1. Surgical Planning Laboratory http://www.slicer.org -1- Brigham and Women’s Hospital Slicer Training 1: Loading and Viewing Data

2. Surgical Planning Laboratory http://www.slicer.org -2- Brigham and Women’s Hospital Welcome to 3D Slicer

3. Surgical Planning Laboratory http://www.slicer.org -3- Brigham and Women’s Hospital Goal of this tutorial Guiding you step by step through the process of Loading and Viewing Data within Slicer

4. Surgical Planning Laboratory http://www.slicer.org -4- Brigham and Women’s Hospital Material Slicer2.5: https://share.spl.harvard.edu/share/birn/public/so ftware/slicer2.5/slicer2.5-opt-win32-2005-05- 23.zip Tutorial Data: tutorial-with-dicom.zip QuestionsAnswers 20 Exercises

5. Surgical Planning Laboratory http://www.slicer.org -5- Brigham and Women’s Hospital Goal of the tutorial Final Result of the series of exercises

6. Surgical Planning Laboratory http://www.slicer.org -6- Brigham and Women’s Hospital Overview of Training 1 Part 1: Slicer Interface Part 2: Loading Data Part 3: Viewing Data

7. Surgical Planning Laboratory http://www.slicer.org -7- Brigham and Women’s Hospital Slicer Interface Viewer Menu Tk window

8. Surgical Planning Laboratory http://www.slicer.org -8- Brigham and Women’s Hospital Slicer Menu Main Menu Panels Sliders Buttons Select the Volumes Module

9. Surgical Planning Laboratory http://www.slicer.org -9- Brigham and Women’s Hospital Panels and Tabs Each panel has tabs along the top. Leftmost tab is Help. Panel may contain controls and displays. The Panel of the Volumes Module appears

10. Surgical Planning Laboratory http://www.slicer.org -10- Brigham and Women’s Hospital Slicer Modules Click on More The list of Modules appears.

11. Surgical Planning Laboratory http://www.slicer.org -11- Brigham and Women’s Hospital Submenus File –Opening files –Saving files –Close –Exit View –Selecting view mode Help –Links to Slicer information

12. Surgical Planning Laboratory http://www.slicer.org -12- Brigham and Women’s Hospital Viewer window Upper part is 3D Viewer Lower part is 2D Viewer –3 separate views –Independent controls

13. Surgical Planning Laboratory http://www.slicer.org -13- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -14- Brigham and Women’s Hospital Overview of Training 1 Part 1: Slicer Interface Part 2: Loading Data Part 3: Viewing Data

15. Surgical Planning Laboratory http://www.slicer.org -15- Brigham and Women’s Hospital Loading Data Slicer can load Volumes Models Scenes = Volumes + Models

16. Surgical Planning Laboratory http://www.slicer.org -16- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -17- Brigham and Women’s Hospital 1.Main  Data  Add Volume  Props 2. From Properties Change Basic  DICOM DICOM Volumes

18. Surgical Planning Laboratory http://www.slicer.org -18- Brigham and Women’s Hospital 3. Select DICOM Volume A dialog box appears 4. Select directory and click OK DICOM Volumes DICOM panel appears Slicer searches for every DICOM file.

19. Surgical Planning Laboratory http://www.slicer.org -19- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -20- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -21- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -22- Brigham and Women’s Hospital Loading DICOM Volumes The DICOM Header information panel appears …Slicer loads the data Click Apply

23. Surgical Planning Laboratory http://www.slicer.org -23- Brigham and Women’s Hospital Loading DICOM Volumes The Viewer contains the DICOM volume

24. Surgical Planning Laboratory http://www.slicer.org -24- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -25- Brigham and Women’s Hospital The Header section of the Props tab appears. Loading Volumes without Header

26. Surgical Planning Laboratory http://www.slicer.org -26- Brigham and Women’s Hospital 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. Loading Volumes without Header 2 1 The Header section of the Props tab appears.

27. Surgical Planning Laboratory http://www.slicer.org -27- Brigham and Women’s Hospital 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. 3 4 5 6 7 3 4 5 6 7

28. Surgical Planning Laboratory http://www.slicer.org -28- Brigham and Women’s Hospital 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. Loading Volumes without Header 8 9 10 8 9 Click Apply to read in the volume.

29. Surgical Planning Laboratory http://www.slicer.org -29- Brigham and Women’s Hospital Loading Volumes without Header The spgr volume appears in the Viewer

30. Surgical Planning Laboratory http://www.slicer.org -30- Brigham and Women’s Hospital Loading Data Slicer can load Volumes Models Scenes = Volumes + Models

31. Surgical Planning Laboratory http://www.slicer.org -31- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -32- Brigham and Women’s Hospital Loading Models The model of the vessels appears in the Viewer.

33. Surgical Planning Laboratory http://www.slicer.org -33- Brigham and Women’s Hospital Loading Data Slicer can load Volumes Models Scenes = Volumes + Models

34. Surgical Planning Laboratory http://www.slicer.org -34- Brigham and Women’s Hospital Loading a Scene File  Open Scene. Find the scene tutorial.xml file, Double-click it, …Wait for the volumes and models to load.

35. Surgical Planning Laboratory http://www.slicer.org -35- Brigham and Women’s Hospital Loading a Scene tutorial Scene

36. Surgical Planning Laboratory http://www.slicer.org -36- Brigham and Women’s Hospital Overview of Training 1 Part 1: Slicer Interface Part 2: Loading Data Part 3: Viewing Data

37. Surgical Planning Laboratory http://www.slicer.org -37- Brigham and Women’s Hospital Manipulating Model The model appears in the 3D Viewer : Rotate the model: with left mouse button. Zoom the model: with right mouse button.

38. Surgical Planning Laboratory http://www.slicer.org -38- Brigham and Women’s Hospital Model Opacity 1.Click on Models in the Main Menu 2.Select the Display Tab The properties Panel of the model appears 3. Opacity Set the opacity of the Skin model to 0.5

39. Surgical Planning Laboratory http://www.slicer.org -39- Brigham and Women’s Hospital Model Opacity Skin model Opacity = 0.5

40. Surgical Planning Laboratory http://www.slicer.org -40- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -41- Brigham and Women’s Hospital Model Visibility Vessels model Visibility 0ff

42. Surgical Planning Laboratory http://www.slicer.org -42- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -43- Brigham and Women’s Hospital Viewing 3D Models Show None  Models have disappeared

44. Surgical Planning Laboratory http://www.slicer.org -44- Brigham and Women’s Hospital 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. Surgical Planning Laboratory http://www.slicer.org -45- Brigham and Women’s Hospital Viewing Volumes (1 of 5) The Axial, Sagittal and Coronal Images appear in the Viewer

46. Surgical Planning Laboratory http://www.slicer.org -46- Brigham and Women’s Hospital Viewing Volumes (1 of 5) 1.View Menu contains different options to visualize the data Select the 3D View

47. Surgical Planning Laboratory http://www.slicer.org -47- Brigham and Women’s Hospital Viewing Volumes 3D view: focuses on 3D.

48. Surgical Planning Laboratory http://www.slicer.org -48- Brigham and Women’s Hospital Viewing Volumes (1 of 5) 1.View Menu contains different options to visualize the data Select 4x512

49. Surgical Planning Laboratory http://www.slicer.org -49- Brigham and Women’s Hospital Viewing Volumes 4x512 view: larger image views to see details

50. Surgical Planning Laboratory http://www.slicer.org -50- Brigham and Women’s Hospital Viewing Volumes (1 of 5) 1.View Menu contains different options to visualize the data Select 1x512

51. Surgical Planning Laboratory http://www.slicer.org -51- Brigham and Women’s Hospital Viewing Volumes 1x512 view: one large, three small images.

52. Surgical Planning Laboratory http://www.slicer.org -52- Brigham and Women’s Hospital Viewing Volumes (1 of 5) 1.View Menu contains different options to visualize the data Select 4x256

53. Surgical Planning Laboratory http://www.slicer.org -53- Brigham and Women’s Hospital Viewing Volumes 4x256 view: smaller equal-sized images. Come back to Normal View

54. Surgical Planning Laboratory http://www.slicer.org -54- Brigham and Women’s Hospital 2D Viewer 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. 1 2 1 2 3 3

55. Surgical Planning Laboratory http://www.slicer.org -55- Brigham and Women’s Hospital Superimpose Bg (background): displays volume in background layer. Fg (foreground): displays volume in foreground layer. –Superimposed over the background layer. 4 5 4 5

56. Surgical Planning Laboratory http://www.slicer.org -56- Brigham and Women’s Hospital 2D Viewer Lb : displays label map Displays results of a segmentation. Left click on Lb in the Axial View and select the Label Map named all

57. Surgical Planning Laboratory http://www.slicer.org -57- Brigham and Women’s Hospital 2D Viewer Images in the label map layer appear as outlines around the structures that were segmented.

58. Surgical Planning Laboratory http://www.slicer.org -58- Brigham and Women’s Hospital 2D Viewer Left Click on Fg in the Axial View and select the Volume named all

59. Surgical Planning Laboratory http://www.slicer.org -59- Brigham and Women’s Hospital 2D Viewer The volume is superimposed to the images

60. Surgical Planning Laboratory http://www.slicer.org -60- Brigham and Women’s Hospital Image Fusion Fade slider: fades between foreground and background. Set the Fade slider to 0.5

61. Surgical Planning Laboratory http://www.slicer.org -61- Brigham and Women’s Hospital 2D Viewer Fade slider effect

62. Surgical Planning Laboratory http://www.slicer.org -62- Brigham and Women’s Hospital Clipping Models Clipping: cutting away sections of a model at one or more selected slices. The model is removed from one side of each selected slice, revealing the image of each selected slice and the rest of the visible model. Models  Display tab

63. Surgical Planning Laboratory http://www.slicer.org -63- Brigham and Women’s Hospital 1. Click on Show all to make all the models visible 2. Right-click the Skin Model in the list. A drop-down menu appears. 3. Select Clipping. 4. Select the Clip tab of the Models panel Clipping Models

64. Surgical Planning Laboratory http://www.slicer.org -64- Brigham and Women’s Hospital Clipping Models Click + or - to select which side of each slice to clip on. Set the sides to: Red Slice + Yellow Slice – Green Slice -

65. Surgical Planning Laboratory http://www.slicer.org -65- Brigham and Women’s Hospital Clipping Models Clipping Model Result

66. Surgical Planning Laboratory http://www.slicer.org -66- Brigham and Women’s Hospital Conclusion Intuitive Interface for Loading/Visualizing Data Each Slicer module contains tools for –Visualizing –Registering –Segmenting – Modeling –Quantifying Open-source tool for developing your own module