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Slicer Tutorial 7 Saving Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
Acknowledgments <ul><li>National Alliance for Medical Image Computing </li></ul><ul><li>NIH U54EB005149  </li></ul><ul><li...
Disclaimer <ul><li>It is the responsibility of the user of 3DSlicer </li></ul><ul><li>to comply with both the terms of the...
Material <ul><li>Slicer 2.6 </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started </li><...
Goal of this tutorial Guide you step-by-step through the process of  saving data  within Slicer.
Saving Data <ul><li>Slicer can save </li></ul><ul><li>Volumes …………………. </li></ul>
Saving Data <ul><li>Slicer can save </li></ul><ul><li>Volumes …………………. </li></ul><ul><li>Models ……………………………….. </li></ul>
Saving Data <ul><li>Slicer can save </li></ul><ul><li>Volumes …………………. </li></ul><ul><li>Models ……………………………….. </li></ul><...
Scene <ul><li>A  Scene  in 3DSlicer can be composed of several  </li></ul><ul><li>volumes ,  fiducials  and  3D models .  ...
Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes  </li></ul><ul><li>Part 3: S...
Loading a Scene Select  File  OpenScene  in the  Main Menu. Load the file  tutorial.xml  in the directory   Tutorial-with...
Loading a Scene Slicer loads the  scene   tutorial   in the  Viewer .
Loading a Scene <ul><li>The Scene  tutorial.xml  is composed of  </li></ul><ul><li>a gray levels volume:  SPGR </li></ul>
Loading a Scene <ul><li>The Scene  tutorial.xml  is composed of  </li></ul><ul><li>a gray levels volume:  SPGR </li></ul><...
Loading a Scene <ul><li>The Scene  tutorial.xml  is composed of  </li></ul><ul><li>a gray levels volume:  SPGR </li></ul><...
Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes  </li></ul><ul><li>Part 3: S...
Saving Volumes Select the module Editor in the Main Menu Click on the button  Save Select the Panel  Volumes  in the Edito...
Saving Volumes Left-click on the  Volume to Save  button and select the volume  all Click on the button   Save Enter the  ...
Saving Volumes Select the directory  Tutorial_with_dicom/tutorial/labels to save the existing labelmap with the new name  ...
Saving Volumes A message warns the user that the volume should not be saved, because it has not been changed since the las...
Saving Volumes Slicer writes the labelmap volume   SavedLabelmap   on the disk,  and generates a MRML file   SavedLabelmap...
Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes  </li></ul><ul><li>Part 3: S...
Saving Models Select the module  ModelMaker  in the Main Menu Select the tab  Save  in the module  ModelMaker
Saving Models Click on the button   Save Select the model  Vessels   as the  Active Model  to be saved Enter the new name ...
Saving Models Save the model  SavedVessels  in the directory  Tutorial_with_dicom/tutorial/ models
Saving Models A message warns the user that the Model has not been changed since the last time it was saved.  Click on  OK...
Saving Models Slicer writes the file  SavedVessels.vtk  in the directory  Tutorial_with_dicom/tutorial/models
Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes  </li></ul><ul><li>Part 3: S...
Saving a Scene <ul><li>A scene in Slicer can be composed of several volumes and several models. </li></ul>
Saving a Scene <ul><li>A scene in Slicer can be composed of several volumes and several models. </li></ul><ul><li>All the ...
Saving a Scene Select the section  File   in the  Main Menu Select  Save Scene As
Saving a Scene The window  Save As File   for the scene name appears. Slicer sets the default name  for the scene to  data.
Saving a Scene Enter the name  SavedScene,  select the directory  Tutorial_with_dicom/tutorial,  and click on  Apply.
Saving a Scene The file  SavedScene.xml  has been created in the directory  Tutorial_with_dicom/tutorial
Saving a Scene Select  Save Scene With Options  The  options  of the Scene including the  settings  from the  modules  and...
Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes  </li></ul><ul><li>Part 3: S...
Saving Images of a Scene Manipulate the models and volumes within the Viewer, and choose a view of the data that you would...
Saving Images of a Scene Select  Set Save 3D View Parameters  in  File
Saving Images of a Scene Set the  Save Mode  to  Single view  Enter the File prefix   SavedView Select the  directory /tut...
Saving Images of a Scene Set the  File Type  to  PNG Check the option   Include slice windows   to save the anatomical vie...
Saving Images of a Scene Slicer saves the image of the Viewer as the PNG file  SavedView001.PNG
Saving Images of a Scene The resulting PNG file can be included in an article or a PowerPoint presentation.
Conclusion <ul><li>Saving data processed with Slicer  </li></ul><ul><li>MRML description of the Scene elements location  <...
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Data Saving-3767

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Transcript of "Data Saving-3767"

  1. 1. Slicer Tutorial 7 Saving Data Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D.
  2. 2. Acknowledgments <ul><li>National Alliance for Medical Image Computing </li></ul><ul><li>NIH U54EB005149 </li></ul><ul><li>Neuroimage Analysis Center </li></ul><ul><li>NIH P41RR013218 </li></ul>
  3. 3. Disclaimer <ul><li>It is the responsibility of the user of 3DSlicer </li></ul><ul><li>to comply with both the terms of the license </li></ul><ul><li>and with the applicable laws, regulations </li></ul><ul><li>and rules. </li></ul>
  4. 4. Material <ul><li>Slicer 2.6 </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Slicer2.6_Getting_Started </li></ul><ul><li>Sample Tutorial Data: tutorial-with-dicom.zip </li></ul><ul><li>http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 </li></ul>Questions Answers Exercises
  5. 5. Goal of this tutorial Guide you step-by-step through the process of saving data within Slicer.
  6. 6. Saving Data <ul><li>Slicer can save </li></ul><ul><li>Volumes …………………. </li></ul>
  7. 7. Saving Data <ul><li>Slicer can save </li></ul><ul><li>Volumes …………………. </li></ul><ul><li>Models ……………………………….. </li></ul>
  8. 8. Saving Data <ul><li>Slicer can save </li></ul><ul><li>Volumes …………………. </li></ul><ul><li>Models ……………………………….. </li></ul><ul><li>Scenes ……………………………….... </li></ul>
  9. 9. Scene <ul><li>A Scene in 3DSlicer can be composed of several </li></ul><ul><li>volumes , fiducials and 3D models . </li></ul><ul><li>It is represented by an .xml file written in </li></ul><ul><li>Medical Reality Modeling Language (MRML), that </li></ul><ul><li>lists the elements of the Scene and their attributes. </li></ul><ul><li>Several views of the same Scene can be saved in 3DSlicer. </li></ul>
  10. 10. Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes </li></ul><ul><li>Part 3: Saving Models </li></ul><ul><li>Part 4: Saving Scenes </li></ul><ul><li>Part 5: Saving Images of a Scene </li></ul>
  11. 11. Loading a Scene Select File  OpenScene in the Main Menu. Load the file tutorial.xml in the directory Tutorial-with-dicom/tutorial
  12. 12. Loading a Scene Slicer loads the scene tutorial in the Viewer .
  13. 13. Loading a Scene <ul><li>The Scene tutorial.xml is composed of </li></ul><ul><li>a gray levels volume: SPGR </li></ul>
  14. 14. Loading a Scene <ul><li>The Scene tutorial.xml is composed of </li></ul><ul><li>a gray levels volume: SPGR </li></ul><ul><li>a segmented volume: all </li></ul>
  15. 15. Loading a Scene <ul><li>The Scene tutorial.xml is composed of </li></ul><ul><li>a gray levels volume: SPGR </li></ul><ul><li>a segmented volume: all </li></ul><ul><li>three models: Skin, Ventricles, Vessels </li></ul>
  16. 16. Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes </li></ul><ul><li>Part 3: Saving Models </li></ul><ul><li>Part 4: Saving Scenes </li></ul><ul><li>Part 5: Saving Saving Images of a Scene </li></ul>
  17. 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. 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. 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. 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. 21. Saving Volumes Slicer writes the labelmap volume SavedLabelmap on the disk, and generates a MRML file SavedLabelmap.xml.
  22. 22. Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes </li></ul><ul><li>Part 3: Saving Models </li></ul><ul><li>Part 4: Saving Scenes </li></ul><ul><li>Part 5: Saving Images of the Scene </li></ul>
  23. 23. Saving Models Select the module ModelMaker in the Main Menu Select the tab Save in the module ModelMaker
  24. 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. 25. Saving Models Save the model SavedVessels in the directory Tutorial_with_dicom/tutorial/ models
  26. 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. 27. Saving Models Slicer writes the file SavedVessels.vtk in the directory Tutorial_with_dicom/tutorial/models
  28. 28. Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes </li></ul><ul><li>Part 3: Saving Models </li></ul><ul><li>Part 4: Saving Scenes </li></ul><ul><li>Part 5: Saving Images of the Scene </li></ul>
  29. 29. Saving a Scene <ul><li>A scene in Slicer can be composed of several volumes and several models. </li></ul>
  30. 30. Saving a Scene <ul><li>A scene in Slicer can be composed of several volumes and several models. </li></ul><ul><li>All the volumes and all the models have to be saved separately before saving a Scene. </li></ul>
  31. 31. Saving a Scene Select the section File in the Main Menu Select Save Scene As
  32. 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. 33. Saving a Scene Enter the name SavedScene, select the directory Tutorial_with_dicom/tutorial, and click on Apply.
  34. 34. Saving a Scene The file SavedScene.xml has been created in the directory Tutorial_with_dicom/tutorial
  35. 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. 36. Tutorial 7: Overview <ul><li>Part 1: Loading a Scene </li></ul><ul><li>Part 2: Saving Volumes </li></ul><ul><li>Part 3: Saving Models </li></ul><ul><li>Part 4: Saving Scenes </li></ul><ul><li>Part 5: Saving Images of a Scene </li></ul>
  37. 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. 38. Saving Images of a Scene Select Set Save 3D View Parameters in File
  39. 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. 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. 41. Saving Images of a Scene Slicer saves the image of the Viewer as the PNG file SavedView001.PNG
  42. 42. Saving Images of a Scene The resulting PNG file can be included in an article or a PowerPoint presentation.
  43. 43. Conclusion <ul><li>Saving data processed with Slicer </li></ul><ul><li>MRML description of the Scene elements location </li></ul><ul><li>Open-Source environment </li></ul>
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