1. Session 1 Loading and Viewing Data
National Alliance for Medical Image Computing
3DSlicer Training Workshop
NCBC AHM
Session 1 Loading and Viewing Data
Sonia Pujol, Ph.D.
Randy Gollub, M.D., Ph.D.

2. Acknowledgments National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218

3. 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. Welcome to 3D Slicer

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

6. Material Slicer 2.6 Sample Tutorial Data: tutorial-with-dicom.zip
Sample Tutorial Data: tutorial-with-dicom.zip
Exercises
Questions
Answers

7. Goal of the tutorial
Final result of the series of exercises

8. Overview Part 1: Slicer Interface Part 2: Loading Data
Part 3: Interacting with Data

9. Slicer Interface
Menu
Viewer
Tk window

10. Select the Volumes Module
Slicer Menu
Select the Volumes Module

11. The Panel of the Volumes Module appears
Panels and Tabs
The Panel of the Volumes Module appears

12. Slicer Menu
Panels
Sliders
Buttons
Control Window

13. Main Menu Observe the different options of the Main Menu File
Opening files
Saving files
Closing files
Exit
Modules
Slicer Modules
Help
Links to Slicer Modules information
View
Selecting view mode

14. Observe the Viewer Window
Upper part is 3D Viewer
Lower part is 2D Viewer
3 separate views Independent
controls

15. Slicer Modules The architecture of Slicer is modular
Select Modules in the SubMenu

16. Slicer Modules The list of Slicer Modules categories appears SettingsIO
Application
Filtering
Segmentation
Registration
Measurement
Visualization
Examples
Unfiled
Alpha
The list of Slicer Modules categories appears

17. Slicer Modules: tutorials
Settings IO
Application
Filtering
Segmentation
Registration
Measurement
Visualization
Examples
Unfiled
Alpha
fMRIEngine ………. SlicerTraining 5
vtkFreeSurferReaders ... SlicerTraining 6

18. Slicer Modules: tutorials
Settings IO
Application
Filtering
Segmentation
Registration
Measurement
Visualization
Examples
Unfiled
Alpha
fMRIEngine ………. SlicerTraining 5
vtkFreeSurferReaders ... SlicerTraining 6
Editor …………….. SlicerTraining 2
Level-Sets ……….. SlicerTraining 3
EMBrainAtlasClassifier…SlicerAdvanced

19. Slicer Modules: tutorials
Settings IO
Application
Filtering
Segmentation
Registration
Measurement
Visualization
Examples
Unfiled
Alpha
fMRIEngine ………. SlicerTraining 5
vtkFreeSurferReaders ... SlicerTraining 6
Editor …………….. SlicerTraining 2
Level-Sets ……….. SlicerTraining 3
EMBrainAtlasClassifier…SlicerAdvanced
DTMRI ……………. SlicerTraining 4
Converting DWI data to Nrrd File Format…SlicerTraining 8
Converting Tensors data to Nrrd File Forma t9

20. Overview Part 1: Slicer Interface Part 2: Loading Data
Part 3: Interacting with Data

21. Loading Data
Slicer can load
Volumes …………………..

22. Loading Data Slicer can load Volumes ………………….. Models …………………….
A model is a 3D reconstruction of the anatomy

23. Loading Data Slicer can load Volumes ………………….. Models …………………….
A model is a 3D reconstruction of the anatomy
Scenes …………………….
Scene = Volume + Model

24. Putting together Images and Surface
Loading Data
Slicer Advantage
Putting together Images and Surface

25. Data representation Volume = collection of image files
Image file = header + raw data
The header contains the parameters of the image.
Header
Raw Data

26. Loading DICOM Volumes
Click on Add Volume in the Slicer Menu

27. Loading DICOM Volumes The Panel Props appears by default.
Left-click on the Menu
Properties and change Basic
to DICOM

28. The DICOM panel appears
Loading DICOM Volumes
The DICOM panel appears
Click on Select DICOM Volume

29. Loading DICOM Volumes Select the directory dicom in
the Tutorial-with-dicom dataset

30. The list of DICOM studies appears.
Loading DICOM Volumes
The list of DICOM studies appears.
Click OK

31. Slicer loads the dicom study
Loading DICOM Volumes
Slicer loads the dicom study
Name : The name that the
volume will have within Slicer
Change to something descriptive: Cortex and click on Header

32. Loading DICOM Volumes The DICOM Header information panel appears
Click Apply

33. Loading DICOM Volumes
Slicer loads the
DICOM volume of
the brain

34. Visualization Support
Control Window: displays a zoomed view of the position of the mouse on the selected image
Move the mouse inside an anatomical view

35. Visualization Support
The value of the gray level of the pixel under the cursor appears in the corresponding slice

36. Viewing Volumes
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 inside the Viewer
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

37. Viewing Volumes
The Axial, Sagittal and Coronal Images appear in the Viewer
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

38. Manipulating the images
Rotation
Position the mouse on the images inside the Viewer
Left-click and move the mouse to the left
Move the mouse button to the left
Linux/Unix/Windows
Mac users
The images move to the left

39. Manipulating the images
Zoom In
Position the mouse on the images inside the Viewer
Right-click and move the mouse down
Press the apple button, click and move the mouse button down
Linux/Unix/Windows
Mac users
The viewer gets closer to the model

40. Manipulating the images
Zoom Out
Position the mouse on the images inside the Viewer
Right-click and move the mouse up
Press the apple button, click and move the mouse button up
Linux/Unix/Windows
Mac users
The viewer moves away from the model

41. Viewing Volumes The View Menu contains
different options to visualize the data
Select the 3D View
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

42. Viewing Volumes 3D View focuses on 3D
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

43. Viewing Volumes The View Menu contains
different options to visualize the data
Select 4x512
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

44. Viewing Volumes 4x512 view: larger image views to see details
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

45. Viewing Volumes The View Menu contains
different options to visualize the data
Select 1x512
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

46. Viewing Volumes 1x512: one large Transverse view and three small
images
1x512 COR:
one large Coronal view
and three small images
1x512 SAG:
one large Sagittal view
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

47. Viewing Volumes The View Menu contains different options to visualize
the data
Select 4x256
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.

48. Come back to Normal View
Viewing Volumes
4x256 view: smaller equal-sized images
Slicer has multiple configurations to present image volumes. By default, the normal view is selected. In normal view, the viewer window is divided into two sections.
The upper portion of the view window shows the 3D formatted version. In the lower quarter of the viewer window, a 2D multi-plane formatted version of the volume is shown.
Come back to Normal View

49. 2D Viewer Three 2D windows (red, yellow, and green)3 1
Three 2D windows (red, yellow, and green)
Slider selects which slice of volume to display
Field shows the slice number 1
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.) 2 3

50. 2D Viewer Bg (Background): displays volume in background layer4 5
Bg (Background): displays volume in background layer
Fg (Foreground): displays volume in foreground layer
Superimposed over the background layer 4
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.) 5

51. Volumes without Header
Motivations:
The DICOM file format incorporates all the parameters that Slicer requires to render the data
Other images files types may not

52. Volumes without Header
Motivations:
The DICOM file format incorporates all the parameters that Slicer requires to render the data
Other images files types may not
Slicer has a simple protocol for
loading volumes without header

53. Volumes without Header
1. Main  Data
2. Add Volume
3. Browse to find the first image of the Volume spgr in the directory tutorial
4. Select first image I.001 of volume to load, and click Open
5. Click on Manual
6. Click on Apply

54. 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

55. Volumes without Header3 4 5 6 7 3 4 5 6 7
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.

56. Volumes without Header8
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. 8 9 10 9 10
Click Apply to load the volume.

57. Volumes without Header
The spgr volume appears in the Viewer

58. Loading Data Slicer can load Volumes ………………….. Models …………………….
A model is a 3D reconstruction of the anatomy
Scenes …………………….
Scene = Volume + Model

59. Loading Models In the main Menu select the module Data and Click on
Add Model.
Technical Note: The data format for the models that Slicer reads in is vtkPolyData.

60. Loading Models The Props tab of the module Models appears
Select the model named Vessels in the directory tutorial/models
Technical Note: The data format for the models that Slicer reads in is vtkPolyData.
Click on Apply

61. The model of the vessels appears in the Viewer.
Loading Models
The model of the vessels appears in the Viewer.
Technical Note: The data format for the models that Slicer reads in is vtkPolyData.

62. Loading Data Slicer can load Volumes ………………….. Models …………………….
A model is a 3D reconstruction of the anatomy
Scenes …………………….
Scene = Volume + Model

63. Loading a Scene A Scene is represented as an Xml file.
Select File  Open Scene
in the Main Menu
Select the file tutorial.xml in the directory Tutorial-with-dicom/tutorial.
To open a scene later:
Click File.
Click Open Scene.
Find the scene .xml file, double-click it, and wait for the volumes and models to load.

64. The viewer displays the tutorial Scene
Loading a Scene
The viewer displays the tutorial Scene
To open a scene later:
Click File.
Click Open Scene.
Find the scene .xml file, double-click it, and wait for the volumes and models to load.

65. Loading a Scene
The elements of the Scene are listed in the Menu Window
To open a scene later:
Click File.
Click Open Scene.
Find the scene .xml file, double-click it, and wait for the volumes and models to load.

66. Overview Part 1: Slicer Interface Part 2: Loading Data
Part 3: Interacting with Data

67. Manipulating a Model Windows/Linux/Unix users
Rotate the model: with left mouse button
Zoom the model: with right mouse button
Mac users
Rotate the model: with mouse button
Zoom the model: with apple button and mouse button

68. Put the mouse on the 3D Slicer icon
Manipulating a Model
Put the mouse on the 3D Slicer icon

69. The Control Window appears
Manipulating a Model
The Control Window appears

70. Position the mouse on the R letter (Right) inside the window
Manipulating a Model
Position the mouse on the R letter (Right) inside the window

71. The View Panel shows the model from the right side of the patient
Manipulating a Model
The View Panel shows the model from the right side of the patient

72. Click on the Spin button
Manipulating a Model
Click on the Spin button

73. The model starts spinning inside the Viewer Panel.
Manipulating a Model
The model starts spinning inside the Viewer Panel.

74. Click on the Rock button
Manipulating a Model
Click on the Rock button

75. The model starts rocking inside the Viewer Panel.
Manipulating a Model
The model starts rocking inside the Viewer Panel.

76. Manipulating a Model
Come back to initial orientation of the Viewer Panel by clicking on the A letter (Anterior) inside the window.

77. Models representation
A model is a 3D representation
of the anatomy.
Type W (Wireframe) in the Main Window

78. Models representation
The triangles of the Model become visible in the Viewer.
Type S (Surface) to come back to Surface Mode rendering

79. 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

80. Model Opacity
Skin model
Opacity = 0.5

81. 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 models

82. Vessels model Visibility 0ff

83. 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
Viewing Models
The Display tab of the Models panel controls which models are visible in Slicer.
Click Show All to display all models in the 3D Viewer.
Click Show None to display none of the models in the 3D Viewer.
Clicking the name of a model in the list turns its visibility on and off.
Right-clicking the name of a model in the list displays a menu of display options for that model.

84. Viewing 3D Models Show None: the models have disappeared
Viewing Models
The Display tab of the Models panel controls which models are visible in Slicer.
Click Show All to display all models in the 3D Viewer.
Click Show None to display none of the models in the 3D Viewer.
Clicking the name of a model in the list turns its visibility on and off.
Right-clicking the name of a model in the list displays a menu of display options for that model.

85. 2D Viewer Lb: displays label map Displays results of a segmentation
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)
Left click on Lb in the Axial View and select the Label Map named None

86. 2D Viewer Lb: displays label map Displays results of a segmentation
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)
The segmented volume named all disappears from the 2D Viewer.

87. 2D Viewer Lb: displays label map Displays results of a segmentation
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)
Left click on Lb in the Axial View and select the Label Map named all.

88. 2D Viewer Lb: displays label map Displays results of a segmentation
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)
The segmented volume named all appears in the 2D Viewer.

89. 2D Viewer
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)
Images in the label map layer appear as outlines around the structures that were segmented.

90. 2D Viewer
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)
Left Click on Fg in the Axial View and select the Volume named all in the Axial, Sagittal and Coronal slices.

91. Image Fusion Fade slider: fades between foreground and background.
Set the Fade slider to 0.5
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)

92. 2D Viewer The volume all is superimposed on the images
There are three 2D windows (red, yellow, and green). You can select both grayscale and label map images into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale images into the first (red) 2D window as the background layer.
In each 2D window, the slider selects which slice of the volume to display. The numerical field shows the slice number.
The V toggle button controls whether the selected slice is visible in the 3D viewer or not. In the figure above, only the slice from the green window is visible in the 3D viewer.
There are Or (scan order), Bg (background), Fg (foreground), and Lb (label map) buttons for each of the three 2D windows.
Use Or to change the scan order in each 2D window. For example, you can use the Axial view in the first 2D window, the Coronal in the second, and the Saggital in the third window. Or you can use the Coronal view in the first and the other two views in the other two windows. Or you can set each view individually, to suit your need.
Use Bg to select which volume to put in the background layer.
Use Fg to select a volume for the foreground layer, which is superimposed over the background layer.
Use Lb to select label map images for the label map layer, to display results of a segmentation. Images loaded into the label map layer will appear as outlines around the structures that were segmented. (You can use Slicer to create label maps, and also to make models from them. See the User's Guide for more information.)

93. 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.
Clipping
Clipping is cutting away sections of a model at one or more selected slices. On one side of each selected slice, the model is removed, revealing the image of each selected slice and the rest of the visible model.
To turn clipping on:
On the Display tab of the Models panel, right-click the model's name in the list.
A drop-down menu appears. Select Clipping.
To control clipping:
Select the Clip tab of the Models panel.
Select which side of a slice to clip the model on, as follows:
Color Slice means: means:
red Axial slices Superior Inferior
yellow Sagittal slices Right Left
green Coronal slices Posterior Anterior
Click + or - to select which side of each slice to clip on.
In the sample below, the right-superior-posterior part of the cortical surface has been clipped.
Select the Models  Display tab

94. Clipping Models 2. Right-click the Skin model in the list
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. Check that the Clipping option is selected.
4. Set the opacity of the Skin model to 1.0.
5. Select the Clip tab of the Models panel.
Clipping
Clipping is cutting away sections of a model at one or more selected slices. On one side of each selected slice, the model is removed, revealing the image of each selected slice and the rest of the visible model.
To turn clipping on:
On the Display tab of the Models panel, right-click the model's name in the list.
A drop-down menu appears. Select Clipping.
To control clipping:
Select the Clip tab of the Models panel.
Select which side of a slice to clip the model on, as follows:
Color Slice means: means:
red Axial slices Superior Inferior
yellow Sagittal slices Right Left
green Coronal slices Posterior Anterior
Click + or - to select which side of each slice to clip on.
In the sample below, the right-superior-posterior part of the cortical surface has been clipped.

95. Clipping Models
Click + or - to select which side of each slice to clip on.
Set the sides to:
Red Slice +
Yellow Slice -
Green Slice -
Clipping
Clipping is cutting away sections of a model at one or more selected slices. On one side of each selected slice, the model is removed, revealing the image of each selected slice and the rest of the visible model.
To turn clipping on:
On the Display tab of the Models panel, right-click the model's name in the list.
A drop-down menu appears. Select Clipping.
To control clipping:
Select the Clip tab of the Models panel.
Select which side of a slice to clip the model on, as follows:
Color Slice means: means:
red Axial slices Superior Inferior
yellow Sagittal slices Right Left
green Coronal slices Posterior Anterior
Click + or - to select which side of each slice to clip on.
In the sample below, the right-superior-posterior part of the cortical surface has been clipped.

96. Clipping Models Clipping Model Result Clipping
Clipping is cutting away sections of a model at one or more selected slices. On one side of each selected slice, the model is removed, revealing the image of each selected slice and the rest of the visible model.
To turn clipping on:
On the Display tab of the Models panel, right-click the model's name in the list.
A drop-down menu appears. Select Clipping.
To control clipping:
Select the Clip tab of the Models panel.
Select which side of a slice to clip the model on, as follows:
Color Slice means: means:
red Axial slices Superior Inferior
yellow Sagittal slices Right Left
green Coronal slices Posterior Anterior
Click + or - to select which side of each slice to clip on.
In the sample below, the right-superior-posterior part of the cortical surface has been clipped.

97. Conclusion Intuitive Interface for Loading and Visualizing Data
Slicer Outcome = fusion of Volumes and Surface
Open-source tool for developing your own module