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Data Loading and Visualization

Slicer3 Training Compendium. Data Loading and Visualization. Sonia Pujol, PhD Randy Gollub, MD, PhD. Material. This course requires the installation of the Slicer3 software and training dataset accessible at the following locations: Slicer 3 Software

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Data Loading and Visualization

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  1. Slicer3 Training Compendium Data Loading and Visualization Sonia Pujol, PhD Randy Gollub, MD, PhD

  2. Material This course requires the installation of the Slicer3 software and training dataset accessible at the following locations: • Slicer 3 Software http://www.na-mic.org/Wiki/index.php/Slicer:Slicer3 • Training Dataset 1 http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 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.

  3. Data This course is built upon three datasets of a single healthy subject brain: Pre-computed Label Map MR DICOM GRASS MR Nrrd SPGR

  4. 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.

  5. 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

  6. Part 1: Loading and visualizing multiple volumes simultaneously

  7. 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

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

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

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

  11. Loading Volumes Click on Select Volume File

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

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

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

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

  16. 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)

  17. Exploring the data Click on the choose view icon

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

  19. Exploring the data The axial slices of the dicom volume appear in the 3D viewer.

  20. Exploring the data Click on the slices fit to window icon

  21. Exploring the data Slicer automatically adjusts the dimensions of the image to the size of the window.

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

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

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

  25. Loading Volumes Click on Select Volume File

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

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

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

  29. Visualizing multiple volumes To simultaneously view the dicom and the nrrd volumes, left click on the drop-down menu to the right of theForeground icon and select the image 001.dcm Click on the links icon.

  30. Visualizing multiple volumes Use the slider from the Slice View controller to fade between Background and Foreground views.

  31. Visualizing multiple volumes Click on either the Background icon or the Foreground icon to display the Nrrd or the DICOM volumes in the Slice Viewer

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

  33. Loading a label map Click on Select Volume File

  34. 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

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

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

  37. Visualizing Multiple Volumes Background Viewer Left click the drop-down menu to the right of the B icon and select the labelmap all Label Viewer Left click the drop-down menu to the right of the L icon and select None

  38. Visualizing Multiple Volumes Foreground Viewer Left click on the drop-down menu to the right of the F icon and select the volume spgr

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

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

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

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

  43. Part 3: Loading and visualizing 3D models

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

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

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

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

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

  49. Visualizing a 3D model Use the slider to lower the opacity of the 3D model.

  50. Visualizing a 3D model The 3D models of the vessels and the ventricles appear through the skin.

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