Users Guide

Complete Guide to Using Slicer The Users Guide is a complete reference to using Slicer. To get started quickly, try the QuickStart There is also a Tutorial to teach you how to use Slicer.

1. Introduction to Slicer     a. Disclaimer     b. Slicer Platforms     c. Getting Slicer     d. Slicer Support	2. Installation Instructions     a. Installing on Solaris     b. Installing on Windows     c. Installing on Linux     d. Installing on Mac OS X     e. Installing at BWH     f. Installing on OpenMR     g. Sample Data
3. Overview	4. Loading Data     a. Loading Volumes with Headers     b. Loading Volumes without Headers     c. Loading DICOM Volumes     d. Loading Label Maps     e. Loading Models     f. Opening Scenes
5. Viewing Data in Slicer     a. Images Available for Viewing     b. Viewing Volumes     c. Viewing 3D Models in Slicer	6. Modifying Data     a. Before Editing Data     b. Editing Data
7. Saving Data     a. Saving Label Maps     b. Saving Models     c. Save Scene     d. Saving the Active Slice     e. Saving the 3D View	8. Modules     a. Common Modules     b. Other Modules     c. Acquiring New Modules
9. Specific Module Instructions     a. Modules A-H     b. Modules I-N     c. Modules O-Z	10. Glossary

1. Introduction to Slicer

Slicer is a freely available, open-source software research tool with emphasis on:

• Research for guiding biopsies and craniotomies
• Research of diagnostic visualization and surgical planning
• Facilitating research into brain shift and volumetric studies in the lab

Slicer can help users:

• visualize medical image data
• register (align) multiple images for comparison
• segment images to isolate anatomical structures
• create 3-dimensional surface area models based on 2-dimensional data
• perform measurements on images

Slicer has a modular structure so that users can select the functions they need. Users can also develop their own modules, either for their own use or to share with others. Slicer modules are written in Tcl, Tk, and VTK.

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1a. Disclaimer

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 these purposes and may not under any circumstances whatsoever be used for clinical purposes.

The 3D Slicer software has not been approved by the FDA and is not intended for treating or diagnosing human subjects, and the recipient and user will not use the 3D Slicer software for such purposes.

The 3D Slicer copyright holders and contributors, Brigham and Women's Hospital, and all affiliated organizations shall not be liable for any damages arising out of the use of 3D Slicer by any party for any purpose.

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1b. Slicer Platforms

Slicer is available on a variety of popular medium- to high-end platforms, including:

• Sun UltraSPARC workstations running Sun Solaris 2.8 (also known as Solaris 8 or SunOS 5.8) and OpenGL 1.2
• PCs running Windows 98, Windows NT, Windows 2000, ow Windows XP.
• Computers running Red Hat Linux 7.3.
• Apple Macintosh computers running Mac OS 10.2.
• Other platforms (such as IRIX): we give out all source code, so users can compile it for their operating system.

Solaris

Slicer runs on Sun UltraSPARC workstations with:

• Sun Solaris 2.8 (also known as Solaris 8 or SunOS 5.8)
• OpenGL 1.2
• 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

Slicer runs on PCs with:

• Windows 98, Windows NT, or Windows 2000
• 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 +
• Colors: 16 bit color +

Linux

Slicer runs on Linux systems with:

• Red Hat Linux 7.3
• 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

Slicer runs on Apple Macintosh computers with:

• Mac OS 10.2
• We are working on hardware requirements.

Other Platforms

Since Slicer's source code is freely available, users can compile it for other operating systems.

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1c. Getting Slicer

How to Get Slicer

When you submit this Agreement, we will check your submission. If all the fields are correctly filled out, you will then receive instructions via email explaining how to download the software using FTP. You should receive an email reply within a day. If you do not receive a reply, please contact us at slicer@ai.mit.edu.

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 these purposes and may not under any circumstances whatsoever be used for clinical purposes.
The 3D Slicer software has not been approved by the FDA and is not intended for treating or diagnosing human subjects, and the recipient and user will not use the 3D Slicer software for such purposes.
The 3D Slicer copyright holders and contributors, Brigham and Women's Hospital, and all affiliated organizations shall not be liable for any damages arising out of the use of 3D Slicer by any party for any purpose.

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1d. Slicer Support

The Slicer license does not include support. However, we do respond to feedback and queries where possible and at our discretion.

Sources of support include:

• User's mailing list: to join the user's mailing list, send a request to:
  slicer-users-request@massmail.spl.harvard.edu
• Developer'ss mailing list: to join the developer's mailing list, send a request to:
  slicer-devel-request@massmail.spl.harvard.edu
• Slicer developers:
  slicer@ai.mit.edu

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2. Installation Instructions

Installation is slightly different on different platforms.

• Solaris
• Windows
• Linux
• Mac OS X
• At BWH
• For the Open MR

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2a. Installing on Solaris

Solaris installation instructions

Compatibility

System Requirements

• Memory: Minimum: 128 MB.
• Disk Space: 35 MB to download the installer, which expands to about 140 MB. The tutorial data set requires 37 MB.
• Processor Speed: Has run successfully on a 450-MHz machine; a faster processor speed is recommended.

Installation Steps

1. Download the desired version of the slicer.tar.gz file to your computer. (Instructions about how to download the most recent version were emailed to you upon receipt of your signed Software License Agreement. If you have not filled this out yet, click here.)
    
2. At a shell prompt, type the following commands to uncompress the file and create a slicer2 directory:

   gunzip slicer.tar.gz
   tar xf slicer.tar

   
    
3. The slicer2/slicer_variables.tcl file automatically sets up the SLICER_HOME environment variable to point to the directory where the slicer2 directory is installed.
    
4. Move the slicer2 directory into a shared system directory that every user can access. Create a symbolic link from a directory that is in every user's PATH environment variable to slicer2/slicer2-solaris-sparc. For example, this may be /usr/local/bin.
    
5. Launch Slicer by typing the following command at a shell prompt:

   slicer2-solaris-sparc

Frequently Asked Questions
How can I load an existing data set? At the shell prompt, type slicer2-solaris-sparc followed by the name of your MRML file.
Was King Louis XIV a good decorator? He transformed a mere hunting lodge into the dazzling royal residence that is Versailles.

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2b. Installing on Windows

Windows Installation Instructions

Compatibility

System Requirements

• Memory: Minimum: 128 MB; recommended: 256 MB or greater.
• Disk Space: 27.3 MB to download the installer, which expands to about 107.5 MB. The tutorial data set requires 37 MB.
• Processor Speed: Has run successfully on a 333-MHz machine with Windows 98; a faster processor speed is recommended.
• Graphics Card: Some older video cards and some laptops restrict the amount of memory allocated to graphics functions and may result in reduced image quality.
• Screen Resolution and Colors: Minimum screen resolution: 1024 x 786; recommended: 1280 x 1024. Minimum colors: 16 bit color; prefer: 32 bit color. (Note: 24 bit color works on most machines, but may cause some rendering problems.)

Installation Steps

1. If you already have an older version of Slicer installed, uninstall it. Simply delete the Slicer program files. There are no Registry entries to change.
    
2. Download the Windows version of Slicer onto your computer. (Instructions about how to download the most recent version were emailed to you upon receipt of your signed Software License Agreement. If you have not filled this out yet, click here.)
    
3. Double-click the zip file to start WinZip, and extract the files, using folder names.
   
   When the installation has completed, browse to that directory and double click the slicer2-win32-86.exe executable.

Frequently Asked Questions
What if I need more detailed instructions for installing with Windows NT? Look in the Developer's Guide
How can I always load a particular data set? Create a Slicer shortcut, right click on it and select Properties. In the Target text box, type the name of the MRML file you wish to open. Then click OK. You can change the name of the new shortcut by selecting the name, clicking the name once, typing the new name, and clicking Enter.
How can I uninstall Slicer? Delete the directory in which you extracted it.

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2c. Installing on Linux

Linux Installation Instructions

Compatibility

System Requirements

• Memory: Minimum: 128 MB.
• Disk Space: 33 MB to download the installer, which expands to about 125 MB. The tutorial data set requires 37 MB.
• Processor Speed: Has run successfully on a 450-MHz machine; a faster processor speed is recommended.

Installation Steps

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2d. Installing on Mac OS X

Mac OS X Installation Instructions

Compatibility

Slicer 2.4 and later are compatible with Mac OS X.
Panther and Tiger are supported in 2.6, but going forward Panther may not be supported. Intel based Mac support is still in the beta stages, only available on the CVS development head as of end of 2006.
Test versions are available for PowerPC and Intel Macs.

System Requirements

Slicer requires Mac OS 10.2 or greater.

Installation Steps

There is no installation. Open the archive and run the executable from inside the X server.

Slicer 2.6 Notes for Mac OS X Users.

Frequently Asked Questions
What are the platform requirements for Mac OS X? We're working on that.

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2e. Installing at BWH

SPL Installation Instructions

Please run the current version, 2.4.1 built for the SPL from the 2.4 release code with the addition of the vtkAG module: slicer24.
slicer2 will run version 2.1b1.

Alternatively, you can download the source code for your operating system (see above), and compile pointing to these libraries:
/projects/birn/slicer2/lib/solaris8

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2f. Installing on OpenMR

OpenMR Installation Instructions

WARNING

These instructions are out of date. Use at your own risk.

Accounts

Install everything as the "surg" user, and always run Slicer as the "surg" user.

Install the Software Packages

Unzip packages (from the ftp site) to create the following directory structure inside a main directory named "slicer":

• pkg -- contains all packages downloaded for installation
   
• slicer-1.2.2 -- most recent version of Slicer
   
• go -- old version of Slicer that was stable on monk during Arya's tenure
   
• bin -- executable scripts for all Slicer versions

Perform the following:

1. Edit "slicer-1.2.2/program/slicer" to set the SLICER_HOME environment variable.
    
2. Copy the "slicer" file to the "bin" directory mentioned above.
    
3. Add the above "bin" directory to the "PATH" environment variable in surg's "~/.tcshrc" file.

Edit Tcl Files to Change Defaults in New Slicer

The files listed in the table below are located relative to the directory:
slicer/slicer-1.2.2/program

Tcl File Edits
tcl-modules/Locator.tcl Add "LocatorSetActive SignaSP" at the end of the LocatorBuildGUI procedure.
tcl-modules/Twin.tcl Edit "set Twin(screen) 0" to become "set Twin(screen) 1". Edit any other lines as desired to change the size and position of the window. For example:   set Twin(xPos) 30   set Twin(yPos) 0   set Twin(width) 550   set Twin(height) 440
tcl-main/MainView.tcl Edit "viewBgColor" in "MainViewInit" to be "Black" instead of "Blue"

Edit Init Files to Change Defaults in Old Slicer

Edit the file "slicer/go/program/slicer.init" so that the "View" variables are as follows:

View ( boreDisplay Image boreScreen 1 boreRender 0 boreWidth 570 boreHeight 426 borePosition 25 0

Start the "SPL Server" on the Imaging Workstation

./spl_server

Run the New Slicer

1. At the command prompt, type "slicer".
2. Go to the "Twin" module and click "On".
3. Go to the "Locator" module and click "Connect".

Run the Old Slicer

1. At the command prompt, type "go".
2. Go to the "Realtime" module, and click "Bore" and "Connect".

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2g. Sample Data

You can download a file called tutorial.tar.gz at https://share.spl.harvard.edu/share/birn/public/software/tutorial.tar.gz.

1. Download tutorial.tar.gz.
2. Uncompress tutorial.tar.gz with WinZip, gunzip, or a similar utility.
3. Untar the tar file. The tutorial.tar file contains the tutorial.xml file.
4. Open the tutorial.xml file in Slicer. (Click File, then Open Scene, then select tutorial.xml.)
   The tutorial.xml file contains both volumetric data and 3D models.

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3. Overview

After Slicer starts, two windows appear.

The Menu window provides menus for accessing the features of Slicer. A brief explanation of the Menu window will make it easier to refer to its parts later. At the top of the Menu window there are File, View, Help, and Modules submenus. Under the submenus is a group of buttons known as the Main menu. Clicking a button on the Main menu will take you to the panel associated with that Slicer feature. There are tabs along the top of each panel. The leftmost tab on each panel is the Help for that feature. You can toggle a scrollbar on and off for the panel with this button.

Clicking More in the Menu window lists the modules available in your version of Slicer. Since Slicer consists of many optional modules, your list of modules may not match the list below.

Here are some sample modules: Anatomy: saves files from a Slicer scene to use with the SPL Anatomy Browser. Anno: controls the annotation displayed in the 2D and 3D viewer. Colors: enables you to create your own color palette. Custom: enables you to create your own modules for Slicer. CustomCsys: lets developers add a Coordinate System actor to their module. EMSegment: implements the "Expectation-Maximization-Segment" algorithm. 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. Guidance: positions two spherical targets (red and yellow) in the 3D view window to support reformatting volumes. Locator: connects Slicer to a server that feeds a real-time stream of coordinates from a device called the locator. Measure: provides measuring tools to calculate Surface Area, Volume, and Cross Sectional Area. MeasureVol: measures the volume of a segmented structure in a label map. ModelCompare: shows point correspondences and models in 2D. ModelHierarchy: displays the hierarchy of models. Options: reorganizes the order of the modules and hides unnecessary modules. Realtime: enables the locator's real-time coordinates to control Slicer. SessionLog: records information about a segmentation session for Slicer development purposes. Slices: selects the slices to display in the 3D viewer window. Tester: allows the developer to test modules. TetraMesh: reads in a Tetrahedral Mesh and converts it into a model. View: customizes the size of the viewer window. The stereo mode allows viewing the 3D window in 3 dimensions, using red/blue glasses. 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.

The Viewer window (below) displays volumes and models.

In the Normal view mode, the upper part of the Viewer window is the 3D Viewer and the lower part is the 2D Viewer, for displaying 2D slices.

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4. Loading Data

Slicer can load several different types of data, including:

• volumes (such as MR slices);
• models (3D surfaces);
• scenes (Slicer views of data).

Volumes

A volume is a collection of volume elements (voxels) of an image. A slice is a portion of a volume.

Slicer can read medical image volumes of various types (including GE Signa and Genesis data, DICOM (digital imaging and communications in medicine) slices, and non-header image data). If Slicer does not recognize the header automatically, you must enter the necessary information manually, so that Slicer can read the volume correctly.

Models

A model is a 3D surface.

Technical Note: The data format for the models that Slicer reads in is vtkPolyData. Model files have a suffix of .vtk.

Scenes

A scene is a description of a Slicer view, including path names to volumes and models, as well as viewing options.

Scenes are saved in an XML file. Scene files have a suffix of .xml.

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4a. Loading Volumes with Headers

To load volumes that have headers:

1. In the Data panel, click Add Volume. The Props tab of the Volumes panel appears.

   

2. To find the first image file, click Browse. A dialog box appears.
3. Select the first image of the volume that you would like to load, and then click Open. (The number of the last image in the volume will automatically appear in the Number of Last Image field.)
4. Leave Image Headers on Auto.
5. Using the Image Data radio buttons, select whether your images are grayscale or label maps (the output of a segmentation).
6. The Name field is the name that your volume will have within Slicer.
7. You may enter a description in the optional Description field, such as "Presurgical_SPGR".
8. When you are done making changes, click Apply to read in the volume. Your data will now appear in the 2D portion of the Viewer window.

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4b. Loading Volumes without Headers

If the volume does not have a header, it is necessary to manually input the information to read the volume:

1. In the Data panel, click Add Volume. The Props tab of the Volumes panel appears.

   

2. To find the first image file, click Browse. A dialog box appears.
3. Select the first image of the volume that you would like to load, and then click Open. (The number of the last image in the volume will automatically appear in the Number of Last Image field.)
4. Set Image Headers to Manual.
5. Click Apply. The Header section of the Props tab appears.
6. Change the default values to the values of your volume, namely, the physical parameters of the pixels that make up your volume. These parameters include:

File Pattern: The pattern for naming the files, expressed in C language syntax. For example, a file named skin.001 has a pattern of %s.%03d, and a file named skin.1 has %s.%d for a pattern.(For more information on C language syntax, see http://www.cppreference.com/stdio_details.html#printf.) Image Size: Number of pixels of the image in the x and y directions. (For square pixels, they are the same.) Pixel Size: Size of each pixel in the x and y directions. (For square pixels, they are the same.) Slice Thickness: The z dimension of the voxel. Scan Order: LR = left to right IS = inferior to superior PA = posterior to anterior Scalar Type: The data format of the pixel. Generally, it is Short (16 bit integer). Slice Tilt: The tilt of the gantry during an MRI. Num Scalars: The number of scalar components for each voxel. Gray-level data has 1. Color data has 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: This parameter, and the values Swap and No Swap, are placeholders for future use.

7. When you are done, click Apply to read in the volume. Your data will now appear in the 2D portion of the Viewer window.

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4c. Loading DICOM Volumes

Note: 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. Also, any oblique scans are shown as the nearest approximate scan order (axial, sagittal, or coronal).

Note Also: Slicer assumes that the subject is scanned supine (face up). Scans of prone subjects (face down) may be flipped.

To load DICOM volumes:

1. Click Add Volume in the Data panel. The Props tab of the Volumes panel appears.

   

2. From the Properties pull-down menu, select Dicom.
3. Click Select DICOM Volume.



4. A dialog box appears. Select the directory to start searching for volumes in, and click OK. The whole directory structure will be traversed to find every DICOM file. Important information, such as the name and ID of the patient, the study UID (unique identifier), and the series UID, will be extracted from each DICOM file. Note: If you have a large number of files, this is a  slow process.



5. After the search, a new dialog box appears showing patient, studies, series, and files. (By default, all files of the first series of the first study of the first patient will appear.) Select a patient, a study of this patient, a series of this study, and the files of this series. Then click OK.
6. After clicking OK, the header data of the first file will be extracted. You may select additional files. Clicking Extract Header will show their header information. You can check and modify the extracted values by clicking Header.
7. In the Basic panel, you can use the Image Data radio buttons to select whether your images are grayscale or label maps (the output of a segmentation).
8. The Name field is the name that your volume will have within Slicer. You may change this to something descriptive, for example "Presurgical SPGR".
9. You may enter a description in the optional Description field.
10. Click Apply to set your Name and Description choices.
11. Finally, click Apply to read in the volume. Your data will now appear in the 2D portion of the Viewer window.

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4d. Loading Label Maps

To load a label map:

1. In the Data panel, click Add Volume. The Props tab of the Volumes panel appears.

   

2. Click Label Map for Image Data.
3. To find the first image file, click Browse. A dialog box appears.
4. Select the first image of the volume that you would like to load, and then click Open. (The number of the last image in the volume will automatically appear in the Number of Last Image field.)
5. Leave Image Headers on Auto.
6. The Name field is the name that your volume will have within Slicer.
7. You may enter a description in the optional Description field, such as "Presurgical SPGR".
8. When you are done making changes, click Apply to read in the volume.
9. Since label maps are saved without headers, a message will appear warning that no header information was found. Click OK.
10. Click Apply to use the default header information, or change the header information and then click Apply. Your data will now appear in the 2D portion of the Viewer window.

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4e. Loading Models

A model is a 3D surface.

Technical Note: The data format for the models that Slicer reads in is vtkPolyData.

To load models:

1. In the Data panel, click Add Model. The Props tab of the Models panel appears.

   

2. To find the model file, click Browse. A dialog box appears.

   

3. Select the model that you would like to load, and click Open.
4. The Name field is the name that your model will have within Slicer. You may change this to something descriptive, like "Vessels".
5. From the Color pull-down menu, you can select your model's color as it will appear in the 3D Viewer.
6. Finally, click Apply to read in the model.

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4f. Opening Scenes

You may have scenes that you have saved using Save Scene, Save Scene As, or Save Scene with Options.
You can open or import a scene. When you open a scene, the current scene closes and the new one opens. When you import a scene, the current scene remains and the new one is added.

To open a scene:

1. Click File. A drop-down menu appears.

   

2. Click Open Scene.
3. Find the scene .xml file, double-click it, and wait for the volumes and models to load.

To import a scene:

1. Click File. A drop-down menu appears.

   

2. Click Import Scene.
3. Find the scene file (usually .xml or .mrml), double-click it, and wait for the volumes and models to load.

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5. Viewing Data in Slicer

Slicer can be used to create many kinds of scenes, including:

• A single series of grayscale images
• A complex scene comprised of several grayscale and segmented data sets
• 3D models, such as the composite scene below of a grayscale MR dataset of an orange, with a single section of the orange highlighted (in red), and the rest of the orange displayed (in orange)

Selecting the View mode

To select the View mode:

1. Click View. A drop-down menu of available view modes appears.
2. Select a view mode from the menu. The view will change to reflect your selection.

Different View modes are useful for different situations. Most users prefer the Normal (shown above) or 4D view for observing data after they are done editing and creating a scene. Users also prefer the 4x512 view during the editing process.

View modes include:

• Normal

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5a. Images Available for Viewing

The List tab shows a list of the items comprising the current scene, which includes all loaded volumes.

To use the List tab:

1. Click Data, then click the List tab. This panel appears.
   
2. If you right-click on any item in the list, a drop-down menu appears that lets you edit, cut, paste, or delete the item.

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5b. Viewing Volumes

After loading volumes, you can optimize how you view them.

Slicer has multiple configurations to display 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.

2D Window Controls

• There are three 2D windows (red, yellow, and green). You can select both grayscale and label map volumes into each of the 2D windows. For example, Slicer will automatically put the Axial grayscale volumes 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 is an Or (scan order), Bg (background), Fg (foreground), and Lb (label map) button 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 volumes for the label map layer, to display results of a segmentation. Volumes 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.)
• 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.

Adjusting Window/Level

By adjusting the Window/Level of the volume, you can optimize displaying the region of interest of gray-scale volumes. 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.

To adjust the Window/Level of a volume:

1. Click Volumes on the Main menu.
   
   The Volumes panel appears.
2. Select the Display tab.
3. From the Active Volume pull-down menu, select a volume.

   

4. Move the sliders, or click Auto, to adjust the display properties of the volume.

Using Threshold to Display

By adjusting the Threshold of the volume, you can limit the display to labels whose values fall within the threshold range.

To adjust the Threshold of a volume:

1. Click Volumes on the Main menu.
   
   The Volumes panel appears.
2. Select the Display tab.
3. From the Active Volume pull-down menu, select a volume.

   

4. Toggle Apply to apply or not apply the threshold. Apply is selected automatically if you select Auto, or move the Lo or Hi sliders.
5. Move the Lo slider to the lower limit you want, or click Auto for automatic threshold.
6. Move the Hi slider to the upper limit you want, or click Auto for automatic threshold.

To define the upper and lower limit of the Threshold sliders:

1. Click Volumes, then click the Other tab. This tab appears.

   

2. Select either Auto or Manual for Slider Range.
3. Enter values for the Low and High values of the Slider Range.

Color Palette

You can select a color scheme to colorize your gray-scale volume. This can help you distinguish different regions of interest better.

Use the Palette pull-down menu (on the Display tab of the Volumes panel) to select one of seven available color schemes:
Gray, Iron, Rainbow, Ocean, Desert, InvGray, or Label.

Image Fusion

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.

In the example below, the images in the background are grayscale (non-brain) images and the images in the foreground are label map or segmented (brain) images.

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5c. Viewing 3D Models in Slicer

You can view models (3D surfaces) in Slicer.

Selecting Models

The Display tab of the Models panel controls which models are visible in Slicer.

• 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.
• Click Show All to display all models in the 3D Viewer.
• Click Show None to display none of the models in the 3D Viewer.

Controlling the 3D View

• Left-click the view and move the mouse to rotate the view.
• Click the middle button (or Alt-Left button) on the view and move the mouse to move the view left, right, up, or down.
• Right-click the view and move the mouse to change the zooming factor, making the view larger or smaller.

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 Image Fusion 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 snaps the 3D view to align with the selected major axis. Click R (Right), L (Left), P (Posterior), A (Anterior), I (Inferior), or S (Superior) to snap the image to each direction.
• The arrows pointing up, down, left, and right rotate the 3D view incrementally in the selected direction. Click the arrow and the 3D view will rotate.
• FOV stands for Field Of View, which determines how much of the image to display. If the image is too small, enter a larger value for FOV. If the image is too large, enter a smaller value for FOV.
• 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

Opacity is how non-transparent a model is. (The higher the opacity, the less transparent the model is.)

You can control the Opacity of each model.

By default, Slicer creates models that are completely opaque (opacity = 1).
Setting the opacity to 0 makes the model completely transparent.

Adjust the opacity in either of two ways:

• On the Display tab of the Models panel, adjust the Opacity slider next to the model's name in the model list.

  

• On the Props tab of the Models panel, set the Active Model, and use the Opacity slider below.

  

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.

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:

1. On the Display tab of the Models panel, right-click the model's name in the list.

   

2. A drop-down menu appears. Select Clipping.

To control clipping:

1. Select the Clip tab of the Models panel.

   

2. 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.

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6. Modifying Data

Slicer has a set of effects (tools) for modifying image data. Most of these are oriented toward segmenting the image data, that is, separating anatomical structures visually.

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6a. Before Editing Data

Beginning the Editing Process

Before you start editing:

• If you have multiple copies of grayscale or label maps that are part of your scene, select the one you currently want to edit.
• Click View to change the view mode to 4x512.

Important notes:

• Slicer creates (in memory) a working version of the data that reflects your edits (called a label map). When saved, the default file name of this working copy is called Working.
• When you have finished editing, make sure to save your changes. Slicer will remind you if you have unsaved volumes and will display the names of unsaved volumes.
• Slicer will strip the headers off the images when you save your data. Slicer encodes the geometry and orientation of your data in a MRML (Medical Reality Modeling Language) file. You can save, reload, and repeatedly update your MRML file until you have created the scene you want.

1. On the Main menu, click Editor.
   
   The Volumes tab appears:
2. 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.
3. Select NEW for the Working Labelmap, and enter a Descriptive Name for this segmentation. For example, if you are segmenting the ventricles of the brain, you might name this segmentation "ventricles".
4. Click Start Editing. The Effects tab appears:
5. Select the Active Slice to edit by clicking Red, Yellow, or Green. For each individual effect, you can choose whether to apply changes to this active slice, nearby slices, or the entire volume.
6. After editing a single slice, continue to the next slice.

About the Editing Effects

Some considerations are common to all the editing effects:

• Select the correct input volume of data to edit, so that the edits will be applied properly.
• Set the scope of your edits properly: one slice (the one on the screen that you are currently editing); three slices (the current slice and the slices on either side of the current slice); or the entire volume. For some effects, such as drawing, it only makes sense to have the scope of the edits be the current slice. For other effects, such as thresholding, it makes sense to apply the changes to the entire 3D volume.
• When you select any of the effects, the following row of buttons appears: The button labels are abbreviations for the effects (except for PhaseWire and Measure Island). The selected button is the current effect. A description appears under the row of buttons.
• The right-most button is Undo (Un), which becomes available after you apply any effect. If you click Un, it undoes (or reverses) the last applied effect.

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6b. Editing Data

Using the Editing Effects

• Threshold
• Erode
• Change Label
• Draw
• Identify Islands
• Remove Islands
• Change Island
• Save Island
• Measure Island
• PhaseWire
  
  
• After Segmenting

Threshold effect

The goal of thresholding is to limit the output image to only those pixels whose signal intensity is between the lower and upper bounds you select. In the new output volume, all the pixels will have a single label (the Output color).
Threshold is useful for separating the anatomy of interest from surrounding anatomy, based on the signal intensity of the anatomy of interest. For example, Threshold works well for segmenting bone in CT data.

To use Threshold:

1. Click Threshold. This panel appears:
2. Select the Input Volume.
3. Select the Scope and Interact ranges.
4. Click Output and select a color, or enter an Output color number. You can also enter an optional label for what that color will represent. For instance, in this example, the chosen color is 2 (orange) and the label is 'skin'.
5. Adjust the Lo slider to exclude points whose signal intensity is too low.
6. Adjust the Hi slider to exclude points whose signal intensity is too high.
7. Click Apply to apply the thresholding effect. Slicer will update the Working volume with your new label of thresholded data.

Results of thresholding

In the example below, we are segmenting the CT skull bone. Thresholding has changed the label to be blue. Notice that the skull is well-defined and separated from the rest of the image.

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).

1. Click Erode. This panel appears:
2. Select the Input Volume.
3. Select the Scope range. Multi Slice applies the one-slice erosion to each slice. 3D treats the whole volume at once.
4. 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.
5. Enter 0 for the Fill value.
6. Enter the number of times to apply the effect in the Iterations field.
7. Select 4 for Neighborhood Size for less erosion or 8 for more erosion.
8. Select Active to apply Erode to the active view. Select Native to apply Erode to the original view.
9. 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:

Change Label effect

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.

To use Change Label:

1. Click Change Label. This panel appears:
2. Select the Input Volume.
3. Select the Scope range.
4. Enter a Value to change. This is the value of label of pixels in the Input Volume that Slicer will change.
5. 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.
6. Click Apply to apply the change label effect. Slicer will update the Working volume with your newly labeled data.

Draw effect

The Draw effect lets you specify pixels by drawing directly on them using the mouse.
Draw is useful when automatic methods cannot segment the data correctly.

To use Draw:

1. Click Draw. This panel appears:
2. Click Output and select a color, or enter an Output color number. This is the new value that pixels you draw on will receive.
3. 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.
4. 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.
5. 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.
6. Select the Render range.
7. Select the Shape that the left mouse represents in the draw window.
8. Click on the region of interest, using the left mouse button, and Slicer will draw as specified with the Mode. 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.

   Note: If you encircle too much of an image in a particular slice, use Draw with Black output to create polygons around the extraneous areas; this acts like an eraser. You may also delete the last selected point of your polygon by selecting Delete Selected.

9. 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.
10. When you have finished drawing the outline of the region of interest, click Apply. Slicer will fill the region of interest with the Output color.

Identify Islands effect

The Identify Islands effect automatically assigns a unique label to each "island" in the designated "sea", namely, the area containing the islands.
Identify Islands is useful when many separate islands have the same label, but belong to different structures.

To use Identify Islands:

1. Click Identify Islands. This panel appears:
2. Select the Input Volume.
3. Select the Scope range.
4. Enter Min Threshold and Max Threshold values to identify islands in a certain intensity range.
5. Click any part of the "sea", namely, the area containing the islands. The islands within that area will receive a unique label.

Remove Islands effect

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.

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.

1. Click Change Island. This panel appears:
2. Select the Input Volume.
3. Select the Scope and Render ranges.
4. 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.
5. 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:

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.

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:

1. Click Measure Island. This panel appears:
2. Select the Input Volume.
3. Select the Scope range.
4. 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.
5. 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, the following formula is used:
size * pixel_size * pixel_size * (thickness + spacing)

PhaseWire effect

PhaseWire is a semi-automatic effect to outline features on images by following edges or contours.
Using PhaseWire is a rapid way to outline a feature.
Warning: PhaseWire does not work in all versions of Slicer, and may cause Slicer to crash.

To use PhaseWire:

1. Click PhaseWire. This panel appears:
2. Click Basic. (Only the Basic features work.)
3. Click Output and select a color, or enter an Output color number. This is the new value that pixels you outline will receive.
4. Select the Render range.
5. Select the Shape of the outline in the draw window. Polygon will close the shape that you outline by selecting points, when you click Apply. Lines will draw lines between points you select. Points will create points of color where you select.
6. Select the Image Feature Size.
7. Click the left mouse on the edge of the feature that you want to outline. Release the mouse button, but follow the edge with the mouse.
   If the "wire" starts to stray from the edge, click the mouse button to pull in the wire.
8. To undo the last mouse click, click Undo Last Click.
9. To start the outline process again, click Clear Contour.
10. When you have finished drawing the outline of the region of interest, click Apply. If Polygon is selected, Slicer will fill the region of interest with the Output color. If Lines is selected, Slicer will outline the region of interest with the Output color.

After Segmenting

Save your segmented data (called a "label map").

1. On the Main menu, click Editor.
   
   The Editor panel appears.
2. Click the Volumes tab. The Volumes tab appears.
3. Select Save.
4. Select the name of your label map for Volume to Save.
5. Select a file name. It is often simplest to use the same name as the Volume to Save.
6. Save this file to the appropriate directory.

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7. Saving Data

There are several ways to save data in Slicer.

• To save label maps and other volumes, use Editor button ==> Volumes panel ==> Save.
• To save models, use ModelMaker button ==> Save panel ==> Save.
• To save a scene as an XML file, use Save Scene, Save Scene As, or Save Scene with Options (File submenu). The XML file lists the elements of the scene and their attributes.
• To save one of the slices as a TIFF file, use Save Active Slice or Save Active Slice As (File submenu).
• To save a picture of the 3D view as a TIFF file, use Save 3D View or Save 3D View As (File submenu).
• To save user preferences, like background color or view mode, into a special Options.xml file, use Save Current Options (File submenu).

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7a. Saving Label Maps

After you create a label map, you can save the label map volume.

To save the label map:

1. On the Main menu, click Editor.
   
   The Editor panel appears.
2. Click the Volumes tab. The Volumes tab appears.

   

3. Select Save.
4. Select the name of your label map for Volume to Save.
5. To select a file name, do one of the following:
   • To use an existing file name, click Save.
   • To use a new file name, enter the Filename Prefix. (It is often simplest to use the same name as the Volume to Save.)
6. Click Save. The Save Volume dialog box appears.
7. Select the path and click Save.

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7b. Saving Models

After you create a model, you can save the model.

To save the model:

1. On the Main menu, click ModelMaker.
   
   The ModelMaker panel appears.
2. Click the Save tab. The Save tab appears.

   

3. Select the Active Model.
4. Enter the File Prefix, which can include a path. (The file suffix is .vtk.)
5. Click Save. The Save Model dialog box appears.
6. Select the path and click Save.

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7c. Save Scene

You can save a description of the current scene. This does not save any volumes, label maps, or models, but does save the path names to those files in an XML file. You can then open them all again later, just by opening the scene file.
Note: Before saving the scene, you should save any new volumes, label maps, and models separately first.
Note: The default directory to save files in is SLICER_HOME.

To save a description of the current scene:

1. Click File. A drop-down menu appears.

   

2. 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 path, and with no options, select Save Scene.
   • To use another file name or path, select Save Scene As and enter your own file name.
   • Use Save Scene With Options to include options in the scene description. Options include view mode, field of view (FOV), background color, and other preferences you set. Options are saved to file named Options.xml.
   • To save only the current viewing options, without saving the scene itself, select Save Current Options.

To open a saved scene later:

1. Click File.
2. Click Open Scene.
3. Find the scene file (usually .xml or .mrml), double-click it, and wait for the volumes and models to load.

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7d. Saving the Active Slice

There are two ways to save the active slice in the TIFF file format. The active slice is the one that you clicked last.

To save the active slice:

1. Click File. A drop-down menu appears.

   

2. 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 and path, select Save Active Slice.
   • To use another file name or path, select Save Active Slice As and enter your own file name.

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7e. Saving the 3D View

There are two ways to save a 2D projection of the 3D scene in the TIFF file format.

To save the 3D view:

1. Click File. A drop-down menu appears.

   

2. 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 and path, select Save 3D View.
   • To use another file name or path, select Save 3D View As and enter your own file name.

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8. Modules

In addition to the basic functionality already mentioned, Slicer also includes a number of modules developed for specific tasks. Developers can create modules and share them with other Slicer users.

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8a. Common Modules

Clicking More in the Menu window lists the modules available in your version of Slicer. (You can also select modules by clicking the Modules catagorized submenu.) Since Slicer consists of many optional modules, your list of modules may not match the list below.

Here are some sample modules: View: customizes the size of the viewer window. The stereo mode allows viewing the 3D window in 3 dimensions, using red/blue glasses. Anno: controls the annotation displayed in the 2D and 3D viewer. Slices: selects the slices to display in the 3D viewer window. Colors: enables you to create your own color palette. 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. Measure: provides measuring tools to calculate Surface Area, Volume, and Cross Sectional Area. MeasureVol: measures the volume of a segmented structure in a label map.

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8b. Other Modules

Other modules include:

• 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 segmentation algorithm.
• Custom: a template to help you to create your own modules for Slicer.
• Anatomy: saves files from a Slicer scene to use with the Surgical Planning Lab's Anatomy Browser.
• CustomCsys: lets developers add a Coordinate System actor to their module.
• ModelHierarchy: displays the hierarchy of models.
• Options: reorganizes the order of the modules and hides unnecessary modules.
• SessionLog: records information about a segmentation session for Slicer development purposes.
• Tester: allows the developer to test modules.
• 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.

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8c. Acquiring New Modules

Acquiring New Modules

Independently developed modules are often checked into the Slicer code archives, and are tested for possible distribution in future releases.
Sometimes they are published on the Web sites of the groups that have developed them, or are announced on the Slicer users or developers mailing lists.
A new module will have to be compiled to be compatible with your version of Slicer, so you must have a version of Slicer that includes source code and .vtk header files.

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9. Specific Module Instructions

Here are instructions about using specific modules. To start a module:

1. In the Menu window, click More. The list of available modules appears.
2. Click the module from the list.

Alternatively, click Modules and select a module category from the submenu. Select the module from the drop-down menu.

• Modules A-H
• Modules I-N
• Modules O-Z

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9a. Modules A-H

Using Modules A-H

• Anatomy
• Anno
• BIRNDUP
• Colors
• CorCTA
• CrossSection
• Custom
• CustomCsys
• DTMRI
• EMSegment
• Endoscopic
• Fiducials
• Guidance

Anatomy module

The Anatomy module lets you save Slicer scenes as files for the SPL Anatomy Browser.
There is one tab: Anatomy.

Anatomy tab

The Anatomy tab lets you save the current scene for the SPL Anatomy Browser.

To use the Anatomy tab:

Click the Anatomy tab. The panel at left appears. Enter the Scene name. Enter the Output directory for the created file. Enter the Directory for temporary files. This directory will contain temporary files while the output file is being created. After the file is created, you can delete the files in the temporary directory. Click Volume and select the volume from the drop-down list. Click Label map and select the label map from the drop-down list. NOTE: Labels must match the model order inside the MRML file and have consecutive label numbers. Click Shrink to change the size of the 3D Viewer to 384-by-384 pixels, which is the standard of the SPL Anatomy Browser. Click Restore window to change the size of the 3D Viewer to full size. Select a name for the view from the list, or click Add to enter a new name for the list. To delete a name, select the name and click Delete. Click Go! to create the file. The file appears in the Output directory.

Anno module

Slicer can display graphical and text annotations on images in the Viewer window. The Anno module lets you control these annotations. This can be useful for orienting images correctly, and for formatting images for output. There are two tabs: Visibility and Mode.
To save annotation options, click File, then click Save Current Options. This will save your options to a file called Options.xml.

Visibility tab

The Visibility tab provides controls for determining which annotations will be visible.

To use the Visibility tab:

Click the Visibility tab. The panel at left appears. To display a 3D wireframe cube, click 3D Cube. To display 3D coordinate axes, click 3D Axes. To display letters that label the 3D coordinate axes, click 3D Letters. To display colored 3D outlines around each slice, click 3D Outline around slices. To display a crosshair on 2D slices, click Crosshair. To display hash marks on the crosshair on 2D slices, click Hash marks. NOTE: Crosshair must be on to display hash marks. To display text on 2D slices (including axis labels, coordinate values, and foreground and background values), click Slice window text.

3D Cube on	3D Axes on	3D Letters on	3D Outline around slices on

Crosshair on	Hash marks on	Slice window text on

Mode tab

The Mode tab lets you choose:

• coordinate system displayed on slices
• precision to display pixel values
• whether axes or cube should follow the focal point

Click the Mode tab. The panel at left appears. Select the coordinate system to display with the Slice Cursor, as follows: Click RAS to select RAS coordinates, which give the coordinates of the slice cursor as the physical location in Right-left, Anterior-posterior, Superior-inferior form, in millimeters. Click IJK to select IJK coordinates, which give the coordinates of the slice cursor in terms of which pixel on which slice. Click XY to select XY coordinates, which give the coordinates of the slice cursor as the number of pixels from the left and from the bottom, respectively. Select how to display the values of the foreground and background of the pixel on the 2D Viewer, as follows: Click 1 to display the values as integers. Click 1.00 to display the values to two decimal places. Click full to display the values to all decimal places. Click Axes follow focal point to have the coordinate axes follow the focal point when you move the mouse in the 3D Viewer. Click Cube follows focal point to have the bounding cube follow the focal point when you move the mouse in the 3D Viewer.

BIRNDUP module

The BIRNDUP module acts as an interface to deidentify and upload DICOM volumes to BIRN (Biomedical Informatics Research Network). There is one tab: BIRNDUP.

BIRNDUP tab

The BIRNDUP tab runs the interface to deidentify and upload DICOM volumes.

To use the BIRNDUP tab:

Click the BIRNDUP tab. The panel at left appears. To choose an active volume, click Active Volume and select a volume from the drop-down list. Click Run Interface to start the BIRN Deidentification and Upload Pipeline.

Colors module

The Colors module lets you:

• create color names and associate colors with each name
• associate one or more labels with each color name
• define color properties, including how ambient, diffuse, and specular a color is
• load predefined sets of colors

Edit Colors tab

The Edit Colors tab provides controls for creating color names, defining color properties, and associating colors and labels with color names.

To use the Edit Colors tab:

Click the Edit Colors tab. The panel at left appears. To create a new Color Name, enter the name and click Add. To delete an existing Color Name, select the name in the list and click Delete. To associate a label with a Color Name, select the name in the list, enter the label in the Label field, and click Add. To remove a label from a Color Name, select the Color Name in the list, select the Label in the list, and click Del. To adjust color properties, select the Color Name in the list, then adjust the sliders for: Red Green Blue Ambient: how much light the material is emitting. A value of 1 is a light source. Diffuse: how much light the material is reflecting in random directions. Specular: how shiny the material is, from reflecting light like a mirror. Power: the intensity of the specular reflection. Then click Update.

Load Colors tab

The Load Colors tab lets you load predefined sets of colors.
To use the Load Colors tab:

Click the Load Colors tab. The panel at left appears. Click Browse and select a MRML file that contains color definitions, then click Load.

CorCTA module

The CorCTA module extracts centerlines for vessels.
There is one tab: Centerlines.

Centerlines tab

The Centerlines tab provides controls for extracting centerlines from a label map. NOTE: This can take a long time.

To use the Centerlines tab:

Click the Centerlines tab. The panel at left appears. Click Input volume to select a loaded label map. Enter a Model name for this use. Select Lines to generate lines. Select Fiducials to generate fiducial points. Select Surfaces to generate surfaces. Select Smooth lines to smoothe the generated lines. Enter a Segment length in mm. Click Extract Centerlines to generate centerlines using the specified parameters.

CrossSection module

The CrossSection module lets you position a virtual camera in the scene, and view what the camera sees in a second window. You can also have the camera move along a pre-defined path. This is useful for examining structures that can't be viewed from outside the model.
There are three tabs: Display, Path, and Advanced.

Display tab

The Display tab lets you control what is displayed, and how large the display is.

To use the Display tab:

Click the Display tab. The panel at left appears. To change the width of the CrossSection View, click choose and select a width from the drop-down menu. Alternatively, enter the Width. To toggle the Main View display (namely, the 3D Viewer with the virtual camera), click Show Main View. To toggle the CrossSection View display (namely, what the virtual camera sees in the scene), click Show CrossSection View. To toggle the 2D Viewer display, click Show 2D Slices. To toggle hiding the CrossSection View on exiting, click Hide CrossSection View on Exit.

Main View, with camera pointing out	CrossSection View

Path tab

The Path tab lets you describe a path along which the virtual camera will move. The virtual camera will display the scene from the path as it moves. You can set the path using automatic and advanced settings.

To use the Path tab automatically:

Click the Path tab, then click Automatic. The panel at left appears. Click Choose an Active Model and select an active model from the list. To select a start point, move the cursor on the model and press p. To select a different start point, click Select another point, then select a start point. To select an end point, move the cursor on the model and press p. To select a different end point, click Select another point, then select an end point. Click Extract Centerline to automatically generate a path from start point to end point.

Custom module

The Custom module is a sample module for developers. It contains typical labels and controls to show how to add a Slicer module. The source code is at http://www.na-mic.org/ViewVC/index.cgi/slicer2/Base/tcl/tcl-modules/Custom.tcl?root=Slicer2&view=log.
There is one tab for illustration purposes.

CustomCsys module

The CustomCsys module is a sample module for developers. It shows how to display and control a Csys actor. The source code is at http://www.na-mic.org/ViewVC/index.cgi/slicer2/Base/tcl/tcl-modules/CustomCsys.tcl?root=Slicer2&view=log.
There is one tab: Coord Sys.

Coord Sys

The Coord Sys tab allows you to translate and rotate the Csys actor.

To use the Coord Sys tab:

Click the Coord Sys tab. The panel above appears. The Csys actor appears in the 3D Viewer. To translate the Csys actor, left-click on one of the axes and move the mouse in the desired direction. To rotate the Csys actor, right-click on one of the axes and move the mouse in the desired direction.

DTMRI module

The DTMRI module allows users to create displays and perform calculations for diffusion tensor MRI research.
There are seven tabs: Convert, Disp, ROI, Scalars, Save, Advanced, and Devel.

Convert

The Convert tab allows the user to convert volumes into DTMRI volumes.

To use the Convert tab:

Click the Convert tab. The panel at left appears. Click Input Volume and select a loaded volume from the drop-down list. Enter the Number of Gradient Directions (usually 6). Enter first and last diffusion-weighted Gradient image numbers at the first slice location. Enter first and last Baseline (non-gradient, not diffusion-weighted) image numbers at the first slice lodation. Enter a list of diffusion gradient direction vectors. Click Convert Volume to convert the volume.

Display

The Display tab allows the user to control the display of DTMRI volumes.

To use the Display tab:

Click the Display tab. The panel at left appears. Click Active DTMRI and select a DTMRI volume from the drop-down list. Select the type of 3D View Settings, either DTMRIs to view the 3D DTMRI as transparent slices or default to return to the Slicer default settings. Next to Display Glyphs, click On to display each DTMRI as a glyph, or Off to not display glyphs. Select where to display glyphs: Red to display in the leftmost slice, Yellow to display in the center slice, Green to display in the rightmost slice, or Vol to display in the volume. Next to Display 'Tracts', click On to display all tracts, Off to hide all tracts, or Delete to clear all tracts. Click Visualization Menu to select one of the following options: Click Glyphs to control display of glyphs. Click Glyph Type and select Axes, Lines, Ellipsoids, or Boxes from the drop-down list. If displaying DTMRI as lines, click Max to use the eigenvector corresponding to the largest eigenvalue, Middle to use the eigenvector corresponding to the middle eigenvalue, or Min to use the eigenvector corresponding to the smallest eigenvalue. Click Color by and select whether to color DTMRI according to Linear, Planar, or Spherical measures, or according to Max, Middle, Min, or MaxMinusMiddle eigenvalue, or according to relative anisotropy (RA) or fractional anisotropy (FA), or according to the direction of the major eigenvector. Next to Scalar Bar, click On to display a bar showing the correspondence between numbers and colors or Off to hide the bar. Select Scalar Range as either Auto to use the largest and smallest scalars to define the range, or Manual to choose the range using the Lo and Hi sliders. Click Tracts to control display of tracts. Click Color to select the color for the tracts. Select Color by as either SolidColor to use solid color on streamlines or MultiColor to color by scalars from the data. Enter Max Length, the maximum propagation distance, beyond which tractography will stop. Enter Step Size, the integration step length to use when following a path. Enter Smoothness (along), the length of each displayed tube segment. Enter Radius, the initial thickness of each displayed tube. Enter Smoothness (around), the number of sides on each displayed tube. Enter Direction, the number of directions to follow from each initial point (1 or 2). Click AutoTracts to automatically start tractography from each voxel in an ROI. Click ROI Labelmap and select the label map to seed tracts from the drop-down list. Click Label to select the color to use to seed the tracts. Click Seed 'Tracts' in ROI to begin seeding a tract from each point in the ROI. This can take a long time. Click SaveTracts to save visible tracts. Click Save tracts in model file to save the currently visible tracts as a model. Click Save tracts in vtk file to save currently visible tracts as a polyline. FOR DEVELOPERS ONLY.

ROI

The ROI tab tbd.

To use the ROI tab:

Click the ROI tab. The panel at left appears.

Scalars

The Scalars tab tbd.

To use the Scalars tab:

Click the Scalars tab. The panel at left appears. Click Active DTMRI and select a DTMRI volume from the drop-down list. Click Create Volume to select the type of volume to produce, including grayscale volume from Trace, Determinant, RelativeAnisotropy, FractionalAnisotropy, LinearMeasure, PlanarMeasure, SphericalMeasure, MaxEigenvalue, MiddleEigenvalue, and MinEigenvalue, and 3-component color volume from ColorByOrientation, D11, D22, and D33. Next to ROI, click None to derive the scalar volume from the entire DTMRI volume using no ROI, Threshold to mask the DTMRI using the thresholded area defined in the ROI before creating the scalar volume, or Mask to mask the DTMRI using the label map volume defined in the ROI tab before creating the scalar volume. Enter the Scale Factor to multiply by the output image for better viewing.

Save

The Save tab tbd.

To use the Save tab:

Click the Save tab. The panel at left appears. Click Active DTMRI and select a DTMRI volume from the drop-down list. Click Save Tensor to save the tensor in vtk file format. Click Save streamlines in scaled IJK to save streamlines.

EMSegment module

The EMSegment module lets you automatically segment a volume using the Expectation-Maximization optimization technique (see http://www.ai.mit.edu/people/tkapur/phdthesis1999.pdf for further information). This produces an intensity-based classification of voxels in the image into different tissue classes.
There are four tabs: EM, Class, CIM, and Setting.

EM tab

The EM tab provides a step-by-step process for segmenting images.

To use the EM tab:

Click the EM tab. The panel at left appears. NOTE: This is Step 1 of a four-step process. Available volumes appear in the Volume List. Select the aligned grayscale volumes to segment and click => to move to the Input Greyscales list. Click Step2.

The panel at left appears. NOTE: This is Step 2 of a four-step process. Enter the following information: No. of Classes: the number of classes to segment the image into. Iterations: the number of times to run the algorithm. Values between 10 and 20 are suggested. Boundary Min and Boundary Max: the slices along each IJK direction to segment. These three limits define the boundary box. Click Step3.

The panel at left appears. NOTE: This is Step 3 of a four-step process. For each of the number of classes you entered in Step 2: Assign a label to the class by clicking Assign Label and selecting or defining a label. Enter a value for the global probability of this class. Assign a probability map by clicking Assign Probability Map and selecting a probability map from the drop-down list. Generate an intensity distribution by clicking either Auto or Manual. If you click Manual, use Ctrl-Left mouse button to take samples for the class. Click Next to configure the next class, or Prev to configure the previous class. Click Class Overview to display the configuration for all classes. To start the EM Segmentation process, click Run. NOTE: This can take a long time (several hours), depending on the number of iterations, the number of slices, and the number of classes.

Class tab

The Class tab lets you configure more complicated classes.
To use the Class tab:

Select the class from the drop-down menu at the top. To use samples to calculate the Mean and Covariance, check the Use Sample box. Otherwise, to enter values manually, leave Use Sample unchecked and enter Mean and Covariance. Enter the Probability for this class. Click Prob. and select a probability map from the drop-down list. Enter the Shape Parameter. This defines the importance of the shape constraints in the overall structure's posterior calculation, with 1 being very important and 0 being totally unimportant. Enter the Prob Data Weight to assign a weight to the probability. Enter the Input Channel Weights to assign a weight to the input channel. To display the class distribution for this class, click Class Distribution. To display the class overview, click Class Overview. To promote this class to a super class, check the Super Class box. This panel appears: Enter a Name for this super class. Enter the Class Probability for this super class. Enter the number of classes for this super class. Enter the Probability Data Weight for this super class. Enter the Input Channel Weights for this super class. To display the class distribution for this class, click Class Distribution. To display the class overview, click Class Overview.

CIM tab

The CIM tab lets you define how neighboring voxels affect the probability of a given voxel. CIM stands for class interaction matrix.
To use the CIM tab:

Click Edit to edit the class interaction matrix. The panel at left appears. To define the location of the neighbor with respect to the voxel, click West, East, North, South, Up, or Down. Enter probabilities in the Class Interaction Matrix. Each column represents the current voxel, and each row represents the neighbor of that voxel.

Click CIM. Click Train to train the class interaction matrix. The panel at left appears. NOTE: Before training the class interaction matrix, use the Class to define every class and use the EM tab to segment the volume. Click Step 3 to select the segmented image. Click Run Algorithm to start training for MRF (Markov Random Field) parameters.

Setting tab

The Setting tab lets you configure and save advanced parameters for the EM algorithm.
To use the Setting tab:

Click Setting. The panel at left appears. Enter advanced parameters for the EM algorithm. To save settings, click Save Setting.

Endoscopic module

The Endoscopic module lets you position a virtual endoscopic camera in the scene, and view what the camera sees in a second window. You can also have the camera move along a pre-defined path. This is useful for examining structures that can't be viewed from outside the model.
There are four tabs: Display, Camera, Path, and Advanced.

Display tab

The Display tab lets you control what is displayed, and how large the display is.

To use the Display tab:

Click the Display tab. The panel at left appears. To toggle the Main View display (namely, the 3D model with the virtual camera), click Show Main View. To toggle the Endoscopic View display (namely, what the virtual camera sees in the scene), click Show Endoscopic View. To toggle the 2D Viewer display, click Show 2D Slices. To toggle hiding the Endoscopic View on exiting, click Hide Endoscopic View on Exit.

Main View, with camera pointing out	Endoscopic View

Camera tab

The Camera tab lets you set the location and orientation of the camera within the scene.
To use the Camera tab:

Click the Camera tab. The panel at left appears. Click either absolute (to position camera with respect to the world coordinate system) or relative (to position camera with respect to the current camera position). Use the sliders to adjust the Camera Position, or enter values in the fields. Click reset to set parameters back to their original values. Use the sliders to adjust the Camera Orientation, or enter values in the fields: Yaw is rotation right (positive) or left (negative). Pitch is rotation up (positive) or down (negative). Roll is rotation around the direction of view, clockwise (positive) or counterclockwise (negative). Click reset to set parameters back to their original values. You can also use the 3D Gyro to change the position or orientation of the camera. Toggle 3D Gyro on by clicking Use the 3D Gyro. Axes appear on the camera symbol. Left-click and move an axis to change the position of the camera. Right-click and move an axis to change the orientation of the camera.

Yaw = 45 degrees	Yaw = 315 degrees

Path tab

The Path tab lets you describe a path along which the virtual camera will move. The virtual camera will display the scene from the path as it moves. You can set the path manually or automatically.

To use the Path tab manually:

Click the Path tab, then click Manual. The panel at left appears. To use an existing path, click Select a Path and select a path from the list. Otherwise, to define a new path, enter a name in the create a new Path field. To create landmarks (namely, the points between which the segments of the path run), position the endoscope within the scene and click Add Landmark. The landmark will become part of the path. A small sphere will appear in the scene at the landmark location, with an arrow showing direction. To modify a landmark, select the landmark in the scene and press q. Change the position or orientation of the landmark, then click Update. To delete a landmark, select the landmark in the scene and press d. The selected landmark is deleted. To move the camera along the path, click Show Fly Through Panel. The Fly-Through Panel below appears. To move the camera along the path, click Fly-Thru. The virtual camera will move along the path. To start the camera back at the beginning of the path, click Reset. To stop the camera during its motion along the path, click Stop. To move to a specific frame, use the Frame slider, or enter a value in the Frame field. To change the speed of the virtual camera along the path, use the Speed slider, or enter a value in the Speed field. To specify the number of points per millimeter, enter a value in the unlabeled field.

To use the Path tab automatically:

Click the Path tab, then click Automatic. The panel at left appears. Click Choose an Active Model and select an active model from the list. To select a start point, move the cursor on the model and press p. To select a different start point, click Select another point, then select a start point. To select an end point, move the cursor on the model and press p. To select a different end point, click Select another point, then select an end point. Click Extract Centerline to automatically generate a path from start point to end point. To move the camera along the path, click Show Fly Through Panel. The Fly-Through Panel below appears. To move the camera along the path, click Fly-Thru. The virtual camera will move along the path. To start the camera back at the beginning of the path, click Reset. To stop the camera during its motion along the path, click Stop. To move to a specific frame, use the Frame slider, or enter a value in the Frame field. To change the speed of the virtual camera along the path, use the Speed slider, or enter a value in the Speed field. To specify the number of points per millimeter, enter a value in the unlabeled field.

To use advanced path options:

Click the Advanced tab. The panel at left appears. To change the size of a voxel, enter a value for VoxelSize. To limit the maximum distance displayed, enter a value for Max. Dist. Use the Visualization plane offset slider to change the offset of the visualization plane. To use the exponential decrease algorithm to compare distances and select the center point, click Use exponential decrease. To use the squared decrease algorithm to compare distances and select the center point, click Use squared decrease. To use the linear decrease algorithm to compare distances and select the center point, click Use linear decrease. If you load a 3D model without 2D slices, you can define a 2D surface to intersect with the model. This intersection defines a label map. To view this label map, click Visualize LabelMap. You can color the model to indicate distance from the outside. This is useful for visualizing the the centerline path that Slicer can generate automatically. To view this coloring, click Visualize DistanceMap.

Advanced tab

The Advanced tab lets you configure the appearance of the camera itself and the angle that its lens subtends.
To use the Advanced tab:

Click the Advanced tab. The panel at left appears. To toggle display of the camera, click Camera. To change the size of the camera, use the Size slider, or enter a value in the Size field. To change the color of the camera lens, click the color bar next to Camera Lens. A window will open. Select or create a color. To change the color of the camera boxs, click the color bar next to Camera Box. A window will open. Select or create a color. To toggle display of the focal point, click Focal Point. To change the color of the focal point, click the color bar next to Focal Point. A window will open. Select or create a color. To toggle display of the 3D gyro, click 3D Gyro. To change the size of the 3D gyro, use the Size slider, or enter a value in the Size field. To change the angle that the lens subtends, use the Lens Angle slider, or enter a value in the Lens Angle field To toggle showing the inside of models, click Show Inside Models.

Fiducials module

The Fiducials module lets you create and manage fiducial points. Fiducial points are reference points on a 2D slice or a 3D model. They are useful for making measurements and establishing landmarks for analysis.
There are two tabs: Display and Edit.

Edit tab

The Edit tab lets you create and edit lists of fiducial points.

To use the Edit tab:

Click the Display tab. The panel at left appears. To create a new fiducials list, enter a name for the new list in the Create a Fiducials List field. Otherwise, to use an existing list, click Fiducials List and select an existing list. The points in the list should appear in the list on the panel. To add new fiducial points to the list, place the cursor where you want the point and press p. The new point should appear in the list, and on the Viewer. To select or unselect a fiducial point, place the cursor on the point and press q. To delete a fiducial point, place the cursor on the point and press d. To delete the active list, click Delete Active List.

Sample Fiducial Points

Display tab

The Display tab lets you control which fiducial points are displayed, and how large the display is.

To use the Display tab:

Click the Display tab. The panel at left appears. To display all the fiducial points, click Show All. To display none of the fiducial points, click Show None. To display some of the fiducial points, toggle each list of points by clicking on its name To change the size of the symbol for each fiducial point, use the Symbol Size slider next to the name of the list. To change the size of the text for each fiducial point, use the Text Size slider next to the name of the list.

Guidance module

The Guidance module lets you select and display two target points in the 3D Viewer. You can reformat slices perpendicular to a line between these two target points. This is useful for reformatting slices between two landmarks, such as the incision point and the target tissue of the surgery.
There is one tab: Target.

Target tab

The Target tab lets you position and use the two target points.

To use the Target tab:

Click the Target tab. The panel at left appears. To position the red target point click Red. To position the yellow target point, click Yellow. Click Show Target. The selected target point appears on the 3D Viewer. Change the Target Position with the sliders. To use the active target point as the focal point (center of rotation in 3D Viewer), click Use as Focal Point. This can be useful to examine an off-center model. To reposition the image along the line between the target points, click View Trajectory.

Using Guidance

3D Viewer with 2 target points	After clicking View Trajectory

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9b. Modules I-N

Using Modules I-N

• LDMMViewer
• Locator
• Measure
• MeasureVol
• ModelCompare
• ModelHierarchy
• Navigator

LDMMViewer module

The LDMMViewer module is tbd.
There is one tab: LDMM.

Locator module

The Locator module connects Slicer to a server that feeds a real-time stream of coordinates from a device called the locator. This is useful in the operating room to allow the surgeon to navigate the volume by pointing to a location with a probe that is tracked. They can use the probe to select a new plane for scanning, or to zero on on an area to scan again. It is also used as a base for developing navigation tools for ultrasound, CT, laser ablation, and the MR Robot project.
NOTE: The Realtime module provides real-time processing of images acquired using Locator.
There are three tabs: Tracking, Server, and Handpiece.

Server tab

The Server tab lets you specify the source of the data for the Locator.

To use the Server tab:

Click the Server tab. The panel at left appears. Click Active Server to select the source of Locator data. The choices include: Select File to read Locator positions from a text file. Then click Prefix and select the text file to read positions from. Enter a value for the Update Period. Select SignaSP to read Locator positions and real-time images from a server process running on the GE Signa SP workstation. Enter Server Connection parameters, including Host name, Port number, and Update Period. Specify the Patient Position by selecting either Head-first or Feet-first for Entry; Supine, Prone, Left-decub, or Right-decub for Patient; and Front or Side for Table. Select Images to read existing images on disk to emulate real-time images coming from a Signa SP scanner. Then click Prefix and select the first image file to read images from. Enter a value for the Image increment and Update Period. Select Csys to display a Csys actor that indicates the position and orientation of the Locator. Click Csys to display the Csys actor.

Tracking tab

The Tracking tab lets you specify the source of the data for the Locator.

To use the Tracking tab:

Click the Tracking tab. The panel at left appears. Click Connect to toggle the connection to the server (chosen using the Server tab). Click Pause to pause the stream of data from the server. Click Show Locator to toggle display of the Locator in the 3D Viewer. Click Handle to toggle display of a handle at right angles to the Locator. Click Guide to toggle display of the guide from the tip of the locator. Click Add Fiducial to create a fiducial point at the current location. Click Delete Fiducial to remove a fiducial point. In the Locator can Drive Slices area, select whether the User or the Locator will drive (position) reformatted slices. To save (or read from) a real-time volume, select the Realtime Volume, or enter the file Prefix and click Save or Read.

Handpiece tab

The Handpiece tab lets you configure the display of the Locator in the 3D Viewer.

To use the Handpiece tab:

Click the Handpiece tab. The panel at left appears. Enter the Offset from Tip values, including Normal (direction along tip of Locator's needle), Trans. (Transverse, perpendicular to the Normal along the Handle), and N x T (N cross T is a vector perpendicular to both Normal and Transverse, using the right-hand rule). NOTE: You can use Offset from Tip to simulate a longer Locator. This can be useful if the Locator is attached to a surgical device and you want to know the location of the device rather than the location of the Locator. Enter the Size values, including Normal (length along tip of Locator's needle), Trans. (transverse, perpendicular to the Normal along the Handle), and Radius of the Locator. Enter the Position & Orientation values, giving the R (Right-left), A (Anterior-posterior), and S (Superior-inferior) coordinates for N (the Normal), T (the Transverse), and P (the cross-product of Normal and Transverse). Create a Color for the Locator, using Red, Green, and Blue sliders.

Measure module

The Measure module calculates geometric measurments on structures, including position, distance, angle, intersection, volume, and surface area. This is useful for determining sizes of structures for diagnosis, comparison, or planning.
There is one tab: Measure.

Measure tab

The Measure tab calculates position, distance, angle, intersection, volume, and surface area for a model.

To use the Measure tab:

The Measure module requires a model that includes fiducial points. You can use the Fiducials module to create fiducial points for a model. Click the Measure tab. The panel at left appears. From the Models drop-down list, select a loaded model that has fiducial points. From the Measure drop-down menu select one of: Position: to determine the position of the fiducial points. Distance: to determine the distance between the fiducial points. At least two fiducial points are necessary. Angle: to determine the angle defined by three fiducial points. Intersection: to determine the intersection point of two lines defined by four coplanar fiducial points. Volume: to determine the volume enclosed by at least four fiducial points. Surface: to determine the surface area of the volume enclosed by at least four fiducial points. The calculated value of the selected measurement appears. To clear output from the list, click Clear Output.

MeasureVol module

The MeasureVol module measures the geometric volume, in milliliters, of each label within an image volume. This is useful for making measurements.
There are two tabs: Measure and Results.

Measure tab

The Measure tab lets you specify the volume to measure and an output file for the results.

To use the Measure tab:

Click the Measure tab. The panel at left appears. Select the image Volume whose geometric volume you want to measure. To include the entire image volume, click Basic. Otherwise, to include only part of the image volume, click Advanced, then enter the upper and lower limits of slices in each of the three dimensions. Only labels within these limits will count toward the geometric volume. To send the results of the volume measurement to an existing file, click Browse and select the file. Otherwise, to specify a new file, enter the file name in the Output File field. Click Measure Volume. When the volume has been measured, a window will appear. To view the output file, click Yes. Otherwise, click No. The results appear on the Results tab.

Results tab

The Results tab displays the results of the volume measurement.

To use the Results tab:

Click the Results tab. The panel at left appears. Remember that you can have the results go to a file for later study, by specifying an Output File name on the Measure tab.

ModelCompare module

The ModelCompare module compares models with an identical number of nodes or displays any models. This is useful for examining the similarities and differences among models that may have been altered without losing nodes.
There are two tabs: Correspond and Array Display.

Correspond tab

The Correspond tab lets you compare models with an identical number of nodes.

To use the Correspond tab:

Click the Correspond tab. The panel at left appears. To select all models, click All. To deselect all models, click None. To toggle models on or off, click the model's name. Enter Sphere Scaling, which is the sphere placed on the model when you run the correspondence. The calculation for the sphere's radius is .15 multiplied by the scaling factor. Enter value for Keep Every Nth Node. Click Run to compare selected models. A comparision appears, showing corresponding nodes.

Array Display tab

The Array Display tab lets you display several models together. NOTE: Models are translated for easy visualization.

To use the Array Display tab:

Click the Array Display tab. The panel at left appears. To select all models, click All. To deselect all models, click None. To toggle models on or off, click the model's name. Enter Transform Name for this transform. Enter Models Per Row to display. Enter values for Row Offset and Column Offset. Click Run to perform the transform for display. Click Undo to undo the transform.

ModelHierarchy module

The ModelHierarchy module lets you view, create, and delete model hierarchies.
There is one tab: Hierarchy.

Hierarchy tab

The Hierarchy tab lets you view, create, and delete hierarchies.

To use the Hierarchy tab:

Click the Hierarchy tab. The panel at left appears. The current hierarchy, if any, of the current model appears. To create a new hierarchy for the current model, click Create. A new hierarchy appears in the list. To create a new group in the hierarchy, click Create group. A dialog appears. Enter the name of the new group, then click Ok. A new group appears in the list. To delete the hierarchy, click Delete. A dialog appears. Click Yes.

Navigator module

The Navigator module lets you navigate models in 3D Viewer, Endoscopic View, and Flattened View independently in a single display. This is useful for observing structures in context.
There are two tabs: Navigate and Options.

Navigate tab

The Navigate tab lets you select the model and flattened view.

To use the Navigate tab:

Click the Navigate tab. The panel at left appears. To choose the 3D model to navigate, click 3D Model and select the model from the list. To choose a loaded flattened view to navigate, click Flattened View and select the view from the list. To load a flattened view, click Browse, then select the flattened view, then click Choose. Click Run to display the selected items. When the selected items appear, use the usual controls to navigate each display independently.

Options tab

The Options tab lets you specify which displays to retain after exiting.

To use the Options tab:

Click the Options tab. The panel at left appears. To toggle hiding the Flattened View on exiting, click Remove Flattened View Upon Exit. To toggle hiding the Endoscopic View on exiting, click Remove Endoscopic View Upon Exit.

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9c. Modules O-Z

Using Modules O-Z

• Options
• OsteoPlan
• Realtime
• SessionLog
• Slices
• Tester
• TetraMesh
• Twin
• View
• VolRend
• VolumeMath

Options module

The Options module lets you control and load display options, including font size and modules listed.
There are three tabs: Props, Gui, and Modules.

Props tab

The Props tab allows you to load saved sets of options.

To use the Props tab:

Click the Props tab. The panel at left appears. To choose a saved and loaded set of options, click Active Option and select the set of options from the drop-down list. Click Basic for basic properties or Advanced for advanced properties. Enter the Program name. Enter the Contents. Click Apply to use the entered settings.

Gui tab

The Gui tab allows you to specify the font size.

To use the Gui tab:

Click the Gui tab. The panel at left appears. Click Font Size and select a font size from the drop-down list.

Modules tab

The Modules tab allows you to specify which modules to list, and in what order.

To use the Modules tab:

Click the Modules tab. The panel at left appears. To load all modules, click Load ALL Modules. Toggle each module loaded or not loaded by clicking the module's name in the list. To move a module up in the list, click Up next to the module's name. To move a module down in the list, click Down next to the module's name. Click Apply to use the entered settings.

OsteoPlan module

The OsteoPlan module is used by the Massachusetts General Hospital Oral & Maxillofacial Surgery department.
There are four tabs: Landmarks, Cut, Reorient, and Rx.

Realtime module

The Realtime module lets you process in real time the data acquired via the Locator module. You can process the incoming Realtime image with a selected Baseline image to produce a Result image.
There is one tab: Processing.

Processing tab

The Processing tab sets up real-time processing of images acquired via the Locator module.

To use the Processing tab:

Click the Processing tab. The panel at left appears. Click Realtime Volume to select the real-time volume. To use an existing baseline image, select the Baseline Volume and enter a Prefix. To save to this volume, click Save. To read from this volume, click Read. To copy the real-time volume to the baseline volume, click Copy Realtime. To save the result, select the Result Volume and enter a Prefix. Click Save. Select an Effect from the drop-down list. Click On to start processing, Off to stop processing, and Pause to pause processing.

SessionLog module

The SessionLog module lets you keep a log of Slicer sessions for research and other purposes. There are two tabs: Start Here and Log.

Start Here tab

The Start Here tab lets you start logging and choose a file to record log entries.

To use the Start Here tab:

Click the Start Here tab. The panel at left appears. Click Log File and browse to select a text file to record log entries in. To start logging, click Start Logging.

Log tab

The Log tab lets you display the current log.

To use the Log tab:

Click the Log tab. The panel at left appears. Click Show Current Log to display the current log.

Slices module

The Slices module lets you control the selection and display of slices when in 3D view mode. There is one tab: Controls.

Controls tab

The Controls tab provides the same controls as the 2D Viewer.

To use the Controls tab:

Click the Controls tab. The panel at left appears. The controls include: 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. You can also enter the number of a slice directly in the numerical field. The V toggle button controls whether the selected slice is visible in the 3D viewer or not. There is an Or (scan order), Bg (background), Fg (foreground), and Lb (label map) button 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.) Select the Active Slice by clicking Red, Yellow, or Green. Click Save Active to save the active slice. Enter a name in the text field to use for the saved slice. Click Show Advanced Slice Controls to change the Zoom and Slice Increment for the active slice.

Tester module

The Tester module allows developers to source files as part of the testing process. Developers can make changes to modules, then source the module to see how it works.
There are two tabs: Source and Watch.

Source tab

The Source tab allows selecting modules to source.

To use the Source tab:

Click the Source tab. The panel at left appears. To choose a file to source, click File to Source and browse for the file. To load a main module, click Main and select the module from the drop-down list. To reload a main module, click Reload next to the main module's name. To load a module, click Module and select the module from the drop-down list. To reload a module, click Reload next to the module's name. To load a shared module, click Shared and select the module from the drop-down list. To reload a shared module, click Reload next to the shared module's name. To choose a new module to source, click New Module to Source and browse for the file.

Watch tab

The Watch tab has not been implemented.

TetraMesh module

The TetraMesh module reads in a tetrahedral mesh, which can be converted into a model in two ways. Assuming that the mesh has integer scalars, surfaces can be extracted, producing one color-coded model for each scalar. Regardless of whether the mesh has integer scalars, edges can be extracted, producing a model consisting of color-coded lines that connect each node.
There are four tabs: Read/Write, Props, Visualize, and View.

Read/Write tab

The Read/Write tab allows reading, writing, and selecting tetrahedral meshes.

To use the Read/Write tab:

Click the Read/Write tab. The panel at left appears. To choose a loaded tetrahedral mesh, click Active TetraMesh and select a mesh from the drop-down list. To choose a tetrahedral mesh file, click Tetrahedral Mesh and browse for the file. To use a loaded volume for alignment, click Alignment Volume and select the volume from the drop-down list. To read the tetrahedral mesh file, click Read. The selected mesh file is read. To write a tetrahedral mesh file, click Write. The mesh is written to the selected mesh file. To read in a new tetrahedral mesh file, click Create New. A new mesh is read.

Props tab

The Props tab controls properties of the tetrahedral mesh.

To use the Props tab:

Click the Props tab. The panel at left appears. To choose a loaded tetrahedral mesh, click Active TetraMesh and select a mesh from the drop-down list. To choose a tetrahedral mesh file, click Tetrahedral Mesh and browse for the file. Click Clipping to turn clipping on. Use the Opacity slider to adjust the opacity. To use a loaded volume for alignment, click Alignment Volume and select the volume from the drop-down list. Click Apply to apply the selected properties. Click Cancel to cancel the selected properties.

Visualize tab

The Visualize tab allows controls how to process the mesh.

To use the Visualize tab:

Click the Visualize tab. The panel at left appears. To choose a loaded tetrahedral mesh, click Active TetraMesh and select a mesh from the drop-down list. There are several options for processing the tetrahedral mesh. Click Surface to grab surfaces of the mesh. To use cell data as part of the process, click Use Cell Data. To smooth normals as part of the process, click Smooth Normals. Click Edges to grab edges of the mesh. Click Nodes to use nodes of the mesh. Enter the Sphere Scaling, which is the sphere placed on the model when you run the correspondence. The calculation for the sphere's radius is .15 multiplied by the scaling factor. To skip nodes, enter a value for Keep Every Nth Node. Click Scalars to use mesh scalars. Enter the Sphere Scaling, which is the sphere placed on the model when you run the correspondence. The calculation for the sphere's radius is .15 multiplied by the scaling factor. To skip nodes, enter a value for Keep Every Nth Node. Click Vectors to use vectors in the mesh. Enter the Arrow Scaling factor. To skip nodes, enter a value for Keep Every Nth Node. Click Tensors to use tensors in the mesh. Enter the Arrow Scaling factor. To skip nodes, enter a value for Keep Every Nth Node. Click Process to start processing.

View tab

The View tab controls viewing the tetrahedral mesh and controlling clipping.

To use the View tab:

Click the View tab. The panel at left appears. Toggle between parallel and perspective view by clicking Parallel. Enter a value for the Scale. To clip all regions that satisfy the constraints of all clipping planes, click Intersection. To clip all regions that satisfy the constraints of at least one clipping plane, click Union.

Twin module

The Twin module displays a second copy of the 3D Viewer, which you can configure to appear on a different screen number on UNIX systems. With two graphics cards, they are numbered 0 and 1. This can be useful for a remote viewer, in a classroom situation, or to provide a display during surgery.
There is one tab: Twin.

Twin tab

The Twin tab configures the Twin screen for display.

To use the Twin tab:

Click the Twin tab. The panel at left appears. To turn the Twin screen on, click On. To turn the Twin screen off, click Off. To pause updating the Twin screen, click Pause. Enter values for the Twin screen, including X Position, Y Position, Width, Height, and Screen Number (0 or 1, if your computer has two graphics cards). Click Apply to use values for the Twin screen.

View module

The View module provides controls for changing the appearance of displays in the Viewer window. This can be useful for medical imaging and for preparing images for publication. There are four tabs: View, Texture, Fog, and Lights.
To save view options, click File, then click Save Current Options. This will save your options to a file called Options.xml.

View tab

The View tab provides controls for:

• changing the size of the 3D Viewer
• changing the color of the background of the 3D Viewer
• turning on the Closeup Window
• enabling stereo mode
• saving the current view as a graphics file

Click the View tab. The panel at left appears. To change the size of the 3D Viewer, enter values for Width and Height. To change the color of the background of the 3D Viewer, click Blue, Black, or Midnight. The Closeup Window magnifies the 2D Viewer window around the mouse cursor. (This is not available for PCs.) To turn the Closeup Window on or off, click On or Off. Stereo mode allows viewing the 3D Viewer in 3D with red/blue, crystal eyes, or interlaced glasses. Click Stereo to turn stereo mode on or off. When stereo viewing is on, select the stereo viewing mode by clicking either RedBlue, CrystalEyes, or Interlaced. To save the current view as a graphics file, click Save View. The view will be saved when you left-click the 3D Viewer. To save the view whenever the 3D Viewer is rendered, leave Save View selected. The following options are available: To include both the 3D Viewer and the 2D Viewer, select with slice windows. To include only the 3D Viewer, deselect with slice windows. Enter the Directory where you want to save the current view as a graphics file. Enter the File Prefix of the graphics files. Enter the Next frame #, which will be appended to the File Prefix for the next saved file. Select the File type for the format of the graphics file. Available formats include: BMP JPEG PNG PNM PostScript TIFF

Texture tab

The Texture tab provides controls to render slices in the 3D Viewer, including:

• resolution of the image
• changing the color of the background of the 3D Viewer
• turning on the Closeup Window
• enabling stereo mode
• saving the current view as a graphics file

Click the Texture tab. The panel at left appears. Enter the Resolution (number of pixels left-to-right and top-to-bottom). Higher values (up to the resolution of your source images) give better quality. Smaller values render faster. Interpolate smoothes the image. To smooth the image, click On. To see the unsmoothed pixels, click Off.

Resolution = 512; Interpolate off	Resolution = 64; Interpolate off	Resolution = 64; Interpolate on

Fog tab

The Fog tab lets you add fog to 3D images, which mixes the color of the 3D object with the background color. This produces a three-dimensional effect that allows users to distinguish structures in the foreground from structures in the background of the image.

To use the Fog tab:

Click the Fog tab. The panel at left appears. To enable fog, click On. To disable fog, click Off. Select linear, exp, or exp2 to choose how the fog changes with distance. Adjust the Start and End sliders to determine where the fog begins and ends.

Fog off	Fog on

Lights tab

The Lights tab lets you adjust the lighting of a 3D object. Usually, the LightKit arrangement of lights lets the user distinguish structures better.

To use the Lights tab:

Click the Lights tab. The panel at left appears. Select Headlight for simple lighting or LightKit for more realistic lighting. Adjust the Light Intensity slider to make the scene brighter or darker.

VolRend module

The VolRend module provides controls over rendering volumes. There are two tabs: Settings and Transfer Functions.

Settings tab

The Settings tab lets you control how to render volumes.

Click the Settings tab. The panel at left appears. To choose a loaded reference volume, click Ref Volume and select a volume from the drop-down list. To toggle hiding the volume on exiting, click Hide Volume on Module Exit. Choose the type of interpolation by clicking Nearest Neighbor or Linear Interpolation. Choose the Ray Casting or 2D Texture Mapping technique. For Ray Casting: Enter the Sample Distance. Choose the method of volume rendering by clicking Composite, MIP (maximum intensity projection), or Isosurface. Choose whether to Interpolate First or Classify First. Click Refresh View to redraw the display of the volume.

Transfer Functions tab

The Transfer Functions tab lets you specify color and opacity functions over the volume.

Click the Transfer Functions tab. The panel at left appears. The Scalar Opacity Box defines the function that assigns the opacity value for a given voxel value. The Color Transfer Box defines the function that assigns the color value for a given voxel value. The Gradient Opacity Box defines the opacity gradient, which is multiplied by the Scalar Opacity value to give the final opacity value. Click Refresh View to redraw the display of the volume. To read in saved transfer functions, click Read and browse to the file. To save the current transfer functions, click Save and specify a file name.

VolumeMath module

The VolumeMath module does arithmetical, statistical, and logical functions on input volumes. There are three tabs: Math, Distance, and Logic.

Math tab

The Math tab performs arithmetical and statistical operations on volumes.

Click the Math tab. The panel at left appears. Click the operation to perform, including: Click Subtract to subtract the values of one volume from another. Volumes should have the same spacing and number of voxels. Click Volume2 to select the volume to subtract from. Click Volume1 to select the volume to subtract from Volume2. Click Volume3 to select the output volume, or create a new output volume. Click Add to add the values of one volume to another. Volumes should have the same spacing and number of voxels. Click Volume2 to select one volume to add. Click Volume1 to select the other volume to add. Click Volume3 to select the output volume, or create a new output volume. Click Resample to resample one volume in the coordinates of another. Click Resample to select the volume to resample. Click in the coordinates of to select the volume whose coordinates to use. Click and put the result in to select the output volume, or create a new output volume. Click View/change Resampling Params to set resampling parameters, including interpolation mode, origin, extent, and spacing. Click Abs to calculate the absolute value of a volume. Click Absolute Value to select the volume to calculate. Click and put the result in to select the output volume, or create a new output volume. Click DistMap to calculate a distance map for a volume. Click Distance Map to select the volume to calculate. Click and put the result in to select the output volume, or create a new output volume. Click Hausdorff to calculate the Hausdorff distance map for two volumes. Click V2 to select one volume. Click V1 to select the other volume. Click and put the result in to select the output volume, or create a new output volume. Click Multiply to multiply the values of one volume by another. Click Volume2 to select one volume to multiply. Click Volume1 to select the other volume to multiply. Click Volume3 to select the output volume, or create a new output volume. Click Statistics to calculate the minimum, maximum, mean, and standard deviation of the non-zero values of a volume. Click Calculate Statistics of to select volume. Click Mask to mask one volume with a label map. Click Volume to Mask to select the volume to mask. Click Label Map to select the label map. Click Masked Output to select the output volume, or create a new output volume. Click Mask to select the color for the mask. Click MaskStat to calculate statistics of a volume masked with a label map. Click Volume to Mask to select the volume to mask. Click Label Map to select the label map. Click Masked Output to select the output volume, or create a new output volume. Click Mask to select the color for the mask. Click Browse to select a file to save the statistics. Click Cast to output values of the volume in various forms. Click Volume to Cast to select the volume. Click Cast Output to select the output volume, or create a new output volume. Click Output Type to form of the output, including Char, UnsignedChar, Short, UnsignedShort, Int, UnsignedInt, Long, UnsignedLong, Float, and Double. Click Run to perform the selected calculation.

Distance tab

The Distance tab calculates distance between voxels. This tab is not operational.

Logic tab

The Logic tab performs a logical AND between volumes.

Click the Logic tab. The panel at left appears. Click Label to select the label value to operate on. Click Volume2 to select one volume. Click Volume1 to select the other volume to AND. Click Volume3 to select the output volume, or create a new output volume.

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10. Glossary

Glossary

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