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3D Visualization

3D Visualization

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3D Visualization

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  1. 3D Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School Leonardo da Vinci (1452-1519), Virgin and Child Alte Pinakothek, München

  2. Slicer3 • An end-user application for image analysis • An open-source environment for software development • A software platform that is both easy to use for clinical researchers and easy to extend for programmers

  3. Material This course requires the installation of the Slicer3 software and training dataset • Slicer 3 Software: www.slicer.org/pages/Downloads • Training Dataset: SlicerSampleVisualization.tar.gz 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. Data This course is built upon three datasets of a single healthy subject brain: Pre-computed Label Map MR DICOM GRASS MR Nrrd SPGR tar –zxvf SlicerSampleVisualization.tar.gz

  5. Learning objective Following this tutorial, you’ll be ableto load and visualize volumes within Slicer3,and to interact in 3D with structural images and models.

  6. Overview • Loading and visualizing multiple volumes simultaneously • Loading and visualizing segmented structures overlaid on grayscale images • Loading and visualizing 3D models • Loading and saving a scene

  7. Launch Slicer3 • If you have downloaded a pre-compiled version of the software, launch Slicer3 from the directory Slicer3 3.2.2008-08-08/: Mac/Linux Run ‘./Slicer3’ in Slicer3-3.2.2008-08-08/ Windows Run ‘./Slicer3’ in Program Files/Slicer3 3.2.2008-08-08/ or launch Start All Programs  Slicer3 3.2.2008-08-08/Slicer

  8. Slicer3 Slicer3-build Slicer3-lib Launch Slicer3 • If you have built a version of Slicer3 on your machine, launch Slicer3 from the directory Slicer3-build: Mac/Linux/Windows Run ‘./Slicer3’ in Slicer3-build/

  9. Slicer3 GUI Menu Toolbar • The Graphical User Interface (GUI) of Slicer3 integrates five components: • the Menu Toolbar • the Module GUI Panel • the 3D Viewer • the Slice Viewer • the Slice and 3D View Controller 3DViewer Module GUI Panel Slice Viewer Slice and 3D View Controller

  10. Part 1: Loading and visualizing multiple volumes simultaneously

  11. Loading Volumes The Data module is the module displayed by default in the GUI.

  12. Loading Volumes Left-click on the module selection menu to load the module Volumes

  13. Loading Volumes The panel of the module Volumes appears in the interface.

  14. Loading Volumes Click on Select Volume File

  15. Loading Volumes Browse to find the first image 001.dcm of the dataset located in the directory SlicerSampleVisualization/dicom and click on Open

  16. Loading Volumes Select Image Origin: Centered Click on Apply to load the DICOM dataset

  17. Loading Volumes The DICOM images appear in the Background display of the 2DViewer.

  18. Loading Volumes Click on the tab Info to display the characteristics of the DICOM volume

  19. Viewing Volume Information • The information contained in the DICOM header appears in the interface: • Volume dimensions: 256 x 256 x 124 • Volume Spacing: 0.9375x0.9375x1.3 mm • Scan Order: LR • Scalar Type: Short • Image Origin: (-79.95, 119.53,119.53)

  20. Exploring the data Click on the choose view icon

  21. Exploring the data Select the red slice onlylayout from the menu

  22. Exploring the data The axial slices of the dicom volume appear in the 3D viewer. Slicer automatically adjusts the dimensions of the image to the size of the window.

  23. Exploring the data Browse the images using the slider to display the ventricles (~slice 38)

  24. Exploring the data Click on the conventional layout icon to come back to the standard view

  25. Loading Volumes Click on the ‘adjust slices fit to window’ icon

  26. Loading Volumes Click on Select Volume File

  27. Loading Volumes Browse to find the header file of the volume spgr.nhdr located in the directory SlicerSampleVisualization/nrrd and click on Open.

  28. Loading Volumes Select Image Origin: Centered and Click on Apply

  29. Loading Volumes The spgr images appear in the Background display of the 2DViewer.

  30. Loading Volumes Select the module Data from the Modules Menu.

  31. Loading Volumes The two datasets 001.dcm ad spgr.nhdr are loaded in Slicer.

  32. Overview • Loading and visualizing multiple volumes simultaneously • Loading and visualizing segmented structures overlaid on grayscale images • Loading and visualizing 3D models • Loading and saving a scene

  33. Part 2: Loading and visualizing segmented structures overlaid on grayscale images

  34. Loading a label map Come back to the module Volumes and click on Select Volume File

  35. Loading a label map Browse to find the header file all.nhdr of the label map dataset located in the directory SlicerSampleVisualization/nrrd and click on Open

  36. Visualizing a label map Set Image Origin to Centered, Check the Label Map box and click on Apply

  37. Visualizing a label map Slicer displays the label map all in the Label layer

  38. Visualizing Multiple Volumes Foreground Viewer Left click the drop-down menu to the right of the F icon and select the labelmap all Label Viewer Left click the drop-down menu to the right of the L icon and select None

  39. Visualizing Multiple Volumes Background Viewer Left click on the drop-down menu to the right of the B icon and select the volume spgr

  40. Visualizing Multiple Volumes Use the slider to fade between the labelmap all (Foreground) and the spgr volume (Background). Select Manipulate Slice Views

  41. Visualizing Multiple Volumes Select the red slice only layout from the menu Select the Red Slice View mode

  42. Visualizing Multiple Volumes Browse to display the segmented ventricles overlaid on the spgr images (~slice 41)

  43. Overview • Loading and visualizing multiple volumes simultaneously • Loading and visualizing segmented structures overlaid on grayscale images • Loading and visualizing 3D models • Loading and saving a scene

  44. Part 3: Loading and visualizing 3D models

  45. Loading a 3D model Select the module Models from the main menu

  46. Loading a 3D model Click on Load Model Directory and select the directory models: SlicerSampleVisualization/models/

  47. Loading a 3D model Slicer loads the 3D models of the skin, the ventricles and the vessels.

  48. Loading a 3D model Click on the Display panel to access the module’s display components

  49. Loading a 3D model Select the model Skin.vtk and scroll down in the Display window to display the icon Set Color.

  50. Visualizing a 3D model Click on the icon Set Color and choose a new color for the 3D model of the head.