1. Pujol S, Gollub R -1- National Alliance for Medical Image Computing Data Loading and Visualization Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard Medical School

2. Pujol S, Gollub R -2- National Alliance for Medical Image Computing 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. Pujol S, Gollub R -3- National Alliance for Medical Image Computing 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.

4. Pujol S, Gollub R -4- National Alliance for Medical Image Computing Data This course is built upon three datasets of a single healthy subject brain: MR DICOM GRASS MR Nrrd SPGR Pre-computed Label Map

5. Pujol S, Gollub R -5- National Alliance for Medical Image Computing Learning objective Following this tutorial, youll be able to load and visualize volumes within Slicer3, and to interact in 3D with structural images and models.

6. Pujol S, Gollub R -6- National Alliance for Medical Image Computing 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. Pujol S, Gollub R -7- National Alliance for Medical Image Computing Launch Slicer3 Slicer3 Slicer3-build Slicer3-lib Launch Slicer3 from the directory Slicer3-build Mac/Linux Run./Slicer3 in Slicer3-build/ Windows Run./Slicer3.exe in Slicer3-build/

8. Pujol S, Gollub R -8- National Alliance for Medical Image Computing Slicer3 GUI 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 Slice Viewer 3DViewer Module GUI Panel Slice and 3D View Controller Menu Toolbar

9. Pujol S, Gollub R -9- National Alliance for Medical Image Computing Part 1: Loading and visualizing multiple volumes simultaneously

10. Pujol S, Gollub R -10- National Alliance for Medical Image Computing Loading Volumes The Data module is the module displayed by default in the GUI.

11. Pujol S, Gollub R -11- National Alliance for Medical Image Computing Loading Volumes Left-click on the module selection menu to load the module Volumes

12. Pujol S, Gollub R -12- National Alliance for Medical Image Computing Loading Volumes The panel of the module Volumes appears in the interface.

13. Pujol S, Gollub R -13- National Alliance for Medical Image Computing Loading Volumes Click on Select Volume File

14. Pujol S, Gollub R -14- National Alliance for Medical Image Computing Loading Volumes Browse to find the first image 001.dcm of the dataset located in the directory SlicerSampleVisualization/dicom and click on Open

15. Pujol S, Gollub R -15- National Alliance for Medical Image Computing Loading Volumes Select Image Origin: Centered Click on Apply to load the DICOM dataset

16. Pujol S, Gollub R -16- National Alliance for Medical Image Computing Loading Volumes The DICOM images appear in the Background display of the 2DViewer.

17. Pujol S, Gollub R -17- National Alliance for Medical Image Computing Loading Volumes Click on the tab Info to display the characteristics of the DICOM volume

18. Pujol S, Gollub R -18- National Alliance for Medical Image Computing 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)

19. Pujol S, Gollub R -19- National Alliance for Medical Image Computing Click on the choose view icon Exploring the data

20. Pujol S, Gollub R -20- National Alliance for Medical Image Computing Select the red slice only layout from the menu Exploring the data

21. Pujol S, Gollub R -21- National Alliance for Medical Image Computing Exploring the data The axial slices of the dicom volume appear in the 3D viewer.

22. Pujol S, Gollub R -22- National Alliance for Medical Image Computing Exploring the data Click on the slices fit to window icon

23. Pujol S, Gollub R -23- National Alliance for Medical Image Computing Exploring the data Slicer automatically adjusts the dimensions of the image to the size of the window.

24. Pujol S, Gollub R -24- National Alliance for Medical Image Computing Exploring the data Browse the images using the slider to display the ventricles (~slice 38)

25. Pujol S, Gollub R -25- National Alliance for Medical Image Computing Exploring the data Click on the conventional layout icon to come back to the standard view

26. Pujol S, Gollub R -26- National Alliance for Medical Image Computing Loading Volumes Click on the adjust slices fit to window icon

27. Pujol S, Gollub R -27- National Alliance for Medical Image Computing Loading Volumes Click on Select Volume File

28. Pujol S, Gollub R -28- National Alliance for Medical Image Computing Loading Volumes Browse to find the header file of the spgr volume spgr.nhdr located in the directory SlicerSampleVisualization/nrrd and click on Open.

29. Pujol S, Gollub R -29- National Alliance for Medical Image Computing Loading Volumes Select Image Origin: Centered and Click on Apply

30. Pujol S, Gollub R -30- National Alliance for Medical Image Computing Loading Volumes The spgr images appear in the Background display of the 2DViewer.

31. Pujol S, Gollub R -31- National Alliance for Medical Image Computing Visualizing multiple volumes To simultaneously view the dicom and the nrrd volumes, left click on the drop-down menu to the right of the Foreground icon and select the image 001.dcm Click on the links icon.

32. Pujol S, Gollub R -32- National Alliance for Medical Image Computing Visualizing multiple volumes Use the slider from the Slice View controller to fade between Background and Foreground views.

33. Pujol S, Gollub R -33- National Alliance for Medical Image Computing 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

34. Pujol S, Gollub R -34- National Alliance for Medical Image Computing 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

35. Pujol S, Gollub R -35- National Alliance for Medical Image Computing Part 2: Loading and visualizing segmented structures overlaid on grayscale images

36. Pujol S, Gollub R -36- National Alliance for Medical Image Computing Loading a label map Click on Select Volume File

37. Pujol S, Gollub R -37- National Alliance for Medical Image Computing 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

38. Pujol S, Gollub R -38- National Alliance for Medical Image Computing Visualizing a label map Set Image Origin to Centered, Check the Label Map box and click on Apply

39. Pujol S, Gollub R -39- National Alliance for Medical Image Computing Visualizing a label map Slicer displays the label map all in the Label layer

40. Pujol S, Gollub R -40- National Alliance for Medical Image Computing 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

41. Pujol S, Gollub R -41- National Alliance for Medical Image Computing Visualizing Multiple Volumes Foreground Viewer Left click on the drop- down menu to the right of the F icon and select the volume spgr

42. Pujol S, Gollub R -42- National Alliance for Medical Image Computing Visualizing Multiple Volumes Select Manipulate Slice Views Use the slider to fade between the labelmap all (Background) and the spgr volume (Foreground).

43. Pujol S, Gollub R -43- National Alliance for Medical Image Computing Visualizing Multiple Volumes Select the Red Slice View mode Select the red slice only layout from the menu

44. Pujol S, Gollub R -44- National Alliance for Medical Image Computing Visualizing Multiple Volumes Browse to display the segmented ventricles overlaid on the spgr images (slice 41)

45. Pujol S, Gollub R -45- National Alliance for Medical Image Computing Visualizing Multiple Volumes Browse to display the segmented ventricles overlaid on the spgr images (~slice 41)

46. Pujol S, Gollub R -46- National Alliance for Medical Image Computing 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

47. Pujol S, Gollub R -47- National Alliance for Medical Image Computing Part 3: Loading and visualizing 3D models

48. Pujol S, Gollub R -48- National Alliance for Medical Image Computing Loading a 3D model Select the module Models from the main menu

49. Pujol S, Gollub R -49- National Alliance for Medical Image Computing Loading a 3D model Click on Load Model Directory and select the directory models: SlicerSampleVisualization/models/

50. Pujol S, Gollub R -50- National Alliance for Medical Image Computing Loading a 3D model Slicer loads the 3D models of the skin, the ventricles and the vessels.

51. Pujol S, Gollub R -51- National Alliance for Medical Image Computing Loading a 3D model Click on the panel Hierachy and Display to access the modules display components

52. Pujol S, Gollub R -52- National Alliance for Medical Image Computing Visualizing a 3D model Select the model Skin.vtk Click on the icon Set Color and choose a new color for the 3D model of the head.

53. Pujol S, Gollub R -53- National Alliance for Medical Image Computing Visualizing a 3D model Use the slider to lower the opacity of the 3D model.

54. Pujol S, Gollub R -54- National Alliance for Medical Image Computing Visualizing a 3D model The 3D models of the vessels and the ventricles appear through the skin.

55. Pujol S, Gollub R -55- National Alliance for Medical Image Computing Visualizing a 3D model Select the model Vessels.vtk and change the color of the vasculature

56. Pujol S, Gollub R -56- National Alliance for Medical Image Computing Manipulating a 3D model Click on the R letter (Right) in the control window

57. Pujol S, Gollub R -57- National Alliance for Medical Image Computing Manipulating a 3D model The 3D Viewer shows the model from the right side of the patient

58. Pujol S, Gollub R -58- National Alliance for Medical Image Computing Manipulating a 3D model Position the mouse in the 3D Viewer, hold down the left mouse button and drag to rotate the model.

59. Pujol S, Gollub R -59- National Alliance for Medical Image Computing Manipulating a 3D model Hold down the right mouse button, and move the mouse up and down to zoom out and in.

60. Pujol S, Gollub R -60- National Alliance for Medical Image Computing Manipulating a 3D model Click on the A letter to display the standard Anterior View. Click on the Spin icon

61. Pujol S, Gollub R -61- National Alliance for Medical Image Computing Manipulating a 3D model The model starts spinning inside the Viewer Panel.

62. Pujol S, Gollub R -62- National Alliance for Medical Image Computing Manipulating a 3D model Click on the icon Rock

63. Pujol S, Gollub R -63- National Alliance for Medical Image Computing Manipulating a 3D model The model starts rocking inside the Viewer Panel.

64. Pujol S, Gollub R -64- National Alliance for Medical Image Computing Manipulating a 3D model Click on the Slice Visibility icon to display the slices in the 3D Viewer

65. Pujol S, Gollub R -65- National Alliance for Medical Image Computing Manipulating the images The anatomical slices appear in the 3D Viewer.

66. Pujol S, Gollub R -66- National Alliance for Medical Image Computing Manipulating the images Use the sliders to slice through the volume in the anterior-posterior direction.

67. Pujol S, Gollub R -67- National Alliance for Medical Image Computing Manipulating the images Set the opacity of the Skin model to 1.0, and select the option clipping

68. Pujol S, Gollub R -68- National Alliance for Medical Image Computing Manipulating the images Scroll down and expand the component Clipping.

69. Pujol S, Gollub R -69- National Alliance for Medical Image Computing Manipulating the images Set the Red Slice Clipping, Yellow Slice Clipping and Green Slice Clipping to Negative Space

70. Pujol S, Gollub R -70- National Alliance for Medical Image Computing Manipulating the images Slicer displays the result of the clipping.

71. Pujol S, Gollub R -71- National Alliance for Medical Image Computing 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

72. Pujol S, Gollub R -72- National Alliance for Medical Image Computing Part 4: Loading and saving a Scene

73. Pujol S, Gollub R -73- National Alliance for Medical Image Computing Saving Data Click on File and Select Save

74. Pujol S, Gollub R -74- National Alliance for Medical Image Computing Saving Data The list of elements currently loaded into Slicer3 appears.

75. Pujol S, Gollub R -75- National Alliance for Medical Image Computing Saving Data Click on Scene File to browse to the location where the scene will be saved

76. Pujol S, Gollub R -76- National Alliance for Medical Image Computing Saving Data Enter the name MyScene.mrml, and click on Save

77. Pujol S, Gollub R -77- National Alliance for Medical Image Computing Saving Data Check the box Save Scene and click on Save

78. Pujol S, Gollub R -78- National Alliance for Medical Image Computing Creating Scene Snapshots Select the module Data, and click on Create Scene Snapshot

79. Pujol S, Gollub R -79- National Alliance for Medical Image Computing Creating Scene Snapshots Enter the Snapshot Name MySceneSnapshot1 and click on OK

80. Pujol S, Gollub R -80- National Alliance for Medical Image Computing Creating Scene Snapshots Select a Superior view of the dataset, and click on Create Scene Snapshot

81. Pujol S, Gollub R -81- National Alliance for Medical Image Computing Creating Scene Snapshots Enter the name MySceneSnapshot2 and click on OK

82. Pujol S, Gollub R -82- National Alliance for Medical Image Computing Creating Scene Snapshots Select File Save and click on Save to include the two scene snapshots in the saved scene

83. Pujol S, Gollub R -83- National Alliance for Medical Image Computing Saving Data Select File Close Scene in the main menu and click on OK

84. Pujol S, Gollub R -84- National Alliance for Medical Image Computing Saving Data The elements of the previous scene disappear from the Viewer.

85. Pujol S, Gollub R -85- National Alliance for Medical Image Computing Saving Data Select File Load Scene from the main menu

86. Pujol S, Gollub R -86- National Alliance for Medical Image Computing Saving Data Select the file myScene.mrml and click on Open

87. Pujol S, Gollub R -87- National Alliance for Medical Image Computing Loading a Scene Slicer loads the elements from the scene myScene.mrml

88. Pujol S, Gollub R -88- National Alliance for Medical Image Computing Loading a Scene Browse to select MySceneSnapshot2, and click on Restore

89. Pujol S, Gollub R -89- National Alliance for Medical Image Computing Loading a Scene Slicer restores scene snapshot MySceneSnapshot2

90. Pujol S, Gollub R -90- National Alliance for Medical Image Computing 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

91. Pujol S, Gollub R -91- National Alliance for Medical Image Computing Conclusion Interactive interface to load and manipulate grayscale volumes and labelmaps 3D interaction with anatomical views Open-source platforms for Linux, Mac and Windows

92. Pujol S, Gollub R -92- National Alliance for Medical Image Computing Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218