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Slicer Training 1 Loading and Viewing Data

Slicer Training 1 Loading and Viewing Data. Sonia Pujol, Ph.D. Randy Gollub, M.D., Ph.D. Acknowledgments. National Alliance for Medical Imaging NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218. Disclaimer. It is the responsibility of the user of 3DSlicer

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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 Imaging 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 this tutorial Guiding you step by step through the process of Loading and Viewing Data within Slicer

  6. Material • Slicer2.5: https://share.spl.harvard.edu/share/birn/public/software/slicer2.5/slicer2.5-opt-win32-2005-05-23.zip • Tutorial Data: tutorial-with-dicom.zip 35 Exercises Questions Answers

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

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

  9. Slicer Interface Menu Viewer Tk window

  10. Slicer Menu Main Menu Panels Sliders Select the Volumes Module Buttons Control Window

  11. Panels and Tabs The Panel of the Volumes Module appears • Each panel has tabs along the top • Leftmost tab is Help • Panel may contain controls and displays

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

  13. Slicer Modules Settings IO Application Filtering Segmentation Registration Measurement Visualization Examples Unfield Alpha The list of Slicer Modules appears

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

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

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

  17. 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

  18. Overview of Training 1 • Part 1: Slicer Interface • Part 2: Loading Data • Part 3: Interacting with Data

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

  20. Loading Data Slicer Power Putting together Images and Surface

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

  22. 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)

  23. Loading Volumes: Overview 1. Main  Data 2. Add Volume Props tab of Volumes panel appears 3. Browse to find the first image 4. Select first image of volume to load, and click Open The number of the last image automatically appears 5.Apply

  24. DICOM Volumes 1. Main  Data  Add Volume  Props 2. From Properties Change Basic DICOM

  25. DICOM Volumes A DICOM panel appears 3. Select DICOM Volume A dialog box appears 4. Select directory and click OK Slicer searches for every DICOM file.

  26. DICOM Volumes • Name The name that the volume will have within Slicer • Optional Description You may enter a description. 5.Change to something descriptive: “Cortex“ 6. Click Header

  27. Loading DICOM Volumes The DICOM Header information panel appears …Slicer loads the data 7. Click Apply

  28. 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 The value of the gray level of the pixel under the cursor appears in the corresponding slice

  29. 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

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

  31. 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

  32. 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

  33. 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

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

  35. Viewing Volumes 3D View focuses on 3D

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

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

  38. Viewing Volumes (1 of 5) The View Menu contains different options to visualize the data Select 1x512

  39. Viewing Volumes 1x512 view: one large, three small images

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

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

  42. 2D Viewer 2 • Three 2D windows (red, yellow, and green) Both grayscale and label map images in windows • Slider selects which slice of volume to display • Field shows the slice number 3 1 1 2 3

  43. Superimpose 4 • Bg (Background): displays volume in background layer • Fg (Foreground): displays volume in foreground layer Superimposed over the background layer 5 4 5

  44. 2D Viewer • Lb: displays label map Displays results of a segmentation 6 6 Left click on Lb in the Axial View and select the Label Map named all

  45. 2D Viewer Images in the label map layer appear as outlines around the structures that were segmented.

  46. 2D Viewer Left Click on Fg in the Axial View and select the Volume named all

  47. Volumes without Header Motivations: • The DICOM file format incorporates all the parameters that Slicer requires to render the data • Other images files types may not Slicer has a simple protocol for loading volumes without header

  48. Volumes without Header 1. Main  Data 2. Add Volume 3. Browse to find the first image of the Volume spgr 4. Select first image I.001 of volume to load, and click Open 5.Click on Manual 6. Click on Apply

  49. Volumes without Header • Preview • small icon-size images in bottom panel (default size is 32x32 pixels) • List Headers • displays header information • Check • displays information about how to group the data • helps to show when slices are missing • useful when several DICOM acquisitions are lumped together. Click OK

  50. Volumes without Header The Header section of the Props tab appears. File Pattern: Pattern of file names, in C syntax. Example: a file named skin.001 has a pattern of %s.%03d. Image Size: Number of pixels of image in x and y directions. 1 2

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