving Models Save the model SavedVessels in the directory Tutorial_with_dicom/tutorial/ models
- 26. 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. Saving Models Slicer writes the file SavedVessels.vtk in the directory Tutorial_with_dicom/tutorial/models
- 28. 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. Saving a Scene A scene in Slicer can be composed of several volumes and several models.
- 30. 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. Saving a Scene Select the section File in the Main Menu Select Save Scene As
- 32. Saving a Scene The window Save As File for the scene name appears. Slicer sets the default name for the scene to data.
- 33. Saving a Scene Enter the name SavedScene, select the directory Tutorial_with_dicom/tutorial, and click on Apply.
- 34. Saving a Scene The file SavedScene.xml has been created in the directory Tutorial_with_dicom/tutorial
- 35. Saving a Scene Select Save Scene With Options The options of the Scene including the settings from the modules and the background color set a re saved in the file SavedScene.xml .
- 36. 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. 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. Saving Images of a Scene Select Set Save 3D View Parameters in File
- 39. Saving Images of a Scene Set the Save Mode to Single view Enter the File prefix SavedView Select the directory /tutorial to save the view
- 40. Saving Images of a Scene Set the File Type to PNG Check the option Include slice windows to save the anatomical views The Output zoom option provides a higher resolution image. Click on Save View Now
- 41. Saving Images of a Scene Slicer saves the image of the Viewer as the PNG file SavedView001.PNG
- 42. Saving Images of a Scene The resulting PNG file can be included in an article or a PowerPoint presentation.
- 43. Conclusion Saving data processed with Slicer MRML description of the Scene elements location Open-Source environment