Introduction Welcome to 3D Slicer!.

Introduction Welcome to 3D Slicer!

Overview of Training What is Slicer? Uses of Slicer Getting Slicer
How to Use Slicer Loading Data Viewing Data Modifying Data Saving Data

What is Slicer?

Slicer Slicer is: freely available, open-source software
for visualizing registering segmenting modeling quantifying medical image data

Slicer Structure Modular Many existing modules.
Can develop own modules. Languages Tcl / C++ Tk VTK

Slicer Development …an ongoing collaboration between:
MIT Artificial Intelligence Lab Surgical Planning Lab (SPL) Part of Brigham & Women's Hospital (BWH) An affiliate of Harvard Medical School Developers can share modules.

Acknowledgements Biomedical Informatics Research Network (BIRN)
Brigham and Women's Hospital (BWH) Harvard Medical School Johns Hopkins University Massachusetts Institute of Technology (MIT) National Center for Research Resources (NCRC) National Science Foundation (NSF)

Disclaimer 3D Slicer is NOT for clinical use.
The 3D Slicer software, and the contents of the 3D Slicer documentation, are intended for educational, research, and informational purposes only. 3D Slicer, or information derived from 3D Slicer, may be used only for research and may not under any circumstances whatsoever be used for clinical purposes. The 3D Slicer software is not intended for treating or diagnosing human subjects, and the recipient and user will not use the 3D Slicer software for those purposes. The 3D Slicer copyright holders and contributors, Brigham and Women's Hospital, and all affiliated organizations assume no responsibility for the use of 3D Slicer for unintended purposes. Disclaimer: 3D Slicer is NOT for clinical use. The 3D Slicer software, and the contents of the 3D Slicer documentation, are intended for educational, research, and informational purposes only. 3D Slicer, or information derived from 3D Slicer, may be used only for research and may not under any circumstances whatsoever be used for clinical purposes. The 3D Slicer software is not intended for treating or diagnosing human subjects, and the recipient and user will not use the 3D Slicer software for those purposes. The 3D Slicer copyright holders and contributors, Brigham and Women's Hospital, and all affiliated organizations assume no responsibility for the use of 3D Slicer for unintended purposes.

Uses of Slicer

Some Uses of Slicer Image-guided medicine
Viewing image data: 2D and 3D Image analysis Registration (aligning data sets) Segmentation (extracting 3D structures) Generating 3D surface models Quantitative analysis: distances, angles, surface areas, and volumes

Users A variety of users and organizations employ Slicer for many tasks.

Medical Research Visualizing anatomical structures Comparative studies
Quantitative measurements Generating figures for publication

Diagnostic Research Viewing anatomical structures
Comparing images from different sources Changes over time Post-operative differences

Surgical Planning Viewing anatomical structures 3D models
Stages of procedures

Intra-operative Imaging
Integrated Slicer with an open MR scanner Full array of pre-operative data Exploring anatomical changes during surgery Tracks surgical instruments Applied in dozens of neurosurgical cases at BWH Routinely used for 1-2 research cases per week.

Getting Slicer

Platforms Slicer is available on a variety of popular medium- to high-end platforms Any modern PC or workstation with a graphics chip should work fine

Solaris (1 of 2) Sun UltraSPARC workstations running:
Sun Solaris 2.8 (also known as Solaris 8 or SunOS 5.8) OpenGL 1.2

Solaris (2 of 2) Hardware: Memory: 128 MB+
Disk Space: 35.6 MB for installer, which expands to 145 MB + 37 MB for tutorial data set Processor Speed: 450 MHz +

Windows (1 of 2) PCs running: Windows 98 Windows NT / 2000 / XP

Windows (2 of 2) Hardware Memory: 128 MB +
Disk Space: 11.5 MB for installer, which expands to 45 MB + 37 MB for tutorial data set Processor Speed: 333 MHz + Screen Resolution: 1024 x 786 + 1280 x 1024 suggested Colors: 16 bit color +

Linux Red Hat Linux 7.3 Hardware: Memory: 128 MB+
Disk Space: 31.6 MB for installer, which expands to 119 MB + 37 MB for tutorial data set Processor Speed: 450 MHz +

Mac OS X Apple Macintosh computers running: Mac OS 10.2
X Windows Server Hardware Recent Vintage Computer We are working on exact requirements.

Other Platforms Source code is freely available.
Users can compile it for their operating system.

Getting Slicer License: slicer/license.html For research only Download slicer2 and install Includes documentation Sample data available

Running Slicer Run the executable for your platform.
On platforms other than Windows, Linux, Solaris, or Mac OS X, you will need to compile Slicer source code before running. Contact the developer list for help.

Support User’s mailing list:
Developer’s mailing list:

How to Use Slicer Slicer interface Loading data Viewing data
Modifying data Saving data

Slicer Interface Graphical User Interface The Menu window
Buttons, menus, sliders, input boxes Panels, tabs Graphical viewer

Submenus File Opening files Saving files Close Exit View
Selecting view mode Help Links to Slicer information

Main menu Group of buttons Data Volumes Models Alignments Editor
ModelMaker

Panels and Tabs Clicking a Main menu button opens a panel.
Each panel has tabs along the top. Leftmost tab is Help. Panel may contain controls and displays.

Viewer window Upper part is 3D Viewer Lower part is 2D Viewer
3 separate views Independent controls

Modules Slicer is modular. Some sample modules:
View: customizes size of viewer window. Anno: controls annotation displayed. Slices: selects slices to display in 3D. Colors: creates color palette. Measure: calculates Surface Area, Volume, and Cross Sectional Area. MeasureVol: measures volume of segmented structures in a label map. Other modules: Locator: connects Slicer to a server that feeds a real-time stream of coordinates from a device called the locator. Realtime: enables the locator's real-time coordinates to control Slicer. Guidance: positions two spherical targets (red and yellow) in the 3D view window to support reformatting volumes. EMSegment: implements the "Expectation-Maximization-Segment" algorithm. Anatomy: saves files from Slicer scene to use with the SPL Anatomy Browser. CustomCsys: lets developers add a Coordinate System actor to their module. Endoscopic: places and controls a virtual endoscope in Slicer's scene, and presents the endoscope's view in a second window. Fiducials: adds fiducial points on models in the 2D or 3D viewer windows. SessionLog: records information about a segmentation session for Slicer development purposes. TetraMesh: reads in a Tetrahedral Mesh and converts it into a model. VolRend: selects the volume rendering method: Composite, MIP (Maximum Intensity Projection), or Isosurface. VolumeMath: adds and subtracts volumes; finds the distance between two points in a volume. ModelCompare: shows point correspondences and models in 2D.

Exercise: 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.

Loading Data Slicer can: Load volumes of image data Load models
Load saved scenes

Loading Volumes Volume: a collection of volume elements (voxels) of an image. Example: A slice is an example of a volume. Slicer reads many medical image types: GE Signa GE Genesis DICOM (digital imaging and communications in medicine) Non-header images General procedure: Main  Data  Add Volume

Volumes with Headers (1 of 2)
Main  Data Data panel appears. Click Add Volume. Props (Properties) tab of Volumes panel appears. To find first image, click Browse. A dialog box appears. Select first image of volume to load, and click Open. The number of the last image in the volume automatically appears in the Number of Last Image field.

Volumes with Headers (2 of 2)
Leave Image Headers on Auto. Image Data buttons: select whether images are grayscale or label maps. Label map: the output of a segmentation. Name field: the name that volume will have within Slicer. Change to something descriptive: “Cortex“. Description field: You may enter a description. Click Apply to read in the volume. Your data appears in the 2D portion of the Viewer window.

Exercise: Volume with Header
Main  Data: Data panel appears. Click Add Volume: Props tab appears. Click Browse: Tutorial  spgr Click I.001 and click Open. Number of Last Image appears. Click Apply. Images appear in bottom of Viewer. Click Main  Data  List. Volume I is in list

Volumes without Headers (1 of 4)
Similar to “with headers”, but needs more manual input. Main  Data Data panel appears. Click Add Volume. Props (Properties) tab of Volumes panel appears. To find first image file, click Browse. A dialog box appears. Select first image of volume to load, and click Open. The number of the last image in the volume automatically appears in the Number of Last Image field.

Set Image Headers to Manual. Click Apply. The Header section of the Props tab appears. Change default values for volume. 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.

More default values to change. Pixel Size: Size of each pixel in the x and y directions. (For square images, they are equal.) Slice Thickness: The 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.

Still more default values to change. 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. Click Apply to read in the volume. Your data appears in the 2D Viewer window.

Exercise:Volume w/out Header
Main  Data: Data panel appears. Click Add Volume: Props tab appears. Click Browse: Tutorial  labels Click all.001 and click Open. Number of Last Image appears. Click Apply. “No header information found”: click OK. Examine default data values. Volume all appears in Data  List.

Loading DICOM Volumes (1 of 4)
Digital Imaging and COmmunications in Medicine Slicer reads most, not all, the many DICOM flavors. From Main menu, click Data. The Data panel appears. Click Add Volume. The Props panel appears. From Properties pull-down menu, select Dicom. Click Select DICOM Volume. A dialog box appears. Select directory and click OK. Slicer searches for every DICOM file. A dialog box appears showing patient, studies, series, and files. DICOM (digital imaging and communications in medicine) is a complicated standard. Slicer is not capable of reading all flavors of it. Slicer assumes that the slices of the volume are stored in separate files, that they are not compressed, and that the header data is correct (contains the correct values of the study and the series UIDs). Slicer uses the following method to determine the correct slice order. First, it tries to find the Image Number (0x0020,0x0013) data element. If that is not present, it tries the Slice Location (0x0020,0x1041) data element. If neither data element is available, the files will be ordered as they were found, possibly not in the correct order. Also, Slicer has a restriction that the slice thickness and spacing must be the same for every slice. ***** In last mentioned dialog box, by default, all files of the first series of the first study of the first patient will appear.

Select or deselect images to load. Selected images are green; deselected images are red. Increasing or Decreasing: loads images in either order. Preview: displays small icon-size images in bottom panel. The default size is 32x32 pixels. You can change the size of the previewed images. List Headers: displays header information about image. 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. In this window, options include: Select or deselect images to load. Selected images are shown in green and deselected images are shown in red. Click Increasing or Decreasing to load images in increasing or decreasing order. Click Preview to display images as small icon-size images in the bottom panel. You can change the size of the previewed images. The default size is 32x32 pixels. Click List Headers to display header information about the geometry of each image in the series. Click Check to display information about the volume and how to group the data. With DICOM data, the organization of the data is not always apparent. Check examines the slice location and thickness of each image in the volume to make sure all slices are the same distance apart. This helps to show when slices are missing. This is also useful when several DICOM acquisitions are lumped together. After the data is organized properly, click OK. Click Extract Header. This displays the information extracted from the headers describing the dataset.

Select a patient, a study of this patient, a series of this study, and the files of this series. Then click OK. The header data of the first file will be extracted. (You may select additional files.) To show header information, click Extract Header. To check and modify the extracted values, click Header. On Basic panel, use Image Data buttons to select whether images are grayscale or label maps.

Name field: the name that volume will have within Slicer. Change to something descriptive: “Cortex“. Description field: You may enter a description. Click Apply to save Name and Description. Click Apply to read in the volume. Your data appears in the 2D portion of the Viewer window.

Loading Models A model is a 3D surface. Main  Data Click Add Model.
Props tab appears. Click Browse. In dialog box, select the model to load (VTK PolyData format), and click Open. Name field: name within Slicer. Make descriptive: “Cortex“. From Color pull-down menu, select color for the 3D Viewer. Click Apply to read in the model. Technical Note: The data format for the models that Slicer reads in is vtkPolyData.

Exercise: Loading Model
Main  Data  Add Model. Props tab appears. Click Browse: Tutorial  models Click model file (.vtk) and click Open. Click Color and select color for model. Click Apply to read in the model. Technical Note: The data format for the models that Slicer reads in is vtkPolyData.

Opening a Saved Scene Click File. Click Open Scene.
Find the scene .xml file. Double-click file. Wait for the volumes and models to load. 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.

Viewing Data Slicer offers many ways to view 2D and 3D data.
A single series of grayscale images A complex scene with several grayscale and segmented data sets 3D models, such as this scene: MR dataset of an orange a single section of the orange (in red) the rest of the orange (in orange)

Viewing Volumes (1 of 5) Slicer has multiple ways to display image volumes. Default is Normal view: two sections. Upper portion: 3D formatted version. Lower portion: 2D multi-plane formatted version. 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.

Viewing Volumes (2 of 5) 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.

Viewing Volumes (3 of 5) 4x512 view: larger image views to see details

Viewing Volumes (4 of 5) 1x512 view: one large, three small images.

Viewing Volumes (5 of 5) 4x256 view: smaller equal-sized images.

2D Viewer (1 of 3) 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. V toggle button controls whether slice is visible in 3D Viewer. Here, only slice from green window is visible in 3D 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.)

2D Viewer (2 of 3) Or (scan order): changes scan order in each 2D window. Example, Axial view in red window, Coronal in yellow, and Saggital in green. Bg (background): displays volume in background layer. Fg (foreground): displays volume in foreground layer. Superimposed over the background layer. 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.)

2D Viewer (3 of 3) Lb (label map): displays label map in label map layer. Displays results of a segmentation. Images in the label map layer appear as outlines around the structures that were segmented. Slicer can create label maps and models. 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.)

Adjusting Window/Level
Optimizes display of the region of interest of gray-scale images. Click Volumes on Main menu. Volumes panel appears. Select the Display tab. From Active Volume pull-down menu, select a volume. Adjust Win so that dark areas are black, not gray. Adjust Lev until dark areas become barely visible. Can also click Auto. Adjusting Window/Level By adjusting the Window/Level of the volume, you can optimize displaying the region of interest of gray-scale images. Adjust the Level value until the dark areas become barely visible. Then adjust the Window value so that the bright areas are not saturated into white. You may need to go back and forth to readjust until you have optimally displayed your data.

Color Palette Selects color scheme to colorize a gray-scale volume.
Helps distinguish different regions of interest better. Click Volumes on Main menu. The Volumes panel appears. Select the Display tab. From Palette pull-down menu, select one of seven color schemes: Gray, Iron, Rainbow, Ocean, Desert, InvGray, or Label. Use the Palette pull-down menu (on the Display tab of the Volumes panel) to select a color scheme to colorize your gray-scale volume. This can help you distinguish different regions of interest better. You can select one of seven available color schemes: Gray, Iron, Rainbow, Ocean, Desert, InvGray, or Label.

Image Fusion Fades from background (Bg) layer image to foreground (Fg). Useful for checking alignment. Or coverage of a label map. Use Fade vertical slider (lower left of Menu window). Above: background images are grayscale and foreground images are label map. Use the Fade vertical slider (in the lower left of the Menu window) to fade from the images displayed in the background (Bg) layer to the images displayed in the foreground (Fg) layer. This is useful for checking alignment or coverage of a label map, for example.

Exercise: Viewing 2D (1 / 5)
Load the I.001 volume as in previous exercise. Click V on Red, Yellow, Green 2D views. Select the view: View  3D: Examine 3D view. View  4x512: Examine large views. View  1x512: Examine single large view that rendered in red panel. View  4x256: Examine smaller views. View  Normal: Examine normal view. View: try Black, Blue, Midnight, White.

Click green V button: image is visible in 3D Viewer. Use green slider to select the slice. Click Or, then select scan order in each 2D window. Click Bg to select the background layer. Click Fg to select the foreground layer.

Click Volumes on Main menu. Select the Display tab. From Active Volume pull-down menu, select I volume. Adjust Win so that dark areas are black, not gray. Adjust Lev until dark areas become barely visible. Examine view. Try clicking Auto.

Click Volumes on Main menu. Select the Display tab. From Palette pull-down menu, select color scheme. Observe how 2D view changes.

Use Fade vertical slider (lower left of Menu window). Fade from background (Bg) layer image to foreground (Fg).

Viewing 3D Models Display tab of Models panel.
Which models are visible. Click Show All to display all models in the 3D Viewer. Click Show None to display none of the models in the 3D Viewer. Click name of model in the list to turn Visibility on and off. Right-clicking name of a model in the list displays a menu of display options for that model. 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.

Controlling the 3D View To rotate the view:
Left-click the view and move the mouse. To move view left-right, up-down: Click the middle button (or Alt-Left button) on view and move the mouse. To change the size of the view (zoom): Right-click the view and move the mouse up and down.

User Interface Panel (1 of 2)
Move the cursor over the Slicer icon. The user interface panel appears. Affects 3D Viewer.

User Interface Panel (2 of 2)
Fade slider: fades between foreground and background. Click R (Right), L (Left), P (Posterior), A (Anterior), I (Inferior),or S (Superior) to align in that direction. Click up, down, left, and right arrows to rotate. FOV: Field Of View, the size of the image. Spin: rotates image horizontally. Parallel: toggles between parallel and perspective projection. Scale: scale for parallel projection. Controlling the scene with the user interface panel Move the cursor over the Slicer icon: The user interface panel appears: The controls on the user interface panel include: The slider on the left between Fade and Exit is useful when you have data in the foreground and background. When the slider is at the top, it will display only the foreground dataset; when it is at the bottom, it will display only the background dataset. When the slider is in between, it will blend the two data sets. This is particularly useful when you are registering two data sets, and want to see how accurate the registration is. The head icon rotates the 3D view. Click R (Right), L (Left), P (Posterior), A (Anterior), I (Inferior), or S (Superior) to rotate the image in each direction. The arrows pointing up, down, left, and right can rotate the 3D view in the appropriate direction. Click the arrow and the 3D view will rotate. FOV stands for Field Of View, which is the size of your image. If the image is too small, enter a larger value for FOV. If the image is too large, enter a smaller value for FOV. Save 3D saves the current 3D scene. Enter a name for the scene in the field. Slicer saves the scene to the directory where you started Slicer. Parallel toggles between a parallel projection (which preserves parallel lines, and displays an object the same size regardless of how far from the observer) and a perspective projection (which displays closer objects as larger than farther objects).

Opacity of Model Opacity: how non-transparent a model is.
The higher the opacity, the less transparent. Default: Slicer creates perfectly opaque models (opacity=1). Two ways to change opacity: On the Display tab of the Models panel, adjust Opacity slider next to the model's name in the model list. On Props tab of Models panel, set Active Model, and use Opacity slider.

Color of Model You can select colors for models.
Click Models on Main menu. The Models panel appears. Select the Props tab. Click Color. Enter a description of what that color will represent. Color You can select colors for models. Click Color (on the Props tab of the Models panel) to select a color. Enter a description of what that color will represent.

Load model as in previous exercise. Click Models button on Main menu. Click Display tab: observe which models are loaded. Click name of model: turn Visibility on and off. Right-click name of model: observe display options for that model.

Left-click 3D view and move mouse: Rotates the view Click middle button (or Alt-Left button) on 3D view and move mouse: Moves view left-right, up-down. Right-click 3D view and move mouse up and down. Changes size of view (zoom).

User Interface Panel: bottom of Main window. Move cursor over the Slicer icon. Move Fade slider: fades between foreground and background. Click Right, Left, Posterior, Anterior, Inferior, or Superior to align in that direction. Click up, down, left, right arrows to rotate. Enter FOV: changes the size of image. Parallel: toggles parallel/perspective projection. Spin: rotates image horizontally. Scale: changes scale: larger for smaller image.

First way to change opacity: Click Models button. Click Display tab. Adjust Opacity slider. Second way to change opacity: Click Props tab. Select Active Model.

Color of model: Click Models on Main menu. Select the Props tab. Select Active Model. Click Color. Select color. Click Apply.

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. On the Display tab of the Models panel, right-click the model's name in the list. A drop-down menu appears. Select Clipping. Select the Clip tab of the Models panel. Select which side of a slice to clip the model on. 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.

Clipping Example Click + or - to select which side of each slice to clip on. In this example, the right-superior-posterior part of the cortical surface has been clipped.

Exercise: Clipping Data
Load model as in previous exercise. Click Models button. Click Display tab. Right-click the model's name in the list. Click Clipping to turn clipping on. Click Clip tab. Click + or - to select which side of each slice to clip on.

Modifying Data Slicer has many tools for manipulating and modifying data. Many tools start the same way: On Main menu, click Editor. The Volumes tab appears. Click Start Editing. The Effects tab appears. Select tool. Select Input Volume. Select slices to modify: Scope and Interact

Segmentation Segmentation: separating and labeling anatomical structure images. Result is a label map. Semi-automatic process using editing tools. Include thresholding, morphological operations, island-removal, and free-hand drawing. Segment data in 3D or slice-by-slice. Merge volumes to construct complex images. Example: segment skin from an MR scan. Segmentation Guide You can segment volumetric data semi-automatically using editing tools such as thresholding, morphological operations, island-removal, free-hand drawing, and more. top 3a. Introduction You can apply editing effects to the data on a 3D or slice-by-slice basis. For instance, you can perform slice-by-slice editing on either the axial, coronal, or sagittal slices simply by clicking on the appropriate slice. In addition, you may apply each effect to either the original volume, or a working volume. Furthermore, you may apply multiple editing effects to the working volume, and, when finished, merge the working volume with a composite volume to overlay smaller structures onto larger ones. For example, we can segment skin automatically from an MR scan, by applying a threshold at the first trough of the histogram (where the noise and signal lobes overlap) and then storing the binary output in the working volume. We next remove islands in the working volume, and finish with an erosion and dilation to smooth the edges. At this point, we copy this working volume to the composite volume. Next, we can segment the brain in the working volume. All non-zero voxels of the working volume can overwrite the composite volume to form a combination of skin and brain. One strength of our system is that you can visualize effects by overlaying the working volume translucently on the original volume and exploring the result in the 3D view.

Segmenting Data On the Main menu, click Editor.
The Editor panel appears. Click the Volumes tab. The Volumes tab appears. Click Setup. The name of data appears in Original Grayscale field. Select NEW for the Working Labelmap. Enter name for this segmentation. Example: "ventricles". Click Start Editing. The Effects tab appears. Segmenting Data To segment data: On the Main menu, click Editor. The Editor panel appears. Click the Volumes tab. The Volumes tab appears. Click Setup. The name you assigned to the original series of data should be present in the Original Grayscale field. These are the images you will segment. Select NEW for the Working Labelmap, and enter a name for this segmentation. For example, if you are segmenting the ventricles of the brain, you might name this segmentation "ventricles". Click Start Editing. The Effects tab should appear.

Threshold Tool Threshold: automatically outlines structures based on voxel value. Lo slider: excludes low-intensity voxels. Hi slider: excludes high-intensity voxels. Click Output and select a color, or enter an Output color number. Click Apply. The outlined areas are called "islands". Threshold: Automatically selects and outlines various structures based on a certain voxel value. Threshold is very useful for brain, ventricles, and skin models of the head for example. On the Threshold panel, adjust the sliding scales to select only the structures you desire. The outlined areas are called "islands". Check some of the original data images to ensure that you are segmenting only what you want. Click Apply. The function will segment the selected areas.

Results of Thresholding
This example is segmenting CT skull bone. Thresholding has changed the label to blue. Notice that the skull is well-defined and separated from the rest of the image.

Exercise: Thresholding (1/2)
Load volume as in previous exercise. Click Editor button. Click Volumes tab. Click Setup button. On Original Grayscale drop-down list, select volume. Select NEW for the Working Labelmap. Enter “Descriptive Name". Click Start Editing.

Exercise: Thresholding (2/2)
Click Threshold or Th. Click Output, select a color for selected voxels. Use Lo slider to exclude low-intensity voxels. Use Hi slider to exclude high-intensity voxels. Example: if 140 is a common value on 2D Viewer, let Lo=130 and Hi=150. Choose Scope: 1 Slice or 3D. Choose to filter 1 Slice, 3 Slices, or 3D. Click Apply. Result: label map.

Change Label Tool Changes the value of the label of pixels to another value. Useful when merging two data sets together, and you want to keep the data sets distinct from each other. Click Change Label. Enter Value to change. Click Output and select a color, or enter a color number. Click Apply. The new output color will replace the value. The Change Label effect changes the value of the label of pixels to another value. Change Label is useful when you are merging two data sets together and you want to keep the data sets distinct from each other. Change Label: Click Change Label. This window appears: Select the Input Volume. Select the Scope range. Enter a Value to change. This is the value of label of pixels in the Input Volume that Slicer will change. Click Output and select a color, or enter an Output color number. This is the new value that pixels with the Value to change will receive. Click Apply to apply the change label effect. Slicer will update the Working volume with your newly labeled data.

Exercise: Change Label
Use on label map or original volume. On Editor, Effects tab, click CL or Change Label. Enter Value to change. Click Output and select a color. Choose Scope: 1 Slice or 3D. Click Apply. The new output color replaces the value.

Change Island Tool Changes color of an island*.
*Island: a group of connected pixels with the same label. Useful after thresholding, to separate anatomy further. Click Change Island. Click New Label and select a color, or enter a color number. Click any part of the island. Pixels that are part of that island will receive the New Label value. Change Island effect The Change Island effect changes the label of an "island" of pixels. Slicer considers an island to be a group of connected pixels that have the same label. Change Island is useful when, after applying an effect (particularly thresholding) to the volume, you still are not able to separate the anatomy you are interested in. For example, surrounding areas may have the same signal intensity as the anatomy of interest, as in the case below: separating the skull is difficult because surrounding points have the same label as the skull itself. To use Change Island: Click Change Island. This window appears: Select the Input Volume. Select the Scope and Render ranges. Click New Label and select a color, or enter a New Label color number. This is the new label value that pixels in the selected island will receive. Click any part of the island. The pixels that are part of that island will receive the New Label value. Results after using Change Island:

Change Island Example Before After

Exercise: Change Island
Use on island in label map or original volume. On Editor, Effects tab, click CI or Change Island. Click New Label and select a new color. Click any part of the island. Changes island to New Label value.

Measure Island Tool Calculates the volume of an island of pixels.
Click Measure Island. Click Island Label and select a color, or enter a color number. Click any part of the island. Slicer will display the Size, in pixels. Also displays the size of the Largest island within the selected Scope. Measure Island effect The Measure Island effect calculates the volume of an island of pixels. Slicer considers an island to be a group of connected pixels that have the same label. To use Measure Island: Click Measure Island. This window appears: Select the Input Volume. Select the Scope range. Click Island Label and select a color, or enter an Island Label color number. Measure Island will calculate the volume of the pixels with the Island Label color in the selected island. Click any part of the island. Slicer will display the Size, in pixels, of the island you clicked. Slicer will also display the size of the Largest island within the selected Scope. To calculate the total volume of the selected island, use the following formula: size * pixel_size * pixel_size * (thickness + spacing)

Exercise: Measure Island
Use on island in label map or original volume. On Effects panel, click Measure Island. Click Island Label and select pixel color. Select 1 Slice or 3D for Scope. Click any part of the island. Observe Size of island in pixels. Observe size of Largest island within Scope. Measure Island effect The Measure Island effect calculates the volume of an island of pixels. Slicer considers an island to be a group of connected pixels that have the same label. To use Measure Island: Click Measure Island. This window appears: Select the Input Volume. Select the Scope range. Click Island Label and select a color, or enter an Island Label color number. Measure Island will calculate the volume of the pixels with the Island Label color in the selected island. Click any part of the island. Slicer will display the Size, in pixels, of the island you clicked. Slicer will also display the size of the Largest island within the selected Scope. To calculate the total volume of the selected island, use the following formula: size * pixel_size * pixel_size * (thickness + spacing)

Erode & Dilate Tool Removes pixels at border of all islands.
Separates two partially connected structures; removes many small islands. Dilate: adds pixels around all islands. Click Erode. Click Value to Erode and select color, or enter color number. Erode acts only on pixels with selected color. Fill value: 0. Iterations: number of times to apply. Neighborhood Size: 4 for less erosion, 8 for more. Click Erode, Dilate, Erode & Dilate, or Dilate & Erode. Erode effect The Erode effect removes pixels at the border of all islands. Slicer considers an island to be a group of connected pixels that have the same label. Dilation is the opposite effect, and adds pixels around the borders of all islands. Erode is useful for separating two distinct pieces of anatomy that are only partially connected, or for removing many small islands, some of which are connected to the anatomy of interest (as shown below). To use Erode: Click Erode. This window appears: Select the Input Volume. Select the Scope range. Multi Slice applies the one-slice erosion to each slice. 3D treats the whole volume at once. Click Value to Erode and select a color, or enter a Value to Erode color number. Erode will act only on pixels with the selected Value to Erode color. Enter 0 for the Fill value. Enter the number of times to apply the effect in the Iterations field. Select 4 for Neighborhood Size for less erosion or 8 for more erosion. Select Active to apply Erode to the active view. Select Native to apply Erode to the original view. Click either: Erode to remove pixels with the Value to Erode from around islands. Dilate to add pixels with the Value to Erode around islands. Erode & Dilate to erode, then dilate. Dilate & Erode to dilate, then erode. Results after using Erode:

Erode Example Before After

Exercise: Erode & Dilate
Use Threshold to change values: use vivid color. Click V for green 2D image. Editor  Volumes tab  Start Editing Effects tab: Green Active Slice, Erode. Value to Erode: use Threshold value. Scope: 3D Click Dilate: threshold value spreads. Click Erode: threshold value area shrinks.

Draw Tool (1 of 2) Draw: specifies pixels for segmenting by drawing directly on them. Useful when automatic methods cannot segment data correctly. Click Draw. Click Output and select a color, or enter color number. Pixels you draw on get this color. Point Radius: fineness of line. 1 or 2 selects individual points. Mode: behavior of left mouse button. Draw: for drawing on points. Select: for selecting points. Move: for moving selected points. Draw effect The Draw effect lets you specify pixels for segmenting by drawing directly on them. Draw is useful when automatic methods cannot segment the data correctly. To use Draw: Click Draw. This window appears: Click Output and select a color, or enter an Output color number. This is the new value that pixels you draw on will receive. Enter a value for the Point Radius, which controls how fine each line of the drawing is. Using a value of 1 or 2 allows you to select individual points. Select the Mode of the left mouse button in the draw window. Draw is for drawing on points. Select is for selecting points. Move is for moving selected points. If the Mode is Select or Move, you can use: Select All to select all points. Deselect All to deselect all points. Delete Selected to delete selected points. Delete All to delete all points. Select the Render range. Select the Shape that the left mouse represents in the draw window. Draw on the region of interest (ROI), using the left mouse button. You can use the right mouse button to zoom in and out on the area. The middle mouse button (or Alt-Left button) moves the image in the window. To clear the list of points after you click Apply, click Yes. To keep the same points in a list after you click Apply, click No. When you have finished drawing the outline of the ROI, click Apply. Slicer will fill the ROI with the Output color.

Draw Tool (2 of 2) Select All: selects all points.
Deselect All: deselects all points. Delete Selected: deletes selected points. Delete All: deletes all points. Shape: shape of left mouse in the draw window. Draw on the region of interest (ROI) with left mouse button. Click Apply. Slicer will fill the ROI with the Output color. Mistake? Use Draw with Black output to erase. Delete last selected point of polygon with Delete Selected.

Exercise: Draw Load volume. Editor  Volumes tab  Start Editing
Effects tab: Green Active Slice, Draw. Click Output: select color. On 2D Viewer, choose area to draw around. Click mouse on edge of area. Move mouse around area, clicking as you move. When area outlined, click Apply. Area is covered by selected color.

Remove Islands Tool Remove Islands: Automatically removes areas based on size. Useful for removing small areas that should not have been thresholded. Example: use an area of 10 to remove all islands less than 10 voxels in size. Remove Islands: Automatically removes areas based on size. Remove Islands is useful for removing small areas that should not have been thresholded. For example, if you use a value of "10", all islands less than 10 voxels in size will be removed.

Exercise: Remove Islands
Use Threshold on volume. Click Remove Islands or RI. Min. Island Area: 10 Label of the sea: 0 Scope: 3D Click on 2D Viewer in sea (outside island). Eliminates the smaller islands.

Save Island Tool Save Island retains the selected island, and removes disconnected pixels with the same label. Useful for separating a single connected structure from other structures. Save Island effect Save Island will retain the selected island, and remove disconnected pixels with the same label. Save Island is useful for separating a single connected structure from other structures.

Exercise: Save Island Color some voxels using Threshold or Draw.
Click Save Island or SI. Scope: 3D Click an island in 2D Viewer. Warning: all other same-colored islands disappear.

Saving Segmented Data Segmented data: a label map
On the Main menu, click Editor. The Editor panel appears. Click the Volumes tab. The Volumes tab appears. Select Save. Select the name of your label map for Volume to Save. Select a file name. Simplest to use same name as the Volume to Save. Save file to the appropriate directory. Save your segmented data (called a "label map"). On the Main menu, click Editor. The Editor panel appears. Click the Volumes tab. The Volumes tab appears. Select Save. Select the name of your label map for Volume to Save. Select a file name. It is often simplest to use the same name as the Volume to Save. Save this file to the appropriate directory.

Exercise: Saving Label Map
Use any of the previous methods to create a simple label map. Example: Threshold. Click Editor  Volumes tab  Save Select the Volume to Save. Add file name to end of Filename Path. Click Save.

Manual Registration Registration: aligning two medical images together. Click Data on the Main menu. The Data panel appears. Select volume(s) and/or model(s) to move. Click Data. Click one volume. Click Add Transform. Click Alignments. Click Manual. Use the translation and rotation sliders to align one image with the other. Registration Registration is the process of aligning two medical image data sets together. Slicer supports rigid, manual registration. The user can specify which volume to move, and then intuitively translate and rotate that volume by clicking and dragging the images in the 2D windows. The user can display the reference volume as the background layer (Bg) of the slices, and display the registered volume as the foreground layer (Fg) translucently (Image Fusion slider). Click Data on the Main menu. The Data panel appears. Select the volume(s) and/or model(s) that you would like to move with this transform. Click Data. Click one of the volumes. This will highlight the volume. Click Add Transform to surround them with a transform. This will create an identity matrix. Click Alignments. Click Manual. Move the slider in the user interface panel at the bottom-left (near the Exit and Fade buttons) so that both volumes are visible. Use the translation and rotation sliders to move one dataset into alignment with the other. You can also drag one dataset to align it with the other dataset. Furthermore, with one button click, the user can employ the result of manual registration as an initial pose for automatic registration using the method of maximization of mutual information. This method is of general utility, and other implementations of it have performed well in an NIH-sponsored test. In Slicer, registration is done on the Alignments panel. The following steps show how to add a Transform to the MRML (Medical Reality Modeling Language) scene: Click Add Transform to surround them with a transform. Change the values in the Matrix at the top of the transform. Double-click Matrix. The Alignments panel appears. Adjust the translation and rotation sliders to set the Matrix. You can also use the mouse in the slice windows to translate and/or rotate the volume.

Automatic Registration
Slicer can perform automatic registration. Automatic registration can use manual registration as starting point. Click Alignments. Click Auto. Select matrix created by manual registration. Select the reference volume and the volume to move. Click Run. Automatic registration will run. This will take a few minutes, including initialization and a series of displays that appear and disappear. Automatic Registration Slicer has the ability to perform automatic registration. However, it is a good idea to start with a manual registration, as described above, before letting the automatic registration refine the alignment. To perform automatic registration: Click Alignments. Click Auto. Select one of the matrices generated in the manual registration phase. Select the reference volume and the volume to move. Click Run. The automatic registration will run. This will take a few minutes, including initialization and a series of displays that appear and disappear. If we save this new scene and examine the resulting .xml file, there is a new text entry for the matrix: Matrix name='manual7' matrix=' ' Note that the numbers in this matrix (resulting from automatic registration) are very similar to those for manual registration, but are more precise.

Exercise: Registration
Load volume from spgr folder. Load label map from labels folder. Use as Fg and Bg. Toggle between them to show misaligned. Click Alignments  Auto. Select Volume to Move and Reference Volume. Click Intensity  Good and Slow. Click Start. This can take a long time.

Making Models Model: a three-dimensional surface.
Use output of segmentation process (label maps) to create models. The bounding surfaces of the label maps are extracted and represented as a collection of triangles. Decimation reduces the number of triangles: can be rendered more quickly little observable loss in detail example: a typical brain surface is reduced from about 500,000 triangles to 150,000. Making Models The output of the segmentation process is a set of label maps, where pixels take on values corresponding to tissue type. To create three-dimensional models, the bounding surfaces of the label maps are extracted and represented as a collection of triangles using marching cubes (a smoothing algorithm). Decimation then reduces the number of triangles to a quantity that can be more quickly rendered with little observable loss in detail. For example, a typical brain surface is reduced from approximately 500,000 triangles to 150,000.

From Label Map to Model Click ModelMaker on the Main menu.
On Create tab of ModelMaker panel, use the Volume pull-down menu to select label map. Largest label in this volume is automatically selected. Or click Label to select another color, or enter the label value in the field. Enter a Name for the model. Change values of Smooth and Decimate parameters. Click Create and wait for the model to be created. The model will appear in the 3D Viewer. To create a model from a label map: Click ModelMaker on the Main menu. On the Create tab of the ModelMaker panel, use the Volume pull-down menu to select the label map to use. The largest label in this volume is automatically selected. To make a model from another pixel value, either click Label to select a color, or enter the label value in the field. Enter the Name for the model. Change the values of the Smooth and Decimate parameters, if necessary. Click Create and wait for the model to be created. The model will appear in the 3D Viewer. To save the model: Click the Save tab in the ModelMaker panel. Select the model from the pull-down menu. Optionally enter a file name. Click Save. A dialog box will appear. Save it to the appropriate directory. The file will be saved as a .vtk file. To save the scene, including the new model: Click File. Click Save Scene or Save Scene As.

Model Example Before After

Exercise: Making a Model
Load label map. ModelMaker  Create tab. Select label map from Volume pull-down menu. Select Label to model (smaller area = faster). Enter a Name. Enter Smooth (larger = faster, smoother). Enter Decimate (larger = slower, fewer triangles). Click Create. To save: Save tab, click Save. To create a model from a label map: Click ModelMaker on the Main menu. On the Create tab of the ModelMaker panel, use the Volume pull-down menu to select the label map to use. The largest label in this volume is automatically selected. To make a model from another pixel value, either click Label to select a color, or enter the label value in the field. Enter the Name for the model. Change the values of the Smooth and Decimate parameters, if necessary. Click Create and wait for the model to be created. The model will appear in the 3D Viewer. To save the model: Click the Save tab in the ModelMaker panel. Select the model from the pull-down menu. Optionally enter a file name. Click Save. A dialog box will appear. Save it to the appropriate directory. The file will be saved as a .vtk file. To save the scene, including the new model: Click File. Click Save Scene or Save Scene As.

Manipulating Model The model appears in the 3D Viewer.
Rotate the model: with left mouse button. Translate the image: with middle mouse button (or Alt-Left button). Zoom the image: with right mouse button. Hide and unhide the model: click name of model on the Models panel. Change opacity of model: use sliding scale next to name of model on the Models panel.

Saving Data Slicer can save data in many ways.

Saving Volumes After creating new label map data, it may be necessary to save the new volume of data. On the Main menu, click Editor. The Volumes tab appears. Click Save. From the menu, select the label map to save and click Save. The Save Volume dialog box appears. Select the path and click Save. Saving Volumes After creating new label map data with the Slicer edit features, it may be necessary to save the new volume of data. To save the volume: On the Main menu, click Editor. The Volumes tab appears. Click Save. From the menu, select the label map to save and click Save. The Save Volume dialog box appears. Select the path and click Save.

Saving Models On the Main menu, click ModelMaker. Click the Save tab.
From the menu, select the model to save and click Save. The Save Model dialog box appears. Select the path and click Save. The model will be saved as a .vtk file, which identifies the file as a model. Saving Models To save a model: On the Main menu, click ModelMaker. Click the Save tab. From the menu, select the model to save and click Save. The Save Model dialog box appears. Select the path and click Save. The model will be saved as a .vtk file, which identifies the file as a model.

Saving the Scene There are several ways to save the scene in Slicer.
Use Save Scene to save as an XML file. The XML file lists the elements of the scene and their attributes. Use Save 3D View to save a picture of the 3D View. Use Save Active Slice to save one slice. Use Save Current Options to save user preferences, like background color or view presets, into a special Options.xml file. Saving the Scene There are several ways to save where you are in Slicer. Use Save Scene to save as an XML file. The XML file lists the elements of the scene and their attributes. Use Save 3D View to save a picture of the 3D View or Save Active Slice to save one of the slices. Use Save Current Options to save user preferences, like background color or view presets, into a special Options.xml file.

Save Scene You can save a description of the current scene.
Includes pathnames to the volumes and models. Can later open them all, just by opening the scene file. Before saving scene, save any new volumes and models. Click File. A drop-down menu appears. To save file with default file name (data.xml) and no options, select Save Scene. To use another file name, select Save Scene As and enter file name for the scene. Use Save Scene With Options to include options in the scene description. Save Scene You can save a description of the current scene. This saves the pathnames to the volumes and models in an XML file. You can later open them all again, just by opening the scene file. Note: Before saving the scene, you should save any new volumes and models first. To save a description of the current scene: Click File. A drop-down menu appears. There are several ways to save the scene, depending on your preferences for file name and options. To save the file with the default file name (data.xml) and no options, select Save Scene. To use another file name, select Save Scene As and enter your own file name for the scene. Use Save Scene With Options to include Options in the scene description. These include view presets, background color, and other preferences you set in this Slicer session. 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.

Opening a Saved Scene Click File. Click Open Scene.
Find the scene .xml file, double-click it, and wait for the volumes and models to load. 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.

Save Images You can save 3D View or Active Slice as TIFF files.
Active Slice: the one that you clicked on last. To save the 3D View: Click File. A drop-down menu appears. To save with default file name, select Save 3D View. Or select Save 3D View As and enter file name. To save the Active Slice: To use default file name, select Save Active Slice. Or select Save Active Slice As, enter file name. Save Images You can save the 3D View and the Active Slice as TIFF files. Note that the Active Slice is the one that you clicked on last. To save the 3D View: Click File. A drop-down menu appears. There are two ways to save the 3D View, depending on your preferences for file name. To save the file with the default file name, select Save 3D View. To use another file name, select Save 3D View As and enter your own file name for the 3D View. To save the Active Slice: There are two ways to save the Active Slice, depending on your preferences for file name. To save the file with the default file name, select Save Active Slice. To use another file name, select Save Active Slice As and enter your own file name for the Active Slice.

Save Current Options You can save your preferences, including:
View Presets set under the Slicer graphic in the Menu window. Settings from the Modules tab on the Options panel. Background Color set using View. Click File. A drop-down menu appears. Click Save Current Options. Saves preferences to a file named Options.xml in the current directory. When running Slicer from that directory, it will use your saved preferences. Save Current Options You can save your preferences in Slicer. Among the features you can save are: The View Presets that you set under the Slicer graphic in the Menu window. The settings from the Modules tab on the Options panel. The Background Color set using View. (Note: You can set this differently for each of your View Presets.) To save your preferences: Click File. A drop-down menu appears. Click Save Current Options. This will save your preferences to a file named Options.xml in the current directory. Whenever you run Slicer from that directory, it will find the Options.xml file, and set things up using your saved preferences.

Extending Slicer Slicer is modular.
You can extend Slicer by adding new modules. See Developer’s Guide for more information.

Introduction Welcome to 3D Slicer!.

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