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Slicer Training 1: Loading and Viewing Data

Slicer Training 1: Loading and Viewing Data. Welcome to 3D Slicer . Goal of this tutorial. Guiding you step by step through the process of Loading and Viewing Data within Slicer. Material.

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Slicer Training 1: Loading and Viewing Data

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  1. Slicer Training 1: Loading and Viewing Data

  2. Welcome to 3D Slicer

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

  4. 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 20 Exercises Questions Answers

  5. Goal of the tutorial Final Result of the series of exercises

  6. Overview of Training 1 • Part 1: Slicer Interface • Part 2: Loading Data • Part 3: Viewing Data

  7. Slicer Interface Menu Viewer Tk window

  8. Slicer Menu Main Menu Panels Sliders Select the Volumes Module Buttons

  9. 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.

  10. Slicer Modules Click on More The list of Modules appears.

  11. Submenus • File • Opening files • Saving files • Close • Exit • View • Selecting view mode • Help • Links to Slicer information

  12. Viewer window • Upper part is 3D Viewer • Lower part is 2D Viewer • 3 separate views • Independent controls

  13. 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.

  14. Overview of Training 1 • Part 1: Slicer Interface • Part 2: Loading Data • Part 3: Viewing Data

  15. Loading Data Slicer can load • Volumes • Models • Scenes = Volumes + Models

  16. 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

  17. DICOM Volumes • Main  Data  Add Volume  Props • 2. From Properties Change Basic DICOM

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

  19. DICOM Volumes • Select or Deselect images to load: Selected images are green, Deselected images are red. • Increasing or Decreasing Loads images in either order.

  20. DICOM Volumes • 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. Also useful when several DICOM acquisitions are lumped together.

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

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

  23. Loading DICOM Volumes The Viewer contains the DICOM volume

  24. Loading 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

  25. Loading Volumes without Header The Header section of the Props tab appears.

  26. Loading 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

  27. 3 4 5 3 4 6 5 6 7 7 Loading Volumes without Header Pixel Size in the x and y directions. Slice Thickness z dimension of the voxel. Scan Order: • LR = left to right • IS = inferior to superior • PA = posterior to anterior Scalar Type: Data format of the pixel. Generally, it is Short (16 bit integer). • Slice Tilt: The tilt of the gantry during an MRI.

  28. 8 9 10 Loading Volumes without Header 8 • Num Scalars: • Number of scalar components for each voxel. Gray-scale data: 1. Color data: 3. • Little Endian: • In little-endian architectures, the rightmost bytes are most significant. In big-endian architectures (Slicer default), the leftmost bytes (those with a lower address) are most significant. • DTI data, Swap, No Swap: Placeholders for future. 9 10 Click Apply to read in the volume.

  29. Loading Volumes without Header The spgr volume appears in the Viewer

  30. Loading Data Slicer can load • Volumes • Models • Scenes = Volumes + Models

  31. Loading Models • A model is a 3D surface. 1. MainData Add Model Props tab appears. 2. Browse 3. Name field Give a name within Slicer. 4. Color pull-down menu select color for the 3D Viewer 5. Click Apply to read in the model. In dialog box, select the model named Vessels and click Open. Make descriptive: “Vessels“.

  32. Loading Models The model of the vessels appears in the Viewer.

  33. Loading Data Slicer can load • Volumes • Models • Scenes = Volumes + Models

  34. Loading a Scene File Open Scene. Find the scene tutorial.xml file, Double-click it, …Wait for the volumes and models to load.

  35. Loading a Scene tutorial Scene

  36. Overview of Training 1 • Part 1: Slicer Interface • Part 2: Loading Data • Part 3: Viewing Data

  37. Manipulating Model The model appears in the 3D Viewer: Rotate the model: with left mouse button. Zoom the model: with right mouse button.

  38. Model Opacity • Click on Models in the Main Menu • Select the Display Tab The properties Panel of the model appears 3. Opacity Set the opacity of the Skin model to 0.5

  39. Model Opacity Skin model Opacity = 0.5

  40. Model Visibility Visibility on and off by left clicking on the name of model in the list Left Click on the Vessels Button in the list of the models

  41. Model Visibility Vessels model Visibility 0ff

  42. Global Visibility Show All to display all models in the 3D Viewer. Click Show None to display none of the models in the 3D Viewer

  43. Viewing 3D Models Show None Models have disappeared

  44. Viewing Volumes (1 of 5) 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 in the Viewer

  45. Viewing Volumes (1 of 5) The Axial, Sagittal and Coronal Images appear in the Viewer

  46. Viewing Volumes (1 of 5) • View Menu contains different options to visualize the data Select the 3D View

  47. Viewing Volumes 3D view: focuses on 3D.

  48. Viewing Volumes (1 of 5) • View Menu contains different options to visualize the data Select 4x512

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

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

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