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Slicer Training 1 Loading and Viewing Data

Slicer Training 1 Loading and Viewing Data

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Slicer Training 1 Loading and Viewing Data

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  1. Slicer Training 1 Loading and Viewing 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. Welcome to 3D Slicer

  5. Goal of the tutorial Guiding you step by step through the process of Loading and Viewing Data within Slicer

  6. 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 Exercises Questions Answers

  7. Goal of the tutorial Final result of the series of exercises

  8. Overview • Part 1: Slicer Interface • Part 2: Loading Data • Part 3: Interacting with Data

  9. Menu Viewer Tk window Slicer Interface

  10. Slicer Menu Select the Volumes Module

  11. Panels and Tabs The Panel of the Volumes Module appears

  12. Panels Sliders Buttons Control Window Slicer Menu

  13. File • Opening files • Saving files • Closing files • Exit • Modules • Slicer Modules • View • Selecting view mode • Help • Links to Slicer Modules information Main Menu Observe the different options of the Main Menu

  14. Viewer window Observe the Viewer Window • Upper part is 3D Viewer • Lower part is 2D Viewer 3 separate views Independent controls

  15. Slicer Modules The architecture of Slicer is modular Select Modules in the SubMenu

  16. Slicer Modules Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfiled Alpha The list of Slicer Modules categories appears

  17. fMRIEngine ………. SlicerTraining 5 • vtkFreeSurferReaders ... SlicerTraining 6 • Editor …………….. SlicerTraining 2 • Level-Sets ……….. SlicerTraining 3 • DTMRI ……………. SlicerTraining 4 Slicer Modules: tutorials Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfiled Alpha

  18. Exercise 1: Slicer GUI • Launch Slicer. • Observe Main window and Viewer window. • Click File, View, Help, and Modules • Examine submenus • Click Main Menu buttons: Data, Volumes, Models, Alignments, Editor, and ModelMaker • Click tabs • Examine panels • Click More • Click modules: click tabs, examine panels

  19. Overview • Part 1: Slicer Interface • Part 2: Loading Data • Part 3: Interacting with Data

  20. Loading Data Slicer can load • Volumes …………………..

  21. Loading Data Slicer can load • Volumes ………………….. • Models ……………………. A model is a 3D reconstruction of the anatomy

  22. Loading Data Slicer can load • Volumes ………………….. • Models ……………………. A model is a 3D reconstruction of the anatomy • Scenes ……………………. Scene = Volume + Model

  23. Loading Data Slicer Advantage Putting together Images and Surface

  24. Header Header Header Header Raw Data Raw Data Raw Data Raw Data Data representation • Volume = collection of image files • Image file = header + raw data The header contains the parameters of the image.

  25. Header Header Header Header Raw Data Raw Data Raw Data Raw Data Data representation • Volume = collection of image files • Image file = header + raw data The header contains the parameters of the image. • Representation of an image: 2D Array of pixels containing the intensity values a Pixel (a,b) b Intensity I (a,b)

  26. Loading DICOM Volumes Click on Add Volume in the Slicer Menu

  27. Loading DICOM Volumes The Panel Props appears by default. Left-click on the Menu Properties and change Basic to DICOM

  28. Loading DICOM Volumes The DICOM panel appears Click on Select DICOM Volume

  29. Loading DICOM Volumes Select the directory dicom in the Tutorial-with-dicom dataset

  30. Loading DICOM Volumes The list of DICOM studies appears. Click OK

  31. Loading DICOM Volumes Name : The name that the volume will have within Slicer Slicer loads the dicom study Change to something descriptive: Cortex and click on Header

  32. Loading DICOM Volumes The DICOM Header information panel appears Click Apply

  33. Loading DICOM Volumes Slicer loads the DICOM volume of the brain

  34. Visualization Support • Control Window: displays a zoomed view of the position of the mouse on the selected image Move the mouse inside an anatomical view

  35. Visualization Support The value of the gray level of the pixel under the cursor appears in the corresponding slice

  36. Viewing Volumes V toggle button controls whether slice is visible in 3D Viewer Click on the three V buttons to display the Axial, Sagittal and Coronal images inside the Viewer

  37. Viewing Volumes The Axial, Sagittal and Coronal Images appear in the Viewer

  38. Manipulating the images • Rotation Position the mouse on the images inside the Viewer Left-click and move the mouse to the left The images move to the left

  39. Manipulating the images • Zoom Position the mouse on the images inside the Viewer Right-click and move the mouse down The viewer gets closer to the model

  40. Manipulating the images • Zoom Position the mouse on the images inside the Viewer Right-click and move the mouse up The viewer moves away from the model

  41. Viewing Volumes The View Menu contains different options to visualize the data Select the 3D View

  42. Viewing Volumes 3D View focuses on 3D

  43. Viewing Volumes The View Menu contains different options to visualize the data Select 4x512

  44. Viewing Volumes 4x512 view: larger image views to see details

  45. Viewing Volumes The View Menu contains different options to visualize the data Select 1x512

  46. Viewing Volumes 1x512: one large TRANSVERSE view and three small images 1x512 COR: one large CORONAL view and three small images 1x512 SAG: one large SAGITTAL view and three small images

  47. Viewing Volumes The View Menu contains different options to visualize the data Select 4x256

  48. Viewing Volumes 4x256 view: smaller equal-sized images Come back to Normal View

  49. 2D Viewer 2 • Three 2D windows (red, yellow, and green) • Slider selects which slice of volume to display • Field shows the slice number 3 1 1 2 3

  50. 2D Viewer 4 • Bg (Background): displays volume in background layer • Fg (Foreground): displays volume in foreground layer Superimposed over the background layer 5 4 5