Essential Training Guide

Analyze 10.0

1999 - 2010 AnalyzeDirect, Inc. 1986 - 2010 BIR, Mayo Clinic

Analyze 10.0 Essential Training Guide

Table of Contents

Getting Started and Loading Data into Analyze

Analyze Basics ......................................................................................................................................................................................... 7 Exercise 1 : DICOM Tool Quick Configuration..................................................................................................................................... 14 Exercise 2 : DICOM Tool Advanced ...................................................................................................................................................... 16 Exercise 3 : Switching On Support for Additional Formats ............................................................................................................... 22 Exercise 4 : Load As Loading and Resizing Anisotropic Data........................................................................................................... 25 Exercise 5 : Import/Export Converting Raw Data into Images ........................................................................................................... 26 Exercise 6 : Import/Export Volume Tool ............................................................................................................................................... 28 Exercise 7 : Saving Data Out of Analyze .............................................................................................................................................. 29

Display and Visualization

Exercise 8 : Multiplanar Sections ......................................................................................................................................................... 31 Exercise 9 : Oblique Sections Oblique Resizing of Volumes ............................................................................................................. 36 Exercise 10 : Oblique Sections Manual AC-PC Realignment ............................................................................................................. 40 Exercise 11 : Volume Compare ............................................................................................................................................................. 42 Exercise 12 : Volume Render Basic Rendering Controls ................................................................................................................... 43 Exercise 13 : Volume Render Advanced Rendering Controls ............................................................................................................ 46 Exercise 14 : Volume Render Tissue Map Tool.................................................................................................................................... 49 Exercise 15 : Volume Render Movie Making with the Sequence Tool ............................................................................................... 51 Exercise 16 : Volume Render Fix Tool .................................................................................................................................................. 54 Exercise 17 : Volume Render Creating a Merged Image..................................................................................................................... 57 Exercise 18 : Volume Render Creating A High Definition Volume Rendering 60 Exercise 19 : Volume Render Parametric Mapping ............................................................................................................................. 61 Exercise 20 : Surface Render Surface Map Creation and Display ..................................................................................................... 63 Exercise 21 : Virtual Endoscopy Interactive Generation of Endoscopic Views 65 Exercise 22 : Virtual Endoscopy Endoscopic Movie Generation ...................................................................................................... 67 Exercise 23 : Image Calculator Image Manipulation ........................................................................................................................... 72 Exercise 24 : Image Calculator SubRegion Data ................................................................................................................................. 74 Exercise 25 : Image Algebra Formula for Image Manipulation .......................................................................................................... 77 Exercise 26 : Histogram Operations Histogram Normalization ......................................................................................................... 79 Exercise 27 : Spatial Filters ................................................................................................................................................................... 80

Analyze 10.0 Essential Training Guide

Table of Contents

Getting Started and Loading Data into Analyze

Exercise 28 : Image Edit Manual Segmentation of Grayscale Data. ................................................................................................... 82 Exercise 29 : Image Edit Manual Segmentation and Object Map Creation.......................................................................................84 Exercise 30 : Morphology Morphological-Based Segmentation. ........................................................................................................ 86 ............................................................................................................................ 87 Exercise 31 : Watershed Automated Segmentation. Exercise 32 : Multispectral Classification............................................................................................................................................. 88 Exercise 33 : Object Extractor Automated Brain Segmentation......................................................................................................... 90 Exercise 34 : Object Extractor Extracting Multiple Objects................................................................................................................ 94 Exercise 35 : Surface Extractor Polygonal Surface Extraction.......................................................................................................... 96 Exercise 36 : Surface Extractor Contour Surface Extraction. ............................................................................................................. 99

Registration

Exercise 37 : Registration 3-D Surface Registration......................................................................................................................... 101 Exercise 38 : Image Registration 3-D Registration using MRI and PET. .......................................................................................... 102 Exercise 39 : Image Registration Mutual Information Registration. ................................................................................................. 106

Measurement

Exercise 40 : Line Profile Calculating Image Intensities Along a Straight Line 109 Exercise 41 : Region of Interest Defining Regions.............................................................................................................................111 Exercise 42 : Region of Interest Defining Regions and Volume Measurements 115 Exercise 43 : Region of Interest Measuring Objects in Object Maps................................................................................................119 Exercise 44 : Region of Interest Histogram Analysis........................................................................................................................ 122 Exercise 45 : Importing .Stat Files to Excel....................................................................................................................................... 125 Exercise 46 : Stereology Estimating Volume. ..................................................................................................................................... 126 Exercise 47 : Object Counter Counting Cells..................................................................................................................................... 127 Exercise 48 : Tree Analysis In Depth Examination of Coronary Arteries 129

Analyze 10.0 Essential Training Guide

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Add Ons
Exercise 49 : SISCOM........................................................................................................................................................................... 133 Exercise 50 : Mayo 3D Brain Atlas....................................................................................................................................................... 136 Exercise 51 : T2 Projection. .................................................................................................................................................................. 139 Exercise 52 : Volume Metrics............................................................................................................................................................... 140

ITK
Exercise 53 : ITK Filters........................................................................................................................................................................ 142 Exercise 54 : ITK Segment 2-D. ............................................................................................................................................................ 143 Exercise 55 : ITK Segment 3-D. ............................................................................................................................................................ 145 Exercise 56 : ITK Registration. ............................................................................................................................................................. 147

Analyze 10.0 Essential Training Guide

Analyze 10.0

Analyze Basics

Analyze 10.0 Essential Training Guide

Introduction
Welcome to the Analyze 10.0 Essential Training Guide. This document provides an overview of Analyze 10.0 core functionality through 56 exercises that guide new users step-by-step through basic and advanced Analyze procedures. A fully comprehensive overview of all Analyze 10.0 module functionality can be found in the Users Guide and Tutorials located under the Help menu within the software. If you have not installed Analyze 10.0, please refer to the Analyze 10.0 Installation Instructions provided with the software.

Installing Tutorial Data In order to work through the Essential Training Guide exercises and Analyze Tutorials, you need to install the tutorial Data from the Resources CD. To install the tutorial Data: 1. 2. 3. Insert the Analyze Resources CD into your computer. Open Analyze 10.0 and choose Help > Tutorials. Click Install Tutorial Data at the bottom of the Tutorials window. Note, if the tutorial data has already been installed this button will not appear. In the window returned, specify the path to the tutorial data, for example D:\TutorialData (where D:\ is equal to your CD-ROM drive). Click Install. All of the tutorial data will be copied from the Resources disk to the $:\BIR\images\TutorialData folder (where $ is the install directory, e.g. C:\ on a Windows system).

Quick Reference Button Reference: Displays PowerBar button or tool button referenced in that exercise step. The button will be next to the step that it refers to. Often, the step only mentions the file path, but the button is displayed as a shortcut. Example: Open the DICOM Tool (File > DICOM Tool).

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Analyze 10.0 Essential Training Guide

Analyze Basics
The Main Analyze Window

The main Analyze window is the first operational window that appears when Analyze is opened. The main Analyze window does not perform any imaging functions, but it does coordinate all the modules within the Analyze package and acts as a file manager for loaded data. It consists of three major components: the Analyze workspace, where all of the loaded data, represented as icons are managed; the Analyze menu, where individual Analyze modules are selected; and the Analyze PowerBar, which provides icon-based shortcuts to the most frequently used Analyze modules

Analyze Menu PowerBar Tabbed Analyze Workspace Image Data Icon

Loading Data into Analyze Image data is loaded into Analyze using one of the load modules (Load, Load As, DICOM Tool, or Import/Export) from the File menu in the main Analyze window. Most of the individual Analyze modules also support data loading directly within the module (File > Load within the module). To load DICOM data, use the DICOM module, for more information on how to use this module, please refer to Exercises 1-2 of this Guide. To load all other data into Analyze, refer to Exercises 3-6 of this Guide. The tutorial data used in the Essential Training Guide exercises can be loaded into Analyze using the Load module (File > Load). It is assumed that the data was installed to $:\BIR\images\TutorialData (where $ is the install directory, e.g. C:\ on a Windows system) according to the Installing Tutorial Data instructions on page 6.

Analyze 10.0 Essential Training Guide

Analyze Basics

The Analyze Workspace

Once data is loaded into Analyze it will appear as an icon in the Analyze workspace and is available to all of the modules in the Analyze package. To load data into a module, select the image icon in the Analyze workspace (the icon will appear framed in red when selected) and open the desired module from the Analyze menu or PowerBar. If multiple icons are selected at the time the module is opened, one of the two actions will occur: 1. 2. If the opened module supports or requires multiple volumes, the volumes are used in the order selected. If multiple loaded volumes are not supported, then multiple instances of the module are invoked.

note To select multiple data sets hold down the <Ctrl> key while making selections with the mouse. Alternatively use the left mouse button to select the first data set and the middle button (if available) to select additional data sets.

Analyze 10.0 Essential Training Guide

Analyze Basics

Right Mouse Button Menu The Analyze workspace is an area with additional options. When the right mouse button is clicked in the workspace, a menu will appear. The menu provides the following options: Unload: Unload selected data from the Analyze workspace Info: Display the header information for a selected data set Rename: Change the name of a selected data set Edit Header: Modify the header information of a selected data set Append: Append selected data Unappend: Unappend 4D multi-volume data sets, or RGB data sets Select All: Select all data sets in the Analyze workspace Invert Selected: Invert your selection of data in the Analyze workspace Arrange: Arrange data sets by Name, Size or Modify Time Current Directory: View and modify the Current Directory location Workspace Directory: View and modify the Workspace Directory location Session Log: Stores information that might be useful to the Analyze support team and software developers, should a problem ever arise with one of the modules.

Main Analyze Window Quick Keys <Ctrl><a> Selects all of the files in the workspace. <Shift><Left Mouse Click> Selects all files between first and shifted selections. Double clicking on a data set in the workspace restarts the last module used with that data. If there is not a module associated with the data, the Multiplanar Sections module will open by default.

Analyze 10.0 Essential Training Guide

Analyze Basics

The Analyze Menu

The File menu contains the modules that are used to input and output data, as well as the standard Save, Save As and Exit options. The Display menu contains the Analyze modules that involve the display, visualization, and manipulation of image data: Multiplanar Sections Oblique Sections Volume Compare Volume Render Surface Render Virtual Endoscopy Movie The Process menu contains the Analyze modules that are used for processing and classifying image data: Image Calculator Image Algebra Histogram Ops Spatial Filters Filter Designer 3-D FFT The Segment menu provides facilities for image segmentation: Image Edit Morphology Watershed Multispectral Classification Object Extractor Surface Extractor

The Register menu contains all of the Analyze tools for image registration: 2-D Registration 2-D Non-rigid Registration Point to Surface 3-D Surface Registration 3-D Voxel Registration 3-D Non-rigid Registration The Measure menu contains an extensive selection of measurement modules: Line Profile Region of Interest Stereology Object Counter Tree Analysis The Apps menu option contains add-on modules available for Analyze: SISCOM Mayo 3-D Brain Atlas* DTI* T2 Projection* Volume Metrics* The ITK menu contains modules that provide access to the Insight Toolkit (ITK): Filter Segment 2-D Segment 3-D Registration

Analyze 10.0 Essential Training Guide

*These modules require the purchase of an additional license

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Analyze Basics

The Analyze Menu

Additional items available in the Analyze menu include: The Other menu contains utilities and modules for configuration and resource monitoring. Resources: The Resource Monitor assists in maintaining system resources at a level that does not impede proper execution of Analyze. The resources being monitored and displayed are Swap space, Workspace, and user specified directory Disk space. For all three, the Resource Monitor reports the amount of space used, space available or free, and total capacity. PowerBar Editor: the PowerBar Editor is an option that appears in all Analyze modules that contain PowerBar options. Options: The Options item allows you to switch on and off workspace features such as the PowerBar, and the pop-up icon names which are shown when the mouse cursor is moved over an image in the workspace. You can also configure Add-On modules to be switched on or off. AppDefaults Editor: The AppDefaults Editor provides several tools for managing and changing defaults or user preferences for the Analyze workspace and specific Analyze modules. For further information about the AppDefaults Editor please reference the Users Guide (Help > Users Guide).

The Help menu provides access to several important Analyze resources: Users Guide: Provides detailed information on each Analyze module. Tip of the Day: Can be set to display an Analyze tip each time Analyze is opened. Tutorials: Tutorial exercises covering some of the main Analyze functions. Note, you must have selected to install the Tutorials during initial Analyze installation. Analyze Update: Checks to make sure Analyze is up-to-date, also will download and install any necessary updates. Online Support: Provides a direct link to the AnalyzeDirect Support home page. Analyze Demos: Provides a direct link to a list of Help Movies Copyrights: Documentation of Analyze Copyrights. About: Provides version, system, and environment information.

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Analyze Basics

Main Analyze PowerBar Directly below the menu bar in the main Analyze window you will find the PowerBar of icons. The icons on this main Analyze PowerBar provide shortcuts to the most commonly used Analyze modules. By default, the main Analyze PowerBar contains icons for: Load As, DICOM Tool, Multiplanar Sections, Oblique Sections, Volume Render, Movie, Object Extractor, 3D Voxel Registration, Region of Interest, and Exit. Module-Specific PowerBars In addition to the main Analyze window, you can also find a PowerBar in each Analyze module. The icons included on the PowerBar of each Analyze module provide shortcuts to the most commonly used tools and options within that specific module. PowerBar Editor - Customizing PowerBars Customizing Analyze PowerBars is a quick and easy way to streamline your work flows and routine processes. To customize the PowerBar displayed within any Analyze window, you can use the PowerBar Editor found under the windows Other menu (Other > PowerBar Editor). Using the PowerBar Editor [A], you can: Add/Remove PowerBar icons: To add an icon to the PowerBar, select it in the PowerBar Editor list (selected icons appear highlighted in black). To remove an icon, deselect it in the PowerBar Editor list. Change the order of PowerBar icons [B]: With the PowerBar Editor open, drag-and-drop an icon on the PowerBar to a new location. Create additional PowerBars: To create multiple PowerBars for the main Analyze window or an Analyze module, click the New button [C] in the PowerBar Editor and then select the desired icons for the new PowerBar. You can scroll through the PowerBars using the up/down arrow buttons added to the far left of the PowerBar [D].
Analyze 10.0 Essential Training Guide

note Be sure to press Save [E] in the PowerBar

Editor if you wish to keep your PowerBar changes for future sessions. Otherwise, changes will be lost upon existing the Analyze module, or Analyze.

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Analyze 10.0

Loading Data Into Analyze

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Exercise 1 : DICOM Tool Quick Configuration

The DICOM Tool expands DICOM support in Analyze, enabling the indexing of collections of DICOM images through a local database file. This exercise will demonstrate how to create a database and then how to import DICOM data into the database. Note: If you are a previous BirPacs user please contact support@[Link] for instructions on migrating your database to the DICOM Tool. 1. 2. Open the DICOM Tool (File > DICOM Tool). The DICOM Tool will detect that there is no database present; a dialog box will be returned asking you if you would like to create a new database or browse for an existing database, click Create a new local database.
note If this is not the first time you have accessed the DICOM Tool, you can access the Create New Image Database window by selecting File > Create Database.

3.

The Create New Image Database window (Figure 1) allows you to specify a database name and file system directory, configure a DICOM receiver for the database (optional), configure a database server (optional), and specify the source of initial DICOM images (optional). The Local Database Name will default to SystemName_PortNumber; change the Local Database Name to TEST_5679 [A]. On your systems local disk create a folder called AnalyzeDB ($:/AnalyzeDB) Click the Local Database Directory button in the Create New Image Database window. In the Browse for Folder window returned navigate to the location of the new AnalyzeDB folder ($:/AnalyzeDB), select the folder, and click OK. You have now specified the location of your local database [B]. To create the local database click the Create Local Database button [C]. Once the database has been created a dialog box will be returned stating All Done, click OK.
Figure 1

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Exercise 1 : DICOM Tool Quick Configuration

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To import DICOM data into the DICOM Tool right-click anywhere in the white space and select Import DICOM Images from the menu (Figure 2). Alternatively, select File > Import DICOM Images. In the Browse for Folder window returned navigate to and select the folder $:\BIR\ images\TutorialData\ImportExportTutorial, then click OK. A dialog box will be returned asking you to confirm that you would like to Import all DICOM files found below <C:/BIR/images/TutorialData/ImportExportTutorial>, click Yes to confirm. All 121 DICOM images contained within the folder will be copied into the database. The DICOM Tool will automatically sort and index the data by patient, study, series, and volume. Data can be selected and viewed in the DICOM Tool (Figure 3). To load a selected data set into the Analyze workspace click Load Volume [D]; if you wish to resize or resample the data click Load As, this will load the selected data into the Load As module (see exercise 4 for instructions on how to use the Load As module).

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Figure 2

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Figure 3 Analyze 10.0 Essential Training Guide 15

Exercise 2 : DICOM Tool Advanced

The DICOM Tool expands DICOM support in Analyze, enabling the indexing of collections of DICOM images through a local database file. With the DICOM Tool, databases can be created, updated, and shared with other users with file system access to the images and the database file. This exercise will demonstrate how to create a database, configure a DICOM receiver and Database sender and then how to import DICOM data into the database. Note: If you are a previous BirPac user please contact support@[Link] for instructions on migrating your database to DICOM tool. 1. 2. Open the DICOM Tool (File > DICOM Tool). If you have already completed exercise 1, choose File > Create Database. If the DICOM Tool detects that no database is present, a dialog box will be returned asking you if you would like to create a new database or browse for an existing database, click Create a new local database.

Specification of the Database Name and Directory 3. In the Create New Image Database window you can specify the database name and file system directory, specify a DICOM receiver for the database (optional), specify database server (optional), and specify the source of initial DICOM images (optional). The Local Database Name will default to SystemName_PortNumber; change the Local Database Name to TEST2_5679.
note Any name can be chosen for the local database, however when creating multiple databases, following a coherent naming convention will simplify database management.

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The Local Database Directory option enables you to specify the directory on your system in which the database and all of the DICOM images will be stored. i. On your systems local disk create a folder called AnalyzeDB ($:/AnalyzeDB). Note that if you have completed exercise 1, DICOM Tool - Quick Configuration, this folder should already exist. Once the directory has been created, click Local Database Directory [A] in the Create New Image Database window, and navigate to the location of the new AnalyzeDB folder ($:/AnalyzeDB). Select the folder and click OK. You have now specified the location of your database.
16 Figure 1

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Analyze 10.0 Essential Training Guide

Exercise 2 : DICOM Tool Advanced

Specification of a DICOM Receiver (optional)

6.

The Configure DICOM Receiver option allows you to configure a DICOM receiver for the database. This step is optional, if you do not want to configure the receiver please move on to step 8, otherwise check the Configure DICOM Receiver option [B]. DICOM Receiver configuration requires three key pieces of information: the Receiver AET, the Receiver Port on the local system, and the directory where the DCMTK executable programs are installed. i. DICOM Receiver AET: By default is set to SystemName_PortNumber. To reflect the receivers connection to the database defined in step 4, change the DICOM Receiver AET to TEST2_5679. DICOM Receiver Port: Specifies the TCP/IP port number on which the DICOM Receiver listens for connections to receive messages. For this exercise, the DICOM Receiver Port can remain 5679. DCMTK Path: The DCMTK executable files are automatically installed with Analyze in the $:\BIR\DCMTK-3.5\$System_Type$\bin directory (where $System_Type$ is your system platform, e.g. PC_NT) and the DCMTK Path will point to this directory by default. However, if Analyze is being run from a network rather than local installation, the DCMTK files should be installed locally and this path should point there.

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Exercise 2 : DICOM Tool Advanced

Specification of a Database Server (optional)

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The Configure Database Server option allows you to configure an optional database server to manage automatic updates and multiple client access to the database over a network. The database server is a dedicated process attached to one database and accessible by system name and port number. It responds to connection requests, SQL statements, and requests for images, and polls the image storage area for newly received images to register. Configuring and installing a database server is very similar to configuring the DICOM receiver. This step is optional, if you do not want to configure the database server please move on to step 10, otherwise check the Configure Database Server option [C]. The Database Server fields are used to configure the database server process that controls access to the database. i. Service Name: The name by which the servicer is identified, for this exercise use TEST2_5679.
note On Windows systems this becomes the name of the Windows Service; on UNIX systems it is used to name the daemon script which starts, stops and checks server status.

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Host System: Identifies the system name this program is running on. You can create servers to run on your system, and any server should be attached to a database local file system. Port Number: Specifies the port number client systems will use to connect to server. It cannot be the same port as the one used by the DICOM receiver (STORESCP). For this exercise set the port to 5680. Update Frequency: Specifies the interval in minutes at which the server will poll the image storage directory to see if the DICOM receiver has deposited images to be in the database. For this exercise, you can leave this set to 5. Server Logging: Creates a log file of the database server for diagnostics.
tip It is recommend using a closely related port number so they can be easily remembered; e.g., if the receiver is running at port n, run that database server at port n+1.

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Exercise 2 : DICOM Tool Advanced

Specification of the Source of Initial Images (optional)

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The Source of Initial Images option allows you to specify a directory containing DICOM images; click Source of Initial Images [D]. In the Browse for Folder window returned, navigate to the $:\BIR\images\ TutorialData directory, select the ImportExportTutorial folder, and click OK.

Creating the Database Server 12. To create the local database, click Create Database Server [E]. Note, creating a Database Server requires administrative privileges; a dialog box will automatically be returned stating that you will receive a prompt from your operating system, click OK. You will then need to enter the administrator password. The DICOM Tool will now copy the DICOM images from the initial source to the location (if selected) specified in step 5. The data will automatically be sorted and indexed by patient, study, series, and volume. Once the process is complete, the Create New Image Database window will automatically be dismissed and the data will now be available in the DICOM Tool (figure 2).

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Viewing and Loading Data 15. 16. Data can be selected from the Patient information panel [F] in the DICOM Tool. Select the data set with the Patient Name MR SIGNA LX 1.0T and Patient ID 337. The data set will be highlighted, note the other information panels will automatically update with relevant Study, Series, and Volume information (when available). Note there are two data sets available for selection in the Series information panel [G] below. Select Series 102.
Figure 2 Analyze 10.0 Essential Training Guide 19

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Exercise 2 : DICOM Tool Advanced

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Review the data slice-by-slice by using the Slice Number slider bar under the image display. Right-click on the image display to open the Intensity window (figure 3). Here you can change the intensity display of the image; use the slider bar to take the Maximum intensity level down to 500. The image display will interactively update. Click Done to dismiss the Intensity window. To load this data set into the Analyze workspace, click Load Volume. The data set will automatically load into the Analyze workspace.

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Figure 3

Other DICOM Tool Options 21. Move the cursor over any of the information panels and right-click. The menu returned provides most of the options available for management of the images in the DICOM database, these options include: Refresh: Deselects any selected data and refreshes the data Configure Columns: Configure the column properties for the data display Configure Search: Focus the scope of the displayed data with an information search Show Server Info: Enable/disable display of recent databases and remote AETs Update DB: Register any recently received unregistered images in the database Query Current AET: Perform query retrieve on remote AET to retrieve images DB Update Status: Enable/disable display of Database Update Status Import DICOM Images: Copy and register images from the file system to the database Load Patient: Load patient data from files Export Patient: Export patient data to files Delete Patient: Delete the patient data from the database Send Patient: Send patient data to listening server Anonymize Patient: Anonymize the patient information (only available from the patient pane)

note If you wish to resize or resample the data use the Load As button option, this will load the selected data into the Load As module (see exercise 4 for instructions on how to use the Load As module).

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Exercise 2 : DICOM Tool Advanced

22. 23. 24. 25. 26. 27. 28.

On your systems local disk create a folder called test_export ($:/test_export). Select the Patient Name MR dataset Brain and then right-click and select the Export Patient option (figure 4). In the Browse for Folder window returned, navigate to and the new test_export directory, then click OK. The DICOM images will be exported out to this directory. Now navigate to the test_export directory on your systems local disk; note the file names have changed to new DICOM UIDs. In the DICOM Tool, with MR data set Brain still selected, right-click and select the Delete Patient option. A dialog box will be returned asking you to confirm that this is what you want to do, click Yes. A delete confirmation window will be returned, click OK to dismiss it. To import this data back into the DICOM Tool right-click in any of the information panels and select the Import DICOM Images option. In the window returned navigate to and select the test_export directory on your system disk, then click OK. You will be asked if you would like to Import all DICOM files found below <$:/test_export >, click Yes to import these images back into the database. The data will be automatically sorted and imported into the DICOM Tool database, and the data set will appear in the Patient information panel.
tip Multiple databases can be created for the DICOM Tool, so multiple DICOM receivers can be configured for the tool; you can select different databases from the Local Databases drop-down menu option.
Figure 4

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Close the DICOM module before proceeding to the next exercise.

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Exercise 3 : Switching On Support for Additional Formats

Analyze supports over 45 different file formats. By default, only the most common formats are enabled. The Import/Export modules External Libraries tool can be used to enable and disable these formats. This exercise will show you how to use the External Libraries tool to switch on support for additional formats. 1. 2. 3. Open the Import/Export module (File > Import/Export). To view the file formats currently supported in Analyze, choose Help > Formats. File formats currently supported are listed in the bottom Formats section of the Supported Formats window (figure 1). When a format is selected, the associated properties will automatically become checked in the Properties section of the window. Experiment by checking several different formats and noting their properties. Click Done to dismiss the window. Open the External Libraries tool (Tools > External Libraries). The External Libraries tool provides a graphical interface listing all formats supported by Analyze (figure 2). The green and red status indicators note whether a format is currently Loaded (L) and Configured (C) - green indicating yes and red indicating no. If you wish to switch on support for a specific file format (for example, PICKERMRI), click on the format in the External Libraries tool. A Configure X Format window will be returned (where X is equal to the selected format) (figure 3). In the Configure X Format window, click Load Now to change the Currently Loaded status to a green Yes.
note Users running multiple operating systems need to configure support for each file format for each operating system. The Platforms option allows the format to be configured for all operating systems (ALL) or for a specific operating system (SPECIFIED).

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Exercise 3 : Switching on Support for Additional Formats

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Click OK. A dialog box will be returned stating that your [Link] file will be updated, click OK (figure 4). The format is now supported by Analyze. If you would like to load and configure all supported formats for your system, click Max in the External Libraries tool. All image file formats will now be supported by Analyze. The L and C status indicators will appear green next time you open the External Libraries tool (figure 5).
Figure 4

note Each file format enabled increases the amount of memory used by your system; it also increases the time taken for a module to open. However, this is typically only an issue on older systems or systems where memory resources are scarce.

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Click Done to close the External Libraries tool. Close the Import/Export module before proceeding to the next exercise.

Figure 5

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Exercise 3 : Switching on Support for Additional Formats

Supported File Formats

Analyze
AnalyzeAVW UNKNOWN VolumeFile OBJMAP ANALYZEIMG ANALYZESCRN used internally for memory mapping, supports all data types, 2D, 3D, and 4D. enables reading raw binary data into images, and exporting image data as raw. enables lists of 2D files to be used as a 3D entity enables object maps to be treated as regular images old Analyze 7.5 format, i.e. .hdr & .img pairs old Analyze 7.5 format of old Screen Edit program

Video
QUICKTIME YUV AVI MPEG1 common movie format single frame color video format video format used by Microsoft Windows standard movie format

Standard Radiological File Formats

DICOM ACR/NEMA PAPYRUS2 PAPYRUS3 NIfTI the standard medical image file format based on Mallincrodt ctn_3_0_3. precursor to DICOM 3D extensions to DICOM from OSIRIS 3D extensions to DICOM from OSIRIS Neuroimaging file format

Raster
BMP GIF JPG PBM PGM PPM PIC PNG PS SGI SUNRASTER TARGA TIFF XBM XWD Microsoft Windows Bitmap a common color indexed format common format featuring lossy compression ascii and binary formats used in Portable Bitmap Library grayscale Portable Bitmap Library 24 bit Color Protable Bitmap Library format used by Softimage Portable Network Graphics output to a PostScript raster dump format used by Silicon Graphics format used by Sun Microsystems a common color format tagged information file format, a common format an ascii c programming language format used by the X Windows system X Windows dump

Vendor-Specific Radiological File Formats

GE9800 GEADVANCE GEADVANTAGE GESIGNA GESTARCAM INTERFILE PICKER MRI SIEMENSCT SIEMENSMAGVIS CTI 7CTI IMATRON SMIS BRUCKER MRI BIO RAD VARIAN FDF older CT format Advance, nulcear medicine format format for CT and MRI older MRI format Signa 4.x older PET format a standard format for nuclear medicine old MRI format used by Picker old Siemens CT format Somatom DR3 Siemens Magnetom Vision (MRI format) PET format used by CTI, early version of ECAT7 PET format used by CTI; CTIECAT7 proprietary CT format proprietary MRI format proprietary MRI format proprietary format Varian MRI format

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Exercise 4 : Load As Loading and Resizing Anisotropic Data

Scanner acquired data is rarely isotropic (cubic) which means that the voxel width, height, and/or depth have different sizes (most often a different slice thickness than the in-plane resolution). This exercise will demonstrate how to load an anisotropic (non-cubic) volume image with the same resolution as when acquired, and then load it again to resize the volume image to create an isotropically sampled volume (cubic) for further use in Analyze. 1. 2. 3. 4. 5. Open the Load As module (File > Load As). Click File [A] and navigate to and select the MRI_Head.avw data set in the $:\BIR\images\TutorialData directory. Uncheck the Auto Exit After Load option [B] and click Load. The data will be loaded into the Analyze workspace as it was acquired (anisotropic). To load the data as isotropic (cubic), select the Resize tab [C] (figure 1). Check the Force Cubic option [D] and click Load; the data will be resampled at the cubic resolution and then loaded. The highest spatial resolution in the acquired volume image is used as the cubic resolution for resampling. Two volumes are now loaded into the Analyze workspace, MRI_Head and MRI_Head0. The latter volume is the cubic volume. To examine the effects of this isotropic sampling, proceed to Exercise 8: Multiplanar Sections. If a specific cubic voxel resolution is desired, the voxel size can be changed. To set the output voxel dimension to 1.5 mm, enter 1.5 in the Output Voxel Size field [E] and press <Enter>. Notice that the Output Axis Dimensions and Memory fields automatically adjust when the voxel dimension is changed. It is also possible to set a specific dimension for the resulting volume image. For example, if you wanted an output volume with an X dimension of 200, enter 200 in the Output X Axis Dimension field [F] and press <Enter>. Again, the other parameters will automatically adjust. You may encounter data sets that are too large to be accommodated by the computer on which you are running (usually due to memory limitations), particularly at the resampled cubic resolution. Specifying a maximum memory size while the Force Cubic option is checked forces each parameter to adjust to the largest value possible that still fits within the specified memory size. Enter 16 into the Output Memory Mb field [G]. Close all windows related to the Load As module before proceeding to the next exercise.
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Figure 1

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Exercise 5 : Import/Export Converting Raw Data into Images

Occasionally it is necessary to import raw data or image data of an unknown file format into Analyze. Such data can be imported if pixels are uncompressed and in contiguous images within the file. The Raw Data tool provides several interactive options to view data as images, ASCII strings, or as the actual binary values of bytes and words. Data can be directly loaded into Analyze or converted into Analyze format image files. Most image file formats consist of some initial header information describing the image(s) and the actual image data. This exercise will demonstrate how to convert raw data from a scanner, which currently has no direct file format support in Analyze. 1. 2. 3. 4. Open the Import/Export module (File > Import/Export). Open the Raw Data tool (Tools > Raw Data). With the Files tab selected, click the File button under Input (figure 1). In the Import/Export Input File window returned navigate to the $:\BIR\ images\TutorialData\ImportExportTutorial directory and select the file UNKNOWN1. Select the Image Parameters tab (figure 2). For this exercise, assume that we know that this file contains one 256 x 256 image, a signed 16-bit integer. An image of this size requires 131072 bytes of storage (256 x 256 x 2), however the file size is 137210 bytes. This indicates that there is an additional 6138 bytes of header information present. This needs to be skipped to get to the first byte of image data. Finally, we know that the 16-bit image data in the file is stored in Big-Endian byte format. To accommodate this, set the following parameters: Byte Offset: 6138 [A](or check Auto Offset to compute this automatically) Width: 256 [B] Height: 256 [C] Data Type: signed 16-bit [D] Byte Swap: Pairs (this only needs to be set on a little-endian architecture, i.e., PC-based systems) [E]
Figure 2 Figure 1

5. 6.

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Exercise 5 : Import/Export Converting Raw Data into Images

8.

Check the following Auto options [F]: Display: Image display will update anytime a control parameter is changed. Clear: Image display is cleared before a new image is displayed. Scale: Data is automatically scaled from its entire dynamic range to 8-bits for display. Click Display to view the current image in the main Import/Export window (figure 3). Click Load in the Raw Data tool to load the image specified in the file into the Analyze workspace. Experiment with the display effects by changing the image parameters to incorrect values, use the up and down arrow buttons found next to the Width and Height fields. Click Done to close the Raw Data tool.

9. 10. 11.

12.

Figure 3

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Exercise 6 : Import/Export Volume Tool

Most medical image formats do not support 3-D directly, since each slice in a study is written to a separate file. The Volume Tool provides a way to create a pseudo format for handling groups of 2-D files as a single 3-D entity. Analyze uses the AVW_VolumeFile, or volume file (.vol), as a way to organize a list of 2-D files into a 3-D volume. The files must contain images of the same size and data type. This exercise will show you how to use the Volume Tool to create a volume file from a list of 2-D TIFF files. 1. 2. 3. 4. Open the Import/Export module (File > Import/Export). Open the Volume Tool (Tools > Volume Tool). In the Volume Tool, click Wild Cards. In the window returned (figure 1), click Directory and navigate to $:\BIR\images\ TutorialData\VolumeToolTutorial - the directory containing the 2-D TIFF data for this exercise. The Filter field is set to * by default so everything in the directory is selected. As this directory only contains TIFF data specific to the data set we wish to load, leave the filter as is. Click Apply. The TIFF files will now be copied to the Volume Tool (figure 2). In the Volume Tool, click Verify to ensure that all the slices selected are the same size and data type. A dialog box (figure 3) will be returned upon successful verification stating Verify Succeeds; click Continue. Click Save and save the volume file as TIFF_Head.vol in the $:\BIR\images\ TutorialData directory.
tip The volume file saved can now be loaded into Analyze using the Load or Load As modules. Alternatively you can load the volume file directly into the Analyze workspace from the Volume tool by clicking Load.
Figure 3 Figure 2 Figure 1

5.

6. 7. 8. 9.

10.

Close the Import/Export module before proceeding to the next exercise.

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Exercise 7 : Saving Data Out of Analyze

At some point it will become necessary for you to save your data out of Analyze. This exercise will demonstrate how to do this using the Save module. 1. 2. 3. 4. Select a data set from the Analyze workspace. If there is no data loaded, load MRI_ [Link] from the $:\BIR\images\TutorialData directory. Open the Save module (File > Save). Click File and navigate to the directory where you would like to save the data set and specify a name. Click Save to return to the main module window. Use the Format drop-down menu to specify the format in which you wish to save the data set.
note Only formats enabled in the external libraries tool will be available. To switch on support for additional formats, please refer to Exercise 3: Switching on Support for Additional Formats.
Figure 1

5.

Click Save to save the data set and close the Save module.
tip You can also save your data out of Analyze using the Save As module. The Save As module provides the same tools as the Load As module, allowing you to resize, change orientation, sub-region, and perform other manipulations on your data while saving it out of Analyze.

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Analyze 10.0

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Exercise 8 : Multiplanar Sections

The Multiplanar Sections module allows the user to quickly and easily view image data in the plane of acquisition or in any naturally orthogonal plane. The module contains several tools for easy two-dimensional display, and has the capacity to load volumes, load object maps, select orthogonal orientations, and perform intensity windowing or thresholding. 1. Load the MRI_Head.avw data set from the $:\BIR\images\TutorialData directory. The data set may already be available in the Analyze workspace if you have completed exercise 4, Loading and Resizing Anisotropic Data. Open the Multiplanar Sections module (Display > Multiplanar Sections). Press the Display Section(s) PowerBar button or choose Generate > Display Section(s). This will begin a sequential display of the data, the display may be stopped at any time by clicking anywhere in the main Multiplanar Sections window (figure 1). Since MRI_Head.avw was acquired in the sagittal orientation, this is the default orientation for display purposes. The display orientation can be changed to display images in a transverse, coronal, or sagittal orientation. Use the Orientation PowerBar buttons to change the display orientation or open the Orientation window (Generate > Orientation). To specify a particular slice to view or to begin the sequential display from, open the Slice window (Generate > Slice). Use the Slice slider bar to set the specific slice.
tip The Slice window also contains three display options: Continuous, Single Step, and Page Mode. Continuous sets the display mode to display the slices in a continuous stream. Single Step turns off the continuous display of slices, when Display Section(s) is selected only one slice is displayed. Page Mode sets the display mode to display a page of slices at a time when Display Section(s) is selected. note Since MRI_Head.avw is anisotropic, images will appear squashed in the coronal and transverse orientations. The resized data set MRI_Head0 created in exercise 4, Loading and Resizing Anisotropic data, will display normally in all three orientations.
Figure 1

2. 3.

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Exercise 8 : Multiplanar Sections

Scan Tool 6. The Scan Tool (Tools > Scan) provides an interface for slice-by-slice review. Click either of the green play arrows to start a sequential display of slices, or use the + and - buttons to move one slice at a time. The slider bar can also be used to move through the slices.

Intersecting Sections Tool 7. Open the Intersecting Sections tool (Tools > Intersecting Sections). The Intersecting Sections tool provides an interactive display of intersecting orthogonal sections. To change the angle at which the intersecting sections are viewed, use the View Angle X, Y, and Z slider bars [A]. The view angle can also be changed by clicking in the image display [B] and dragging the image to a new view. Use the Slice X, Y, and Z slider bars [C] to manipulate the intersecting orthogonal sections. The X slider bar controls the sagittal slice displayed, Y the coronal, and Z the transverse; the slider bar and intersecting sections are also color-coded. The image display will interactively update, allowing the user to navigate through the interior of the data set. The scale of each plane can also be changed using the Scale X, Y, and Z slider bars. To increase the scale of all planes in proportion to each other, uncheck the Individual Axis option; one Scale slider bar [D] will replace the three slider bars, use this to increase and decrease the image size. Right-click on the image display and choose Auto Save. Now, repeat some of the maneuvers described above; when you are finished, right-click again and uncheck the Auto Save option. The maneuvers performed have been recorded and saved to the Analyze workspace. The file can be reviewed with the Movie module (Display > Movie).

8.

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Exercise 8 : Multiplanar Sections

Cube Sections Tool 12. Open the Cube Sections Tool (Tools > Cube Sections). The Cube Sections tool provides an interactive display of orthogonal sections in a three-dimensional viewing cube. The View Angle [A] and Scale [B] options for the Cube Sections tool may be changed as described for the Intersecting Sections tool. Planes can be interactively sliced away in the three orthogonal orientations to revel interior sections of the cube with the Subregion X, Y, and Z double-ended slider bars [C]. As with the Intersecting Sections tool, X controls the sagittal orientation slices displayed, Y the coronal, and Z the transverse; the slider bars and cube sides are also color-coded. After subregioning the data set, right-click on the image display and choose Extract Sub-volume. The subregioned data set will be saved to the Analyze workspace. Click Done to close the Cube Sections tool. Close the Multiplanar Sections module before proceeding to the Additional Task.

13. 14.

15. 16. 17.

Figure 3

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Exercise 8 : Multiplanar Sections

8.1 Creating a Grayscale Data Set with Color Overlaid Objects

Additional Task

The ability to create a grayscale image overlaid with colored objects, also known as an Intensified Volume, can be useful. This exercise will demonstrate how to achieve this using the Multiplanar Sections module. 1. 2. 3. Select the MRI_3D_Head data set in the Analyze workspace and then open the Multiplanar Sections module (Display > Multiplanar Sections). Choose File > Load Object Map and load the MRI_3D_Head.obj object map from the $:\BIR\images\TutorialData directory. When the object map loads the Objects window will automatically open (figure 1). In the Objects window do the following: Set Control by to Attribute Set the Display of all objects to On with the acceptation of the Original and Skin objects. Open the Scan Tool (Tools > Scan) and use the slice slider to review the display of the image date (figure 2). Open the Intensity option (View > Intensity). In the Intensities window, review each of the Object Color modes by selecting each from the Mode drop down menu.
Figure 2 Figure 1

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Figure 3 Windowed Object Analyze 10.0 Essential Training Guide Local Max/Min Object Only Color Edges Edges Only 34

Exercise 8 : Multiplanar Sections

8.1 Creating a Grayscale Data Set with Color Overlaid Objects

Additional Task

6.

Change the Mode back to Windowed Object.

note If you have reviewed the data set using the Display Sections option, make sure you use the Generate > Slice option to set the slice number back to 1.

7. 8. 9.

Next select File > Output Intensified. A message will be returned (figure 4), select Continue. A new Intensified Volume will be saved to the Analyze Workspace. Close the Multiplanar Sections module before proceeding to the next exercise.
Figure 4

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Exercise 9 : Oblique Sections Oblique Resizing of Volumes

Sometimes a particular structure of interest within a data set is not aligned with the orthogonal axes of the 3-D volume. The Oblique Sections module interactively generates any arbitrary plane through a data set and allows reformatting of a series or the entire data set. This exercise will demonstrate how to create an obliquely resampled data set for further analysis with Analyze. 1. 2. 3. 4. Load the Canine_Chest_CT.avw data set from the $:\BIR\images\TutorialData directory. Open the Oblique Sections module (Display > Oblique Sections). Open the Fly tool (Generate > Fly). Use the Fly tool (figure 1) to rotate the current oblique plane from the transverse orientation to the sagittal orientation: i. Click the Roll Right button [A] nine times to rotate the oblique plane into the sagittal orientation. The Fly Value defaults to 10 [B], so for each selection of Roll Right, the plane is rotated by 10 degrees (90 total). Given that the view of this sagittal orientation is as if the body was in a prone position, click the Yaw Counter Clockwise button [C] nine times to rotate the body upright. This is a right lateral view of the chest. If a left lateral view is desired, click the Roll Left button [D] to complete a roll of the oblique plane by 180 degrees (select the button 18 times). Note that the plane appears to rotate through the data set, passing from a right lateral view to a left lateral view.
tip The Fly Value [B] can be changed to make incrementally larger or smaller changes when performing manipulations (e.g. set the Fly Value to 180 and press Roll Left once to rotate 180 degrees).

ii.

iii.

Figure 1

4.

Reset the oblique plane to the central transverse slice by selecting the T Cube at the bottom of the Fly tool [E].

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Exercise 9 : Oblique Sections - Oblique Resizing of Volumes

5. 6.

Open the Matrix Tool (Tools > Matrix) to display the current transformation matrix that reflects this 3-D orientation (figure 2). Now, complete the fly maneuvers as given above to rotate from the transverse orientation to the sagittal orientation again. Note the changes in the transformation matrix in the Matrix tool as these maneuvers are carried out. This demonstrates that the oblique plane manipulation is represented as a full 3-D transformation, with resampling of the data occurring based on the respective 3-D transformation as given in the matrix. Use the Fly tool to select an arbitrary oblique orientation of your choice. For example, click the Roll Right button three times, then the Yaw Clockwise button four times. To save the data set in this oblique orientation, choose File > Output. In the Output window, set Destination to Workspace and change Name to xxx_ myoblique (where xxx are your initials) (figure 3). To resample the entire data set, set Method to Reformat Entire Volume. Since this is an oblique orientation, the resampling space for the new data set may need to be larger than the original, so by default the Change to best fit data option is selected to output a large enough data set to capture all transformed voxels. Click Generate Slices. The resampled data set is now saved to the Analyze workspace. Close the Oblique Sections module before proceeding to the Additional Task. To view your new reformatted data set, open it with the Multiplanar Sections module.
Figure 3 Figure 2

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Exercise 9 : Oblique Sections

9.1 Grid Align Tool

Additional Task

The new Grid Align tools provides users with the ability to interactively reorientate image data using a gird overlay on the current oblique slice, this allows for easy reorientation with reference to structures in the slice. The grid allows for reorientation via translation and yaw of the oblique slice. This task will demonstrate how to reorientate data using the tool. 1. 2. 3. 4. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Oblique Sections module (Display > Oblique Sections). Open the Fly tool (Generate > Fly). Use the Fly tool to set the display orientation to Sagittal by clicking on the S-cube. Next select Generate > Grid Align to apply the grid overlay to the current slice.

Translation: Click to select a point near the center of the grid axis (anywhere within the 36 center boxes). [A] While holding the mouse button down, move your cursor so that the center intersection of the grid is moved to the new desired location. In this example the middle of the cerebellum. [B] Release the mouse button. The image will be translated with the selected region as the new center point. [C]

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Exercise 9 : Oblique Sections

9.1 Grid Align Tool

Additional Task

5. Yaw:

Click on the S-Cube in the Fly tool to reset the image display. Click to select anywhere towards the outside of the grid (anywhere not within the 36 center boxes). [A] While holding the mouse button down, move your cursor to rotate the grid about the center axis. In this example, aligning a grid line along the brain stem. [B] Release the mouse button to apply the Yaw reorientation to the image. [C]

6.

Close all Oblique Sections windows before proceeding to the next exercise.

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Exercise 10 : Oblique Sections Manual AC-PC Realignment

This exercise will review additional manual realignment tools available in the Oblique Sections module. The exercise will explain how to use these tools by demonstrating how to realign the brain along the AC-PC. Please note that the Mayo 3D Brain Atlas add-on provides an interactive AC-PC based alignment tool for realignment of volume image data to the Talairach-Tournoux coordinate and proportional grid system, for more information please review the Mayo 3D Brain Atlas exercise.

1. 2. 3.

Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Then open the Oblique Sections module (Display > Oblique Sections). Once the Oblique Sections module is open, select the Orthogonals (Tools > Orthogonals). In the Orthogonals window (figure 1), move to the mid-sagittal slice where the AC and PC can be identified using the slider bar under the sagittal display pane [A]. It may be helpful to increase the display size of the sagittal slice. To do this, right-click on the pane and select the Size option [B]. At the bottom of the Orthogonal window, select the Interactive Perp Axis option [C] to turn on the interactive generation of the perpendicular axis and the perpendicular oblique. Now, on the sagittal image, move your cursor to either the AC or PC points and select this point with your mouse button. Hold the mouse button down as you drag the line from this point to the other AC or PC point. Release the mouse button when the other point has been selected [D]. This provides the AC-PC axis and generates an oblique image, which is perpendicular to the midpoint of this axis - essentially a coronal image. The Perpendicular Axis window automatically opens (figure 2). This will allow you to note the coordinates of the AC and PC points (Point 1 and Point 2) if desired. Open the Fly tool from the Generate menu in the main Oblique Sections window (Generate > Fly).

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Figure 1

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Exercise 10 : Oblique Sections Manual AC-PC Realignment

9. 10.

Change the Fly Value to 90 (figure 3), and do a Pitch maneuver. This 90 degree pitch places the current oblique image in the plane of the AC-PC line. Now change the Fly Value to a smaller value (e.g. 1 to 5 degrees).
note The anterior part of the brain should be at the top of the oblique image. If it is not, then you can do two more 90 degree pitch maneuvers to flip this oblique plane around 180 degrees.

11.

Viewing the main oblique image, you can use the Roll and Yaw maneuvers to attempt to accommodate brain symmetry in this oblique plane. This is an entirely visual process and shouldnt require much manipulation. Note that you may have to do other smaller manipulations along the way to adjust for the volume being tilted slightly, but you can do this at any time. When satisfied with this transverse-oblique along the AC-PC plane, select File > Output. Change the Method to Reformat Entire Volume to generate the output volume at this new orientation. It is up to you to reformat this back into the original volume size (Maintained), or new output volume that can hold the entire span of the rotated original volume (Change to best fit data). Select Generate Slices to save the AC-PC aligned volume to the Analyze workspace. Close the Oblique Sections module before proceeding to the next exercise.
Figure 3

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Exercise 11 : Volume Compare

The Volume Compare module provides the ability to compare data sets images that have the same spatial resolution. This exercise will provide an overview of the module. 1. Load the MRI_3D_Head.avw and MRI_3D_Brain.avw data sets from the $:\BIR\ images\TutorialData directory. Select both data sets, MRI_3D_Head.avw first and MRI_3D_Brain.avw second. Open the Volume Compare module (Display > Volume Compare). Open the Blend window, select Yellow-Cyan. Click on any of the images and drag your cursor to move through the image display. Alternatively, use the arrow keys and the page up, page down keys to move through the data. From the File menu, select Load First Object Map and load the MRI_3D_Head.obj. Next, load the MRI_3D_Brain.obj object map for the second volume (File > Load Second Object Map). Use the crosshairs to navigate through the data (figure 2). Double click in any pane to log points. To save the Point Log, click Save (figure 3). To save the Fused Volume, select File > Save Fused. Close the Volume Compare module before proceeding to the next exercise.
Figure 1

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Exercise 12 : Volume Render Basic Rendering Controls

The Volume Render module provides a variety of display representations for three-dimensional image data sets. Also provided in the module are tools for volume image editing and measurement. This exercise will demonstrate the different control parameters involved in the process of volume rendering. This includes demonstrating various rendering algorithms that are part of the suite of techniques used to render volume images with Analyze. 1. 2. 3. 4. Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render). Press the Render PowerBar button or choose Generate > Render. Open the Preview window (Generate > Preview).
Figure 1

Thresholding Data 5. 6. 7. 8. Open the Thresholds window (Generate > Thresholds). Set the Threshold Minimum to 85 (figure 1) - all voxels with a value less than 85 are now removed from view. The resulting image can be seen in the Preview window (figure 2). Click Render to display the rendering in the main Volume Render window. Now, set the Threshold Minimum to 145all voxels with a value less than 145 are now removed from view. Click Render.
Figure 2

Controlling the Rotation Parameters 9. 10. 11. Open the Rotation window (Generate > Rotation). The Volume Absolute option is selected by default (figure 3); use the X, Y, and Z slider bars to change the rendering view. Click Render as desired. Select the Screen Relative and Volume Relative options and compare the different rotation methods available. The Screen Relative option specifies that the rotation of the volume be performed relative to the current screen axis, while the Volume

Figure 3 Analyze 10.0 Essential Training Guide 43

Exercise 12 : Volume Render Basics

Relative option specifies that the rotation be performed relative to the current position of the volume axis. 12. 13. 14. Look at the Matrix option, but adjustment is not recommended. Experiment with the Named option views. Select the Change View option and use the arrows to manipulate the rendering view (figure 4). Alternatively, you can click and drag the rendering to a new angle in the image display.
note As the rendering is moved, only the originally viewable voxels are interactively rerendered, providing visual cues to the movement and orientation of the image. Upon release of the mouse button, the full image is rendered at the new orientation.

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When you are familiar with all of the rotation options, select the Front view from the Named option and click Render. Click Done to dismiss the Rotation window.
Figure 4

Rendering Algorithms 17. 18. 19. 20. Open the Render Types window (Generate > Render Type) (figure 5). Experiment with the rendering algorithms. (See Note below). Select the Depth Shading option. View the rendering in the Preview window. Click Render to display the rendering in the main Volume Render window (figure 6). Select the Volume Compositing option. View the rendering in the Preview window. Click Render to display the rendering in the main Volume Render window (figure 7). For more information on the Volume Compositing Tissue Map Type Specific option, please review exercise 13, Volume Render Tissue Map Tool.
note Additional parameters for each render type are available from the Type Specific sub-menu (Generate > Type Specific), explanation of all of these additional options is beyond the scope of this exercise, but more information can be found in the Users Guide (Help > Users Guide).

Figure 6

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Exercise 12 : Volume Render Basics

21.

Select the Maximum Intensity Projection option. Click Render to display the rendering in the main Volume Render window. This render type is normally used with vascular data where the signal is enhanced (usually using contrast), but the dense bone in this data set also shows up well. Try the MIP Weighting option available from with the Type Specific sub-menu (Generate > Type Specific > MIP Weighting). The Before weighting option works very well with this input data (figure 8).

22.

Select the Summed Voxel Projection option and click Render. If the threshold minimum is still set to 145, the Summed Voxel Projection algorithm is actually only adding and averaging the voxels corresponding to bone, ignoring all soft tissue. In most cases, whenever you use the Summed Voxel or Maximum Intensity Projections render types, you may want to set the threshold range to the complete range of the input data. In the Thresholds window (Generate > Thresholds) change the Threshold Minimum to 0 and click Render. Notice that now the Summed Voxel Projection rendering looks like a re-projection X-ray (a Digitally Reconstructed Radiograph DRR) (figure 9).

Figure 8

Figure 9

Figure 10

note When working with anisotropic data, the Interpolated Rays option may help to improve the quality of the rendering.

23.

Select the Surface Projection option. Set the Threshold Minimum back to 145 in the Thresholds window, then click Render. This render type is more effective with different input data, but the effect can be seen using the current surface (figure 10). Select Gradient Shading and click Done to dismiss the Render Types window.

24.

The Clip Tool 25. 26. 27. 28. Open the Clip tool (Generate > Clip). The Clip tool (figure 11) allows a subregion of the volume to be rendered. Experiment with the Clip Plane and Clip Volume parameters. Click Done to close the Clip tool. Close all windows related to the Volume Render module before moving onto the next exercise.
Figure 11

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Exercise 13 : Volume Render Advanced Rendering Controls

Adding the ability to control specific objects in the rendering process provides incredible power and versatility in the creation of unique visualizations. In Analyze, this is possible with the use of object maps. Object maps are special image files that are used in Analyze to partition and identify structures as belonging to a particular segmented object. Voxels in the volume image correspond directly, on a one-to-one basis, with a voxel in the object map, whose value assigns the voxel to a particular segmented object. Each of the objects within the object map can be controlled and manipulated independently. This exercise will begin to explore the power of object control in creating 3-D visualizations, but will only scratch the surface of the endless possibilities for exploration of this 3-D visualization space. 1. 2. Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render).

Defining Objects in an Object Map 3. 4. Choose File > Create Object Map. The Objects window will automatically be returned; dismiss the window for now by clicking Done. Open the Threshold Tool (Tools > Manipulate > Threshold) (figure 1). Set the Minimum Threshold to 85 [A]. Set Change to Object Map [B]. Set Defined Object to ***New*** [C]. Click Threshold Volume to define a new object. Note all voxels from 85 to 255 will be defined as a new object, Object_2. Click Done to close the Threshold Tool. Open the Preview window (Generate > Preview) to interactively review your changes. Open the Objects window (View > Objects). Select Object _2 (if it is not already selected) from the Object drop-down menu. Change the following attributes for Object_2: Click Render to display the rendering in the main Volume Render window (figure 2). In the main Volume Render window, open the Thresholds window (Generate > Thresholds). Set the Threshold Minimum to 145 and click Render.
Figure 2 Figure 1

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Exercise 13 : Volume Render Advanced

9.

Open the Connect Tool (Tools > Manipulate > Connect). Change the Connect Method to Connected Components. Set to Keep the 3 Largest Objects. Click Label Components. The three largest objects will automatically be identified and labeled as new objects (figure 3). Click Done to close the Connect Tool.

tip

Up to 255 different objects can be defined in an object map.

Manipulating Objects 10. 11. In the Objects window (View > Objects) (figure 4), click Reassign Object(s) [A]. In the window returned (figure 5), select: BlueObject from the Reassign from list. From the drop down menu to the right select: YellowObject. Click Apply and then OK to dismiss the window. Note the update in the Preview window. Click Remove Unused [B] in the Objects window to remove BlueObject. Click OK in the dialog box returned. Select the GreenObject from the Object drop-down menu. Then change the following attributes: Name: Bone Color: white Shades: 32 Select the YellowObject from the Object drop-down menu. Then change the following attributes: Name: Rope Color: red Shades: 8 Click Render. In the Thresholds window (Generate > Thresholds), set the Threshold Minimum to 5. Return to the Objects window and set Control by to Attribute [C].

Figure 3

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Exercise 13 : Volume Render Advanced

18. 19.

Set the Display attribute to Off for the Original object. Then, click Render. Open the Render Types window (Generate > Render Type). Select the Object Compositing option, then open the Object Mapping window, (Generate > Type Specific > Object Mapping). Select the Transparency render type (figure 6) and click Render to view the effects. A variety of object attributes can be controlled in the Objects window. Set Attribute to Opacity by selecting it from the drop-down menu. Change the Bone object to 1 (opaque). Click Render (figure 7).

note The Object Mapping is only available if the Object Compositing option is selected. The Transparency render type is only available when an object map has been loaded or created.

20. 21.

Saving an Object Map 22. 23. 24. Object maps can be saved for review or use at a later time, or to load into another Analyze module; choose File > Save Object Map to save the object map. Name the file Cubic_CT_Head_xxx.obj (where xxx are your initials) and specify a location to save the file, then click Save (object maps are saved as .obj files). Close the Volume Render module before proceeding to the next exercise.

Figure 6

Figure 7 Analyze 10.0 Essential Training Guide 48

Exercise 14 : Volume Render Tissue Map Tool

The Tissue Map tool provides a control interface that allows for the creation of unique visualizations. This exercise will demonstrate how to use the tool to generate visualizations of different tissues. 1. 2. 3. 4. 5. 6. Load the CT_Heart.avw data set from the $:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render). Open the Render Types window (Generate > Render Type). Select the Volume Compositing render type (figure 1). Click Render, then click Done to dismiss the window. Open the Tissue Map tool (Generate > Type Specific > Tissue Map). A tissue map is a mapping of the voxel values within a volume to a given color and opacity. The Tissue Map tool provides several control options to aide in the creation of a tissue map for a volume. The Tissue Map tool provides four control points to manipulate which voxel values are mapped to specific colors and opacity (figure 2). Start [A]: The starting voxel value within the volume mapped to a specific color (chosen from the color drop-down menu) with 0% opacity. Min [B]: The minimum voxel value within the volume that will be mapped to a specific color and set opacity (e.g. 44%). Max [C]: The maximum voxel value within the volume that will be mapped to a specific color and set opacity (e.g. 44%). End [D]: The ending voxel value within the volume mapped to a specific color with 0% opacity. Click Render to view the rendering with the default parameters (displayed in the main Volume Render window).
Figure 1

The Tissue Map tool is only available with the Volume Compositing render type

7.

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Figure 2 Analyze 10.0 Essential Training Guide 49

Exercise 14 : Volume Render Tissue Map

9.

Use the slider bars [A] in the Tissue Map tool to set the following (figure 3): Start: 157 Min: 200 Max: 500 End: 3072 Select 60 from the Opacity drop-down menu [B]. Click Render to view the effect of the changes (figure 4). Now, experiment by moving the control points in the graphical display [C]. Click Render as desired. Right-click in the graphical display and select Show Histogram; the volume histogram will be calculated and displayed. This option may help determine voxel values associated with tissues. Several default tissue maps are also available, rightclick in the graphical display and choose Default Tissue Maps > CT1; once loaded, click Render (figure 5). Experiment with adding a second tissue to the tissue map by clicking the + button [D] to the right of the graphical display. Click Render as desired to see the effect. Close the Volume Render module before proceeding to the next exercise.

10. 11. 12.

13.

Figure 3

14. 15.

Figure 4

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Exercise 15 : Volume Render Movie Making with the Sequence Tool

The Volume Render module contains a number of tools for movie generation. This exercise will introduce the Sequence tool. While complicated movies can be created, the goal of this exercise is to demonstrate how to generate a quick, simple movie. For more information, please review the Movie Making with Volume Render Tutorial after you have completed this exercise. The tutorial can be accessed from the Help menu in the main Analyze workspace. 1. 2. 3. 4. Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render). Choose File > Save Renderings (figure 1). In the Save Renderings window, check the Save After Each Render option and change Name to MyTestMovie. The movie that is generated will automatically be saved to the Analyze workspace as MyTestMovie. Click Done to dismiss the Save Renderings window. Open the Sequence tool (Generate > Sequence). By default, the sequence already has one action, Z Rotation. To modify the action click Modify [A], and then click on the red Z Rotation action [B] (figure 2). The Action window will automatically be returned. For the first part of this movie, we will threshold the data set to show the structure of interest, in this case the head. If you have completed Volume Render exercises 11 and 12, you will know that in order to view the head in this data set, we need to increase the threshold minimum to 85. In the Action window, set the following parameters (figure 3): Action Name: Threshold Number of Frames: 36, the default frame display is 12 frames per second. Persistent: Checking the Persistent option will ensure that the minimum threshold parameter set in this action will be retained for the rest of the movie. If not checked, the threshold minimum will be reset after the action is completed. Parameter: Threshold End Minimum: 85
Figure 2

Figure 1

5. 6. 7.

8.

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Figure 3 Analyze 10.0 Essential Training Guide 51

Exercise 15 : Volume Render Sequence Tool

10. 11. 12.

To preview the movie with the new action, first open the Preview window (Generate > Preview). Now, in the Sequence tool, click Sequence [C]. Then, click Make Sequence [D] (figure 4). A dialog box will be returned asking if you would like to Preview or Make the Sequence, click Preview the Sequence. The movie will now be played in the Preview window.
note The Preview the Sequence option is only available when the Preview window is open. If the Preview window is not open, the dialog box will not be returned after clicking Make Sequence, instead the sequence will automatically be generated.

13.

Add another action to the movie. Click Add Action [E] and place the new action on Track 2 in Frame 36 [F]; this will be directly under the last frame of the Threshold action (figure 5). Once the new action has been added, click Modify [G] and then click on the new action to open the Action window. We will now add a rotation to the movie. Set the following parameters for the new action: Action Name: Rotation Number of Frames: 60 Parameter: Rotation End Z: 720 (2 rotations, 360=1 rotation) Click Done to dismiss the window. Review the movie. Click Sequence, and then, with the Preview window open, click Make Sequence. In the dialog box returned, click Preview the Sequence. The movie playing in the Preview window should show the data set being thresholded to the head, followed by two quick rotations about the Z-axis.
tip

Figure 4

14. 15.

16. 17. 18.

Figure 5

To slow the rotation of the data set, simply add more frames in the Action window (e.g. Change Number of Frames from 60 to 120), or only show one rotation by changing the End Z value to 360 from 720.

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Exercise 15 : Volume Render Sequence Tool

19. 20.

To generate the movie, click Sequence again. This time, after clicking Make Sequence, choose Make the Sequence from the dialog box returned. As the sequence is generated, each frame will be displayed in the main Volume Render window. Each frame is also being written to a movie file called MyTestMovie in the Analyze workspace (specified earlier in the Save Renderings window). Once sequence generation is complete, close the Volume Render module. In the Analyze workspace, select the MyTestMovie file and review it using the Movie module (Display > Movie). (figure 6) To save the movie out of Analyze, choose File > Save in the Analyze window. Choose a movie file format (AVI, QuickTime, or AnimatedGIF) from the Format dropdown menu before clicking Save. Close the Movie module before proceeding to the next exercise.
Figure 6

21. 22. 23.

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Exercise 16 : Volume Render Fix Tool

The Fix Tool provides the capability to correct for bad slices within a volume. The tool allows a variety of correction methods for missing or corrupt images that occur in a volume, including removing corrupt images, copying from an adjacent uncorrupted image, and interpolation from a range of uncorrupted images near the corrupt image. This exercise will demonstrate how to use the Fix Tool to correct for bad slices within a volume. 1. 2. 3. 4. 5. 6. 7. Load the VH_Abdomen.avw data set from the $:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render). Open the Preview window (Generate > Preview). Now, open the Thresholds window (Generate > Thresholds). Set the Threshold Minimum to 26; the Preview window will interactively update (figure 1). Note the lines that appear in the image [A]. Open the Ortho Sections tool (Tools > Display > Ortho Sections). In the Ortho Sections tool (figure 2), click on the line in the rendering seen in the top left pane [B]. The three orthogonal views will automatically update. Notice the corrupt image in the transverse orientation [C]. Click Done to close the Ortho Sections tool. Also close the Thresholds and Preview windows.
Figure 1

8.

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Exercise 16 : Volume Render Fix Tool

9. 10. 11. 12. 13. 14.

Open the Fix Tool (Tools > Manipulate > Fix). In the Fix Tool (figure 3), use the Displayed Slice slider bar [D] to locate the first corrupt slice. Note that the first corrupt slice is slice 276. In the Bad Slice(s) portion of the window, set slice 276 as the first bad slice [E]. Now, use the Displayed Slice slider bar to locate the last corrupt slice. Note: the last corrupt slice is slice 279. In the Bad Slice(s) portion of the window, set slice 279 as the last bad slice [F]. Select Interpolate Between the First Good Slice for the correction method [G].
note This method uses linear interpolation to calculate a replacement slice for each bad slice. The value of each voxel is computed using information for each of the good slices on each side of the bad slices. The percentage of each image used is calculated based on the distance from the bad slice to each good slice.

15.

Click Fix Slice(s). A dialog box will be returned, click Change a Copy of the Loaded Volume. The fix will now be applied to a copy of the data set; the fixed data set will be saved to the Analyze workspace as VH_Abdomen0. Click Done to close the Fix Tool. In the main Volume Render window, press the Render PowerBar button or choose (Generate > Render). Note that the lines that appeared in the top of the image are no longer present (figure 4). Close the Volume Render module before proceeding to the additional task.
Figure 3

16. 17.

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Figure 4 Analyze 10.0 Essential Training Guide 55

Exercise 16 : Volume Render Fix Tool

1. Copy from Related Volume Option

Additional Task

The option Copy from Related Volume provides the ability to use a related volume as input for the Fix Tool, allowing images to be copied from the Related Volume to the Loaded Volume. To demonstrate the new fix option we will correct for the corrupt slices in the VH_Abdomen data set, using the fixed slices from the VH_Abdomen0 data set. 1. 2. 3. 4. 5. 6. 7. 8. Select the VH_Abdomen data set in the Analyze workspace and open the Volume Render module (Display > Volume Render). In the main Volume Render window, choose File > Input/Output Ports. The VH_Abdomen data set icon will appear under the Volume port. In the Analyze workspace, select the fixed data set created in the main exercise, VH_Abdomen0. Drag-and-drop VH_Abdomen0 to the Related Volume port in the main Volume Render window (figure 5). Open the Fix Tool (Tools > Manipulate > Fix). As in the main exercise, set slice 276 as the first bad slice and slice 279 as the last bad slice. Select Copy from Related Volume for the correction method. Click Fix Slice(s). Slices 276 through 279 will be copied from the related volume and replace the corrupt slices in the loaded volume. A dialog box will be returned, click Change a Copy of the Loaded Volume. Click Done to close the Fix Tool. In the main Volume Render window, press the Render PowerBar button or choose Generate > Render. Note that the lines that appeared in the top of the image are no longer present (see step 7 in the main exercise). Close the Volume Render module before proceeding to the next exercise.

Figure 1

9. 10.

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Exercise 17 : Volume Render Creating a Merged Image

The Volume Render Merge Tool allows images generated with different render types to be merged into a single image providing users with the ability to create unique visualizations of their image data. This exercise will demonstrate how to use the Merge Tool to create a unique rendering of the brain and ventricles.

Creating the First Image 1. 2. 3. 4. 5. Load the MRI_3D_Head.avw data set from the C:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render). Choose File > Load Object Map and load the MRI_ 3D_Head.obj object map from the $:\BIR\images\TutorialData directory. Open the Preview window (Generate > Preview) Open the Rotation window (Generate > Rotation). In the Rotation window select Named and then select Right. Note that after this point you will not be able to reposition the data. Open the Objects window (View > Objects) and set the Control by option to Attribute. Set the Display attribute to Off for all objects except the Ventricle (figure 1). Next we will use some of the additional rendering options to generate a rendering of the ventricle. Open the Specular Reflection tool and Light tool from the Type Specific menu (Generate > Type Specific > ). In the Specular Reflection tool set the following parameters (figure 2): Specular Reflection to On Factor to 0.32 Exponent to 0.1 Use the Light tool to brighten the image display by moving the Brightness slider to the right (figure 3). Once these parameters are set, click the Render button in the main Volume Render window.
Figure 2 Figure 3 57 Figure 1

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Exercise 17 : Volume Render Creating a Merged Image

11. 12.

Next open the Merge tool from the Tools menu (Tools > Display > Merge). The current rendering will be displayed in the Current port. Click the Current to Previous button to copy the current rendering over to the Previous port (figure 4).
note If you wish to return to this point at a later time, save the rendering by rightclicking in the Previous port and select the Save Previous option.

Figure 5

Creating the Second Image 13. In the Objects window, switch the display of the Ventricle to Off and the display of the Brain to On. Next, change the Attribute from Display to Color and change the Brain color from Pink to White (figure 5). Open the Render Type window (Generate > Render Type) and set the Render Type to Surface Projection (figure 6). Next, open the Surface option from the Generate > Type Specific menu. In the Surface option set Skip to 2 and Thickness to 6 (figure 7). Note the display of the brain from the Preview window. Once these parameters have been set, click on the Render button in the main Volume Render workspace. The Current rendering in the Merge Tool will update.
Figure 4 Figure 7 Figure 6

14. 15.

16. 17.

Merging the Images 18. Right-click on the main image display window in the Merge Tool, set the Merge Type to Average (figure 8). Note the updated display. Right-click and set the Merge Type back to ZBuffer Depth.

Figure 8 Analyze 10.0 Essential Training Guide 58

Exercise 17 : Volume Render Creating a Merged Image

19. 20. 21.

Decrease the Opacity value of the current rendering by moving the Opacity slider bar under the current rendering to the left. An Opacity of 0.32 works well (figure 9). Next, click the Merge to Current button. To save the rendering, select File > Save Renderings. In the Save Renderings window, change the Name to Merged Image and then click on the Save Last Rendering button. The following window may be displayed (depending upon the render options you set).
Figure 9

22.

23.

Select the Intensity Scaled (unsigned 8-bit) option. The rendering will be saved to the Analyze workspace and can be saved out of Analyze as a .jpg, .tiff, or .bmp using the Save module. Close the Volume Render module before proceeding to the next exercise.

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Exercise 18 : Volume Render Creating A High Definition Volume Rendering

The Volume Render module allows for the generation of High Definition Volume Renderings. This exercise will demonstrate how to generate a high definition volume rendering using a CT data set with a Volume Composite with a tissue map overlay. Note the high definition volume renders can be generated with any of the rendering algorithms available in the Volume Render module. 1. 2. 3. 4. 5. Load the CT_Heart.avw data set from the $:\BIR\images\TutorialData directory. Open the Volume Render module (Display > Volume Render). Open the Render Size option from the Generate menu and change the Width and Height of the Render size to 2000x2000. Then click Apply (figure 1). Open the Render Type window from the Generate menu and select Volumetric Compositing, check the Interpolated Rays option (figure 2). Open the Tissue Map tool (Generate > Type Specific > Tissue Map). Right-click on the main tissue map panel and select Load Tissue Map, choose the CT 2 default tissue map. Now open the Perspective Rendering tool (Tools > Display > Perspective) and then click the Perspective Render button (figure 3). In Perspective mode, a ray is cast for every output pixel in the rendering. In this case 4 million (2000x2000) rays are cast through the current field of view (FOV) for the perspective geometry. Note the Render Size controls the number of rays, and the FOV controls the space in the volume through which that number of rays is cast. It may take a little while to render depending on the volume size. Once the rendering is complete, the HDVR will be displayed in the main Volume Render window. To save the rendering, Select File > Save Rendering. Name the rendering HDVR and then click the Save Last Rendering button. Close the Volume Render module before proceeding to the next exercise.
Figure 3
Figure 1

Figure 2

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Exercise 19 : Volume Render Parametric Mapping

Volume Render provides the ability to generate parametric maps when a related volume is loaded and the render type is set to gradient shading. This exercise will demonstrate how to sue the parametric mapping option. 1. Load the SISCOM_Extracted_Brain.avw and SISCOM_4D_ActivityMap.avw data set from the $:\BIR\images\TutorialData\AdditionalData directory.
note The SISCOM_4D_ActivityMap is a multivolume created using the SISCOM module. Each volume represents an activation map generated with a different activity standard deviation. Starting at 0.1 and increasing at a 0.1 intervals to 5.0

2. 3.

Open the Volume Render module (Display > Volume Render). In the Volume Render window, select File > Input/Output Ports (figure 1). Drag-and-drop the SISCOM_Extracted_Brain file from the Analyze workspace into the Volume port. Next, drag-and-drop the SISCOM_4D_ActivityMap from the Analyze workspace into the Related Volume port. Open the Preview window (Generate > Preview). Open the Parametric Mapping window (Generate > Type Specific > Parametric Mapping). In the Parametric Mapping window, set Parametric Mapping to On (figure 2). Review the rendering in the Preview window. If necessary, use the Rotation window (Generate > Rotation) Change View option to maneuver the brain to a desirable orientation (figure 3).
Figure 2

4. 5. 6. 7.

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Exercise 19 : Volume Render Parametric Mapping

8.

Review the effects of changing the Mapping Factor and Map Transparency options in the Parametric Mapping interactively in the Preview window. To view the 4D multivolume over time, use the Which Mapping Volume option. Check Increment after each Render, then press Render, until youve made your way through the volumes (figure 4). Close the Volume Render module before proceeding to the next exercise.

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Exercise 20 : Surface Render Surface Map Creation and Display

Surface Render provides a semi-automated interface for the conversion of object maps into surface maps using the Adapt/Deform algorithm.

1. 2. 3.

Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Surface Render module (Display > Surface Render). Choose File > Load Object Map and load the Cubic_CT_Head object map from the $:\BIR\images\TutorialData directory. The Objects window (View > Objects) will automatically be returned. In the Objects window, set Control by to Attribute and set the Display attribute to Off for the Rope, Left Skin, and Skull objects (figure 1). Choose File > Create Surface Map. The Surfaces window (View > Surfaces) will automatically be returned. In the Surfaces window, click From Object(s). A dialog box will be returned asking if you would like to create the surface map from all currently active objects, click Yes. The objects that have their Display attribute set to On (in the Objects window) will be tiled and a surface map generated. Once the surface map is generated, click Render to display the results (figure 2).
note Where possible, the attributes of the surfaces in the surface map and the objects in the object map should have equivalent values.

4. 5. 6.

Figure 1

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8. 9. 10. 11.

Choose File > Load Surface Map and load the Cubic_CT_Head.smp surface map from the $:\BIR\images\TutorialData directory. Click Render to display the results. Open the Camera tool (Generate > Camera) and set Sort to Front-Back (figure 3). Click Render to display the results. In the Surfaces window set Control by to Attribute. Choose Shading from the Attribute drop-down menu and change the shading of the Right Skin surface to Gouraud.

Figure 2

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Exercise 20 : Surface Render Surface Map Creation and Display

12. 13. 14.

Click Render, note the changes in the rendering (figure 4). Experiment with the different shading options. Choose File > Save Surface Map to save changes made to the surface map. If you wish to export the surface map out of Analyze for use in another application, choose File > Export Surface Map. Surface maps can be exported out of the Surface Render module in the Inventor (.iv) or VRML (.vrml) surface description formats. To learn about more surface rendering tools and options, complete the Additional Task.
Figure 4

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20.1 Advanced Visualization

Additional Task

1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Open the Preview window (Generate > Preview) to view changes prior to rendering. In the Camera tool (Generate > Camera), set FOV to 60. In the Surfaces window (View > Surfaces) select Display from the Attribute dropdown menu and set the Rope, Right Skin, and Left Skin surfaces to Off. Choose Transparency from the Attribute drop-down menu, and set the Skull and Jawbone surfaces to 1.0. Click Render. Open the Rotation window (Generate > Rotation). With the Volume Absolute option selected, set X: -64, Y: -3, Z: 37. Then, click Render. In the Camera tool select the Position option and set the Z position to 300. Click Render and note the changes in the rendering. Now, set the Position coordinates to X: 12, Y: 41, Z: -215. Click Render and note the changes in the rendering (figure 5). In the Rotation window, select the Change View option. Use the arrow buttons or click and drag the rendering to a new view in the image display. Notice that each time the view is modified the image is re-rendered in the main module window. To prevent this, right-click on the Change View image display and deselect Regenerate on Release. Close all windows related to the module before proceeding to the next exercise.
64 Figure 5

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Exercise 21 : Virtual Endoscopy Interactive Generation of Endoscopic Views

Virtual Endoscopy is an important visualization application that results from the ability to create 3-D visualizations from a viewpoint inside of the body. This exercise will familiarize you with the Virtual Endoscopy module, demonstrating basic functionality and various methods of controlling the view. 1. 2. Load the CT_Lungs.avw data set from the $:\BIR\images\TutorialData directory. Open the Virtual Endoscopy module (Display > Virtual Endoscopy).

Basic Controls 3. Position the cursor on the image display near the center of the trachea (the hole in the flat surface) and click once; this will be set as the new Look At point and the Eye position will advance (figure 1).
tip The Eye position advances toward the selected point based on settings in the View Parameters window.

4. 5.

Position the cursor on the flat surface outside of the trachea and click once. The Back PowerBar button can be used to reposition to previous locations; the Forward PowerBar button will move to the next location if one has been defined. Press the Back button once. Position the cursor over the center of the trachea and click several times to navigate into the trachea. Then, press the Back button until you return to the starting location.
Figure 1

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Advanced Controls 7. 8. 9. Open the View Parameters window (Generate > View Parameters). Set the Move Percent to 50. Now, click again on the image display near the center of the trachea; note the effect of increasing the Move Percent (figure 2). The View Parameters window (figure 3) also allows you to specify a location by typing in coordinates. Set the following coordinates: Eye X: 128 Y: 150 Z: 181 Look At X: 125 Y: 142 Z: 120 Up X: 0 Y: 1 Z: 0 Click Render in the View Parameters window to display the location of the coordinates (figure 4).
Figure 4 65 Figure 2

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Exercise 21 : Virtual Endoscopy Interactive Generation of Endoscopic Views

11. 12.

Reset Move Percent to 20 in the View Parameters window and click Done to dismiss the window. Many times when an obvious entry location is not available, the Orthogonal Eye and Look At views are very useful. To enable these views, press the Eye and Look At PowerBar buttons or choose View > Eye and View > Look At. When enabled, three interactive panes become available (figure 5) on either side of the module window, displaying the transverse, coronal, and sagittal sections that intersect with the current Eye position [A] or Look At point [B]. A new Eye position or Look At point can be set by clicking in any of the orthogonal section panes.
tip The Eye position advances toward the selected point based on settings in the View Parameters window (Generate > View Parameters).

13.

Press the Manual Controls PowerBar button or choose Generate > Manual Controls. The Manual Controls will appear in the main module window [C], allowing you to select the translation or rotation actions, the increment, and point(s) to manipulate. To apply a manual action, click the Render button at the bottom of the main module window. Use the interactive Orthogonal Eye/Look At panes and the Manual Control buttons to navigate down into the trachea until you reach the bifurcation of the airway. Press the Show Object PowerBar button or choose Generate > Show Object. The Show Object window allows the Eye position and Look At direction to be manipulated on an exterior rendering. The rendering shows a circle indicating the Eye position and an arrow for the Look At direction (figure 6).
note Since the visualization is created by thresholding, you must be inside the object in order for it to be rendered.

Figure 5

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16.

Close all Virtual Endoscopy windows before proceeding to the next exercise.

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Exercise 22 : Virtual Endoscopy Endoscopic Movie Generation

The Virtual Endoscopy module provides an interactive interface for endoscopic visualization. Often the desired result of such an endoscopic exploration is a detailed endoscopic movie sequence along a specified fly-through path. This exercise will demonstrate how to achieve this by defining a path using key frames then generating all endoscopic renderings along this path. 1. 2. 3. Load the CT_Lungs.avw data set from the $:\BIR\images\TutorialData directory. Open the Virtual Endoscopy module (Display > Virtual Endoscopy). Before beginning to record the movie, move closer to the trachea. Position the cursor near the center of the trachea and click three times to cause incremental movement towards the target. Press the Add Key Frame PowerBar button or choose Generate > Sequence > Add Key Frame to specify the first key frame (this is where the movie will begin). Move closer to the trachea by clicking three more times within the tracheal lumen (figure 1). After the movement towards the trachea has stopped, press the Add Key Frame button to add another key frame. Choose Generate > Sequence > Auto Add Key Frame, this option causes any new viewpoint to automatically be added as a key frame. Continue to click within the tracheal lumen and navigate down to the bifurcation of the airway (approximately 9 clicks) (figure 2). When you reach the bifurcation of the airway, click in the left bronchus to reorient the viewpoint down that specific branch. Click several more times to traverse down the left bronchus. When you have moved down the left bronchus (figure 3), choose Generate > Sequence > Auto Add Key Frame to turn off the Auto Add Key Frame option. To save the sequence, choose Generate > Sequence > Save Sequence. To generate a movie of the sequence, choose Generate > Sequence > Generate Sequence. The full sequence (defined by the key frames) will now be generated by the module; all endoscopic renderings will be generated along the defined path. The fly-through movie will be available in the Analyze workspace and can be viewed with the Movie module (Display > Movie).
Figure 3

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Figure 1

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note Rendering the endoscopic movie may take a few minutes depending upon your system and the size of the movie.
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Exercise 22 : Virtual Endoscopy Endoscopic Movie Generation

22.1 Advanced Maneuvers

Additional Task

1. 2. 3. 4.

After viewing your movie try recreating the movie adding these steps into the main exercise after Step 7. When you reach the bifurcation of the airway, click in the right bronchus. Click two more times to move further into the bronchus (figure 1). Press the Back PowerBar button three times, and then proceed down the left bronchus. At the end of the left bronchus press the Invert Positions PowerBar button, then move back up through the left bronchus towards the trachea. When you reach the trachea choose Generate > Sequence > Auto Add Key Frame to turn off the Auto Add Key Frame option. Choose Generate > Sequence > Generate Sequence to generate the movie (figure 2). Close the Virtual Endoscopy module before proceeding to the next Additional Task.
Figure 1

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Exercise 22 : Virtual Endoscopy Endoscopic Movie Generation

22.2 Generating a Centerline

Additional Task

The Virtual Endoscopy module provides that ability to generate the centerline of an endoscopic structure using the current Eye and Look At points. Key frames are automatically generated between the two points and displayed in the Sequence Edit window once the centerline has been created, allowing an endoscopic sequence to be generated along the centerline, thus reducing the time taken to create fly-through movies. This task will show you how to create a centerline and generate the resulting endoscopic movie. 1. 2. 3. Load the CT_Lungs.avw data set from the $:\BIR\images\TutorialData directory. Open the Virtual Endoscopy module (Display > Virtual Endoscopy). Position the cursor over the center of the trachea and click to navigate into the trachea. Clicking 12 times should position you midway into the trachea (figure 1). Press the Eye and Look At PowerBar buttons to enable the Eye and Look At views. Then press the Show Object PowerBar button to open the Show Object window. In the Show Object window, click on and drag the green arrow (the Look At point) to the end of the airway (figure 2). Use the Look At panels to correct the Look At position, make sure that the Look At position is on the airway (figure 3).
Figure 1

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Exercise 22 : Virtual Endoscopy Endoscopic Movie Generation

22.2 Generating a Centerline

Additional Task

7.

Next select Generate > Generate Centerline. The module will calculate the centerline between the current Eye and Look At points. Once calculated, the Sequence Edit tool will open displaying the automatically generated key frames, the centerline will be displayed in the Show Object window (figure 4).
note If you do not have the Look At point centered exactly in the airway, you will receive an error when generating the centerline. If this happens, reposition your Look At point and try again.

8.

To generate the endoscopic movie, select Generate > Sequence > Generate Sequence. The endoscopic movie based on the centerline will be generated and saved to the Analyze workspace. Close all windows associated with the Virtual Endoscopy module before proceeding to the next Additional Task.
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Exercise 22 : Virtual Endoscopy Endoscopic Movie Generation

22.3 Adding Color to Endoscopic Movies

Additional Task

Movies generated in the Virtual Endoscopy module can be given a quick update by apply a color map using the Multiplanar Sections module. 1. 2. 3. Select the endoscopic fly-through movie from the Analyze workspace and open the Multiplanar Sections module Display > Multiplanar Sections. Open the Intensities window View > Intensities. In the Intensities window set Type to Colormap. Here you can generate your own custom color map or load an existing color map (figure 1). Load the hot_ [Link] from the C:\BIR\images\TutorialData\Colormaps directory. Once loaded, set Range to Data Type and then increase the Max value to 255. To review the movie, select the Display Sections button from the PowerBar (figure 2). To save the color intensified movie, select File > Output Intensified. The color map will be applied to a copy of the movie and saved to the Analyze workspace. Close all windows associated with the Virtual Endoscopy module before proceeding to the next exercise.
Figure 1

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Exercise 23 : Image Calculator Image Manipulation

This exercise will demonstrate how to use the Image Calculator module for rudimentary image processing and manipulation.

1. 2. 3. 4. 5. 6.

Load both the MRI_3D_Head.avw and MRI_3D_Brain_Bin.avw data sets from the $:\BIR\images\TutorialData directory. With the MRI_3D_Head data set selected in the Analyze workspace, open the Image Calculator module (Process > Image Calculator). In the Image Calculator module, the MRI_3D_Head data set icon should appear in the white space above the calculator (figure 1). Click the Multiply button [A] on the calculator. Drag-and-drop the MRI_3D_Brain_Bin data set from the Analyze workspace into the Image Calculator module (white space). This first manipulation demonstrates how to multiply a grayscale data set with a binary data set. The binary brain will act as a mask, all voxels in the grayscale data set that fall within the binary mask will be kept, while the voxels that fall outside will be removed. Click the Equals button [B] on the calculator. A dialog box will be returned stating that the action modifies the loaded volume, click Change a Copy of the Loaded Volume. The masked grayscale data will appear in the Image Calculator module; a copy will be automatically be saved to the Analyze workspace. Click the Multiply button again. Click the Matrix button [C] on the calculator. The Matrix Tool will open (figure 2); set to Rotate around the Z-axis 45 degrees and click Apply. Click Done to close the Matrix Tool. Click the Equals button on the calculator. A Transformation window will be returned; use the default settings and click Transform. The transformed data will appear in the Image Calculator module and the copy in the Analyze workspace will be updated.
note In order to be able to dragand-drop data sets from the Analyze workspace into the module, make sure that the Analyze window is not maximized to full window display.

7. 8. 9. 10. 11. 12. 13.

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Exercise 23 : Image Calculator Image Manipulation

14. 15.

Right-click on the calculator and choose Buttons; the Button Tool will open (figure 3). The Button Tool includes a Palette and Key Pad (figure 3). To add a button to the main calculator, drag-and-drop it from the Palette to the Key Pad area of the Button Tool. Click the Flip button [D] that now appears on the calculator (figure 4). In the Function Options window returned, check the Flip X option and click Apply (figure 5). View the results by clicking the Volume Tool button [E] on the calculator. A copy of the data set (as specified earlier) with the manipulations performed has automatically been saved to the Analyze workspace. Close the Image Calculator module before proceeding to the next exercise.
Figure 3

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Exercise 24 : Image Calculator SubRegion Data

The Image Calculator module performs mathematical operations on volumes, matrices and constant numerical values. The module also contains a number of processing functions including: subregioning (crop), flipping, resizing, shifting etc. This exercise will demonstrate how to use some of these additional processing tools to manipulate your data. 1. 2. 3. 4. 5. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Image Calculator module (Process > Image Calculator). In the Image Calculator module, right click on the white space and select Buttons from the menu options (figure 1). In the Button Tool, select the Region Pad button [A] from the palette on the left, and drag and drop it onto the Key Pad [B] on the right. After the Region Pad button has been moved to the Key Pad, hit Apply. The main Image Calculator key pad will be updated with the additional button option. Close the Button Tool. Now drag and drop your data set from the Analyze workspace onto the Image Calculator process canvas, (the white space. This will load the data set into the module and the volume will appear on the canvas. Hit the Region Pad button [C], the Region Pad buttons Function Option window will be returned (figure 4). In this window you can subregion the data by entering Low and High values for the X, Y and Z options. X Low - Specifies the first column of pixels from each slice to be loaded. X High - Specifies the column end point Y Low - Specifies the first row of pixels from each image to be loaded Y High - Specifies the row end point Z Low - Specifies the first slice from the selected volume to be loaded Z High - Specifies the slice endpoint
Figure 1

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Exercise 24 : Image Calculator - SubRegion Data

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Click on the Interactive button in the Subregion window. Example 1: Subregioning 50 slices in the X. i. ii. Set the X Low value to 25 Set the X High value to 151

Figure 5

Example 2: Subregioning 50 slices in the Y. i. ii. Set the Y Low value to 25 Set the Y High value to 211

Figure 6

Example 3: Subregioning 50 slices in the Z i. ii. Set the Z Low value to 25 Set the Z High value to 162

Figure 7 Analyze 10.0 Essential Training Guide 75

Exercise 24 : Image Calculator - SubRegion Data

10.

Now use the interactive tool to subregion. Use the tool to trace a bounding box around the area you wish to subregion. To define the box, simply click and drag the box on the image display [A]. You can review and adjust the box in all three orthogonal orientations, by using the T, C, or S cube icons to change orientations. You can review your subregion on all slices prior to applying the subregion, use the slice slider bar to navigate through the volume [B]. A subregion defined in the Interactive tool automatically updates in the X,Y and Z high/low values in the Region Pad Function Option window. To apply a subregion to a data set, hit Apply in the Region Pad Function Option window. When you Apply a subregion you will be asked if you would like to apply the changes to the Loaded or if you would like to Change a Copy of the Loaded Volume. Select Change a Copy of the Loaded Volume. The changes made to the copy of the data set will automatically be saved to the Analyze workspace. Close all windows associated with Image Calculator before proceeding to the next exercise.

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Exercise 25 : Image Algebra Formula for Image Manipulation

The Image Algebra module provides an algebraic formula parser, allowing both simple and complex algebraic operations (containing up to 1000 variables and 1000 constants) to be performed on image data. This exercise will demonstrate the use of common algebraic processing and other manipulations with the Image Algebra module. 1. 2. Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData directory. Deselect the Cubic_CT_Head data set in the Analyze workspace, and then open the Image Algebra module (Process > Image Algebra).
note The Image Algebra module remembers parameters from previous Image Algebra sessions. If the module detects parameters from a past session, it will prompt the user to remember or forget these settings.

Thresholding Data 3. 4. 5. 6. 7. 8. You may remember from previous exercises (Volume Render 12 and 13), that the Cubic_CT_Head data set can be thresholded to 145 to show bone. [A] Enter the formula: Output = (a > 145) * a. Press <Enter> (figure 1) [B] Drag-and-drop the Cubic_CT_Head data set from the Analyze workspace into the Image Algebra module under variable a. Click the Output button [C]; in the Parameters window returned, set Name to Bone. Click Done to dismiss the window. Click Go [D] in the main Image Algebra window to begin processing. Once processing is complete, right-click on the Output icon and select Display to examine the data with all voxels less than 145 removed (figure 2). Close the Display tool once the data has been reviewed.
Figure 1

Manipulating Data 9. In the Image Algebra module edit the formula: Output = (a < 145) * a. Press <Enter>. All voxels greater than 145 will now be removed from the data set.

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Exercise 25 : Image Algebra Formula for Image Manipulation

10. 11. 12. 13. 14. 15.

Click the a button to view the parameters for variable a (figure 3). Click Done to dismiss the Parameters window. Click the Output button and change Name to NoBone. Click Done to dismiss the window. Click Go in the main Image Algebra window to begin processing. Once processing is complete, right-click on the Output icon and select Display to examine the data with bone removed. Now, try adding the bone back in with the new formula: Output = (b >= 1) * b + (b < 1) * a. Press <Enter> (figure 4). Since we have reused the a variable, the Image Algebra module will remember the data associated with it from the previous example. However, this is the first time the b variable has been specified, so drag-and-drop NoBone (from Output or the Analyze workspace) to the area under variable b. Click the Output button and change Name to BoneAdded. Click Done to dismiss the window. Click Go to process the new formula (figure 4). Once processing is complete, right-click on the Output icon and select Display to examine the data with the bone added back. Right-click in the formula field and explore some of the example formulas provided. Close the Image Algebra module before proceeding to the next exercise.

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Exercise 26 : Histogram Operations Histogram Normalization

The Histogram Operations module provides the ability to do histogram processing, such as histogram matching, flattening, and equalization (normalization). The goal of this exercise is to demonstrate how to normalize the histograms of SPECT images taken under different conditions. 1. 2. 3. 4. Load both the SISCOM_Ictal_SPECT.avw and SISCOM_Interictal_SPECT.avw data sets from the $:\BIR\images\TutorialData directory. With only the SISCOM_Ictal_SPECT data set selected in the Analyze workspace, open the Histogram Operations module (Process > Histogram Ops). Open the Function window (Generate > Function). In the Function window select Histogram Normalize and set the following parameters (figure 1): Use Histogram: Median Target Value: 150 Image Display: Original and Filtered Histogram Display: On Click Filter. An Input and Output Histogram will automatically be returned. The filtered result will be displayed in the main Histogram Operations window. In the Function window change Action to Memory and click Filter again. A dialog box will be returned stating that the action modifies the loaded volume, click Change a Copy of the Loaded Volume. Drag-and-drop the SISCOM_Interictal_SPECT data set from the Analyze workspace into the main Histogram Operations window. Press the Filter PowerBar button. In the dialog box returned, click Change a Copy of the Loaded Volume. The two new volumes you have created have been normalized to the same value, so equivalent numbers in the images now indicate levels of metabolic activity (figure 2). Additionally, both normalized volumes have automatically been saved to the Analyze workspace. Close the Histogram Operations module before proceeding to the next exercise.
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Exercise 27 : Spatial Filters

The Spatial Filters module enables the application of two-dimensional and three-dimensional filters to image data. This exercise will demonstrate how to apply a filter in the Spatial Filters module to your data. 1. 2. 3. 4. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Spatial Filters module (Process > Spatial Filters). Open the Preview Options window (Generate > Preview Options). Select the Loaded and Preview Volumes option (figure 1). This will preview the original data set and a copy of the data set with any filter applied, side-by-side. Open the Filters window (Generate > Filters). In the Filters window, select the Low Pass filter by clicking the radio button next to the option (figure 2). Now, click Preview [A]. The original data set and the filtered data set will be displayed side-by-side in the main Spatial Filters window (figure 3), the filtered data set appears on the right. Preview several other filters, noting the effect of each. To apply a filter to the data set, click Filter [B] in the Filters window. A dialog box will be returned stating that the action modifies the loaded volume, click Change a Copy of the Loaded Volume. A filtered copy of your volume will be saved to the Analyze workspace. Close the Spatial Filters module before proceeding to the next exercise.
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Exercise 28 : Image Edit Manual Segmentation of Grayscale Data

The Image Edit module provides a number of manual segmentation tools. This exercise will demonstrate how to segment grayscale data using the auto trace tool. For a full overview of all the segmentation tools in the module, please review the Image Edit tutorial available from the Help menu in the Analyze window. 1. 2. 3. 4. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Image Edit module (Segment > Image Edit). Open the Slice window (Generate > Slice), and use the slider bar to move to Slice 122. In the main Image Edit window, select the Auto Trace tool [A]. Position the cursor near the center of the brain and click to set a seed point. The Image Edit window will automatically update to display Auto Trace parameters (figure 1). Use the double-ended slider bar at the bottom of the window [B] to adjust the threshold range until a reasonable trace of the brain is obtained. A threshold minimum of 34 and maximum of 129 works well for this data set. Select the Delayed Flood Fill tool and place a fill point outside the auto-traced region (click on the background). Select the Auto Trace tool again and click Apply & Advance [C]. A dialog box will be returned stating that note An edited version of the data set will the action modifies the loaded volume, be automatically saved to the Analyze click Change a Copy of the Loaded workspace. Volume. The area outside the trace will be highlighted in red, and then the next slice will appear in the image display (the slice number can be seen in the lower left corner of the image display [D]). Review the edited slice by opening the Edit Review Tool (Tools > Edit Review) (figure 2). In the main Image Edit window, you will notice that when the module advanced to slice 123 (step 8) the seed point and auto trace parameters set in step 5 were copied forward. The trace should have automatically adjusted to the brain on this slice. If not, the seed point may have been copied forward to an area outside the brain or to a voxel with a different grayscale value. Use the Move button and adjust the seed point.

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Exercise 28 : Image Edit Manual Segmentation of Grayscale Data

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If the trace needs no further adjustment and the Delayed Flood Fill point is still positioned outside the trace, click Apply & Advance and edit 19 more slices, finishing on slice 142. In the Edit Review tool, change the orientation to Coronal and then Sagittal, note the slice edits in these orientations (figure 3). To create a rendering of the edited data complete the Additional Task.

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28.1 Rendering Segmented Data

Additional Task

1. 2. 3. 4. 5. 6.

Continue to segment the data set until approximately slice 181 to remove the entire top of the head. Close the Image Edit module. Select the MRI_3D_Head0 data set in the Analyze workspace and then open the Volume Render module (Display > Volume Render). Open the Thresholds window (Display > Thresholds). Set the Minimum threshold level to 50, then click Render. The rendering will be displayed in the main Volume Render window (figure 4). Close the Volume Render module before proceeding to the next exercise.

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Exercise 29 : Image Edit Manual Segmentation and Object Map Creation

As discussed in Exercise 13: Volume Render Advanced Controls, object maps are special image files that are used in Analyze to partition and identify structures as belonging to a particular segmented object. This exercise will demonstrate how to create an object map containing manually segmented objects. 1. 2. 3. 4. 5. 6. 7. 8. 9. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Image Edit module (Segment > Image Edit). Choose File > Create Object Map. The Objects window (View > Objects) will automatically be returned (figure 1). Click Add Object [A] to create a new empty object (Object_2). Change Name from Object_2 to Brain [B]. Click Done to dismiss the Objects window. Open the Slice window (Generate > Slice), and use the slider bar to move to Slice 122. At the bottom of the main Image Edit window, set Change to Object Map and choose Brain from the Defined Object drop-down menu [C]. Select the Auto Trace tool, the Image Edit window will automatically update to display Auto Trace parameters (figure 2). Position the cursor near the center of the brain and click to set a seed point. Use the double-ended slider bar [D] at the bottom of the window to adjust the threshold range until a reasonable trace of the brain is obtained. A threshold minimum of 34 and maximum of 129 works well for this data set. Select the Delayed Flood Fill tool and place a fill point inside the auto-traced region (click inside the region). Select the Auto Trace tool again. Click Apply & Advance. The next slice will appear in the image display (the slice number is displayed in the lower left corner [E]).
note If you did not set the Change option to Object Map (step 7) the defined region will appear black in the Edit Review tool.
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Exercise 29 : Image Edit Manual Segmentation and Object Map Creation

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View the edited object map by opening the Edit Review Tool (Tools > Edit Review). Select the Previous option in the Edit Review tool. The change can also be viewed by selecting the Sagittal option. With the Auto Trace tool selected, continue to segment slices by clicking Apply & Advance in the main Image Edit window. Segment the brain on 20 slices (to slice 142).
tip If the auto trace does not apply to a slice, or leaks to unwanted structures, try the following: 1) adjust the threshold range, 2) draw a limit after selecting the Add Limit button, or 3) turn on the Auto Limit option and adjust the Gap Size. Additionally, the auto trace can be adjusted on a slice by moving the seed point with the Move button selected.

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To save the created object map for use in other Analyze modules, choose File > Save Object Map. Save the object map as xxx_mybrain.obj (where xxx are your initials).

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29.1 Viewing the Object Map in Volume Render

Additional Task

1. 2. 3. 4. 5.

In the Analyze workspace, select the MRI_3D_Head data set and open the Volume Render module (Display > Volume Render). Choose File > Load Object Map and load the xxx_mybrain.obj object map (saved earlier in step 16). Open the Objects window (View > Objects). Set Control by to Attribute and set the Display attribute to Off for the Original object. Click Render. You should see a rendering of the object you created in the Image Edit module. Use the Rotation window (Generate > Rotation) to generate different views of the object (figure 2).

Figure 1 Analyze 10.0 Essential Training Guide 85

Exercise 30 : Morphology Morphological-Based Segmentation

The Morphology module applies 1-D, 2-D, or 3-D mathematical morphological transformations and object topology operations to a data set. This exercise will demonstrate the morphological segmentation tools available in the module by showing how to segment the brain from an MRI data set. 1. 2. 3. 4. 5. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Morphology module (Segment > Morphology). From the Generate menu, open the Slice tool. Move the slice slider to slice 130. Open the Step Editor window (Generate > Step Editor) (figure 1). Click the Threshold button [A]. In the Step 1: Threshold window returned, set the Threshold Min to 65. Click Threshold Volume. In the window returned, select Change a Copy of the Loaded Volume. Select Generate > Display Section(s) > Current to review that data. Select File > Save Volume. Save the volume as MRI_3D_Head_bin. Click the Erode button [B]. In the Step 2: Erode window, change the Element Depth to 3 and change the value Iterations to 2. Click Erode Volume (figure 2). In the Step Editor window, click Transform Volume. A dialogue box will be returned, select Yes. Click Connect [C]. Change Max. No. of Components to 1. Click Connect Volume. In the Step Editor window, click Conditional Dilate [D]. In the Conditional window, change Element Depth to 3 and change Iteration to 1. Next load the conditional volume by clicking the Volume button. Use the window returned to select the MRI_3D_ Head_bin.avw data set saved in step 7. Press the Cond. Dilate Volume button. To view your segmentation, select Generate > Display Section(s) > Current (figure 3). The binary segmentation is available in the Analyze workspace. To obtain a suitable volume for further analysis multiply the binary volume by the input grayscale volume using the Image Calculator or Image Algebra modules. When you are finished reviewing, close all windows related to the Morphology module before proceeding to the next module.
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note Notice the left side of the Step Editor window; as operations are selected from below the Morph Operations, the sequence of steps is maintained on the left.

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Exercise 31 : Watershed Automated Segmentation

The goal of this exercise is to demonstrate how to automatically strip the skull from in a T1- or T2-weighted MRI scan.

1. 2. 3.

Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Watershed module (Segment > Watershed). The Watershed module default parameters usually allow for a successful segmentation of the brain. Check the Always Display option and view the red pixels that define the Pre-Fill level on different slices and orientations. Do not change the Pre-Fill Value (49). Click Watershed Segment Volume to initialize the automatic segmentation. After the automatic segmentation process has completed, the Results tab is automatically selected (figure 1). Each segmented object will appear as a different random color in the image display. With the Render Selected Object option selected, click on the object that represents the brain in the image display. The Render Tool will automatically be returned (figure 2), allowing you to review the segmented objects from difference orthogonal orientations. You can also click and drag the rendering to a new view in the Render Tool image display. Select the Create Masked Volume from Selected Object option from the Results tab. Then, click again on the object that represents the brain. The Compare window that appears allows you to review the original and segmented volume side-by-side, slice-by-slice in different orthogonal views. The File menu provides options to save the segmented object, the masked volume, and an object map of the segmented object. Choose File > Save Masked Volume. In the window returned, set Destination to Analyze Workspace and then click Save Volume. The object clicked on in step 8 after selecting Create Masked Volume from Selected Object will be saved to the Analyze workspace. Click Done to dismiss the Save Masked Volume window. Close all windows before proceeding to the next exercise.
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Exercise 32 : Multispectral Classification

The goal of this exercise is to demonstrate the use of the Scattergram tool in the Multispectral Classification module to illustrate the various supervised classifiers in the multispectral measurement space. 1. Load the MRI_multi.avw data set from the $:\BIR\images\ TutorialData\MultiSpectralTutorial directory. This file contains a spatially co-registered MRI T1 and T2 volume of the same patient.
note If you use the Load As module to load the data set into Analyze, select Single Multivolume when prompted.

2. 3. 4.

Open the Multispectral Classification module (Segment > Multispectral Classification). Open the Scattergram window (Samples > Scattergrams). In the Scattergram window (figure 1), move the Slice slider bar [A] to slice 14. The T1 and T2 sections are displayed side-by-side along with the scattergram of the pixels. To increase the image display size, change Single to Double in the drop-down menu [B] next to the Slice slider bar. Select the Closed Trace tool and define a small region of white matter (central brain tissue) as class 1 by drawing on the image display. The paired values found in this region are colored red in the scattergram display and on the image displayed in the main Multispectral Classification window (figure 2). Select the Curved Line tool and define a small region of grey matter (peripheral brain tissue) as class 2. Make sure to choose class 2 from the Classes drop-down menu [C] before starting the trace. The paired values will show as green in the scattergram and in the image display.
tip To move a defined region hold <Shift> then click and drag the region to the desired location.
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Exercise 32 : Multispectral Classification

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Select the Closed Trace tool and define a small region of cerebrospinal fluid (in the central ventricles) as class 3. Click Classify Images. The Gaussian Scattergram Classifier window will automatically be returned (figure 3), click Classify. Click Done to dismiss the window. Choose Scattergram & Classified from the drop-down menu below the far right pane of the Scattergram window to view the Gaussian class boundaries derived from the samples (figure 4). By selecting classifiers other than Gaussian Cluster in the Scattergram window before clicking Classify Images, other supervised classifiers can be demonstrated on the same samples. Close the Multispectral Classification module before proceeding to the next exercise.
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Exercise 33 : Object Extractor Automated Brain Segmentation

The Object Extractor module applies thresholding, morphology erosion and dilation, and region growing steps in an attempt to automatically segment an object within a volume. This exercise will demonstrate how to use this module. 1. 2. 3. 4. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Object Extractor module (Segment > Object Extractor). Open the Define Region window (Generate > Define Region) to begin the segmentation process. To define an auto trace on any slice of the volume, first specify a starting slice using the Slice slider bar. Slice 141 is an excellent starting point for this data set. Note that the orientation can be changed using the Extract Options directly below the slider bar. In order to define a threshold range for the auto trace, a seed point must be set. Position the cursor near the center of the brain and click to set a seed point. The Define Region window will automatically update (figure 1) to display auto trace parameters. Use the double-ended slider bar [A] now note Click the Clear Regs button [B] at available to set the Threshold Minimum to 49 and the any time to remove all traces and Maximum to 140. Click Extract Object to start the object extraction process. The grayscale copy of the extracted object will automatically be saved to the Analyze workspace.

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limit ranges. A new starting slice may also be defined if required by clicking the Target Slice button [C].

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Once the process is complete, a rendering of the extracted object will be displayed in the main Object Extractor window. The Render Tool will also automatically be returned, allowing you to view the object from different orientations (figure 2). The resulting extraction can be further examined in the Compare window (Generate > Compare). The Compare window will allow the user to compare the original and segmented volume slice-by-slice. If the extraction is not satisfactory, the data may be re-segmented by clearing the regions in the Define Region window (Generate > Define Region) and selecting a new seed point and threshold range. Close the Object Extractor module before proceeding to the Additional Tasks.
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Exercise 33 : Object Extractor Automated Brain Segmentation

33.1 Extract Options - Creating an Object Map

Additional Task

As introduced in earlier exercises, an object map is a special image file used by Analyze to partition and identify structures as belonging to a particular segmented object. Voxels in the image volume correspond directly, on a one-to-one basis, with a voxel in the object map, whose value assigns the voxel to a particular segmented object. Since object map files can also be loaded into other Analyze modules, the same objects within an image volume can be referenced for a variety of purposes (see Exercise 47: Region of Interest Measuring Objects in Object Maps). This exercise will demonstrate how to create an object map in Object Extractor. 1. 2. 3. 4. Select the MRI_3D_Head.avw data set loaded in the Analyze workspace and open the Object Extractor module (Segment > Object Extractor). Open the Define Region window (Generate > Define Region) and set the Target Slice to 141. Click inside the brain to set a seed point. Set the Threshold Minimum to 49 and the Maximum to 140. Click Extract Options and set the Result to Object (figure 1). A dialog box will be returned asking if you would like to create an object map, click Yes (figure 2). Click Done to dismiss the Extract Options window. In the Define Region window, click Extract Object to start the object extraction process. Once the extraction process is complete the object will be displayed overlaid on the original image data in the main Object Extractor window (figure 3). The Render Tool will also automatically be returned, allowing you to view the object from different orientations. The object map will not be automatically saved, if you wish to save the object map choose File > Save Object Map. Close the Object Extractor module. To learn how to create a binary object with the Object Extractor proceed to the next Additional Task.
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Exercise 33 : Object Extractor Automated Brain Segmentation

33.2 Extract Options - Creating a Binary Object

Additional Task

Occasionally it is necessary to save the segmented object as a binary object, as opposed to a grayscale object like in the first part of this exercise. This additional task will demonstrate how to achieve this. 1. 2. 3. 4. 5. 6. Select the MRI_3D_Head.avw data set in the Analyze workspace and then open the Object Extractor module (Segment > Object Extractor). Open the Define Region window (Generate > Define Region) and set the Target Slice to 141. Click inside the brain to set a seed point. Set the Threshold Minimum to 49 and the Maximum to 140. Click Extract Options and set the Result to Binary (figure 1). Click Done to dismiss the Extract Options window. In the Define Region window, click Extract Object to start the object extraction process. Once the process is complete, a rendering of the extracted object will be displayed in the main Object Extractor window. The Render Tool will automatically be returned again, allowing you to view the object from different orientations. The segmented binary brain will be automatically saved to the Analyze workspace and can now be used with any other Analyze module. Close the Object Extractor module before proceeding to the next Additional Task.
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Exercise 33 : Object Extractor Automated Brain Segmentation

33.3 Extract Options - Automatic Brain Stem Removal

Additional Task

The Object Extractor module now provides the option to automatically remove the brain stem from your segmented brain. This task will demonstrate how to segment and remove the brain stem. 1. 2. 3. 4. 5. 6. Select the MRI_3D_Head.avw data set in the Analyze workspace and then open the Object Extractor module (Segment > Object Extractor). Open the Define Region window (Generate > Define Region) and set the Target Slice to 141. Click inside the brain to set a seed point. Set the Threshold Minimum to 49 and the Maximum to 140. Click Extract Options and set the Remove Stem option to On (figure 1). Click Done to dismiss the Extract Options window. In the Define Region window, click Extract Object to start the object extraction process. Once the process is complete, a rendering of the extracted brain with the brain stem removed will be displayed in the main Object Extractor window. The Render Tool will also automatically be returned (figure 2), allowing you to view the object from different orientations. The segmented grayscale brain will be automatically saved to the Analyze workspace and can now be used with any other Analyze module. Close the Object Extractor module before proceeding to the next exercise.

Figure 1

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Exercise 34 : Object Extractor Extracting Multiple Objects

The Object Extractor module supports the creation of multi-object object maps. This exercise will demonstrate how to achieve this.

1. 2. 3. 4.

Load the CT_Lungs.avw data set from the $:\BIR\images\TutorialData directory. Open the Object Extractor module (Segment > Object Extractor). Open the Define Region window (Generate > Define Region) to begin the segmentation process. To define an auto trace on any slice of the volume, first specify a starting slice using the Slice slider bar. Slice 104 is the default slice, and it is an good starting point for this data set. Position the cursor near the center of the left lung and click to set a seed point. The Define Region window will automatically update (figure 1) to display auto trace parameters. Use the double-ended slider bar [A] now available to set the Threshold Minimum to 18 and the Maximum to 99. Click the Extract Options button, and set the Result to Object (figure 2), select Yes in the window returned. In the Define Regions window, click Extract Object to start the object extraction process. The left lung will be extracted and saved as the object called Extracted. The object will appear red. Open the Define Regions window again, when opened click the Clear Regions button [B]. Next, click in the right lung to set a seed point, set the Threshold Minimum to 18 and the Maximum to 104. Click Extract Object again. The right lung will be extracted and saved as the object called Extracted (2), the object will appear green. In the main Object Extractor module you will see both lungs (figure 3).
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Exercise 34 : Object Extractor - Extracting Multiple Objects

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The render window will now display both lungs in 3D (figure 4). To change the name and color of each object, go to the Objects window (View > Objects). Set Control By to Attribute, and from the drop down menu select the Name and Color attribute options (figure 5). To save the object map for use in other modules, select File > Save Object Map. Close all windows related to the Object Extractor module before proceeding to the next exercise.
Figure 4

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Exercise 35 : Surface Extractor Polygonal Surface Extraction

Polygonal surface extraction is the process of converting an object in the voxel-based volume to a representation of the surface of the object, expressed as sets of vertices and polygons. This conversion must optimally extract a representative surface, with as much detail as possible, but do so with as few vertices and polygons as possible. This exercise will use the Adapt/Deform algorithm to perform such an optimal surface extraction. Often this surface extraction is a precursor to using the surface with other applications, such as CAD/CAM modeling, rapid prototyping (model building), and finite element analysis.

1. 2. 3. 4. 5.

Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Surface Extractor module (Segment > Surface Extractor). Choose File > Load Object Map and load the MRI_3D_Head.obj object map. Open the Extraction Parameters window (Generate > Extraction). Click Objects [A] at the top of the Extraction Parameters window (figure 1). In the window returned, leave the Brain set to On and set all other objects to Off. Click Done to dismiss the window. Create a polygonal surface of the Brain object using the Adapt/Deform algorithm with the default parameters. With the AdaptDeform tab selected click Extract [B]. A dialog box will be returned stating the number of polygons generated. Note the number of polygons (approximately 37,258), then click Done. To create a rendering of the surface model, choose Generate > Render. A surface map will automatically be created for the Brain surface, and the Surfaces window returned. The rendering will be displayed in the main Surface Extractor window (figure 2). In the Extraction Parameters window change the Cube Edge Size [C] to 5 and rebuild the surface by clicking Extract. Note, the number of polygons generated (approximately 12,261), then click Done. Choose Generate > Render to view the extracted surface with the new parameters (figure 3). Increasing the Cube Edge Size will smooth the surface, reducing the number of voxels considered when generating the initial surface estimate, which reduces the polygon count.
Figure 2 Figure 3

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Exercise 35 : Surface Extractor Polygonal Surface Extraction

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Click Reset [D] in the Extraction Parameters window to restore the default parameters (Cube Edge Size of 3). Click Advanced [E] and change the Time Step to 0.5. Click Done to dismiss the window. Rebuild the surface by clicking Extract in the Extraction Parameters window. Note the number of polygons generated (approximately 37,258), then click Done. Choose Generate > Render to view the extracted surface with the new parameters. Increasing the Time Step causes the surface extraction to reach equilibrium faster, producing a smoother surface without altering the polygon count. When the opposite changes are made, the surface will conform to the voxel surface better, resulting in a rougher, more voxelated surface.
note Increasing the resolution increases the processing time, this is demonstrated by setting the Cube Edge Size to 1. In cases where a high resolution (Cube Edge Size of 1) is required, use the Marching Cubes algorithm.

15.

Decreasing the Surface Force and increasing the Spring Constant (also Advanced options) smooths the surface without altering the polygonal count by forcing the polygons to bridge small variations in the voxel surface (the polygons attraction to the surface is reduced and they become harder to bend). Press the Save Surface PowerBar button or choose File > Save Surface > To File to save the extracted surface to disk. In the Save Surface window returned (figure 4) you can select from the following surface description formats in the Format drop-down menu: Alias (.obj), Autocad (.dxf), Compressed Iges (.iges), Iges (.iges), Inventor (.iv), Patran (.out), Poly (.poly), 3D Systems (.stl), Binary 3D Systems (.stl), Vrml (.wrl). Close the Surface Extractor module. To learn about extracting the surface of a binary data set, complete the following Additional Task.
Figure 4

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Exercise 35 : Surface Extractor Polygonal Surface Extraction

35.1 Extracting the Surface of a Binary Data Set

Additional Task

1. 2. 3. 4. 5. 6.

Load the MRI_3D_Brain_Bin.avw data set from the $:\BIR\images\ TutorialData directory. Open the Surface Extractor module (Segment > Surface Extractor). Open the Extraction Parameters window (Generate > Extraction). With the AdaptDeform algorithm tab selected, click Extract. Note the number of polygons generated (approximately 37,504) and choose Generate > Render to view the extracted surface (figure 1). Close the Surface Extractor module before proceeding to the next exercise.
Figure 1

Supported Surface File Formats

Polygonal Formats
Alias Wavefront Autocad IGES Compressed IGES Inventor Patran Poly Binary 3D Systems VRML (.obj) Read and Write (.dxf) Read and Write (.iges) Write only (.iges) Write only (.iv) Write only (.out) Write only (.poly) Read and Write (.stl) Raad and Write (.wrl) Write only

Contour Formats
HP 3D IGES Compressed IGES Pogo 3D Systems Stereolithography ASCII Columns
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(.hpgl) Write only (.iges) Write only (.iges) Write only (.slc) Read and Write (.slc) Read and Write (.txt) Read and Write
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Exercise 36 : Surface Extractor Contour Surface Extraction

Contour surface extraction is the process of converting an object in the voxel-based volume to a representation of the surface of the object, expressed as a series of stacked contours. This surface extraction is a precursor to other applications, such as CAD/CAM modeling, rapid prototyping (model building), and finite element analysis. This exercise demonstrates how to use the Contours algorithm. 1. 2. 3. 4. 5. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Surface Extractor module (Segment > Surface Extractor). Choose File > Load Object Map and load the MRI_3D_Head.obj object map. Open the Extraction Parameters window (Generate > Extraction). Click Objects [A] at the top of the Extraction Parameters window (figure 1). In the window returned, switch the Ventricle to On and set everything else Off. Click Done to dismiss the window. Create a contour surface of the Ventricle object using the Contours algorithm with the default parameters. Select the Contours tab and click Extract. A dialog box will be returned stating the number of slices for which contours were generated. Note the number of slices used (60), then click Done. To create a rendering of the extracted contour model, choose Generate > Render. In the Extraction Parameters window, click Advanced [B] in the Contours tab. Check the Subvolume Extraction option and click Done to dismiss the window (figure 2). Rebuild the contour surface by clicking Extract in the Extraction Parameters window. Note the number of slices used (108). This resamples and reformats the object and thus changes the number of slices. Choose Generate > Render to create a rendering of the extracted contour model (figure 3). Close the Surface Extractor module before proceeding to the next exercise.
Figure 2 Figure 3 Figure 1

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Exercise 37 : Registration 3-D Surface Registration

Surface matching is fast and robust, even in the presence of image noise and incomplete overlap of the image volumes. Both volumes must contain common objects, which must be explicitly segmented from the grayscale image data and saved as a grayscale or binary image. A surface is extracted from both a base object and a match object that are preprocessed from the base volume and match volume, respectively. This exercise will demonstrate how to achieve an optimal registration of two 3D volumes based on corresponding surfaces. 1. 2. 3. 4. Load the Edited_MRI_Head.avw and the Edited_PET_Head.avw data sets from the $:\BIR\images\TutorialData directory. Select the Edited_MRI_Head.avw data set, then while holding down the <Ctrl> key, select the Edited_PET_Head.avw data set. Open the 3-D Surface Registration module (Register > 3-D Surface). Select File > Input/Output Ports to view the import and output ports at the bottom of the main 3-D Surface Registration window. Make sure that Edited_MRI_Head is the base volume, and Edited_PET_Head is the match volume. Open the Blend window (Generate > Blend). Set the Blend Type to Green-Red. Examine the combined images to determine if they need to be registered. Select Generate > Register to register the two volumes. Select File > Save Transformed and save the transformed PET to the Analyze workspace. Close the 3-D Surface Registration module before proceeding to the next exercise.

5. 6. 7. 8. 9.

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Exercise 38 : Image Registration 3-D Registration using MRI and PET

The 3-D Voxel Registration module is an implementation of the Normalized Mutual Information algorithm and allows users to spatially register two volume images. The module contains several unique and powerful algorithms that will allow the precise alignment of 3-D data to be achieved, both quickly and efficiently. This exercise will demonstrate how to register two images of different modalities. 1. 2. Load both the MRI_Head.avw and PET_Head.avw data sets from the $:\BIR\ images\TutorialData directory. In the main Analyze workspace, first select the MRI_Head data set. Then, while holding down the <Ctrl> key, select the PET_Head data set (resulting in both being selected). Open the 3-D Voxel Registration module (Register > 3-D Voxel). Choose File > Input/Output Ports to ensure that MRI_Head is assigned as the Base Volume and PET_Head is assigned as the Match Volume.

3. 4.

Main Interface Features 5. The main interface contains nine image display panes (figure 1). First Column: Displays the Base volume (MRI_Head) Last Column: Displays the Match volume (PET_Head) pre-scaled to the size of the base volume Middle Column: Displays the base and match volumes fused together Rows: Display the volumes in the transverse, coronal, and sagittal orientations 6. By default, the volumes are displayed with cubic voxels. To turn off the cubic display press the Toggle Cubic PowerBar button. For this exercise leave cubic display on.
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Exercise 38 : Image Registration 3-D Registration using MRI and PET

7.

Open the Blend window (Generate > Blend). The Blend window provides different settings to help visually evaluate the registration. Experiment with the different blend options (figure 2) and then click Done to dismiss the window. The crosshair in each of the image display panes can be used to move through the volumes. When the crosshair is moved in any of the panes, the other panes automatically update to display the same volume coordinate. Note, the base and match coordinates are reported at the bottom of the window. Right-click on any of the image display panes to view options for controlling individual tiles, reference lines, image sizes, annotations, and interactivity.

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Registration 10. For this exercise, no parameters need to be changed for a successful registration, the default settings are appropriate. Press the Register PowerBar button or choose Generate > Register. After registration is complete you will see that the PET volume has been scaled, rotated, and translated to match exactly the sagittal MRI. To evaluate the registration, move the crosshair in any of the panes and change the Blend type to Average. To view the current transformation matrix open the Matrix Tool (Tools > Matrix). You may manually enter rotations, translations, and scaling to the matrix by selecting an option and increment (figure 3). You may also save the current matrix as an ASCII floating-point file or load a previously saved matrix. You may also use manual correction buttons in the Manual tool (Tools > Manual) to incrementally change the registration matrix. The buttons move the match volume section in the directions indicated, and then adjust the 3-D matrix depending upon the orientation selected.

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Exercise 38 : Image Registration 3-D Registration using MRI and PET

Saving Transformed and Fused

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To save a copy of the transformed match volume (PET_Head), choose File > Save Transformed; the transformed volume can be saved to disk or to the main Analyze workspace (figure 4). To save the fused volume, choose File > Save Fused; the fused volume can be saved to disk or to the main Analyze workspace. Close the 3-D Voxel Registration module before proceeding to the Additional Task.
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Exercise 38 : Image Registration 3-D Registration using MRI and PET

38.1 Manual Scale Adjustment

Additional Task

The Manual Registration tool in both the 3-D Voxel and Surface Registration modules now provides the ability for users to manually adjust the scale of the Match data prior to registration. This task will demonstrate how to access and use the new Adjust Scale tool. 1. 2. 3. Select the MRI_Head.avw data set. Then while holding down the <Ctrl> key, select the PET_Head.avw data set (resulting in both being selected). Open the 3-D Voxel Registration module (Register > 3-D Voxel). To access the Adjust Scale tool, open the Manual Registration tool from the Tools > Manual menu (figure 1). Check the Adjust Scale option, the Manual Registration tool will update with X, Y, and Z scale tools. Adjust the scale of the Match data up and down in each orientation by click on the arrow up and arrow down keys. Note the display of the Match data each time the scale is adjusted. Close all windows associated with the 3-D Voxel Registration module before proceeding to the next exercise.

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Exercise 39 : Image Registration Mutual Information Registration

This exercise will demonstrate how to adjust a 3-D registration starting position to achieve an optimal registration of two 3-D volume images.

1. 2.

Load both the Register_MRI_Base.avw and Register_MRI_Match.avw data sets from the C:\BIR\images\TutorialData directory. In the Analyze workspace, first select the Register_MRI_Base data set. Then, while holding down <Ctrl> select the Register_MRI_Match data set (resulting in both being selected). Open the 3-D Voxel Registration module (Register > 3-D Voxel). Choose File > Input/Output Ports to ensure that Register_MRI_Base is assigned as the Base Volume and Register_MRI_Match is assigned as the Match Volume. Open the Blend window (Generate > Blend). Select the Red-Green blend and then click Done. The Red-Green blend option will help evaluate the registration. Press the Register PowerBar button or choose Generate > Register. Examine the center Fused column of the main module window (figure 1). As you can see, the registration is not acceptable.

3. 4. 5. 6. 7.

Manual Adjustment 8. 9. 10. 11. Since the registration is not acceptable, manually adjust the starting point of the registration. Open the Manual tool (Tools > Manual). Click Reset Matrix in the Manual tool (figure 2), this will reset the match volume to the original starting position. Now, using the Manual tool options, move the match volume to a better starting position and press Register. If the registration is still not acceptable, return to the Manual tool and click Reset Matrix again.
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Exercise 39 : Image Registration Mutual Information Registration

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Now, select the Coarse adjustment option [A] and press the down arrow button once. Change the orientation from coronal to sagittal by selecting the S-cube [B] and then press the right arrow button once. Press Register. The volumes should now register correctly (figure 3).

Saving 15. To save the transformed match volume (Register_MRI_Match), choose File > Save Transformed; the transformed volume can be saved to disk or to the Analyze workspace. To save the fused volume, choose File > Save Fused; the fused volume can be saved to disk or to the Analyze workspace. Close the 3-D Voxel Registration module before proceeding to the next exercise.

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Exercise 40 : Line Profile Calculating Image Intensities Along a Straight Line

The Line Profile module enables calculation of image intensities along straight lines and freehand traces. Coordinate points and angle measurements can also be made. All measurements can be logged and saved to disk. 1. 2. 3. 4. 5. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Line Profile module (Measure > Line Profile). Open the Slice window (Generate > Slice) to move through the volume image. Set the Slice to 97 and click Done. To calculate the intensity values along a straight line in this slice, select the Line tool in the main Line Profile window (figure 1). Position the cursor on the image and click to begin drawing. The Sequence window (Generate > Sequence) provides X and Y coordinate slider bars for precise positioning of lines. The Profile window (figure 2) will automatically be returned when a line is drawn, displaying the intensity profile of the line. The Profile window allows profiles, statistics, distances, and FWHM (full width half max) measurements to be logged.
note To log FWHM, open the Profile Options window (Generate > Profile) and set Full Width Half Max to On.

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Click Log Profile in the Profile window. To save the Line Profile Log as a .stats file for use in another application (such as Microsoft Excel), select Save in the Log window. Select the Trace tool in the main Line Profile window to draw a freehand trace. Select the Caliper tool (figure 3), an Angle Measure window will automatically be returned. The Caliper tool provides a series of repositionable points and lines, enabling measurement of user-specified angles and distances on a selected slice. The Angle Measure window will automatically update with any repositions. Close the Line Profile module before proceeding to the Additional Task.
tip If a structure of interest is in another orientation, choose Generate > Orientation to choose between transverse, coronal, and sagittal orientations, or define your own oblique orientation.

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Exercise 40 : Line Profile - Calculating Image Intensities Along a Straight Line

40.1 Line Profile Radial Sequence Tool

Additional Task

1. 2. 3. 4. 5. 6. 7.

The Radial Sequence tool in the Line Profile module enables users to sample a radial sequence of profiles. Load the VH_Abdomen.avw data set from the $:\BIR\images\ TutorialData directory. Open the Line Profile module (Measure > Line Profile). Open the Profile Options window (Generate > Profile) and set Full Width Half Max to On. Select the Line tool and then draw a line starting in the middle of the right femur, finishing outside (figure 3). Open the Radial Sequence tool (Generate > Radial Sequence). Set the Angle Increment to 10 (figure 4). When sampling a radial sequence the angle is incremented until a full 360 degrees from the starting position has been sampled. Set Log Profile, Log Stats, and Log FWHM to On. Click Sample Radial Sequence. When the process has run, a Stats Log, Profile Log, and FWHM Log (figure 5) will be returned. To save any of the log files, right click and select Save Log. Close the Line Profile module before proceeding to the next exercise.
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Exercise 41 : Region of Interest Defining Regions

The Region of Interest module allows users to define and measure 3-D regions. This exercise will demonstrate how to use the tools in the module to define regions of interest within a volume image. 1. 2. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Region of Interest module (Measure > Region of Interest).

ROI Interface 3. When the module is opened, an object map is automatically created to store defined regions. To define a new region, make sure that the Object to Define: is set to ***New*** [A] at the bottom of the window (figure 1). The buttons along the left side of the window control the definition of regions on the images [B]. The buttons below the image display allow you to modify the defined regions [C]. The first slice of the volume is automatically displayed when the ROI module is opened. You can move to a different slice using the Show Next and Show Previous Slice PowerBar buttons or by using the Slice slider bar [D]. The currently displayed slice number and orientation can always be seen in the lower left corner of the image display [E].
tip The + and - keyboard keys can also be use to move through the data set.

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Rectangle Tool 6.

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Define a rectangular region on slice 1 using the Rectangle tool. Position the cursor on the image display, then, click and drag the cursor out to size the rectangle, when you release the mouse button the new region [Link] will be created and added to the object map (figure 2). Copy the region to the next slice (slice 2) by pressing the Copy Regions Forward PowerBar button once. Regions can be modified using the buttons found below the image display. Select the Move button. Position the cursor near the region you wish to modify, then click and drag the cursor; any movement of the cursor will move the region. Also try using the Rotate and Scale buttons (found directly to the right of the Move button).
Figure 2

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tip

Holding the <Ctrl> key while sizing will force a square.

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Exercise 41 : Region of Interest Defining Regions

Oval Tool 9. 10. 11. Add a new region to slice 2 using the Oval tool (figure 3). Press Copy Regions Forward to copy the regions to slice 3. Select the Move button again. To move all regions on a slice simultaneously, hold the <Ctrl> key while moving the regions as described in step 7. When you release the mouse button, a dialog box will be returned asking if you would like to Move Regions in: This Slice Only, the Entire Object Map, or Cancel the move, click This Slice Only. Press the Show Next Slice PowerBar button to move to slice 4.
tip
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Polygon Tool 13. Since the Show Next Slice button was pressed, and not the Copy Regions Forward button, there are currently no regions defined on slice 4. Define a region on slice 4 using the Polygon tool. To begin defining the polygonal region, position the cursor on the image display and click once to set a starting point. Move the cursor outward to specify the length and direction of the first polygon side. To set a vertex and begin drawing another side, click once. Double-click to close the polygon (figure 5). If after defining the region it is unsatisfactory, click the Undo button. Press Show Next Slice to move to slice 5.

Holding the <Ctrl> key while sizing will force a circle.

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Figure 5

Manual Trace Tool 17. Define a region on slice 5 using the Manual Trace tool. Position your cursor on the image display, then click and hold the mouse button to begin drawing the trace, release the mouse button to end the trace. The last point of the trace will be automatically connected to the first point of the trace.

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18.

If you make a mistake while tracing, continue holding the mouse button down, and press the <u> keyboard key. The trace will slowly back up from the current position until the <u> key is released. Try this by drawing a line on the image, and while continuing to hold the mouse button down, press the <u> key. Once the trace has backed up half way, release the <u> key and continue your trace in a different direction. To define a region without having to continuously hold down the mouse button, rightclick on the image display and choose the Button Passive option [F]. When Button Passive is selected, simply click on the image display to begin the trace, and then click again when you are ready to end the trace and define the region. The Button Passive option is available for all region definition tools. Right-click and deselect the Button Passive option. Then, click Clear Regions [G] on the left side of the window to clear all regions defined on this slice. With the Manual Trace tool still selected, check the Smart Edge option [H]. The Smart Edge option searches for edges (areas of high gradient) when drawing a trace with the Manual Trace or Spline tools. Click once to begin a trace along an edge in the image display, letting Smart Edge determine the path, click again to lock that portion of the trace. When the region of interest has been defined, double-click to end the trace. Uncheck the Smart Edge option. Press Show Next Slice to move to slice 6.

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Spline Tool 23. Define a new region on slice 6 using the Spline tool. The Spline tool enables the drawing of splines with moveable control points. Position the cursor on the image display and click once to begin drawing a spline, click once again to set a control point. When the region of interest has been defined, double-click to close the spline. To modify the region with the spline control points, select the Move button and then drag any control point to a new location.

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Exercise 41 : Region of Interest Defining Regions

41.1 Intersecting Regions

Additional Task

1.

When objects overlap, the resulting regions may not appear as expected. Since the object map is a one-to-one mapping of the voxels to an object, a voxel cannot be part of more than one object. The Intersections become part of: option (in the lower left hand corner) allows you to control how intersecting regions are handled. Press Show Next Slice to move to slice 7. Choose File > Reset Object Map to clear all regions from the volume. In the dialog box returned, click Continue without Saving. Ensure that Intersections become part of: is set to Defined (figure 7). Select the Rectangle tool and define a region. Now, select the Oval tool and define a region that overlaps the rectangle. The intersecting area becomes part of the region being defined, [Link] (figure 7). Click Undo button and then set Intersections become part of: to Existing. Select the Oval tool and again define a region that overlaps the rectangle. The intersecting area now becomes part of the existing region, [Link] (figure 8). Click Undo and then set Intersections become part of: to New. Select the Oval tool and again define a region that overlaps the rectangle. The intersecting area now becomes a new region, [Link] (figure 9). Close the Region of Interest module before proceeding to the next exercise.
Figure 7

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Exercise 42 : Region of Interest Defining Regions and Volume Measurements

This exercise will demonstrate how to use more advance region definition tools in the Region of Interest module to define objects of interest within a 3-D volume image. The exercise will also show you how to measure these objects. 1. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. The data set may be available in the Analyze workspace if you have completed Exercise 41: ROI Defining Regions. Open the Region of Interest module (Measure > Region of Interest). Using the slice slider below the image display, move to Slice 122. In the main ROI window, select the Auto Trace tool. Position the cursor near the center of the brain and click to set a seed point. The ROI window will automatically update once a seed point is set to display a double-ended slider bar (to specify a threshold range) and other Auto Trace parameters (figure 1). Use the double-ended slider bar to set the threshold minimum to 34 [A] and the threshold maximum to 129 [B]. Then, click Apply [C]. The double-ended slider bar will disappear and the new region will be named [Link]. Press the Copy Regions Forward PowerBar button once. The auto trace will be copied to the next slice. Notice that the auto trace is recalculated for each slice based on the set threshold range. Press Copy Regions Forward until the auto trace has been applied to all the remaining slices containing brain matter, (until approximately slice 181). Once you have copied the region forward to the remaining slices, choose Tools > Show Rendering to open the Render Tool and view a 3-D rendering of the defined object (figure 2). Click Done to dismiss the window. Open the Objects window (View > Objects). Select Object.1 from the Object drop-down menu and change Name of Object.1 to Brain. Click Done to dismiss the window.
tip
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note You can change the image display size within the Size window (View > Size) or with the Magnifier PowerBar buttons.

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If you placed your seed point towards the outside of the brain, it will eventually be copied forward to an area of a slice that does not contain the brain. Select the Move button and move the seed point to the middle of the brain, then, continue to copy the region forward. To learn more about editing regions see the Additional Task at the end of the exercise.
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Exercise 42 : Region of Interest Defining Regions and Volume Measurements

Measuring Regions

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Open the Sample Options window (Generate > Sample Options). In the Sample Options window set the following (figure 3): Sample Type: Object(s), check the Brain object Summing: On Sample: All Slices Sequence Display: Off Log Stats: On Click Configure Log Stats to open the ROI Stats window. The ROI Stats window displays all statistics that can be returned for the Stat Type selected in the Sample Options window (in this case the Intensity Stat Type). All statistics with a check mark in the Log box to the left will be reported in the ROI Stat Log when the defined object is sampled. Click Sample Images. The module will now sample the defined object (Brain). The ROI Stat Log will automatically be returned, displaying the object statistics (figure 4). Click Done; in the dialog box returned click Discard, then Exit. In the Sample Options window switch Summing to Off and Sequence Display to On. Click Sample Images to sample the object again. This time each slice will be displayed as it is sampled as Sequence Display is now set to On. Notice the difference in time taken to sample the entire volume. The object statistics for each slice will be reported in the ROI Stat Log, as Summary is set to Off. In the Sample Options window, set Sample to Slices Specified in Slice Menu. Open the Slice window (Generate > Slice) and set Slice to 122 (the first slice with the object) and Number to 59 (the number of slices after 122 on which the object appears) (figure 5).
Figure 4

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Exercise 42 : Region of Interest Defining Regions and Volume Measurements

20. 21.

Click Sample Images. Only the slices specified in the Slice window will be sampled. Experiment sampling the data with the different Stat Types available in the Sample Options window, for a full explanation of statistic types choose Help > Users Guide in the main ROI window. To learn about editing regions complete the following Additional Task.
Figure 5

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Exercise 42 : Region of Interest Defining Regions and Volume Measurements

42.1 Editing Regions

Additional Task

1.

Using the Show Next and Show Previous Slice PowerBar buttons, review the Brain object (defined previously) slice-by-slice to determine if the auto trace leaked into other structures. On slices where the auto trace leaked, select the Edit Region button and draw in the edge of the brain where the leak occurred. Areas beyond that edge will be removed from the object on that slice. Next, use the slice slider below the image and move to slice 62. Ensure that the Object to Define is set to Brain (at the bottom of the ROI window). Then, trace the brain on slices 62-121 using the Auto Trace or another region definition tool. Once you have traced the Brain object on slices 66-121, choose Tools > Show Rendering to open the Render Tool and view a 3-D rendering of the define object (figure 1). Click Done to dismiss the window. Open the Sample Options window (Generate > Sample Options) and set Summing back to On and Sample to All Slices. Click Sample Images in the main ROI window to sample the Brain object as it is defined on slices 66-181. Choose File > Save Object Map to save the object map with the Brain object. Close the Region of Interest module before proceeding to the next exercise.

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Exercise 43 : Region of Interest Measuring Objects in Object Maps

As well as allowing users to define and measure objects defined in the module the Region of Interest module also allows users to load and measure object maps created in other modules. 1. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. The data set may be available in the Analyze workspace if you have completed exercise 45 or 46. Open the Region of Interest module (Measure > Region of Interest). Choose File > Load Object Map and load the MRI_3D_Head.obj object map from the $:\BIR\images\TutorialData directory. Open the Objects window (View > Objects) and set Control to by Attribute. Notice that this object map contains several objects. With the Display attribute selected, switch the Lenticular and Caudate objects to On. Open the Slice window (Generate > Slice) and navigate through the volume, the objects with the Display attribute set to On will be seen on the images (figure 1). Open the Sample Options window (Generate > Sample Options). In the Sample Options window set the following: Sample Type: Object(s), check Brain Summing: On Sample: All Slices Sequence Display: Off Log Stats: On Click the Sample Images button to sample the Brain object. The ROI Stat Log will automatically be returned, displaying the object statistics (figure 2). Note the volume given is only for the Brain object, not the entire brain. To find the total volume of the brain you need to obtain the volume of the objects that make up the brain in this exercise this includes the Brain, Ventricle, Lenticular, and Caudate objects. Click Done to close the ROI Stat Log; in the dialog box returned click Discard, then Exit.
Figure 2 Figure 1

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Exercise 43 : Region of Interest Measuring Objects in Object Maps

12. 13. 14. 15.

In the Sample Options window, check the Ventricle, Lenticular, and Caudate objects (the Brain object should already be checked). Click Sample Images button. The individual volumes for each object will be returned to the ROI Stat Log. The sum of these volumes is the total brain volume. To have the volume of the objects added together automatically for the total volume, set Combine Objects to Yes under the selection area (figure 3). Click Sample Images. The total brain volume will now be returned to the ROI Stat Log (figure 4)

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Exercise 43 : Region of Interest Measuring Objects in Object Maps

43.1 Volume Measurement - Manual vs. Automated Segmentation

Additional Task

1. 2. 3. 4.

Select File > Load Object Map and load the object map created in Exercise 33: Object Extractor - Automated Segmentation. Follow steps 7-9 in the above exercise to calculate the volume of the Extracted Brain object. Compare the volume returned in the ROI Stat Log (figure 5) to that of the brain volume obtained in step 15. Close the Region of Interest module before proceeding to the next exercise.

Figure 5

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Exercise 44 : Region of Interest Histogram Analysis

This exercise will provide instructions on how to generate a histogram for an individual slice within a volume, an entire volume, and for a defined object.

Sampling a Single Slice 1. 2. 3. 4. 5. 6. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the Region of Interest module from the Measure menu (Measure > Region of Interest). Use the slice slider directly below the image, and move to slice 97. Open the Histograms window (Generate > Histograms). In the Histograms window, set Histogram Display to On and set Log Histogram to On. In the main ROI window click on the image. The module will sample voxel intensity vs. occurrences. The results will be displayed as a histogram and saved to a Histogram Log file. The Histogram Log file can be saved by right-clicking in it and selecting Save Log. Close all windows associated with the ROI module.

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Exercise 44 : Region of Interest - Histogram Analysis

Sampling a Volume

1. 2. 3. 4. 5.

Select the MRI_3D_Head.avw data set and open the Region of Interest module. In the Histograms window, set Histogram Display to On and set Log Histogram to On. Next open the Sample Options window (Generate > Sample Options). In the Sample Options window, set Summing to On and set Sample to All Slices (figure 4). In the main ROI window click on the image display to start the sampling process. The module will sample voxel intensity vs. occurrences for the entire volume. The results will be displayed as a histogram and saved to a Histogram Log file (figure 5). The Histogram Log file can be saved out of Analyze by right-clicking in it and selecting Save Log.
note If you want to sample all slices at the same time, but do not want to sum the information, simply set Summing to Off, intensity vs. occurrence will be reported for each individual slice in the volume. For a quicker sampling time, set Sequence Display to Off.
Figure 5

Figure 4

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Close all windows associated with the ROI module.

Sampling an Object 1. 2. 3. Select MRI_3D_Head.avw and open the Region of Interest module. Select File > Load Object Map and load MRI_3D_Head.obj from the $:\BIR\images\ TutorialData directory. Open the Histogram window (Generate > Histogram).

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Exercise 44 : Region of Interest - Histogram Analysis

4. 5.

In the Histograms window set Histogram Display to On and set Log Histogram to On. Next open the Sample Options window (Generate > Sample Options), and set the following parameters: Sample Type to Object(s) Uncheck all objects except the Brain Summing to On Sample to All Slices

6.

Click on the Sample Images button to start the sampling process. The module will sample voxel intensity vs. occurrences for the brain object. The results will be displayed as a histogram, and also saved to a Histogram Log file (figure 7). The Histogram Log file can be saved out of Analyze by right-clicking in it and selecting Save Log. Close all windows associated with the ROI module before proceeding to the next exercise.

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Exercise 45 : Importing .Stat Files to Excel

ROI Stat Log files (.stats) and Histogram Log files (.hst) can be saved out of Analyze as text files. These text files can be imported into third party statistical applications such as Excel, for further statistical analysis. This exercise will demonstrate how to load a .stats file into Excel. Note that the process for loading a .hst file is identical. 1. 2. 3. 4. 5. 6. 7. Open Excel, then select File > Open. In the Open window, select All Files (*.*) from the File Type drop menu. Navigate to and open the .stats file. The Text Import Wizard will appear. In Step 1 of 3 Under Original Data Type select Delimited and click Next at the bottom of the screen. In Step 2 of 3 of the Text Import Wizard, under the Delimiters select Space, and deselect any other options. Then click Next. Step 3 of 3, in the Data Preview section, simply click Finish at the bottom of the screen. Your stats file will now appear in an excel worksheet.

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Exercise 46 : Stereology Estimating Volume

The Stereology module estimates volume and surface area using the stereological method of point counting. The point counting method consists of overlaying the images entirely with a randomly positioned and oriented systematic array of test points and counting the number of occasions on which a point lies within the feature of interest. 1. 2. 3. Load the Canine_Chest_CT.avw data set from the $:\BIR\images\TutorialData directory. Open the Stereology module (Measure > Stereology). The intensity scaling of the images must be changed so that they are viewable. Open the Intensities window (View > Intensities) and change the Maximum to 145. Click Done to dismiss the window. Open the Grid Parameters window (Generate > Grid) to set up a sampling grid that encompasses the heart (figure 1). The heart first appears around slice 42 and remains visible until slice 94. Set the Starting Grid Slice to 42. Using Stereology, it is not necessary to sample every slice, set the Grid Slide Increment to 3 and Number of Grid Slices to 17. Click Generate Grid. Then, click Done to dismiss the Grid Parameters window.
tip The Orthogonal tool (Tools > Orthogonal) shows the grid point location in the three orthogonal orientations and is helpful on points that are on or near the edge of the heart.

tip

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Open the Size window (View > Size) to increase the size of the image display.
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In the main Stereology window, click in the image display and drag your cursor over all grid points that lie on the heart (figure 2). If points that are not on the heart are mistakenly selected, hold <Shift>, click and drag the cursor over to deselect them. When you are finished selecting points on the current slice, press the Next Slice PowerBar button to move to the next grid slice (specified earlier in the Grid Slice Increment field) and select the appropriate points. Continue in this manner until all grid slices have been examined. Open the Statistics window (Generate > Statistics) to view the estimated volume of the heart. Close the Stereology module before proceeding to the next exercise.
Figure 2

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Exercise 47 : Object Counter Counting Cells

The Object Counter module allows a user to count the number of objects that occur on each slice of a loaded data set. The goal of this exercise is to count and measure cells from light microscopy data. 1. 2. 3. Load the [Link] data set from the $:\BIR\images\TutorialData directory. Open the Object Counter module (Measure > Object Counter). Select the PreProcess tab. This tab allows for correction of intensity fall off near the edges of the image data by applying an Inhomogeneity Correction filter. Using the default settings, click Apply. Select the Connect tab. This tab (figure 1) allows for the specification of region growing parameters used to segment objects, including whether the objects should be segmented in 2D or 3D (for this exercise, we will use 2D). With 2D selected, set the following Connect tab parameters: Max. Size: 3217 Min. Size: 50 Threshold Minimum: 106 (this will allow the cells to be separated from the background)
tip The Max and Min Size parameters can be set by selecting the Interactive Size buttons next their respective text entry fields. Specify each by selecting either button and then drawing an ellipse around the largest/smallest object to be counted. Holding the <Ctrl> key while tracing forces the ellipse to be a circle.

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Click Apply. All of the objects satisfying the size and threshold criteria will be identified and outlined in red on each slice of the volume. Use the Slice slider bar to move through the slices in the data set. Return to slice 1 before proceeding to the next step. Select the Limits tab. This tab allows interactive screening of segmented objects based on position and shape characteristics. With the Position button selected, increase the Y Min to 11 using the arrow key found to the right. This will cause any objects with a Y coordinate less than 11 to be removed (objects along the bottom of the image display in the transverse orientation).
tip

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The Calibrate tab provides the ability to determine the dimensions of pixels in an image. By drawing a line over a known distance in the image, such as on a ruler or structure of known size, the correct pixel dimensions can be established and the image can be calibrated for realworld measurements. Slice thickness can also be entered for 3D data.

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Exercise 47 : Object Counter - Counting Cells

10. 11.

Reduce the X Max to 470 using the arrow key and observe the effect (seen along the right side of the image display). By default, no shape screening is performed on the objects. Select the Circularity button, and check the Restrict Circularity option. Using the slider bar set the Circularity Maximum to 1.8. Experiment with the effects of restricting Intensity, Diameter, Area, Perimeter, and Rectangularity. Select the Edit tab. This tab allows objects to be added, deleted, and modified manually. Select the Measure tab. This tab allows specification of the measurement statistics to be returned in the Object Counter Stats window. To obtain a cell count on each slice click Log Measurements (without checking any of the options). The Object Counter Stats window will be returned, displaying a cell count for each slice (figure 2). Click Done to dismiss the window. In the main Object Counter window select the Measure tab again. Check Area and then click Log Measurements. The Object Counter Stats window will be returned, displaying an object count for each slice and the average area of the objects on each slice. To view the area for each individual object, select the Detailed option at the bottom of the Object Counter Stats window. When the Detailed option is selected, click on any object in the Object Counter Stats window to highlight the object in the image display or vice versa (figure 3). Experiment with other measurements available in the Measure tab. Close the Object Counter module before proceeding to the next exercise.
tip To save the Object Counter Stats as a .stats file for use in another application (such as Microsoft Excel), right-click in the window and select Save Log.
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Exercise 48 : Tree Analysis In Depth Examination of Coronary Arteries

The Tree Analysis module allows users to take an in-depth look at tree-like structures in medical images, such as coronary arteries. Branching angles, segment lengths, and cross sectional areas can all be measured with the module. This exercise will demonstrate how to use Tree Analysis to create, review, and sample a coronary tree. Tree Generation 1. 2. 3. 4. 5. 6. 7. 8. 9. Load the Coronary_CT.avw data set from the $:\BIR\images\TutorialData directory. Open the Tree Analysis module (Measure > Tree Analysis). Open the Slice window (Generate > Slice) and set Slice to 64. Open the Generate Tree window (Generate > Generate Tree). Set the Threshold Minimum to 130 and Maximum to 255. Since the thinning algorithm used in the tree generation process is sensitive to holes within structures it is advised that the Fill Holes option always be left checked. Leave the Shortest Skeleton Branch and the Maximum/Minimum Tree Length fields as their defaults. Set the Approximate Root Location values to X: 56, Y: 69, Z: 125. Note that you can also set the Approximate Root Location by clicking in the main module window. Click Generate Tree. The Tree Plot window will automatically be returned when the extraction is complete. The Tree Plot window can be used to view the trees generated and provides a number of tools for in-depth analysis of the structures.
Figure 1

Tree Display Options 10. 11. 12. To view the trees generated in the extraction process, use the Tree drop-down menu [A] in the Tree Plot window. Select Tree 2. Select all four of the Views buttons [B] to display the left, top, right and bottom views of the tree. Check Render [C] from the Display options at the bottom of each window. A MIP rendering will be displayed behind each view of the trees. Experiment with the different Label and Display options.

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Exercise 48 : Tree Analysis in Depth Examination of Coronary Arteries

13.

Several of the Action options can also be used to manipulate the tree display. With Action set to Zoom, click the + and - buttons to increase or decrease the tree display size. To magnify a specific area in a tree, click and drag a rectangle over the area in any of the displayed views. Now, set Action to Rotate. Click in any of the views and drag the tree to a new rotation angle. To return all views to their default display, right-click on any of the views and select Reset.

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Tree Manipulation 16. A new tree can be added by clicking the New Tree button. With Action set to Add Point, construct the new tree by drawing branches over the rendering in any of the views. The Add Point action can also be used to add branches to an existing tree. An entire tree can also be deleted by selecting the Delete Tree button. Click Undo to recover deleted trees. To only delete branches from a tree, set Action to Delete Branch. Click on a branch in any one of the views to delete it, all branches below it will also be removed from the tree. Set Action to Distance to Root and check the Log option. Click on a point in the tree; the distance to the tree root from that point will be returned to a Tree Distance Log (figure 3). Select Stats at the bottom of the Tree Plot window. The Stats Option window returned allows specification of parameters used to calculate the various tree statistics (figure 4). The location where the resulting stats files are saved can also be set in this window. To calculate stats, press the Calculate Stats button. The Tree Stats window (figure 5) displays the Summary statistics for each branch of the tree. Select the Detailed option from the bottom of the window to view statistics on each of the points in the branches.
tip

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When a point is selected in the Detailed view, a BAP Plot will be returned and the points branch will be highlighted in the Tree Plot window.

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Exercise 48 : Tree Analysis in Depth Examination of Coronary Arteries

48.1 Generating a Fly-Through Movie

Additional Task

1. 2. 3.

Check Internal from the Display options in the Tree Plot window (figure 1). Set Action to Select and click on the point in the tree from which you wish to begin your fly-through movie. The Renderings window will be returned. By default, the Renderings window will display both fly-through sequence views: Away from Root on the left and Toward Root on the right (figure 2). Preview the sequence using the slider bar. To generate the fly-through movie, right-click in the Renderings window and from the Sequence sub-menu, specify the direction of movement and the viewpoint for the movie. The movie will then automatically be saved to the main Analyze workspace and can be viewed with the Movie module (Display > Movie) (figure 3). Close the Tree Analysis and Movie modules before proceeding to the next exercise.

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Exercise 49 : SISCOM
Epilepsy Seizure Focus Localization with SISCOM (Subtraction Ictal SPECT CO-registered to MRI) automates the technique for advanced imaging of epilepsy patients that was developed with Analyze at the Mayo Foundation. This method uses a combination of SPECT and MRI imaging for improved diagnosis of areas of regional activation in the brain during a seizure. The SISCOM technique requires acquisition of ictal (during the seizure) and interictal (resting, or between seizures) SPECT images and an MRI volume spanning the entire brain. This exercise will demonstrate how to use the SISCOM module within Analyze.

1. 2.

Load the data sets SISCOM_Ictal_SPECT.avw, SISCOM_Interictal_SPECT.avw, and SISCOM_MRI.avw from the $:\BIR\images\TutorialData directory. Select the data sets in the following order (hold down the <CTRL> key to select multiple data sets, or click using the middle mouse button): SISCOM_Ictal_SPECT.avw SISCOM_Interictal_SPECT.avw SISCOM_MRI.avw Note the selection order: Ictal, Interictal, MRI. If the data is not loaded in this order the SISCOM procedure will fail to run correctly. Open the SISCOM module (Apps > SISCOM). Open the Register SPECT option (Process > Register SPECT) to compute an activation map. i. ii. iii. iv. Set the Interictal SPECT minimum Cerebral Activity Threshold level to 75 [A]. Note the change in the binary image. Ensure that the Interictal Transformation Type is set to Linear [B]. Use the Activation Level slider bar to set the standard deviation to 2.0 [C]. Next, select the Register and Map button. The Register SPECT tool will automatically register, normalize, subtract, select the statistically significant voxels of activation, and output the activation map based on the parameters specified above. Note that the tool will update, displaying the Activation Map [D].
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Select Next to continue onto the next step of the SISCOM procedure, MRI brain extraction.

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Exercise 49 : SISCOM

6. 7.

The Extract MRI Brain tool allows for segmentation of the brain for SPECT-MRI registration. Right-click in the MRI data display window and select the Intensities option. In the Intensity (MRI) window returned, change the Maximum to 101 then click Done to close the Intensity Tool. Use the slider bar to adjust the minimum and maximum threshold values to obtain the best definition of the cortical boundary as possible. In this case, the threshold values do not need to be adjusted. Select Extract Brain to segment the brain. After segmentation is complete, the extracted brain is automatically displayed in the Extract MRI Brain tool. The segmentation can be reviewed using the Slice slider bar (figure 2). Select Next to continue to the next step, registration of the SPECT data sets to the MRI data sets. The Fuse SPECT & MRI tool will automatically open and immediately run the Match Surfaces process, registering the SPECT data sets to the MRI data set and displaying the Activation Map overlaid on the MRI data set. The activation map and MRI can be reviewed using the orthogonal orientation buttons and the slice slider bar (figure 3). Select Fuse Volumes. The activation map and MRI will be fused and automatically be saved to the Analyze workspace. Select Done to close the Fuse SPECT & MRI tool. Also close the Extract MRI Brain and Register SPECT tools.
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Exercise 49 : SISCOM

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Select the Compare Tool option (Process > Compare Tool). The Compare Tool provides an interface for users to display and visually inspect the accuracy of the registration and fusion of the volumes created in the SISCOM process. Use the drop down menu options under each image [A] to select the volumes to compare (figure 4). Select Done when review is complete. Select the Create Object Map option from the File menu to generate an object map based on the areas of activation. Select Output Object Map. The object map will be automatically saved to the location specified using the File option. The Render tool (figure 5) will automatically open, allowing for interactive review of the object map. Close all windows related to the SISCOM module before proceeding to the next exercise.

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Exercise 50 : Mayo 3D Brain Atlas

The Analyze Mayo 3D Brain Atlas add-on provides a unique 3D implementation of the Talairach anatomical atlas of the human brain. The Mayo 3D Brain Atlas add-on allows for 3D navigation of the atlas and interactive query and reporting of atlas-based coordinates in many common volumetric and neuroanatomical and neurofunctional frames of reference, including TT, MNI, SPM, FSL and ICBM coordinates. In addition, atlas-derived neuroanatomical regions can be output from the module and then utilized directly in many other Analyze modules. This exercise will demonstrate how to use the Mayo 3D Brain Atlas add-on. 1. 2. 3. Load the MRI_3D_Head data set from the C:\BIR\images\TutorialData directory. Select the MRI_3D_Head data set then open the Mayo 3-D Brain Atlas module (Apps > Mayo 3D Brain Atlas). The PowerBar buttons in the main Mayo 3D Brain Atlas window are set up in the sequence of operations performed. The first step to using the atlas is AC-PC based alignment of the loaded image data to the Talairach-Tournoux coordinate and proportional grid system. Open the Align AC-PC window (Tools > Align AC-PC). Use your cursor to move the AC and PC points to the appropriate location on the sagittal image. Enlarging the image may help to identify the AC and PC; right-click on the display and select Size > Double. Note that the left and right arrows and rotation buttons can be used to adjust the data set to correct for symmetry. Select the AC point and move it to the appropriate location. The magnify window will automatically display helping you to determine the precise location of the AC (figure 1). Select the PC point and move it to the appropriate location. Select Align AC-PC. The image volume will realign to the AC-PC. Select Next to open the Extract Brain Tool. A seed point and threshold range are automatically set by the Extract Brain Tool. These can be adjusted if necessary. Check the Fill Holes after Extraction option and then select Extract Brain. The extracted brain can be reviewed using the Slice slider bar (figure 2).
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Exercise 50 : Mayo 3D Brain Atlas

1.

Select Next to open the Adjust Registration tool (figure 3). If needed the atlas can be adjusted. Right-click in any of the orthogonal display panes and select Restrict > None. Note the right-click menu also provides options to display the loaded or extracted volume and increase the display size. The grid can now be manipulated. Move the grid lines in any of the orthogonal displays to adjust the atlas. When you are finished making adjustments, right-click in any of the orthogonal displays and set Restrict back to All. Move the yellow square marker in any of the orthogonal displays to move through the loaded volume. Note that when the marker is moved the name of the atlas region and the coordinates of the current marker point will appear in the lower left-hand corner of the window. To query specific structures by coordinates, navigate back to the main module window and select the Query Atlas button from the PowerBar. The Adjust Registration window and the Query Atlas window work together. The Query Atlas window will return the atlas structure and coordinates for the current location set in the Adjust Registration window. In the Adjust Registration window, move the Yellow marker to a location you wish to query. In the Query Atlas window click the Query button, the structure and location of the Yellow marker will be returned. Check the Query Range option and set the Range to 5. Click the Query button again. All structures with in a 5 voxel range will be reported in the query window (figure 4). Please note: The information returned can be saved as a text file by right-clicking in the Query window and selecting the Save As option. Close the Query Atlas and Adjust Registration windows. To save the atlas as an object map open the Generate Output window by clicking on the Output button in the PowerBar.

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Exercise 50 : Mayo 3D Brain Atlas

1.

In the Generate Output window returned (figure 5), make sure the following options are set: i. Set Output What to Specified Atlas ii. Set Space to Original Volume iii. Set Which Atlas to Transverse iv. Set Output As to Object Map

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Next change Object(s) to Specified and then click on the List button. The Object List window returned allows you to select only the objects you wish to output to the object map, click Done to close the window and then set Object(s) back to All. Select Generate Output. The object map will be saved as AtlasOutput_MRI_3D_ [Link] in the specified directory. Select Done in the Generate Output window and close the Mayo 3D Brain Atlas. To review the Atlas object map created, select the MRI_3D_Head data set from the Analyze workplace and then open the Multiplanar sections module. Select File > Load Object Map and load the object map saved in step 23. Select the Traffic Signal icon to begin the sequence display of the data. Close all windows before proceeding to the next exercise.

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Exercise 51 : T2 Projection
The MRI T2 Optimization Add-On provides the ability to enhance the relative contrast between different tissue types in T2 weighted MR images postacquistion. The add-on uses a piecewise non-linear intensity transformation based on priori knowledge. The prior knowledge is derived from training multiple post-processed data sets acquired at different relaxation (TR) and echo (TE) times. The transformation does not make any assumption on the pulse sequence parameters associated with the image to be projected. This exercise will demonstrate how to use the add-on to enhance a T2 MRI data set. 1. 2. 3. 4. 5. Load the MRI_T2.avw data set from the $:\BIR\images\TutorialData directory. Open the T2 Projection add-on (Apps > T2 Projection) The input, or pre-enhanced, T2 data is displayed on the left side of the window, the post enhanced data is displayed on the right side Click Show Forward, until Slice 15 is displayed. The Relaxation Time (TR) can be adjusted by selecting a value from the TR (msec) drop-down menu. Select 1800. Note that the post-enhanced display updates when a new value is selected. Similarly, the Echo Time (TE) can be adjusted by selecting a value from the TE (msec) drop-down menu. Select 110. To save post-enhanced T2 select the Create Projection button. The projection will be saved to the Analyze workspace. Note the enhanced images are named according to the TR and TE values used. For example MRI_T2_1800-110. Close all windows associated with the T2 Projection module before proceeding to the next exercise.
Figure 1

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Exercise 52 : Volume Metrics

The Volume Metrics Add-On provides tools to assess the quality of multiple associated volumes, allowing the creation of a set of statistics based on the type of metric chosen. The add-on can be used to assess the similarity of two co-registered three dimensional volumes using 15 parametric or 12 non-parametric similarity indices. The add-on can also be used to assess the concordance of different segmentation results with ground truth data using 47 popular binary similarity metrics. This exercise will demonstrate how to compute similarity metric values for two related data sets. Calculating and Logging Metrics 1. 2. 3. Load the MRI_3D_Head.avw and the MRI_3D_Brain.avw data sets from the $:\BIR\images\TutorialData directory. With both volumes selected, open the Volume Metrics module (Apps > Volume Metrics). To calculate all of the statistics for a specific metric option, select the Metric Type [A], then click the Calculate Metrics button [B]. The metrics are calculated and displayed next to each Similarity Value [C]. To log the metrics in a log file, click on the Log Metrics button. The Volume Metrics Log (figure 2) contains all of the metrics that are checked in the main window. To save the metrics log file to disk, right click in the log window and select Save Log. Click Done to close the log screen. Close all of the windows associated with Volume Metrics before proceeding to the next exercise.

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note Volume 1 is the input volume, while Volume 2 is the comparison volume.
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Exercise 53 : ITK Filters

The ITK Filters module enables the application of ITK smoothing, edge-detection, and feature-extraction filters to image data. This exercise will demonstrate how to apply a filter in the ITK Filters module to your data. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the ITK Filters module (ITK > Filter). Open the Preview Options window (Generate > Preview Options). Select the Loaded and Preview Volumes option. This will preview the original data set and a copy of the data set with any filter applied, side-by-side. Open the Filters window (Generate > Filters). In the Filters window, select the Bilateral filter (figure 1). Use the Slice slider bar to determine which slice you would like to preview the filter on; set to Slice 128. Now, click Preview. The main module window will display the filtered slice on the left and original slice on the right (figure 2) Preview several other filters, noting the effect of each. To apply a filter to the data set, simply click Filter in the Filters window. A dialog box will be returned stating that the action modifies the loaded volume, click Change a Copy of the Loaded Volume. A filtered copy of your volume will be saved to the Analyze workspace. Close the ITK Filters module before proceeding to the next exercise.
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Exercise 54 : ITK Segment 2-D

The ITK Segment 2-D module provides an interactive framework for applying sequential processing steps using ITK functions for segmentation of sets of 2-D slices based on region growing and level set methods. This exercise will demonstrate how to use the ITK Segment 2-D module. 1. 2. 3. 4. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the ITK Segment 2-D module (ITK > Segment 2-D). Use the Slice slider bar to move to slice 133, make sure that the image is displayed in the transverse orientation (select the T cube). The SubRegion tab allows the user to limit segmentation to a specific region, helping decrease processing time. Check the Use SubRegion option and set the following values (figure 1): X: 63 and 120 Y: 78 and 152 Z: 1 and 187 Select the Smooth tab. This tab provides several different methods for reducing noise on images. Select the Gradient Anisotropic Diffusion type and click the Default button. Select the Edge tab. This tab provides methods for generating gradient images required for some seed- and mask-based segmentation algorithms. Select the Gradient Magnitude edge type. Select the Seed Based tab. This tab provides different methods for performing seedbased segmentation on the current volume. Select the Fast Marching type. Click once inside of the left ventricle to set a seed point. The right side will no longer be selected, set a second seed point by clicking once inside of the right ventricle (figure 2). Seed points can be reset by right clicking on the image display and selecting Reset Seed(s). Select the Mask Based tab. This tab provides options to enhance features found in the Seed Based tab. Select the Shape Detection type and set the Alpha value to -2.1.
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Exercise 54 : ITK Segment 2-D

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At this point, we have exhausted our enhanced ITK functionality, but there are still some built in post-processing steps that can be performed. Select the Morph tab. This tab allows a number of post-processing steps, for example filling of small holes that still appear in the segmentation. Select the 4-connected Fill Holes option. Select the Output tab. This tab provides a number of output parameters. Change the output type to Binary. If you wish to save this slice, click Save Slice (figure 3). The Process Volume button does apply all steps to the entire volume, but a more successful 3-D segmentation can be performed in the ITK Segment 3-D module (exercise 41). Close the ITK Segment 2-D module before proceeding to the next exercise.

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Exercise 55 : ITK Segment 3-D

The ITK Segment 3-D module provides a framework for 3-D segmentation using ITK algorithms. This exercise will demonstrate how to use the ITK Segment 3-D module. 1. 2. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory. Open the ITK Segment 3-D module (ITK > Segment 3-D).
tip The module displays the data set in all three orthogonal orientations. To update the display click on one of the display panes and move the cursorthe other two orientations will interactively update.

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Select the SubRegion tab (figure 1). Check the Use SubRegion option and set the following values: X: 51 and 127 Y: 36 and 162 Z: 86 and 144 The subregion can also be specified interactively in the image display with the mouse when the Adjust Subregion button (found directly below the image display) is selected. Click Extract SubRegion. Select the Smooth tab. Select the Gradient Anisotropic Diffusion type, and change the Time Step value to 0.0625. Click Smooth Volume. Select the Edge tab. Select the Gradient Magnitude edge type and then click Detect Edge. Select the Seed Based tab and select the Fast Marching algorithm type. Select the New Seed button (directly below the image display), and click to set a seed point in each ventricle. Click Seed Segment to apply the seed-based segmentation.
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You can review the results of the segmentation with the Render Tool (Tools > Render). Click and drag the rendering to rotate it, or click the direction buttons to quickly change views (figure 2). You can leave this tool open, it will update as we modify our segmentation. Select the Mask Based tab. Select the Shape Detection type and set the following and then click Mask Segment. Select the Morph tab and choose the Dilate option and the 3-pass 2D Fill Holes option. Click Apply Morphology. Select the Output tab for options to output the segmentation results. Choose the Binary option and click Output Volume to create a binary mask of our segmented volume in the Analyze workspace (figure 3). Also try selecting the Masked Grayscale option, and use the Output Volume button to output the resulting volume in the Analyze workspace. Close the ITK Segment 3-D module before proceeding to the next exercise.

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Exercise 56 : ITK Registration

The ITK Registration module functions the same as the Analyze 3-D Registration modules with the exception of ITK function specific parameters. The exercise will provide an overview of the module. 1. 2. Load the Register_MRI_Base.avw data set from the $:\BIR\images\ TutorialData directory. Next open the Load As module (File > Load As). Navigate to and select the Register_MRI_Match.avw data set from the $:\BIR\images\TutorialData directory. Select the Resize tab and check the Force Cubic option. Click Load. Select the Register_MRI_Base.avw data set. Then, while holding down the <Ctrl> key, select the Register_MRI_Match.avw data set (resulting in both being selected). Open the ITK Registration module (ITK > Registration). Open the Blend window (Generate > Blend) and set the Blend Option to Red-Green (figure 1). Press the Register PowerBar button or choose Generate > Register. After registration is complete, evaluate the registration by moving the crosshair in any of the panes to navigate through the image data. If you are satisfied with the registration, save a copy of the transformed match volume (Register_MRI_Match), choose File > Save Transformed. The transformed volume can be saved to disk or to the Analyze workspace. If you are unsatisfied with the registration, reset by selecting the Reset Matrix button in the Manual Registration tool (Tools > Manual Registration). Adjusting the Match position manually and the ITK Registration Parameters (Generate > Parameters) (figure 2). For more information about the ITK Registration Parameters, please refer to the ITK Users Guide ([Link]/[Link]). Close the ITK Registration module.
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