Analyze Training Guide

Analyze 12.
Training Guide
1999-2014 AnalyzeDirect, Inc.

1999-2014 BIR, Mayo Clinic
Table of Contents
Training Guide............................................................................ 1
Introduction............................................................................ 4
Analyze Basics....................................................................... 5
Loading Data into Analyze....................................................... 10
DICOM Tool: Quick Configuration.......................................... 11
DICOM Tool: Advanced......................................................... 13
Switching on Support for Additional Formats......................... 19
Supported File Formats......................................................... 21
Load As: Loading & Resizing Anisotropic Data...................... 22
Import/Export: Converting Raw Data to Images.................... 23
Import/Export: Volume Tool................................................... 25
Saving Data Out of Analyze................................................... 26
Display and Visualization......................................................... 27
Multiplanar Sections.............................................................. 28
Multiplanar Sections: Adding Color Overlay...................... 31
Oblique Sections: Oblique Resizing of Volumes..................... 32
Oblique Sections: Grid Align............................................. 34
Oblique Sections: Grid Align............................................. 35
Oblique Sections: Manual AC-PC Realignment..................... 36
Volume Compare.................................................................. 38
Volume Render: Basic Rendering Controls............................ 39
Volume Render: Advanced Rendering Controls..................... 42
Volume Render: Tissue Map Tool.......................................... 45
Volume Render: Movie Making.............................................. 47
Analyze 12.0 Training Guide
Volume Render: High Def Volume Rendering......................... 50

Volume Render: Parametric Mapping.................................... 51
Volume Render: Creating and Modifying Objects................... 52
Volume Render: Fabricate Tool.............................................. 54
Surface Render: Surface Maps............................................. 55
Virtual Endoscopy................................................................. 56
Virtual Endoscopy: Movie Generation.................................... 58
Process..................................................................................... 61
Image Calculator: Image Manipulation................................... 62
Image Calculator: SubRegion Data........................................ 64
Image Algebra: Formula for Image Manipulation.................... 67
Image Repair......................................................................... 69
Image Repair: Repair a Bad Region.................................. 70
Histogram Operations: Histogram Normalization................... 71
Spatial Filters......................................................................... 72
Filter Designer....................................................................... 73
Filter Designer: Defining Filters.......................................... 74
Segmentation........................................................................... 75
Image Edit: Manual Segmentation......................................... 76
Image Edit: Object Map Creation........................................... 78
Volume Edit........................................................................... 80
Volume Edit: Adipose Tissue Segmentation........................... 82
Volume Edit: 4D Segmentation.............................................. 84
Volume Edit: Cerebellum Segmentation................................. 85
Table of Contents
Segmentation (Continued)
Volume Edit: Lung Segmentation.......................................... 87
Volume Edit: Advanced Segmentation................................... 90
Volume Edit: Liver Segmentation .......................................... 93
Morphology........................................................................... 95
Watershed: Automated Segmentation................................... 96
Multispectral Classification.................................................... 97
Object Extractor: Automated Brain Segmentation................. 99
Object Extractor: Creating an Object Map....................... 100
Object Extractor: Creating a Binary Object....................... 101
Object Extractor: Automatic Brain Stem Removal............ 102
Object Extractor: Extracting Multiple Objects........................ 103
Surface Extractor: Polygonal Surface Extraction................... 105
Surface Extractor: Extracting a Binary Data Set............... 107
Surface Extractor: Contour Surface Extraction..................... 108
Registration............................................................................. 109
2D Registration.................................................................... 110
2D Non-Rigid Registration.................................................... 112
3D Surface Registration....................................................... 115
3D Voxel Registration........................................................... 116
3D Voxel Registration: Manual Scale Adjustment............. 119
3D Voxel Registration: Mutual Information............................ 120
3D Non-Rigid Registration.................................................... 122
Measurement........................................................................... 125
Line Profile: Intensity-based Line Measurement.................... 126
Line Profile: Radial Sequence Tool................................... 127
Region of Interest: Defining Regions..................................... 128
Region of Interest: Intersecting Regions........................... 131
Region of Interest: Defining Regions..................................... 132
Region of Interest: Editing Regions.................................. 134
Region of Interest: Measuring Regions................................. 135
Region of Interest: Histogram Analysis................................. 137
Importing .stats files into Excel............................................. 138
Stereology: Estimating Volume............................................. 139
Object Counter: Counting Cells........................................... 140
Tree Analysis........................................................................ 142
Tree Analysis: Generating a Fly-Through Movie................ 144
Apps & Add-Ons...................................................................... 145
SISCOM (Subtraction Ictal SPECT Co-registered to MRI)..... 146
Mayo 3D Brain Atlas............................................................. 149
Diffusion Tensor Imaging (DTI).............................................. 152
T2 Projection........................................................................ 155
Volume Metrics.................................................................... 156
Introduction
Welcome to the Analyze 12.0 Essential Training Guide. This document provides an overview of Analyze 12.0 core functionality through
exercises that guide new users step-by-step through basic and advanced Analyze procedures. A fully comprehensive overview of all Analyze
12.0 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 12.0, please refer to the Analyze 12.0 Installation Instructions provided with the software.
Installing Tutorial Data
Quick Reference
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:
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:
1.
Insert the Analyze Resources CD into your computer.
2.
Open Analyze 12.0 and choose Help > Tutorials.
3.
Click Install Tutorial Data at the bottom of the Tutorials

window. Note, if the tutorial data has already been insatlled
this button will not appear.
4.
In the window returned, specify the path to the tutorial data,

for example D:\TutorialData (where D:\ is equal to your CDROM drive)
5.
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).
Open the DICOM Tool (File > DICOM Tool).
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
Power Bar
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 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.
If the opened module supports or requires multiple volumes, the volumes are used in the order selected.
2.
If multiple loaded volumes are not supported, then multiple instances of the module are invoked.
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
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.
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.
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.
Display
Multiplanar Sections
Oblique Sections
Volume Compare
Volume Render
Surface Render
Virtual Endoscopy
Movie
Process
Image Calculator
Image Algebra
Image Repair
Histogram Ops
Spatial Filters
Filter Designer
3-D FFT
Segment
Image Edit
Volume Edit
Morphology
Watershed
Multispectral Classification
Object Extractor
Surface Extractor
Register
2-D Registration
2-D Non-rigid Registration
Point to Surface
3-D Surface Registration
3-D Voxel Registration
3-D Non-rigid Registration
Measure
Line Profile
Region of Interest
Stereology
Object Counter
Tree Analysis
Apps
SISCOM
Mayo 3-D Brain Atlas*
DTI*
BMA*
T2 Projection*
Volume Metrics*
*These modules require the purchase of an additional license
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.
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.
PowerBar Editor: the PowerBar Editor is an option that

appears in all Analyze modules that contain PowerBar
options.
Tutorials: Tutorial exercises covering some of the main

Analyze functions. Note, you must have selected to install
the Tutorials during initial Analyze installation.
Options: The Options item allows you to switch on and off

workspace features such as the PowerBar, and the popup 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.
Analyze Update: Checks to make sure Analyze is upto-date, also will download and install any necessary
updates.
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).
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.
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, Volume
Edit, 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, 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: 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 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.
Be sure to press Save in the PowerBar Editor if you wish to keep your PowerBar changes for future sessions. Otherwise, changes
will be lost upon exiting the Analyze module, or Analyze.
Analyze 12.0: Essential Training Guide
Loading Data into Analyze
10
DICOM Tool: Quick Configuration
Exercise 1
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@analyzedirect.com for instructions on migrating your database to the DICOM Tool.
1.
2.
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).
4.
The Local Database Name will default to SystemName_PortNumber;

change the Local Database Name to TEST_5679.
5.
On your systems local disk create a folder called AnalyzeDB

($:/AnalyzeDB)
6.
Click the Local Database Directory button in the Create New Image
Database window.
7.
In the Browse for Folder window returned navigate to the location of the
new AnalyzeDB folder ($:/AnalyzeDB), select the folder, and click OK.
You have now specified the location of your local database.
8.
To create the local database click the Create Local Database button.
Figure 1
11
DICOM Tool: Quick Configuration

9.
Exercise 1
Once the database has been created a dialog box will be

returned stating All Done, click OK.
10. 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.
11. In the (Browse for Folder) window returned navigate
to and select the folder $:\BIR\images\TutorialData\
ImportExportTutorial, then click OK.
12. 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.
Figure 2
13. 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.
14. 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; 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).
Figure 3
12
DICOM Tool: Advanced
Exercise 2
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 BirPacs user please contact support@analyzedirect.com for instructions on migrating your database to the DICOM Tool.
1.
2.
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).
4.
The Local Database Name will default to SystemName_PortNumber; change the

Local Database Name to TEST2_5679.
note
5.
Any name can be chosen for the local database, however when creating multiple databases,
following a coherent naming convention will simplify database management.
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
($:/AnalyzeDB). Note that if you have completed exercise 1, DICOM Tool Quick Configuration, this folder should already exist.
ii. Once the directory has been created, click Local Database Directory in the
Create New Image Database window, and navigate to the location of the new
AnalyzeDB folder ($:/AnalyzeDB).
iii. Select the folder and click OK. You have now specified the location of your
database.
Figure 1
13
Exercise 2
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.
7.
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.
ii. 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.
iii. DCMTK Path: The DCMTK executable files are automatically
installed with Analyze in the $:\BIR\DCMTK-3.5.4\$System_Type$\
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.
14
Exercise 2
Specification of a Database Server (optional)

8.
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.
9.
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.
ii. 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.
iii. 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.
iv. 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.
v. 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.
15
Exercise 2
Specification of the Source of Initial Images (optional)

10. The Source of Initial Images option allows you to specify a directory
containing DICOM images; click Source of Initial Images.
11. 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.
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.
13. 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.
14. 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).
Viewing and Loading Data

15. Data can be selected from the Patient information panel in the
DICOM Tool.
16. 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).
17. Note there are two data sets available for selection in the Series
information panel below. Select Series 102.
Figure 2
16
Exercise 2
18. Review the data slice-by-slice by using the Slice Number slider bar under the
image display.
19. 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.
20. To load this data set into the Analyze workspace, click Load Volume. The data
set will automatically load into the Analyze workspace.
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)
Figure 3
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).
17
Exercise 2
22. On your systems local disk create a folder called test_

export ($:/test_export).
23. Select the Patient Name MR dataset Brain and then rightclick and select the Export Patient option (figure 4).
24. In the (Browse for Folder) window returned, navigate to the
new test_export directory, then click OK. The DICOM
images will be exported out to this directory.
25. Now navigate to the test_export directory on your
systems local disk; note the file names have changed to
new DICOM UIDs.
26. In the DICOM Tool, with MR data set Brain still selected,
right-click and select the Delete Patient option.
27. A dialog box will be returned asking you to confirm that this
is what you want to do, click Yes. A delete confirmation
window will be returned, click OK to dismiss it.
28. To import this data back into the DICOM Tool right-click in
any of the information panels and select the Import DICOM
Images option. In the window returned navigate to and
select the test_export directory on your system disk, then
click OK.
29. You will be asked if you would like to Import all DICOM
files found below <$:/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.
30. Close the DICOM module before proceeding to the next
exercise.
Figure 4
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.
18
Switching on Support for Additional Formats
Exercise 3
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.
Open the Import/Export module (File > Import/Export).
2.
To view the file formats currently supported in Analyze, choose Help >
Formats.
3.
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.
4.
Open the External Libraries tool (Tools > External Libraries).
5.
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.
6.
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).
7.
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).
Figure 1
Figure 3
Figure 2
19
Switching on Support for Additional Formats

8.
Click OK. A dialog box will be returned stating that your EXTEND.conf file will
be updated, click OK (figure 4). The format is now supported by Analyze.
9.
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 Import/Export and the External Libraries tool (figure 5).
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.
Exercise 3
Figure 4
10. Click Done to close the External Libraries tool.

11. Close the Import/Export module before proceeding to the next exercise.
Figure 5
20
Supported File Formats

Analyze
AnalyzeAVW

UNKNOWN

Volume File
OBJMAP
AnalyzeImg
AnalyzeScrn
Standard Radiological File Formats

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 3D entity
enables object maps to be treated as regular imgs
old Analyze 7.5 format, i.e. .hdr/.img pairs
old Analyze 7.5 format of old Screen Edit program
Raster
BMP
Microsoft Windows Bitmap
GIF
a common color indexed format
JPG
common format featuring lossy compression
PBM
ascii and binary formats used in Portable Bitmap
Library
PGM
grayscale Portable Bitmap Library
PPM
24 bit Color Portable Bitmap Library
PIC
format used by Softimage
PNG
Portable Network Graphics
PS
output to a PostScript raster dump
SGI
format used by Silicon Graphics
SUNRASTER format used by Sun Microsystems
TARGA
a common color format
TIFF
tagged information file format, a common format
XBM
an ascii c programming language format used by

the X Windows system
XWD X
Windows dump
DICOM
the standard medical image file format based on
Mallincrodt ctn_3_0_3.
ACR/NEMA
precursor to DICOM
PAPYRUS2 3D
extensions to DICOM from OSIRIS
PAPYRUS3 3D
extensions to DICOM from OSIRIS
NIfTI
Neuroimaging file format
Video
QUICKTIME
YUV
AVI
MPEG1
common movie format

single frame color video format
video format used by Microsoft Windows
standard movie format
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
21
Load As: Loading & Resizing Anisotropic Data
Exercise 4
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.
Open the Load As module (File > Load As).
2.
Click File and navigate to and select the MRI_Head.avw data set in the
$:\BIR\images\TutorialData directory.
3.
Uncheck the Auto Exit After Load option and click Load. The data will be
loaded into the Analyze workspace as it was acquired (anisotropic).
4.
To load the data as isotropic (cubic), select the Resize tab (figure 1).
5.
Check the Force Cubic option and click Load; Select Create New and 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.
6.
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.
7.
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 and press <Enter>. Notice that the Output Axis Dimensions and Memory
fields automatically adjust when the voxel dimension is changed.
8.
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 and press <Enter>. Again, the other parameters will
automatically adjust.
9.
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].
Figure 1
10. Close all windows related to the Load As module before proceeding to the next exercise.
22
Import/Export: Converting Raw Data to Images
Exercise 5
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.
Open the Raw Data tool (Tools > Raw Data).
3.
With the Files tab selected, click the File button under Input (figure 1).
4.
In the Import/Export Input File window returned navigate to the $:\BIR\ images\
TutorialData\ImportExportTutorial directory and select the file
UNKNOWN1.
5.
Select the Image Parameters tab (figure 2).
6.
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.
7.
To accommodate this, set the following parameters:

Byte Offset: 6138 (or check Auto Offset to compute this
automatically)
Figure 1
Width: 256
Height: 256
Data Type: signed 16-bit
Byte Swap: Pairs (this only needs to be set on a little-endian
architecture, i.e., PC-based systems)
Figure 2
23
Import/Export: Converting Raw Data to Images

8.
Exercise 5
Check the following Auto options:

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.
9.
Click Display to view the current image in the main Import/Export

window (figure 3).
10. Click Load in the Raw Data tool to load the image specified in the
file into the Analyze workspace.
11. 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.
12. Click Done to close the Raw Data tool.
Figure 3
24
Import/Export: Volume Tool
Exercise 6
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.
Open the Volume Tool (Tools > Volume Tool).
3.
In the Volume Tool, click Wild Cards.
4.
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.
5.
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.
6.
Click Apply. The TIFF files will now be copied to the Volume Tool
(figure 2).
7.
In the Volume Tool, click Verify to ensure that all the slices selected are the
same size and data type.
8.
A dialog box (figure 3) will be returned upon successful verification stating

Verify Succeeds; click Continue.
9.
Click Save and save the volume file as TIFF_Head.vol in the $:\BIR\images\
TutorialData directory.
Figure 1
10. Close the Import/Export module before proceeding to the

next exercise.
Figure 3
Figure 2
25
Saving Data Out of Analyze
Exercise 7
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.
Select a data set from the Analyze workspace. If there is no data loaded, load
MRI_3D_Head.avw from the $:\BIR\images\TutorialData directory.
2.
Open the Save module (File > Save).
3.
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.
4.
Use the Format drop-down menu to specify the format in which you wish to
save the data set.
note
5.
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.
Click Save to save the data set and close the Save module.
Figure 1
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.
26
Display and Visualization
27
Exercise 8
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.
2.
Open the Multiplanar Sections module (Display > Multiplanar Sections).
3.
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).
4.
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).
5.
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.
Figure 1
Scan Tool
6.
tip
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.
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.
28
Exercise 8
Intersecting Sections Tool

7.
Open the Intersecting Sections tool (Tools > Intersecting Sections). The
Intersecting Sections tool provides an interactive display of intersecting
orthogonal sections.
8.
To change the angle at which the intersecting sections are viewed, use the
View Angle X, Y, and Z slider bars. The view angle can also be changed by
clicking in the image display and dragging the image to a new view.
9.
Use the Slice X, Y, and Z slider bars 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.
10. 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 will replace the
three slider bars, use this to increase and decrease the image size.
11. 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).
Figure 2
29
Exercise 8
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 threedimensional viewing cube.
13. The View Angle and Scale options for the Cube Sections tool may be
changed as described for the Intersecting Sections tool.
14. Planes can be interactively sliced away in the three orthogonal orientations
to reveal interior sections of the cube with the Subregion X, Y, and Z
double-ended slider bars. 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.
15. 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.
16. Click Done to close the Cube Sections tool.
17. Close the Multiplanar Sections module before proceeding to the Additional
Task.
Figure 3
30
Multiplanar Sections: Adding Color Overlay
Exercise 8.1
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.
Creating a Grayscale Data Set with Color Overlaid Objects

1.
Select the MRI_3D_Head data set in the Analyze workspace and

then open the Multiplanar Sections module (Display > Multiplanar
Sections).
2.
Choose File > Load Object Map and load the MRI_3D_Head.obj
object map from the $:\BIR\images\TutorialData directory.
3.
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 exception of the
Original and Skin objects.
4.
5.
Open the Scan Tool (Tools > Scan) and use the slice slider to review
the display of the image data (figure 2).
Figure 1
Open the Intensity option (View > Intensities). In the Intensities window,
review each of the Object Color modes by selecting each from the Mode
drop down menu.
Figure 2
Figure 3
Windowed Object
Local Max/Min
Object Only
Color Edges
Edges Only
31
Oblique Sections: Oblique Resizing of Volumes
Exercise 9
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.
Load the Canine_Chest_CT.avw data set from the $:\BIR\images\

2.
Open the Oblique Sections module (Display > Oblique Sections).
3.
Open the Fly tool (Generate > Fly).
4.
Use the Fly tool (figure 1) to rotate the current oblique plane from the
transverse orientation to the sagittal orientation:
v. Click the Roll Right button nine times to rotate the oblique plane into the
sagittal orientation. The Fly Value defaults to 10, so for each selection of
Roll Right, the plane is rotated by 10 degrees (90 total).
vi. Given that the view of this sagittal orientation is as if the body was in a
prone position, click the Yaw Counter Clockwise button nine times to
rotate the body upright. This is a right lateral view of the chest.
vii. If a left lateral view is desired, click the Roll Left button 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.
8.
tip
Reset the oblique plane to the central transverse slice by selecting the T
Cube at the bottom of the Fly tool.
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).
Figure 1
32
Oblique Sections: Oblique Resizing of Volumes

9.
Exercise 9
Open the Matrix Tool (Tools > Matrix) to display the current transformation
matrix that reflects this 3-D orientation (figure 2).
10. 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.
11. 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.
12. To save the data set in this oblique orientation, choose File > Output.
13. In the Output window, set Destination to Workspace and change Name to
xxx_myoblique (where xxx are your initials) (figure 3).
Figure 2
14. 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.
15. Click Generate Slices. The resampled data set is now saved to the Analyze
workspace.
16. Close the Oblique Sections module before proceeding to the Additional Task.
17. To view your new reformatted data set, open it with the Multiplanar Sections
module.
Figure 3
33
Oblique Sections: Grid Align
Exercise 9.1
The Grid Align tools provide users with the ability to interactively reorientate image data using a grid 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.
Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData directory.
2.
Open the Oblique Sections module (Display > Oblique Sections).
3.
Open the Fly tool (Generate > Fly). Use the Fly tool to set the display orientation to Sagittal by clicking on the S-cube.
4.
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).
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.
Release the mouse button. The image will be translated with the selected region as the new center point.
34
Oblique Sections: Grid Align

5.
Exercise 9.1
Click on the S-Cube in the Fly tool to reset the image display.
Yaw
6.
Click to select anywhere towards the outside of the grid (anywhere not within the 36 center boxes).
7.
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.
8.
Release the mouse button to apply the Yaw reorientation to the image.
9.
Close all Oblique Sections windows before proceeding to the next exercise.
35
Oblique Sections: Manual AC-PC Realignment
Exercise 10
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.
Load the MRI_3D_Head.avw data set from the $:\BIR\images\

TutorialData directory. Then open the Oblique Sections
module (Display > Oblique Sections).
2.
Once the Oblique Sections module is open, select the

Orthogonals (Tools > Orthogonals).
3.
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. 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.
4.
At the bottom of the Orthogonal window, select the Interactive

Perp Axis option to turn on the interactive generation of the
perpendicular axis and the perpendicular oblique.
5.
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.
6.
This provides the AC-PC axis and generates an oblique image, which is
perpendicular to the midpoint of this axis - essentially a coronal image.
7.
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.
8.
Open the Fly tool from the Generate menu in the main Oblique Sections
window (Generate > Fly).
Figure 1
Figure 2
36
Oblique Sections: Manual AC-PC Realignment

9.
note
Exercise 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.
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.
10. Now change the Fly Value to a smaller value (e.g. 1 to 5 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.
12. When satisfied with this transverse-oblique along the AC-PC plane, select
File > Output.
13. Change the Method to Reformat Entire Volume to generate the output
volume at this new orientation. The option is available to reformat 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).
14. Select Generate Slices to save the AC-PC aligned volume to the Analyze
workspace.
15. Close the Oblique Sections module before proceeding to the next exercise.
Figure 3
Figure 4
37
Volume Compare
Exercise 11
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.
2.
Open the Volume Compare module (Display > Volume Compare).
3.
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.
4.
From the File menu, select Load First Object Map and load the MRI_3D_
Head.obj.
5.
Next, load the MRI_3D_Brain.obj object map for the second volume (File >
Load Second Object Map).
6.
Use the crosshairs to navigate through the data (figure 2).
7.
Double click in any pane to log points. To save the Point Log,
click Save (figure 3).
8.
To save the Fused Volume, select File > Save Fused.
9.
9. Close the Volume Compare module before proceeding to the

next exercise.
Figure 1
Figure 3
Figure 2
38
Volume Render: Basic Rendering Controls
Exercise 12
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.
Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData

directory.
2.
Open the Volume Render module (Display > Volume Render).
3.
Press the Render PowerBar button or choose Generate > Render.
4.
Open the Preview window (Generate > Preview).
5.
To rotate the image data in this window, click and drag the mouse.
Figure 1
Thresholding Data
6.
Open the Thresholds window (Generate > Thresholds).
7.
Set the Threshold Minimum to 85 (figure 1) - all voxels with a value less than 85
are now removed from view.
8.
The resulting image can be seen in the Preview window (figure 2). Click Render to
display the rendering in the main Volume Render window.
9.
Now, set the Threshold Minimum to 145all voxels with a value less than 145
are now removed from view. Click Render.
Figure 2
39
Exercise 12
Rendering Algorithms
10. Open the Render Types window (Generate > Render Type) (figure 3).
11. Experiment with the rendering algorithms.
12. Select the Depth Shading option. View the rendering in the Preview window. Click
Render to display the rendering in the main Volume Render window.
note
When working with anisotropic data, the Interpolated Rays option may help to improve
the quality of the rendering.
13. 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.
14. Select the Maximum Intensity Projection option. Click Render to display the
rendering in the main Volume Render window.
15. Select the Summed Voxel Projection option and click Render.
16. 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 3
note
Additional parameters for each render type

are available in the Render Types window.
Upon clicking on each Render Type, notice
that type specific parameters will either
become enabled or disabled depending on
whether the parameter is supported.
17. Select Gradient Shading before moving to the next section.
Depth Shading
Gradient Shading
Volume Compositing
Maximum Intensity
Projection
Summed Voxel
Projection
Surface Projection
40
Exercise 12
Clip Tool
18. Open the Clip tool from the Render Type window or from (Generate >
Clip).
19. The Clip tool (figure 5) allows a subregion of the volume to be rendered.
Experiment with the Clip Plane and Clip Volume parameters.
20. Click Done to close the Clip tool.
21. Close all windows related to the Volume Render module before moving
onto the next exercise.
Figurre 5
Figure 6
41
Volume Render: Advanced Rendering Controls
Exercise 13
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 oneto-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.
Load the Cubic_CT_Head.avw data set from the $:\BIR\images\TutorialData directory.
2.
2. Open the Volume Render module (Display > Volume Render).
Defining Objects in an Object Map

3.
Choose File > Create Object Map. The Objects window will automatically be returned;
dismiss the window for now by clicking Done.
4.
Open the Threshold Tool (Tools > Manipulate > Threshold) (figure 1).
Set the Minimum Threshold to 85.
Set Change to Object Map.
Set Defined Object to ***New***.
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.
5.
Open the Preview window (Generate > Preview) to interactively review your changes.
6.
Click Render to display the rendering in the main Volume Render window (figure 2).
7.
In the main Volume Render window, open the Thresholds window (Generate > Thresholds).
Set the Threshold Minimum to 145 and click Render.
Figure 1
Figure 2
42

8.
Open the Connect Tool (Tools > Manipulate > Connect).

Change the Connect Method to Connected Components.
Set to Keep the 3 Largest Objects.
note
Exercise 13
Up to 255 different
objects can be defined
in an object map.
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.
Manipulating Objects
9.
Figure 3
In the Objects window (View > Objects) (figure 4), click Reassign Object(s).
10. 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.
11. Click Remove Unused in the Objects window to remove BlueObject. Click
OK in the dialog box returned.
Figure 4
12. Select the GreenObject from the Object drop-down menu. Then change the
following attributes:
Name: Bone
Color: white
Shades: 32
13. Select the YellowObject from the Object drop-down menu. Then change the
following attributes:
Name: Rope
Color: red
Shades: 8
14. Click Render.
15. In the Thresholds window (Generate > Thresholds), set the Threshold
Minimum to 5.
16. Return to the Objects window and set Control by to Attribute.
Figure 5
43
Exercise 13
17. Set the Display attribute to Off for the Original object. Then, click
Render.
18. Open the Render Types window (Generate > Render Type). Select the
Object Compositing option, then open the Object Mapping window,
(Generate > Type Specific > Object Mapping).
19. Select the Transparency render type (figure 6) and click Render to view
the effects.
20. 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).
Saving an Object Map
Figurre 6
21. 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.
22. 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).
23. Close the Volume Render module before proceeding to the next
exercise.
Figure 7
44
Volume Render: Tissue Map Tool
Exercise 14
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.
Load the CT_Heart.avw data set from the $:\BIR\images\TutorialData

directory.
2.
3.
Open the Render Types window (Generate > Render Type).
4.
Select the Volume Compositing render type (figure 1). Then open the Tissue
Map tool by clicking the Tissue Map button.
5.
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.
6.
The Tissue Map tool provides four control points to manipulate which voxel
values are mapped to specific colors and opacity (figure 2).
Start: The starting voxel value within the volume mapped to a specific
color (chosen from the color drop-down menu) with
0% opacity.
Figure 1
Min: The minimum voxel value within the volume that

will be mapped to a specific color and set opacity (e.g.
44%).
Max: The maximum voxel value within the volume that
will be mapped to a specific color and set opacity (e.g.
44%).
End: The ending voxel value within the volume
mapped to a specific color with 0% opacity.
7.
Click Render to view the rendering with the default

parameters (displayed in the main Volume Render
window).
Figure 2
45
Volume Render: Tissue Map Tool

8.
Exercise 14
Use the slider bars, or type the numbers in the

appropriate text box in the Tissue Map tool to set the
following (figure 3):
Start: 157
Min: 200
Max: 500
End: 3072
9.
Select 60 from the Opacity drop-down menu. Click

Render to view the effect of the changes (figure 4).
10. Now, experiment by moving the control points in the

graphical display. Click Render as desired.
11. 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.
Figure 3
12. Several default tissue maps are also available, rightclick

in the graphical display and choose Default Tissue
Maps > CT2; once loaded, click Render (figure 5).
13. Experiment with adding a second tissue to the tissue
map by clicking the + button to the right of the graphical
display. Click Render as desired to see the effect.
14. Close the Volume Render module before proceeding to
the next exercise.
Figure 4
Figure 5
46
Volume Render: Movie Making
Exercise 15
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.
Choose File > Save Renderings (figure 1).
4.
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.
5.
Click Done to dismiss the Save Renderings window.
6.
Open the Sequence tool (Generate > Sequence).
7.
By default, the sequence already has one action, Z Rotation. To modify the
action click Modify, and then click on the red Z Rotation action (figure 2). The
Action window will automatically be returned.
8.
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.
9.
In the Action window, set the following parameters (figure 3):
Figure 1
Action Name: Threshold

Number of Frames: 36, the default frame display is 12 frames per second.
Figure 2
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 3
47
Exercise 15
10. To preview the movie with the new action, first open the Preview window
(Generate > Preview).
11. Now, in the Sequence tool, click Sequence. Then, click Make Sequence
(figure 4).
12. 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 and place the new
action on Track 2 in Frame 36; this will be directly under the last frame of the
Threshold action (figure 5).
Figure 4
14. Once the new action has been added, click Modify and then click on the new
action to open the Action window.
15. 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)
16. Click Done to dismiss the window.
17. Review the movie. Click Sequence, and then, with the Preview window open,
click Make Sequence.
18. 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.
Figure 5
note
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.
48
Exercise 15
19. To generate the movie, click Sequence again. This time, after clicking Make
Sequence, choose Make the Sequence from the dialog box returned.
20. 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).
21. Once sequence generation is complete, close the Volume Render module.
22. In the Analyze workspace, select the MyTestMovie file and review it using the
Movie module (Display > Movie). (figure 6)
23. 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.
24. Close the Movie module before proceeding to the next exercise.
Figurre 7
49
Volume Render: High Def Volume Rendering
Exercise 16
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.
Load the CT_Heart.avw data set from the $:\BIR\images\TutorialData

directory.
2.
3.
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).
4.
Open the Render Type window from the Generate menu and select
Volumetric Compositing, check the Interpolated Rays option (figure 2).
5.
Click the Tissue Map button to open the Tissue Map tool. Right-click on the
main tissue map panel and select Default Tissue Maps, choose the CT 2 default
tissue map.
6.
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.
7.
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.
8.
Once the rendering is complete, the HDVR will be

displayed in the main Volume Render window.
9.
To save the rendering, Select File > Save

Rendering. Name the rendering HDVR and then
click the Save Last Rendering button.
10. Close the Volume Render module before

proceeding to the next exercise.
Figure 1
Figure 2
Figure 3
50
Volume Render: Parametric Mapping
Exercise 17
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 use 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.
2.
Open the Volume Render module (Display > Volume

Render). In the Volume Render window, select File >
Input/Output Ports (figure 1).
3.
Drag-and-drop the SISCOM_Extracted_Brain file from

the Analyze workspace into the Volume port. Next, dragand-drop the SISCOM_4D_ActivityMap from the Analyze
workspace into the Related Volume port.
4.
Open the Preview window (Generate > Preview).
5.
Open the Parametric Mapping window (Generate > Type

Specific > Parametric Mapping).
6.
In the Parametric Mapping window, set Parametric

Mapping to On (figure 2).
7.
Review the rendering in the Preview window. To rotate the

image, drag and drop the rendering in Preview window
(figure 3).
8.
Review the effects of changing the Mapping Factor

and Map Transparency Value options in the Parametric
Mapping interactively in the Preview window.
9.
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).
10. Close the Volume Render module before proceeding to the

next exercise.
Figure 1
Figure 2
Figure 3
Figure 4
51
Volume Render: Creating and Modifying Objects
Exercise 18
Volume Render is a powerful display module. In the Volume Render module, you can use many different tools to create many different
outcomes. This exercise will demonstrate an amalgamation of Volume Render tools, to create a desired display.
Creating the Object Map

1.
Load the Coronary_CT.avw data set from the $:\BIR\images\TutorialData directory.
2.
Select the data set and open the Volume Render module (Display > Volume Render).
3.
Open the Toggle Preview window (Generate > Preview).
4.
Open the Threshold tool (Tools > Manipulate > Threshold). Use the slider bar to
increase the minimum threshold, note that the preview in the Preview window updates
interactively. Increase the threshold until you have thresholded the heart - 63 is a good
minimum value for this data set.
5.
In the Threshold tool, set Change to Object Map. Set Define Object to ***New***.
6.
Now select the Threshold Volume button. Your object map now contains one object; the
heart.
7.
In the Threshold tool, increase the Threshold Minimum until you see only the vascular
system surrounding the heart, a minimum value of 133 is good. Set Define Object to
***New***.
8.
Select the Threshold Volume button again, Object_3 is created and contains only the
vascular system (figure 2).
9.
Set the Threshold Mimimum to 1 and then close the Threshold tool.
Figure 1
Figure 2
52
Volume Render: Creating and Modifying Objects
Exercise 18
Modifying the Object Display Options

10. Open the Objects window (View > Objects), at the top of the window set
Control By to Attribute. Set the display of the Original to Off, then select
Render.
11. In the main Volume Render module, select Generate > Render Type. In the
Render Type window returned, select Object Compositing and then hit
Render (figure 3). The render will show both the heart and the vessels.
12. In the Objects window, select Name from the Attribute drop down menu and
change the name of Object_2 to Heart, and the name of Object_3 to
Vessels.
Figure 4
13. Now select Color from the Attribute drop down menu and change
the color of the Heart to Pink and the color of the Vessels to Red.
Note that you can just type the name and hit enter to change the
color of the object.
14. Now select Opacity from the Attribute drop down menu and change
the opacity of the Heart to .02. Change the thickness of the Vessels
to 2 (figure 4). You will see the Preview window update (figure 4). To
view the results in the main Volume Render module, hit Render.
15. Experiment with other settings and tools within the Volume Render
module.
Figure 3
16. To save your object map, select File > Save Object Map.
17. Close the Volume Render module before proceeding to the next exercise.
Figure 5
53
Volume Render: Fabricate Tool
Exercise 19
The Volume Render Fabricate Tool allows for the creation of objects from a text file with coordinates or by user defined coordinates. This
exercise will demonstrate how to create objects from a predefined log file. The log file provides a list of the coordinates, the centroids of 61
electrodes from an electrode grid. Using the fabricate tool we will create an electrode object around each coordinate.
1.
Load the Trans_Pre_OP_MRI and open it in the Volume Render

module (Display > Volume Render).
2.
Open the Fabricate Tool (Tools > Manipulate > Fabricate). Click the
Alt button once and then click the File button (figure 1).
3.
Navigate to the log file Electrodes_FabTool.log in the C:/BIR/

Images/TutorialData directory.
4.
Adjust the Radius to 10. This will define an electrodes object with a
radius of 10 voxels. Set Change to Object Map, then from the Defined
Object menu select ***New***.
5.
Click Create.
6.
From the main Volume Render window, open the Preview window
(Generate > Preview). To rotate the image, click and drag the
rendering in the Preview window.
7.
Open the Render Type window (Generate > Render Type), select
Object Compositing, the rendering is shown in figure 3.
Figure 1
Figure 2
Figure 3
54
Surface Render: Surface Maps
Exercise 20
Surface Render provides a semi-automated interface for the conversion of object maps into surface maps using the Adapt/Deform algorithm.
1.
2.
Open the Surface Render module (Display > Surface Render).
3.
Choose File > Load Object Map and load the Cubic_CT_Head object map from the $:\BIR\
images\TutorialData directory.
4.
In the Objects window (View > Objects) returned, set Control by to Attribute and set the
Display attribute to Off for the Rope, Left Skin, and Skull objects (figure 1).
5.
Choose File > Create Surface Map.
6.
In the Surfaces window (View > Surfaces) returned, 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.
7.
Once the surface map is generated, click Render to display the results (figure 2).
8.
Choose File > Load Surface Map and load the Cubic_CT_Head.smp surface map from
the $:\BIR\images\TutorialData directory.
9.
Click Render to display the results.
10. Open the Camera tool (Generate > Camera) and set Sort to Front-Back (figure 3). Click
Render to display the results.
Figure 1
Figure 2
11. In the Surfaces window set Control by to Attribute. Choose Shading from the Attribute dropdown menu and change the shading of the Right Skin surface to Gouraud.
12. Click Render, note the changes in the rendering (figure 4). Experiment with the different shading
options.
13. Choose File > Save Surface Map to save changes made to the surface map.
14. 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.
Figure 3
15. Close the Surface Render module before proceeding to the next exercise.
55
Virtual Endoscopy
Exercise 21
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.
Load the CT_Lungs.avw data set from the $:\BIR\images\TutorialData directory.
2.
Open the Virtual Endoscopy module (Display > Virtual Endoscopy).
Basic Controls
tip
The Eye position advances

toward the selected point
based on settings in the
View Parameters window.
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).
4.
Position the cursor on the flat surface outside of the trachea and click once.
5.
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.
6.
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
Advanced Controls
7.
Open the View Parameters window (Generate > View Parameters).
8.
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).
9.
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
Y: 1
Z: 0
X: 0
Figure 2
Figure 3
10. Click Render in the View Parameters window to display the location of the
coordinates (figure 4).
Figure 4
56
Virtual Endoscopy
Exercise 21
11. Reset Move Percent to 20 in the View Parameters window and click
Done to dismiss the window.
12. 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 or Look At point. 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, 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.
Figure 5
14. 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.
15. 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.
16. Close all Virtual Endoscopy windows before proceeding to the next exercise.
Figure 6
57
Virtual Endoscopy: Movie Generation
Exercise 22
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.
Load the CT_Lungs.avw data set from the $:\BIR\images\TutorialData directory.
2.
Open the Virtual Endoscopy module (Display > Virtual Endoscopy).
3.
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.
4.
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).
5.
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.
6.
Choose Generate > Sequence > Auto Key Frame, this option causes any new viewpoint to
automatically be added as a key frame.
7.
Continue to click within the tracheal lumen and navigate down to the bifurcation of the airway
(approximately 9 clicks) (figure 2).
8.
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.
9.
When you have moved down the left bronchus (figure 3), choose Generate > Sequence > Auto
Key Frame to turn off the Auto Add Key Frame option.
Figure 1
Figure 2
10. To save the sequence, choose Generate > Sequence > Save Sequence.
11. 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.
12. The fly-through movie will be available in the Analyze workspace and can be viewed with the
Movie module (Display > Movie).
note
Rendering the endoscopic movie may

take a few minutes depending upon
your system and the size of the movie.
Figure 3
58
Virtual Endoscopy: Centerline Generation
Exercise 22
The Virtual Endoscopy module provides the 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.
Load the CT_Lungs.avw data set from the $:\BIR\images\

2.
Open the Virtual Endoscopy module (Display > Virtual

Endoscopy).
3.
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).
4.
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.
5.
In the Show Object window, click on and drag the green arrow (the
Look At point) to the end of the airway (figure 2).
6.
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
Figure 3
Figure 2
59
Virtual Endoscopy: Centerline Generation

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.
9.
Close all windows associated with the Virtual Endoscopy module

before proceeding to the next Additional Task.
Exercise 22
Figure 4
60
Process
61
Image Calculator: Image Manipulation
Exercise 23
This exercise will demonstrate how to use the Image Calculator module for rudimentary image processing and manipulation.
1.
Load both the MRI_3D_Head.avw and MRI_3D_Brain_Bin.avw data sets from the $:\BIR\
2.
With the MRI_3D_Head data set selected in the Analyze workspace, open the Image Calculator
module (Process > Image Calculator).
3.
In the Image Calculator module, the MRI_3D_Head data set icon

should appear in the white space above the calculator (figure 1).
4.
Click the Multiply button on the calculator.
5.
Drag-and-drop the MRI_3D_Brain_Bin data set from the Analyze

workspace into the Image Calculator module (white space).
6.
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.
7.
Click the Equals button 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.
8.
The masked grayscale data will appear in the Image Calculator module; a copy will be
automatically be saved to the Analyze workspace.
9.
Click the Multiply button again.
note
In order to be able to drag-anddrop data sets from the Analyze workspace into the module, make sure that
the Analyze window is not maximized
to full window display.
10. Click the Matrix button on the calculator.

11. 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.
Figure 1
12. Click the Equals button on the calculator. A Transformation window will
be returned; use the default settings and click Transform.
13. The transformed data will appear in the Image Calculator module and
the copy in the Analyze workspace will be updated.
Figure 2
62
Image Calculator: Image Manipulation
Exercise 23
14. Right-click on the calculator and choose Buttons;

the Button Tool will open (figure 3).
15. 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.
16. Click the Flip button that now appears on the
calculator (figure 4).
17. In the Function Options window returned, check
the Flip X option and click Apply (figure 5).
18. View the results by clicking the Volume button on
the calculator.
19. A copy of the data set (as specified earlier) with the
manipulations performed has automatically been
saved to the Analyze workspace.
20. Close the Image Calculator module before
Figure 3
Figure 4
Figure 5
63
Image Calculator: SubRegion Data
Exercise 24
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.
Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData

directory.
2.
Open the Image Calculator module (Process > Image Calculator).
3.
In the Image Calculator module, right click on the white space and select
Buttons from the menu options (figure 1).
4.
In the Button Tool, select the Region Pad button from the palette on
the left, and drag and drop it onto the Key Pad on the right.
5.
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.
6.
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.
7.
Hit the Region Pad button, the Region Pad buttons Subregion-Pad
Volume window will be returned (figure 4).
8.
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
Figure 2
Figure 3
Figure 4
64

9.
Exercise 24
Click on the Interactive button in the Subregion window.
Example 1: Subregioning 50 slices in the X.

Set the X Low value to 25
Set the X High value to 162
Example 2: Subregioning 50 slices in the Y.

Set the Y Low value to 25
Set the Y High value to 211
Example 3: Subregioning 50 slices in the Z.

Set the Z Low value to 25
Set the Z High value to 151
65
Exercise 24
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.
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.
11. 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.
12. 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.
13. Close all windows associated with Image Calculator before proceeding
to the next exercise.
66
Image Algebra: Formula for Image Manipulation
Exercise 25
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.
Load the Cubic_CT_Head.avw data set from the $:\BIR\images\

2.
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.
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.
4.
Enter the formula: Output = (a > 145) * a. Press <Enter> (figure 1)
5.
Drag-and-drop the Cubic_CT_Head data set from the Analyze workspace

into the Image Algebra module under variable a.
6.
Click the Output button; in the Parameters window returned, set Name to
Bone. Click Done to dismiss the window.
7.
Click Go in the main Image Algebra window to begin processing.
8.
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.
Figure 2
67
Image Algebra: Formula for Image Manipulation
Exercise 25
10. Click the a button to view the parameters for variable a (figure 3).
Click Done to dismiss the Parameters window.
11. Click the Output button and change Name to NoBone. Click Done
to dismiss the window.
12. Click Go in the main Image Algebra window to begin processing.
13. Once processing is complete, right-click on the Output icon and
select Display to examine the data with bone removed.
14. Now, try adding the bone back in with the new formula: Output = (b
>= 1) * b + (b < 1) * a. Press <Enter> (figure 4).
15. 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.
16. Click the Output button and change Name to BoneAdded. Click
Figure 3
17. Click Go to process the new formula (figure 4).

18. Once processing is complete, right-click on the Output icon and
select Display to examine the data with the bone added back.
19. Right-click in the formula field and explore some of the example
formulas provided.
20. Close the Image Algebra module before proceeding to the next
exercise.
Figure 4
68
Image Repair
Exercise 26
The Image Repair module is a module that includes the ability to designate bad slices or subregions that can be repaired by copying voxels from
neighboring slices, interpolating across neighboring slices, copying from a related volume, or removed from the volume. Subregion repair includes
the ability to blend voxels at the edge of the region.
1.
Load the VH_Abdomen.avw data set from the $:\BIR\images\

2.
Open the Image Repair module (Process > Image Repair).
3.
In the Image Repair module (figure 1), use the Displayed Slice slider
bar to locate the first corrupt slice. Note that the first corrupt slice is
slice 276.
4.
In the Bad Slice(s) portion of the window, set slice 276 as the first
bad slice.
5.
Now, use the Displayed Slice slider bar to locate the last corrupt
slice. Note: the last corrupt slice is slice 279.
6.
In the Bad Slice(s) portion of the window, set slice 279 as the last
bad slice.
7.
Select Interpolate Between the First Good Slices for the

correction method.
8.
Click Repair 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.
9.
Close the Image Repair module before proceeding to the next task.
Figure 1
69
Image Repair: Repair a Bad Region
Exercise 26.1
The Bad Region option provides the user the ability to define only a selected region to be repaired. To demonstrate this option we will use the
VH_Abdomen data set and repair only the corrupt regions.
1.
Select the VH_Abdomen data set in the Analyze workspace and

open the Image Repair module (Process > Image Repair).
2.
As in the main exercise, set slice 276 as the first bad slice and slice
279 as the last bad slice.
3.
Select the Bad Region option, the region boundaries and region
sliders will appear.
4.
Adjust the region sliders until just the corrupt area is defined (figure
1).
5.
Try adjusting the Blend Border and Correction Method. Review

the different results.
6.
Click Repair Slice(s). Slices 276 through 279 will be corrected

according to the region and correction method. A dialog box will be
returned, click Change a Copy of the Loaded Volume.
7.
Close the Image Repair module before proceeding to the next

exercise.
Figure 1
70
Histogram Operations: Histogram Normalization
Exercise 27
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.
Load both the SISCOM_Ictal_SPECT.avw and SISCOM_Interictal_SPECT.

avw data sets from the $:\BIR\images\TutorialData directory.
2.
With only the SISCOM_Ictal_SPECT data set selected in the Analyze

workspace, open the Histogram Operations module (Process > Histogram
Ops).
3.
Open the Function window (Generate > Function).
4.
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
Figure 1
Histogram Display: On
5.
Click Filter. An Input and Output Histogram will automatically be returned. The
filtered result will be displayed in the main Histogram Operations window.
6.
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.
7.
Drag-and-drop the SISCOM_Interictal_SPECT data set from the Analyze

workspace into the main Histogram Operations window.
8.
Press the Filter PowerBar button. In the dialog box returned, click Change a
Copy of the Loaded Volume.
9.
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.
10. Close the Histogram Operations module before proceeding to the next exercise.
Figure 2
71
Spatial Filters
Exercise 28
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.
Open the Spatial Filters module (Process > Spatial Filters).
3.
Open the Preview Options window (Generate > Preview Options).
4.
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.
5.
Open the Filters window (Generate > Filters).
6.
In the Filters window, select the Low Pass filter by clicking the radio button next
to the option (figure 2).
7.
Now, click Preview. 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.
8.
Preview several other filters, noting the effect of each.
9.
To apply a filter to the data set, 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.
Figure 1
Figure 2
10. A filtered copy of your volume will be saved to the Analyze workspace.
11. Close the Spatial Filters module before proceeding to the next exercise.
Figure 3
72
Filter Designer
Exercise 29
The Filter Designer module is a general-purpose 2D image processing tool which performs convolution and deconvolution in the frequency domain
using the Fast Fourier Transform (FFT). This exercise will demonstrate how to use the Filter Designer process functions available when a data set
and its associated Point Spread Function are loaded.
1.
Load the Chromosome_2D_512 and Chromosome_2D_PSF data sets from

C:\BIR\images\TutorialData\ImageProcessingTutorial.
2.
Select Chromosome_2D_512 and open the Filter Designer module (figure 1)

from the Process menu.
3.
Drag and drop the PSF file from the workspace onto the PSF input icon.
4.
Double-click on the Input icon to open the Input Selector window, and double
click on the Output icon to open the Output Viewer.
5.
The Convolver function has automatically been applied to the data. The Fourier
transform of the selected section (slice) of the input volume is multiplied by the
Fourier transform of the selected section (slice) of the PSF volume. The output
is the inverse Fourier transform of the resulting spectrum.
6.
Compare the input (figure 2) and output (figure 3) images.
7.
Right-click on the Output icon and select Store This Section option. The
output data set will be saved to the Analyze workspace. If desired the Filter and
Spectrum generated by the process can also be saved in this manner.
8.
Change the function to Generate > Process > Cross Correlator.
9.
A cross correlation function of the selected section of the input

volume with the selected section of the PSF volume will be
generated.
Figure 1
10. Compare the input and output images.

11. Review the other functions available from the Generate > Process
menu. Adjust the associated parameters to see the effect on the
filtered image data.
Figure 2: Convolver Input
Figure 3: Convolver Output

73
Filter Designer: Defining Filters
Exercise 29.1
Filter Designer is a general-purpose 2D image processing tool, the module allows users to interactively define a representation of a frequency filter.
This exercise will show you how to manually define filters to filter your image data.
1.
Select MRI_3D_Head and open the Filter Designer module (Process

> Filter Designer).
2.
Set the Slice to 100 (Generate > Slice) (figure 1).
3.
In the Filter Designer window draw a Low Pass filter (figure 2).
4.
After releasing the mouse the filter will be applied to the current slice.
5.
Double click on the Output image to view the effect of the low pass
filter (figure 3).
6.
Now in the Filter Designer window, define a High Pass filter (figure 4).
7.
Note the update to the Output image (figure 5).
8.
To save the current filtered image right-click on the output image and
select Store This Selection. Set Change a Copy of Image Data
when prompted. Slice 100 in the data set will be filtered.
9.
To review the filtered data, open it with the Multiplanar Sections

module. The filter has been applied to slice 100.
Figure 1
Figure 2
Figure 3
Figure 5
Figure 4
74
Segmentation
75
Image Edit: Manual Segmentation
Exercise 30
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.
Open the Image Edit module (Segment > Image Edit).
3.
Use the Slice Slider to move to Slice 122.
4.
In the main Image Edit window, select the Auto Trace tool. 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).
5.
Use the double-ended slider bar 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.
6.
Select the Delayed Flood Fill tool and place a fill point outside the auto-traced region
(click on the background).
7.
Select the Auto Trace tool again and click Apply & Advance.
8.
A dialog box will be returned stating that the action modifies the loaded volume, click
Change a Copy of the Loaded 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).
9.
Review the edited slice by opening the Edit Review Tool (Tools > Edit Review)
(figure 2).
note
An edited version of the data set will be automatically saved to the

Analyze workspace.
Figure 1
Figure 2
76
Image Edit: Manual Segmentation
Exercise 30
10. 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.
11. 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.
12. In the Edit Review tool, change the orientation to Coronal and then Sagittal,
note the slice edits in these orientations (figure 3).
13. Close all windows related to Image Edit before moving to the next exercise.
Figure 3
77
Image Edit: Object Map Creation
Exercise 31
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.
Open the Image Edit module (Segment > Image Edit).
3.
Choose File > Create Object Map. The Objects window (View > Objects) will automatically
be returned (figure 1).
4.
Click Add Object to create a new empty object (Object_2).
5.
Change Name from Object_2 to Brain. Click Done to dismiss the Objects
window.
6.
Use the slider bar to move to Slice 122.
7.
At the bottom of the main Image Edit window, set Change to Object Map and
choose Brain from the Defined Object drop-down menu.
8.
Select the Auto Trace tool; the Image Edit window will automatically update to
display Auto Trace parameters (figure 2).
9.
Position the cursor near the center of the brain and click to set a seed point. Use
the double-ended slider bar 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.
Figure 1
10. Select the Delayed Flood Fill tool and place a fill point inside the auto-traced
region (click inside the region).
11. Select the Auto Trace tool again.
12. Click Apply & Advance. The next slice will appear in the image display (the slice
number is displayed in the lower left corner).
Figure 2
78
Image Edit: Object Map Creation
Exercise 31
13. View the edited object map by opening the Edit Review Tool (Tools > Edit Review).
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.
14. Select the Previous option in the Edit Review tool. The change can also be viewed by
selecting the Coronal option (figure 3).
15. 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).
note
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.
Figure 3
16. 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).
17. Close all windows before moving to the next exercise.
79
Volume Edit
Exercise 32
The Volume Edit module provides interactive segmentation tools for manual and semi-automated object definition of structures using an intuitive
3D interface. This exercise will provide an overview of how these tools can be used to interactively build an object map.
1.
Select MRI_3D_Head from the Analyze

Workspace, and open the Volume Edit module
(Segment > Volume Edit).
2.
Click the Add Object button to add a new object.

Change the Name to Skin and Color to Tan.
3.
Select the Semi-Automatic tab, and then select

Threshold.
4.
Adjust the threshold using the double-ended

slider. Set the Minimum Threshold to 44 and the
Maximum Threshold to 255. Click the Define
Object button.
5.
The next step is to extract the brain. Select

Object Extractor, and click the Add Object
button, change the Name to Brain and Color to
Pink. In the Transverse orientation, move to slice
135.
6.
Click to set a seed point within the white matter

(figure 2).
7.
Adjust the Minimum Threshold to 48 and the

Maximum Threshold to 141. Click Extract
Object.
tip
To toggle through intensity display options, press

Ctrl+F9 on your keyboard. Review the options and
decide which is most useful to you.
Figure 1
Figure 2
Figure 3
80
Volume Edit
8.
The brain will be extracted as the second object in the object map.
9.
Once the brain object has been extracted, select the Manual tab.
Exercise 32
10. To extract the ventricles, click the Add Object button. Change the
Name to Ventricles and Color to Green. Select the Auto Trace
tool.
11. Move to Transverse Slice 130 and set a seed point within the
Ventricles.
12. Set the Threshold Minimum to 1 and the Threshold Maximum to
48 (figure 4). If there are unconnected regions that should belong to
the same object, click to set additional seed points.
13. To automatically advance the seedpoints to the next slice, set Auto
Advance to Forward, then click Apply.
14. Click the Apply button until the ventricles are defined. If
needed, click the Reset Seeds button and click to place
new seed points inside the ventricles (figure 5).
15. To review the segmentation on the rendering, right click on
the render window and select Transparency (figure 6). To
rotate the rendering, click and drag with the middle mouse
button.
Figure 4
16. To save the created object map for use in other Analyze
modules, choose File > Save Object Map. Close the
Volume Edit module before proceeding to the next
exercise.
Figure 5
Figure 6
81
Volume Edit: Adipose Tissue Segmentation
Exercise 33
In this exercise we will review the segmentation of visceral and subcutaneous adipose tissue to demonstrate key Volume Edit functionality
including; Edge Strength, Region Growing, and Object Separation. However, this application is one approach used for the segmentation and
separation of fat pads in mice.
1.
Download the CLS_MouseFat.avw data set from www.

analyzedirect.com/data/CLS_MouseFat.zip. Use File >
Load to load the data into Analyze.
2.
Use the Process > Spatial Filters module to apply a 3 x 3

x 3 median filter to the data set. See Exercise 27: Spatial
Filters for instructions on applying a filter to a data set.
3.
Next select the filtered data set (CLS_MouseFat_Med)

and open Segment > Volume Edit.
4.
Click the Intensities button and adjust the Minimum and

Maximum intensity values to improve display of
fat and abdominal wall.
5.
From the Edge Strength tab check the Use

Edge Strength option.
6.
Set the Edge Strength Threshold to 63. Note

that the abdominal wall is shown in red (figure 1).
7.
Next select the Semi-Automatic tab and choose

the Region Grow option.
8.
In the transverse orientation use the slider bar to move to

slice 256. Click intra-abdominal fat then set the Threshold
Minimum to 2230 and the Threshold Maximum to 2540
(figure 2).
9.
Click Extract Object.
Figure 1
10. Repeat to add any additional areas of adipose tissue.

11. In the Objects control panel rename Object_2 to VAT
Figure 2
Figure 3
82
Volume Edit: Adipose Tissue Segmentation
Exercise 33
(Visceral Adipose Tissue).

12. Click Add Object, change the name of the new object to SubQ
(Subcutaneous Adipose Tissue)
13. Select Object Separator. Click to set a seed point in a region of
subcutaneous adipose tissue. Then click to set a second seed point
in a region of visceral adipose tissue (figure 4).
14. Click Separate. The two regions of adipose
tissue will be broken into their respective subcompartments (figure 5).
Figure 4
15. Save the object map by selecting File > Save

Object Map.
16. Note that the VAT and SubQ volumes can
be sampled using the Measure > Region of
Interest module. For more information please
refer to exercise 51: Region of Interest Measuring Objects in Object Maps.
17. Exit the Volume Edit module.
Figure 5
83
Volume Edit: 4D Segmentation
Exercise 34
Segmentation is often the precursor to other image analysis applications such as image measurement. Volume Edit provides a gamut of tools for
a variety of segmentation tasks not only applicable to 2D-ROI and 3D-VOI measurement but also 4D-VOIs. In this exercise we will use the Volume
Edit module to segment the left atrium in the heart using the Object Extractor tool over a series of 18 3-D volumes that span the entire cardiac
cycle. The segmentation result can then be used for a number of applications such as calculation of blood volumes in the region over different
stages of the cardiac cycle or cardiac ejection fraction.
1.
Load the mouse dataset BeatVol from $:\BIR\images\

2.
Use File > Load to load the data set into Analyze.
3.
Next select the BeatVol data set and open Segment >
Volume Edit.
4.
Note that there is an additional Volume control option.

Use the Volume slider to navigate through all 18 volumes.
Set the volume back to 1 when done.
5.
The Segment All Volumes option will be checked by

default, with this option checked the semi-automatic
segmentation task performed on the currently selected
volume will be propagated to each volume in the series.
6.
Click on the Semi-Automatic tab and choose the Object

Extractor option.
7.
Set a seed point in the Left Atrium. Set the Min

Threshold to 154 and the Max Threshold to 255, then
click Extract Object. The Object will be segmented in all
18 volumes. Review the segmentation by moving through
the Volume Slider.
8.
Save the object map by

selecting File > Save
Object Map.
9.
Exit the Volume Edit

module.
Figure 1
84
Volume Edit: Cerebellum Segmentation
Exercise 35
Segmenting structures from surrounding anatomy with a similar grayscale intensity can be difficult. This exercise will demostrate how to utilize the
walls function in Volume Edit to make segmenting the cerebellum from the rest of the brain easier.
1.
Load the MRI_EGV_Brain.avw from the the $:\BIR\images\TutorialData

directory.
2.
Select the data set and open Segment > Volume Edit.
3.
Adjust the intensity range by opening View > Intensities and lowering the
Maximum value to 80.
4.
Select the Walls tab, and check Define walls to limit semi-automated
operations. In the options returned, set Draw Walls and Spline (figure 1).
5.
In the Sagittal view navigate to slice 68. Start setting spline points between
the cerebellum and the rest of the brain. Click Apply on the Walls panel after
completing a spline, or hit A on your keyboard to apply the spline.
note
6.
Always define walls in the same manner. For example if defining from the front to the
back of the brain make sure all walls for defined in this way.
Move forward several slices and define another spline. Repeat across the brain
(figure 2).
Figure 1
Figure 2
85
Volume Edit: Cerebellum Segmentation

7.
Once complete, move back through the slices and

review the walls. Add new walls if needed.
8.
Select the Semi-Automatic tab and select the Object

Extractor option. Click in the cerebellum on a sagittal
slice to set a seed point.
9.
Select a min threshold of 30 and a max of 69 (figure 3).

Click Extract Object.
Exercise 35
10. Lock Object_2 and click Add Object. Set a seed point
in the white matter on a spatially connected transverse
slice, then click Extract Object.
11. Change the name of Object_2 to Cerebellum and
Object_3 to Brain.
12. Save the Object Map (File > Save Object Map) and
open in Measure > Region of Interest to make
measurements of the Brain and Cerebellum objects.
13. Close the module before proceeding to the next
exercise.
Figure 3
Figure 4
Figure 5
86
Volume Edit: Lung Segmentation
Exercise 36
In this exercise we will review lung segmentation from preclinical mouse data. We will cover additional segmentation and processing tools available
in the module, including object separation and morphological operations dilation, erosion, and fill holes.
1.
Download the mouse dataset Mouse_Lungs from www.

analyzedirect.com/data.
2.
Unzip the data and then use File > Load to load the Mouse
data set into Analyze.
3.
Next select Process > Spatial Filters to apply a 3 x 3 x 3

median filter to the data set. See Exercise 27: Spatial Filters
for instructions on applying a filter to a data set.
4.
Next select the filtered data set (Mouse_Lungs_Med) and

open Segment > Volume Edit.
5.
Click Add Object, change the name of the new object to

Lungs.
6.
Next select the Semi-Automatic tab and choose Object

Extractor (figure 1).
7.
Using the slider under the transverse image move

to slice 210, now click inside the lungs to set a
seed point.
8.
Use the threshold slider to define a threshold range

with a minimum of 1200 and maximum of 1550
(figure 2). Then click the Extract Object button.
9.
If necessary repeat the object extraction steps to

add any missed regions to the Lung.
Figure 2
Figure 1
10. To separate the trachea from the lungs add a new

object, click Add Object and name the object
Trachea&Bronchi (figure 3).
Figure 3
87
Exercise 36
11. Next select Object Separator.

Click on the trachea to set a
seed point then click on the
lungs to set a second seed
point. Note you can click
on either the 3-D rendering
or the 2-D slices. Next click
Separate.
12. Review the separation results.
Repeat the object separation
steps to separate any
remaining areas of the trachea
from the lungs (figure 3).
13. Select the Trachea&Bronchi
object in the Object list and
then click the Delete button to
remove the object.
14. To obtain a total lung volume
measurement it may be
necessary to fill any holes in
the lungs. To do this use the
morphological tools in the
Objects window. Select View >
Objects, set Object to Lungs
and then click on the Morph
Objects button.
Figure 3
88
Exercise 36
15. In the Morph Objects window set the following parameters (figure 5):

Objects to Lungs
Operation to Dilate
Element Shape to Jack
Element Size to 5 by 5 by 5
Defined Object to Lungs

16. Click Morph. The Lungs object will be dilated. Now, set the following
parameters (figure 6):

Objects set to Lungs

Operation to Fill Holes
Fill Type to 3 pass 2D; Transverse; and 4-connected
Defined Object to Lungs
17. Click Morph. The Lungs object will be filled.

Figure 4
18. Finally set (figure 7):

Objects to Lungs
Operation to Erode
Element Shape to Jack
Element Size to 5 by 5 by 5
Figure 5
Defined Object to Original

19. Click Morph. The Lungs object will be eroded. Click Done to
dismiss the Morph Objects window.
20. Save the object map by selecting File > Save Object Map.
21. Note that the lung volume can be measured using the Measure >
Region of Interest module. For more information please refer to
Exercise 55: Region of Interest - Measuring Objects in Object
Maps.
22. Exit the Volume Edit module.
Figure 6
Figure 7
89
Volume Edit: Advanced Segmentation
Exercise 37
In this exercise we will review some of the additional tools and options in the Volume Edit module designed to enhance your segmentation
capabilities. The exercise will demonstrate the application of the Edge Strength and Walls tools to set 3D limits on the image data set. The
exercise will then explore the Object Extractor, Object Separator, and Oblique Cutting options.
1.
Download the Cardiac_CT.avw data set from www.

analyzedirect.com/data. Unzip the file and then use
File > Load to load the data set into Analyze.
2.
Select the Cardiac_CT data set and open Segment >

Volume Edit.
3.
In the Edge Strength tab check the Use Edge

Strength.
4.
Set Edge Strength Threshold to 94 (figure 1). Note: The

Edge Strength option allows users to mask the loaded
volume with a threshold range of sobel filter gradients,
aiding with the segmentation of objects.
5.
Next select the Walls tab. Check Define walls to limit

semi-automated operations. Now select Draw Wall
and then set Wall Type to Line (figure 2).
6.
Using the slice slider below the transverse image, move

to slice 138. Draw a line along the mitral valve between
the left ventricle and left atrium (figure 3).
7.
Now move to transverse slice 171. Draw another

line along the mitral valve (figure 4). Note: Using the
transverse slice slider move back to slice 138. Note
that the wall defined between slice 138 and 171 has
interpolated between the two positions over the slices
in between. This wall will act as a 3D limit across the
volume aiding with segmentation of the data. Move
back to slice 171 before proceeding.
8.
In the object control panel click the Add Object button
Figure 1
Figure 2
Figure 3
Figure 4
90
Exercise 37
(figure 5).
9.
Select the Semi-Automatic tab and choose the

Object Extractor option.
10. Using the Sagittal slice slider move to slice 228.

11. Click in the middle of the left atrium to set a seed
point (figure 6). Set the following threshold range:
Minimum: 235 and Maximum: 2213.
12. Click Extract Object (figure 7). Note: The 3D
limits specified by defining walls in the transverse
orientation prevented the aorta from being included as
part of this segmented object.
Figure 5
Figure 6
13. Click the Add Object button and move to transverse

slice 262.
14. Click in the middle of the aorta to set a seed point
(figure 8). Note: The module remembers the previous
threshold range set (if the seed pixel value is within
the threshold range) and will automatically populate
the minimum and maximum threshold values.
15. Click Extract Object (figure 9).
16. To enable the transparency rendering view right-click
on the rendering and select Transparency.
17. Click Add Object.
Figure 7
Figure 8
91
Exercise 37
18. Next select the Object Separator option.

19. On the rendering click to set a seed point on the aorta.
20. Then set a second seed point on the left ventricle below the
aortic valve.
21. Now click Separate. The aorta will be split into two objects
(figure 10).
22. Click Add Object.
23. Now select the Browse tool. Using the middle mouse button
(or the left-mouse button + CTRL key) rotate the rendering of
the heart so you can clearly see the pulmonary vein.
24. Select the Oblique Cutting option and then click on the
pulmonary vein. The Volume Edit interface will update to
show the Oblique Cutting interface. Note: The oblique
plane can be moved or rotated interactively using the
orthogonal images or the rendering.
Figure 9
Figure 10
25. Right-click in the oblique image and select the

Dimensions/Increment option. Set the Width to 50 and
the Height to 50, then click Done.
26. Click the Cut button in the manual control panel to
separate the pulmonary vein into the new object (figure 11).
27. Click Browse to return to the regular Volume Edit interface.
28. Select File > Save Object Map to save your work.
29. Close the Volume Edit module.
Figure 11
92
Volume Edit: Liver Segmentation
Exercise 38
Manual segmentation is often necessary when semi-automatic segmenation fails. While manual segmentation can be time consuming, Analyze has
tools to speed up segmentation time. The propagate regions option uses shaped-based interpolation to extend the definition a region to slices on
which it was not defined. For example, if the user defined a region on every third slice, the tool could be used to fill in the region on the slices in
between.
1.
Load the CT_Liver.avw data set from the $:\BIR\images\

2.
Open the Volume Edit module (Segment > Volume Edit).
3.
Click on the Intensities button and adjust the minimum and

maximum intensities.
4.
Use the slice slider bar underneath the Coronal view and
navigate to slice 100
5.
Select the manual tab and then the Spline Edit tool. Check the
Smart Edge option and set the Sensitivity to 3.
6.
Begin clicking around the outside of the liver on the Coronal

slice 100 (figure 1). Once finished double click to close the
spline.
7.
Once the spline has been closed and the points are correctly
set, click Apply.
8.
Navigate to Coronal slice 125. Use spline edit to define the liver
and click Apply.
9.
Repeat the same process for Coronal slice 150 & 175 (figure 2).
note
- Control points can be moved using the middle mouse button (or
<Shift> + Left mouse button).
- To add a control point click with the left mouse button.
- To delete a control point, right click on the control point and select
Delete Control Point.
Figure 1
Figure 2
93
Volume Edit: Liver Segmentation
Exercise 38
10. Select the Semi Automatic tab and click on the

Propagate Objects option.
11. Set the Propagation Type to the Current Object
and select Coronal.
12. Click Propagate.
13. The module will use shape-based interpolation
to generate regions on the slices between the
defined regions (figure 3).
14. Close the module before proceeding to the next
exercise.
Figure 3
94
Morphology
Exercise 39
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.
Open the Morphology module (Segment > Morphology).
3.
From the Generate menu, open the Slice tool. Move the slice slider to slice 130.
4.
Open the Step Editor window (Generate > Step Editor) (figure 1).
5.
Click the Threshold button. 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.
6.
Select Generate > Display Section(s) > Current to review that data.
7.
Select File > Save Volume. Save the volume as MRI_3D_Head_bin.
8.
Click the Erode button. In the Step 2: Erode window, change the Element
Depth to 3 and change the value Iterations to 2. Click Erode Volume (figure 2).
9.
In the Step Editor window, click Transform Volume. A dialogue box will be
returned, select Yes.
10. Click Connect. Change Max. No. of Components to 1. Click Connect Volume.
Figure 2
11. In the Step Editor window, click Conditional Dilate. 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.
Figure 1
12. To view your segmentation, select Generate > Display Section(s) > Current (figure 3).
13. 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.
14. When you are finished reviewing, close all windows related to the Morphology module
before proceeding to the next module.
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.
Figure 3
95
Watershed: Automated Segmentation
Exercise 40
The goal of this exercise is to demonstrate how to automatically strip the skull from in a T1- or T2-weighted MRI scan.
1.

directory.
2.
Open the Watershed module (Segment > Watershed).
3.
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).
4.
Click Watershed Segment Volume to initialize the automatic segmentation.
5.
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.
6.
With the Render Selected Object option selected, click on the object that
represents the brain in the image display.
7.
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.
8.
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.
9.
Figure 1
The File menu provides options to save the segmented volume, the masked volume,
and create an object map of the segmented object.
10. 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.
11. Close all windows before proceeding to the next exercise.
Figure 2
96
Exercise 41
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.
2.
Open the Multispectral Classification

module (Segment > Multispectral
Classification).
3.
Open the Scattergram window (Samples

> Scattergrams).
4.
In the Scattergram window (figure 1), move

the Slice slider bar 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
next to the Slice slider bar.
5.
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).
6.
Choose class 2 from the Classes drop-down menu before starting

the trace. Select the Curved Line tool and define a small region of
grey matter (peripheral brain tissue) as class 2. The paired values
will show as green in the scattergram and in the image display.
7.
Select the Closed Trace tool and define a small region of

cerebrospinal fluid (in the central ventricles) as class 3.
Figure 1
Figure 2
97
8.
Click Classify Images. The Gaussian Scattergram

Classifier window will automatically be returned (figure 3),
click Classify. Click Done to dismiss the window.
9.
In the main Multispectral Classification window, the

classified image will be returned (figure 4).
Exercise 41
10. 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 5).
11. 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.
12. Close the Multispectral Classification module before
Figure 4
Figure 3
Figure 5
98
Object Extractor: Automated Brain Segmentation
Exercise 42
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.

directory.
2.
Open the Object Extractor module (Segment > Object Extractor).
3.
Open the Define Region window (Generate > Define Region) to begin the
segmentation process.
4.
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 Target Slice directly below the slider bar.
5.
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.
6.
The Define Region window will automatically update (figure 1) to display auto trace
parameters. Use the double-ended slider bar now available to set the Threshold
Minimum to 49 and the Maximum to 140.
7.
Click Extract Object to start the object extraction process. The grayscale copy of
the extracted object will automatically be saved to the Analyze workspace.
8.
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).
9.
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.
Figure 1
10. 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.
11. Close the Object Extractor module before proceeding to the Additional Tasks.
Figure 2
99
Object Extractor: Creating an Object Map
Exercise 42.1
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.
Select the MRI_3D_Head.avw data set loaded in the Analyze

workspace and open the Object Extractor module (Segment
> Object Extractor).
2.
Open the Define Region window (Generate > Define Region)

and set the Target Slice to 141.
3.
Click inside the brain to set a seed point. Set the Threshold
4.
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.
5.
In the Define Region window, click Extract Object to start the

object extraction process.
6.
Once the extraction process is complete the object will be

displayed in the Render Tool (figure 3), allowing you to view the
object from different orientations.
7.
The object map will not be automatically saved, if you wish to

save the object map choose File > Save Object Map.
8.
Close the Object Extractor module. To learn how to create a

binary object with the Object Extractor proceed to the next
Additional Task.
Figure 1
Figure 2
Figure 3
100
Object Extractor: Creating a Binary Object
Exercise 42.2
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.
Select the MRI_3D_Head.avw data set loaded in the Analyze

workspace and open the Object Extractor module (Segment
> Object Extractor).
2.
Open the Define Region window (Generate > Define Region)

and set the Target Slice to 141.
3.
Click inside the brain to set a seed point. Set the Threshold
4.
Click Extract Options and set the Result to Binary (figure 1).
Click Done to dismiss the Extract Options window.
5.
In the Define Region window, click Extract Object to start the

object extraction process.
6.
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.
7.
Close the Object Extractor module before proceeding to the

next Additional Task.
Figure 1
101
Object Extractor: Automatic Brain Stem Removal
Exercise 42.3
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.
Select the MRI_3D_Head.avw data set loaded in the Analyze workspace

and open the Object Extractor module (Segment > Object Extractor).
2.
Open the Define Region window (Generate > Define Region) and set the
Target Slice to 141.
3.
Click inside the brain to set a seed point. Set the Threshold Minimum to 49
and the Maximum to 140.
4.
Click Extract Options and set the Remove Stem option to On (figure 1).
Click Done to dismiss the Extract Options window.
5.
In the Define Region window, click Extract Object to start the object
extraction process.
6.
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 grayscale brain will be automatically
saved to the Analyze workspace and can now be used with any other
Analyze module.
7.
Close the Object Extractor module before proceeding to the next exercise.
Figure 1
Figure 2
102
Object Extractor: Extracting Multiple Objects
Exercise 43
The Object Extractor module supports the creation of multi-object object maps. This exercise will demonstrate the segmentation
and separation of the lungs.
1.
Load the CT_Lungs.avw data set from the $:\BIR\images\

2.
Open the Object Extractor module (Segment > Object Extractor).
3.
Open the Define Region window (Generate > Define Region) to begin
the segmantation process.
4.
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.
5.
Position the cursor near the center of the left lung and click to set a
seed point.
6.
The Define Region window will automatically update (figure 1) to

display auto trace parameters. Use the double-ended slider bar now
available to set the Threshold Minimum to 18 and the Maximum to
99.
7.
Click the Extract Options button, and set the Result to Object (figure
2), select Yes in the window returned.
8.
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.
9.
Open the Define Regions window again, when opened click the Clear
Regions button. Next, click in the right lung to set a seed point, set the
Threshold Minimum to 18 and the Maximum to 104.
Figure 1
10. 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).
Figure 2
Figure 3
103
Object Extractor: Extracting Multiple Objects
Exercise 43
11. The render window will now display both lungs in 3D (figure 4).
12. 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).
13. To save the object map for use in other modules, select File > Save Object
Map.
14. Close all windows related to the Object Extractor module before proceeding to
the next exercise.
Figure 4
Figure 5
104
Surface Extractor: Polygonal Surface Extraction
Exercise 44
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.

directory.
2.
Open the Surface Extractor module (Segment > Surface Extractor).
3.
Choose File > Load Object Map and load the MRI_3D_Head.obj object map.
4.
Open the Extraction Parameters window (Generate > Extraction).
5.
Click Objects 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 (figure 2). Click Done to dismiss the window.
6.
Create a polygonal surface of the Brain object using the

Adapt/Deform algorithm with the default parameters. With the
AdaptDeform tab selected click Extract.
7.
A dialog box will be returned stating the number of polygons

generated. Note the number of polygons (approximately 37,258),
then click Done.
8.
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 3).
9.
In the Extraction Parameters window change the Cube Edge Size to 5

and rebuild the surface by clicking Extract. Note, the number of polygons
generated (approximately 12,261), then click Done.
10. Choose Generate > Render to view the extracted surface with the new
parameters (figure 4). 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 1
Figure 3
Figure 4
105
Surface Extractor: Polygonal Surface Extraction
Exercise 44
11. Click Reset in the Extraction Parameters window to restore the default
parameters (Cube Edge Size of 3).
12. Click Advanced and change the Time Step to 0.5. Click Done to dismiss the
window.
13. Rebuild the surface by clicking Extract in the Extraction Parameters window.
Note the number of polygons generated (approximately 37,258), then click
Done.
14. 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.
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).
Figure 5
16. Choose File > Save Surface > To File to save the extracted surface to disk.
17. In the Save Surface window returned (figure 6) 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),
Ply(.ply) Poly (.poly), 3D Systems (.stl), Binary 3D Systems (.stl), Vrml (.wrl).
18. Close the Surface Extractor module. To learn about extracting the surface of a
binary data set, complete the following Additional Task.
Figure 5
106
Surface Extractor: Extracting a Binary Data Set

1.
Load the MRI_3D_Brain_Bin.avw data set from the $:\BIR\images\

2.
3.
4.
With the AdaptDeform algorithm tab selected, click Extract.
5.
Note the number of polygons generated (approximately 37,504) and choose

Generate > Render to view the extracted surface (figure 1).
6.
Close the Surface Extractor module before proceeding to the next exercise.
Supported Surface File Formats

Polygonal Formats
Alias Wavefront
Autocad
IGES
Compressed IGES
Inventor
Patran
Poly
Binary 3D Systems
VRML
Contour Formats
HP 3D
IGES
Compressed IGES
Pogo
3D Systems Stereolithography
ASCII Columns
Exercise 44.1
Figure 5
(.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
(.hpgl) Write only
(.iges) Write only
(.iges) Write only
(.slc) Read and Write
(.slc) Read and Write
(.txt) Read and Write
107
Surface Extractor: Contour Surface Extraction
Exercise 45
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.

directory.
2.
3.
Choose File > Load Object Map and load the MRI_3D_Head.obj object map.
4.
5.
Click Objects 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
6.
Create a contour surface of the Ventricle object using the Contours algorithm
with the default parameters. Select the Contours tab and click Extract.
7.
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.
8.
To create a rendering of the extracted contour model, choose Generate >

Render.
9.
In the Extraction Parameters window, click Advanced in the Contours tab.

Check the Subvolume Extraction option and click Done to dismiss the
window (figure 2).
10. 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.
Figure 1
Figure 2
11. Choose Generate > Render to create a rendering of the extracted contour
model (figure 3).
12. Close the Surface Extractor module before proceeding to the next exercise.
Figure 3
108
Registration
109
2D Registration
Exercise 46
The 2D Registration module determines geometric transformation parameters which can be used to align 2D images, section to section by
matching common contours or by matching sections to a single base slice. This exercise will demonstrate how to do this using the 2D Registration
module to align a series of misaligned 2D slices.
1.
Load the Spinal_Cord data set from the $:/BIR/images/TutorialData

folder.
2.
Open the 2D Registration module (Register > 2D Registration).
3.
Open the Cursor Link Tool (Tools > Cursor Link).
4.
Choose a Blend from the right-click menu in the upper right pane.
5.
To review the data slice by slice, use the Match Section slider bar.
6.
If required, slice data can be manually adjusted using the manual adjust
control operations.
7.
The % Base Image allows the combined image display (upper right
pane) to fade between the base and match image.
8.
Open the Control window (Generate > Control).
9.
Choose between a Sequential or Single reference registration mode

(figure 2):
Sequential: each slice will register sequentially to its neighbor (ie
slice 2 to slice 1, slice 3 to slice 2, etc.)
Single Reference: will register each slice to a
single base slice (defined with the To Section
slider).
10. The Register Section and Thru slider bars allow

users to determine a range of slices to be registered
(ie slices 10-20 only).
Figure 1
11. Set the registration mode to Sequential, then click

Done.
Figure 2
110
2D Registration
Exercise 46
12. Open the Voxel Match window (Generate > Voxel Match), expand
the Threshold, Sample Region and Search Parameters options
(figure 3).
13. Check the Show Thresholding option the image, the cursor link
tool will update converting the images to binary representations.
Only voxels displayed as white will be considered for the
registration.
14. Set the Minimum threshold value to 5 to eliminate background
noise. Then uncheck the Show Thresholding option.
15. The Sample Region option will allow for defining a region to
consider for registration. See the X Minimum to 69 and the X
Maximum to 333. Then set the Y Minimum to 33 and the Y
Maximum to 237. Reset the Min/Max X and Y values before
proceeding. Note the region is defined on the blended and match
image (figure 4).
16. The Search Parameters option allows users to adjust the X and Y
Translation range, the Z Relation range and the X and Y Scaling
range.
17. Click Register. Select Generate > Transform Slices, set the
Destination to Analyze Workspace, then click Go. The data will be
transformed and saved to the Analyze workspace.
Figure 3
18. Compare the input and output data sets to see the effect of the
registration on the data.
Figure 4
111
2D Non-Rigid Registration
Exercise 47
The 2D Non-Rigid Registration module applies local Normalized Mutual Information (NMI) image registration in a grid of subregions. The optimized
local registration transformations are then interpolated across the image to effect a continuous non-rigid transformation. This exercise will
demonstrate how to register two adjacent sections to correct for the difference stretching forces each section has been subjected to.
1.
Load the AdjacentSections data set from the C:/BIR/images/TutorialData

folder.
2.
Open the 2D Non-Rigid Registration module (Register > 2D Non-Rigid).
3.
Open the Control Window (Generate > Control) (figure 1). Two Registration
Modes are provided, Sections or Slabs.
Sections: allows for each image to be non-rigidly registered to the next.
Slabs: registration will only be performed at Interfaces between slabs,
during transformation the non-rigid transformation is relaxed through the
slab.
4.
Set the Registration Mode to Sections. You can now choose between a
Sequential or Single Reference registration.
Sequential: specifies that each section will register sequentially to its
neighbor.
Single Reference: will register each slice to one
base slice, the To Section slider is used to select
the base.
5.
Select Sequential (figure 2). Do not close the

Control window.
6.
Open the Cursor Link tool (Tools > Cursor Link).

The Cursor Link window displays two sections; the
Base and Match, in their current registration, as
well as the two sections overlaid. Right click in the
overlay window and select a Blend option from the
Blend Mode menu.
Figure 1
Figure 2
112
7.
By default, the Match section displays the current minimum region grid (the
grid of subregions the local NMI is applied to), shown in green. Note there are 4
regions, to adjust the region size use the Minimum Region Size X and Y sliders
To increase the number of regions from 4 to 9, set the X slider to 112 and the Y
slider to 119.
8.
Note the orange box in the overlay window shows the current selected region.
To switch this on in the Base and Match windows right-click and select the
Selected Region option (figure 3).
9.
Manual transformations and rotations can be applied to the current selected

region in the Match image using the Manual Adjustment buttons. Because the
regional displacements are interpolated across the image, some transformations
may also affect adjacent areas of the image. The Resolution options (Coarse,
Medium or Fine) below the Manual Adjustment buttons control the amount of
displacement. Note, Fine resolution is a one pixel translation or one degree
rotation, Coarse is approximately ten.
Exercise 47
10. Click on the Non Rigid Parameters button.

11. In the Non-Rigid Match window (figure 4), review the following options:
Threshold: Check the Show Thresholding option and note the update
in the image display as you adjust the threshold range. Only voxels
displayed as white will be considered for the registration.
Samples: specifies the minimum and maximum sampling density.
Process: these options set limits of confidence on the registration
procedure.
Figure 3
12. To Register the sections sequentially click the Register All Sections
button in the Control window.
13. After registration is complete select Generate > Transform Slices from
the main 2D Non-Rigid Registration window. In the Transformation
window returned, set the Destination to Analyze Workspace and set the
Interpolation option to Linear (default), next click GO. The transformed
image data will be saved to the Analyze workspace.
14. Close the 2D Non-Rigid Registration module.
Figure 4
113
Exercise 47
15. Review the original data and then the registered data (Match2D_out) using the Multiplanar Sections module. Observe the difference in
the slice data between the two data sets, specifically slices 2 and 3 in the registered data set (figure 6).
Figure 5
Figure 6
114
3D Surface Registration
Exercise 48
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.
Load the Edited_MRI_Head.avw and the Edited_

PET_Head.avw data sets from the $:\BIR\images\
2.
Select the Edited_MRI_Head.avw data set, then while

holding down the <Ctrl> key, select the Edited_PET_
Head.avw data set.
3.
Open the 3-D Surface Registration module (Register

> 3-D Surface).
4.
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.
5.
Open the Blend window (Generate > Blend). Set the

Blend Type to Green-Red.
6.
Examine the combined images to determine if they

need to be registered.
7.
Select Generate > Register to register the two

volumes.
8.
Select File > Save Transformed and save the

transformed PET to the Analyze workspace.
9.
Close the 3-D Surface Registration module before

115
3D Voxel Registration
Exercise 49
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.
Load both the MRI_Head.avw and PET_Head.avw data sets from

the $:\BIR\ images\TutorialData directory.
2.
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).
3.
Open the 3-D Voxel Registration module (Register > 3-D Voxel).
4.
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.
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) prescaled 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.
Figure 1
116
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.
8.
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.
9.
Right-click on any of the image display panes to view options for controlling individual
tiles, reference lines, image sizes, annotations, and interactivity.
Exercise 49
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.
11. 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.
12. 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.
Figure 2
13. 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.
Figure 3
117
Exercise 49
Saving Transformed and Fused

14. 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).
15. To save the fused volume, choose File > Save Fused; the fused
volume can be saved to disk or to the main Analyze workspace.
16. Close the 3-D Voxel Registration module before proceeding to the
Additional Task.
Figure 6
118
3D Voxel Registration: Manual Scale Adjustment
Exercise 49.1
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.
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).
2.
Open the 3-D Voxel Registration module (Register > 3-D Voxel).
3.
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.
4.
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.
5.
Close all windows associated with the 3-D Voxel Registration module before
Figure 1
119
3D Voxel Registration: Mutual Information
Exercise 50
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.
Load both the Register_MRI_Base.avw and Register_

MRI_Match.avw data sets from the C:\BIR\images\
2.
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).
3.
Open the 3-D Voxel Registration module (Register > 3-D

Voxel).
4.
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.
5.
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 (figure 1).
6.
Press the Register PowerBar button or choose Generate

> Register.
7.
Examine the center Fused column of the main module

window (figure 1). As you can see, the registration is not
acceptable.
Figure 1
120
3D Voxel Registration: Mutual Information
Exercise 50
Manual Adjustment
8.
Since the registration is not acceptable, manually adjust the starting point
of the registration. Open the Manual tool (Tools > Manual).
9.
Click Reset Matrix in the Manual tool (figure 2), this will reset the match
volume to the original starting position.
10. Now, using the Manual tool options, move the match volume to a better
starting position and press Register.
11. If the registration is still not acceptable, return to the Manual tool and
click Reset Matrix again.
12. Now, select the Coarse adjustment option and press the down arrow
button once.
13. Change the orientation from coronal to sagittal by selecting the S-cube
and then press the right arrow button once.
14. Press Register. The volumes should now register correctly.
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.
Figure 2
16. To save the fused volume, choose File > Save Fused; the fused volume
can be saved to disk or to the Analyze workspace (figure 3).
17. Close the 3-D Voxel Registration module before proceeding to the next
exercise.
Figure 3
121
Exercise 51
Non-rigid registration allows for non-linear deformation in the registration transformation between volumes. This exercise will demonstrate how to
use the 3D Non-Rigid Registration module.
1.
Load both the Heart_Time_Point_1.avw and Heart_Time_Point_2.

avw data sets from the C:\BIR\images\TutorialData directory.
2.
In the Analyze workspace, first select the Heart_Time_Point_1

data set. Then, while holding down <Ctrl> select the Heart_Time_
Point_2 data set (resulting in both being selected).
3.
Open the 3-D Non-Rigid Registration module (Register > 3-D

Non-rigid).
4.
Choose File > Input/Output Ports to ensure that Heart_Time_

Point_1 is assigned as the Base Volume and Heart_Time_Point_2 is
assigned as the Match Volume (figure 1).
5.
To open the Cursor Link tool (figure 2), select Tools > Cursor Link.
The cursor link will allow you to interactively review the data.
6.
To change the orientation, open View > Orientation, select

Coronal. To change the size of the data, select View > Size.
7.
To set a blend mode, right click in the top-right display pane.

Use the Section slider to navigate through the data.
Figure 1
Figure 2
122
8.
Exercise 51
Open the Generate > 3D Non-Rigid NMI window. This window gives
the following options:
Threshold: specifies the clip values applied to the volumes before
attempting registration. Check the Show Thresholding option and
note the update in the Cursor Link image display as you adjust the
threshold range, only voxels displayed in white will be considered
for registration.
Minimum Region Size: specifies the scales at which the
registration is conducted.
Samples: defines the number of samples used in each region for
which the Mutual Information cost function is evaluated.
Process: sets limits of confidence for the registration.
Minimum Entropy: specifies the minimum histogram entropy in a
subregion in order to be registered.
Minimum NMI: specifies the minimum NMI value for a registration
result to be considered valid.
9.
Once you have defined your parameters in the 3D Non-Rigid NMI

window, click Register to initiate the non-rigid registration process.
10. Once the registration is complete, review in the Cursor Link tool
(figure 3).
11. To output the transformed match volume to the Analyze Workspace,
select Generate > Transform.
123
Exercise 51
12. Use the Volume Compare module to compare the original Heart_Time_Point_1 and Heart_Time_Point_2 data sets
(figure 4). Then compare the original Heart_Time_Point_1 and the transformed Heart_Time_Point_2 data set (figure 5).
Figure 4
Figure 5
124
Measurement
125
Line Profile: Intensity-based Line Measurement
Exercise 52
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. Load the MRI_3D_Head.avw data set from the $:\BIR\images\TutorialData
directory.
2.
Open the Line Profile module (Measure > Line Profile).
3.
Use the slice slider to move to slice 97.
4.
To calculate the intensity values along a straight line in this slice, select the Line
tool in the main Line Profile window (figure 1).
5.
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.
6.
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.
7.
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.
8.
Select the Trace tool in the main Line Profile window to draw a
freehand trace.
9.
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.
note
To log FWHM, open the

Profile Options window
(Generate > Profile) and set
Full Width Half Max to On.
Figure 1
10. Close the Line Profile module before proceeding to the Additional Task.
Figure 2
tip
Figure 3
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.
126
Line Profile: Radial Sequence Tool

1.
The Radial Sequence tool in the Line Profile module

enables users to sample a radial sequence of profiles.
2.
Load the VH_Abdomen.avw data set from the $:\BIR\

3.
Open the Line Profile module (Measure > Line Profile).
4.
Open the Profile Options window (Generate > Profile) and

set Full Width Half Max to On.
5.
Select the Line tool and then draw a line starting in the
middle of the right femur, finishing outside (figure 3).
6.
Open the Radial Sequence tool (Generate > Radial

Sequence).
7.
Set the Angle Increment to 10. When sampling a radial

sequence the angle is incremented until a full 360 degrees
from the starting position has been sampled.
8.
Set Log Profile, Log Stats, and Log FWHM to On.
9.
Click Sample Radial Sequence.
Exercise 52.1
10. 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.
11. Close the Line Profile module before proceeding to the next
exercise.
Figure 4
Figure 5
127
Region of Interest: Defining Regions
Exercise 53
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.
Open Region of Interest (Measure > Region of Interest).
ROI Interface
3.
4.
5.
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*** 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 (figure 2). The buttons below the image
display allow you to modify the defined regions (figure 3).
Figure 3
Figure 2
The first slice of the volume is automatically displayed when the ROI module is
opened. You can move to a different slice by using the Slice slider bar or + and - on
your keyboard. The currently displayed slice number and orientation can always be
seen in the lower left corner of the image display.
Figure 1
Rectangle Tool
6.
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 1.Object will be created and added to
the object map (figure 4).
7.
Copy the region to the next slice (slice 2) by pressing the Copy Regions Forward
PowerBar button once.
8.
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).
tip Holding the
<Ctrl> key
while sizing
will force a
square.
Figure 4
128
Exercise 53
Oval Tool
9.
Add a new region to slice 2 using the Oval tool (figure 5).
10. Press Copy Regions Forward to copy the regions to slice 3.

11. 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 8. 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.
12. Move to slice 4.
Polygon Tool
13. There are currently no regions defined on slice 4, define a region on slice 4 using the Polygon
tool.
Figure 5
14. 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 6).
15. If after defining the region it is unsatisfactory, click the Undo button.
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.
Figure 6
129
Exercise 53
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.
19. To define a region without having to continuously hold down the mouse
button, right-click on the image display and choose the Button Passive
option. 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.
20. Right-click and deselect the Button Passive option. Then, click Clear
Regions on the left side of the window to clear all regions defined on this
slice.
21. With the Manual Trace tool still selected, check the Smart Edge option.
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.
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.
Figure 7
24. To modify the region with the spline control points, select the Move button
and then drag any control point to a new location.
130
Region of Interest: Intersecting Regions

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.
2.
Move to slice 7.
3.
Choose File > Reset Object Map to clear all regions from the volume. In
the dialog box returned, click Continue without Saving.
4.
Ensure that Intersections become part of: is set to Defined (figure 8).
5.
Select the Rectangle tool and define a region.
6.
Now, select the Oval tool and define a region that overlaps the rectangle.
7.
The intersecting area becomes part of the region being defined, 2.Object
(figure 8).
8.
Click Undo button and then set Intersections become part of: to
Existing.
9.
Select the Oval tool and again define a region that overlaps the rectangle.
Exercise 53.1
10. The intersecting area now becomes part of the existing region, 1.Object
(figure 9).
11. Click Undo and then set Intersections become part of: to New.
12. Select the Oval tool and again define a region that overlaps the rectangle.
Figure 8
13. The intersecting area now becomes a new region, 3.Object (figure 10).
14. Close the Region of Interest module before proceeding to the next
exercise.
Figure 9
Figure 10
131
Exercise 54
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.

directory.
2.
Open the Region of Interest module (Measure > Region of Interest).
3.
Using the slice slider below the image display, move to Slice 122.
4.
In the main ROI window, select the Auto Trace tool.
5.
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 doubleended slider bar (to specify a threshold range) and other Auto Trace parameters
(figure 1).
6.
Use the double-ended slider bar to set the threshold minimum to 34 and the
threshold maximum to 129. Then, click Apply. The double-ended slider bar will
disappear and the new region will be named 1.Object.
7.
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.
8.
Press Copy Regions Forward until the auto trace has been applied to all the
remaining slices containing brain matter, (until approximately slice 181).
9.
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.
10. 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
Figure 1
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.
Figure 3
132
Exercise 54
Measuring Regions
11. Open the Sample Options window (Generate > Sample Options).
12. 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
13. 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.
14. Click Sample Images. The module will now sample the defined object (Brain).
15. 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.
Figure 4
16. In the Sample Options window switch Summing to Off and

Sequence Display to On.
17. 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.
Figure 5
133
Region of Interest: Editing Regions

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.
2.
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.
3.
Next, use the slice slider below the image and move to slice 62.
4.
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.
5.
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.
6.
Open the Sample Options window (Generate > Sample Options) and set Summing
back to On and Sample to All Slices.
7.
Click Sample Images in the main ROI window to sample the Brain object as it is
defined on slices 66-181.
8.
Choose File > Save Object Map to save the object map with the Brain object.
9.
Close the Region of Interest module before proceeding to the next exercise.
Exercise 54.1
Figure 1
134
Region of Interest: Measuring Regions
Exercise 55
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.

directory. The data set may be available in the Analyze workspace if you have
completed exercise 45 or 46.
2.
Open the Region of Interest module (Measure > Region of Interest).
3.
Choose File > Load Object Map and load the MRI_3D_Head.obj object map from
the $:\BIR\images\TutorialData directory.
4.
Open the Objects window (View > Objects) and set Control by to Attribute.
5.
Notice that this object map contains several objects. With the Display attribute
selected, switch the Lenticular and Caudate objects to On.
6.
Using the slice slider below the image display, navigate through the volume, the
objects with the Display attribute set to On will be seen on the images (figure 1).
7.
Open the Sample Options window (Generate > Sample Options).
8.
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
9.
Click the Sample Images button to sample the Brain object.
Figure 1
10. 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.
Figure 2
135
Region of Interest: Measuring Regions
Exercise 55
11. Click Done to close the ROI Stat Log; in the dialog box returned
click Discard, then Exit.
12. In the Sample Options window, check the Ventricle, Lenticular,
and Caudate objects (the Brain object should already be
checked).
13. 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.
14. To have the volume of the objects added together automatically for
the total volume, set Combine Objects to Yes under the
selection area.
15. Click Sample Images. The total brain
volume will now be returned to the
ROI Stat Log (figure 4).
16. Save the .stats file.
Figure 3
136
Region of Interest: Histogram Analysis
Exercise 56
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.
Open the Region of Interest module (Measure > Region of

Interest).
3.
Use the slice slider directly below the image, and move to slice 97.
4.
Open the Histograms window (Generate > Histograms).
5.
In the Histograms window, set Histogram Display to On and set

Log Histogram to On.
6.
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.
7.
Figure 1
Close all windows associated with the ROI module.
Figure 3
Figure 2
137
Exercise 56
Sampling a Volume
1.
Select the MRI_3D_Head.avw data set and open the Region of

Interest module (Measure > Region of Interest).
2.

3.
Next open the Sample Options window (Generate > Sample

Options).
4.
In the Sample Options window, set Summing to On and set Sample

to All Slices (figure 4).
5.
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 rightclicking in it and selecting Save Log.
note
6.
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 4
Figure 5
138
Exercise 56
Sampling an Object
1.
Select the MRI_3D_Head.avw data set and open the Region of

Interest module (Measure > Region of Interest).
2.
Select File > Load Object Map and load the MRI_3D_Head.obj
from the $:\BIR\images\TutorialData directory.
3.
Open the Histograms window (Generate > Histograms).
4.

5.
In the Sample Options window set the following (figure 7):

Sample Type: Object(s)
Check only the Brain object
Summing: On
Sample: All Slices
6.
7.
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.
Figure 6
Figure 7
139
Importing .stats files into Excel
Exercise 57
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.
Open Excel, then select File > Open.
2.
In the Open window, select All Files (*.*) from the File Type
drop menu.
3.
Navigate to and open the .stats file.
4.
The Text Import Wizard will appear.
5.
In Step 1 of 3 Under Original Data Type select Delimited

and click Next at the bottom of the screen.
6.
In Step 2 of 3 of the Text Import Wizard, under the

Delimiters select Space, and deselect any other options.
Then click Next.
7.
In 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.
140
Stereology: Estimating Volume
Exercise 58
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.
Load the Canine_Chest_CT.avw data set from the $:\BIR\images\

2.
Open the Stereology module (Measure > Stereology).
3.
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.
4.
Open the Grid Parameters window (Generate > Grid) to set up a sampling grid
that encompasses the heart (figure 1).
5.
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.
6.
Click Generate Grid. Then, click Done to dismiss the Grid Parameters
window.
note
Figure 1
Any name can be chosen for the local database, however when creating multiple databases, following a coherent naming convention will simplify database management.
7.
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.
8.
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.
9.
Open the Statistics window (Generate > Statistics) to view the estimated
volume of the heart.
10. Close the Stereology module before proceeding to the next exercise.
Figure 2
141
Object Counter: Counting Cells
Exercise 59
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.
Load the FatCells.avw data set from the $:\BIR\images\TutorialData directory.
2.
Open the Object Counter module (Measure > Object Counter).
3.
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.
4.
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).
5.
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)
note
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. Hold <Ctrl> while tracing forces the
ellipse to be a circle.
6.
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.
7.
Use the Slice slider bar to move through the slices in the data set. Return to slice 1
before proceeding to the next step.
8.
Select the Limits tab. This tab allows interactive screening of segmented objects
based on position and shape characteristics.
9.
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).
Figure 1
142
Object Counter: Counting Cells
Exercise 59
10. Reduce the X Max to 470 using the arrow key and observe the effect (seen
along the right side of the image display).
11. 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.
12. Experiment with the effects of restricting Intensity, Diameter, Area, Perimeter,
and Rectangularity.
13. Select the Edit tab. This tab allows objects to be added, deleted, and
modified manually.
14. Select the Measure tab. This tab allows specification of the measurement
statistics to be returned in the Object Counter Stats window.
Figure 2
15. 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.
16. 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.
17. 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).
18. Experiment with other measurements available in the Measure tab.
19. 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.
Figure 3
143
Tree Analysis
Exercise 60
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.
Load the Coronary_CT.avw data set from the $:\BIR\images\TutorialData

directory.
2.
Open the Tree Analysis module (Measure > Tree Analysis).
3.
Open the Slice window (Generate > Slice) and set Slice to 64.
4.
Open the Generate Tree window (Generate > Generate Tree).
5.
Set the Threshold Minimum to 130 and Maximum to 255.
6.
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.
7.
Leave the Shortest Skeleton Branch and the Maximum/Minimum Tree Length fields
as their defaults.
8.
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.
9.
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. To view the trees generated in the extraction process, use the Tree drop-down menu in
the Tree Plot window. Select Tree 2.
11. Select all four of the Views buttons to display the left, top, right and bottom views of
the tree.
12. Check Render 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.
Figure 2
144
Tree Analysis
Exercise 60
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.
14. Now, set Action to Rotate. Click in any of the views and drag the
tree to a new rotation angle.
15. To return all views to their default display, right-click on any of the
views and select Reset.
Figure 3
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.
17. An entire tree can also be deleted by selecting the Delete Tree
button. Click Undo to recover deleted trees.
18. 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.
Figure 4
19. 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).
20. Select Stats at the bottom of the Tree Plot window.
21. 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.
22. 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.
Figure 5
145
Tree Analysis: Generating a Fly-Through Movie

1.
Check Internal from the Display options in the Tree Plot window (figure 1).
2.
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.
3.
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.
4.
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).
5.
Close the Tree Analysis and Movie modules before proceeding to the next
exercise.
Exercise 60.1
Figure 1
Figure 2
146
Apps & Add-Ons
147
SISCOM (Subtraction Ictal SPECT Co-registered to MRI)
Exercise 61
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.
Load the data sets SISCOM_Ictal_SPECT.avw, SISCOM_Interictal_SPECT.avw,

and SISCOM_MRI.avw from the $:\BIR\images\TutorialData directory.
2.
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 selected in this
order the SISCOM procedure will fail to run correctly.
3.
Open the SISCOM module (Apps > SISCOM).
4.
Open the Register SPECT option (Process > Register SPECT) to compute an
activation map.
i. Set the Interictal SPECT minimum Cerebral Activity Threshold level to 75.
Note the change in the binary image.
ii. Ensure that the Interictal Transformation Type is set to Linear.
iii. Use the Activation Level slider bar to set the standard deviation to 2.0.
iv. Next, select the Register and Map button. The Register SPECT tool will
automatically register, normalize, subtract, select the statistically
significantv oxels of activation, and output the activation map based on the
parameters specified above. Note that the tool will update, displaying the
Activation Map.
5.
Figure 1
Select Next to continue onto the next step of the SISCOM procedure, MRI brain
extraction.
148

6.
The Extract MRI Brain tool allows for segmentation of the

brain for SPECT-MRI registration.
7.
Right-click in the MRI data display window and select the

Intensities option. In the Intensity (MRI) window returned,
change the Maximum to 100 then click Done to close the
Intensity Tool.
8.
Use the slider bar to adjust the minimum and maximum

threshold values to obtain the best definition of the cortical
boundary as possible.
9.
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).
Exercise 61
10. Select Next to continue to the next step, registration of the

SPECT data sets to the MRI data sets.
11. 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).
Figure 2
12. 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.
Figure 3
149
Exercise 61
13. 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 to select the volumes to compare (figure 4). Select
Done when review is complete.
14. Select the Create Object Map option from the File menu to generate
an object map based on the areas of activation.
15. 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.
16. Close all windows related to the SISCOM module before proceeding to
the next exercise.
Figure 4
Figure 5
150
Mayo 3D Brain Atlas
Exercise 62
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, atlasderived 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.
Load the MRI_3D_Head data set from the C:\BIR\images\TutorialData

directory.
2.
Select the MRI_3D_Head data set then open the Mayo 3-D Brain Atlas
module (Apps > Mayo 3D Brain Atlas).
3.
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 TalairachTournoux coordinate and proportional grid system.
4.
Open the Align AC-PC window (Tools > Align AC-PC).
5.
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.
6.
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).
7.
Select the PC point and move it to the appropriate location.
8.
Select Align AC-PC. The image volume will realign to the AC-PC.
9.
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.
Figure 1
10. Check the Fill Holes after Extraction option and then select Extract Brain.
11. The extracted brain can be reviewed using the Slice slider bar (figure 2).
Figure 2
151
Mayo 3D Brain Atlas
Exercise 62
12. 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.
13. 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.
14. 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.
15. To query specific structures by coordinates, navigate back to the
main module window and select the Query Atlas button from the
PowerBar.
16. 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.
Figure 3
17. In the Adjust Registration window, move the Yellow marker to a

location you wish to query.
18. In the Query Atlas window click the Query button, the structure and
location of the Yellow marker will be returned.
19. 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.
20. Close the Query Atlas and Adjust Registration windows.
Figure 4
152
Mayo 3D Brain Atlas
Exercise 62
21. To save the atlas as an object map open the Generate Output
window by clicking on the Output button in the PowerBar.
22. 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
23. 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.
24. Select Generate Output. The object map will be saved as
AtlasOutput_MRI_3D_Head.obj in the specified directory.
Figure 5
25. Select Done in the Generate Output window and close the Mayo 3D
Brain Atlas.
26. 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.
27. Close all windows before proceeding to the next exercise.
153
Diffusion Tensor Imaging (DTI)
Exercise 63
The Analyze MR Diffusion Tensor Imaging add-on computes and saves the primary diffusion maps from diffusion-encoded MRI data. The module
also provides standard visualizations of DTI data and includes white fiber tracking and visualization (Tractography). This protocol will demonstrate
how to compute DTI maps as well as compute and display fibers.
Loading DTI data and Computing DTI Maps

1.
To load in a series of DTI data open the DICOM Tool (File

> DICOM Tool), then import the DICOM images (File >
Import Dicom Images). Navigate to the folder containing
the DTI data, and click OK. A dialogue window will be
returned asking if you would like to import all DICOM files
found below that directory, click Yes.
2.
Select all the DTI files and click Load Volume. In

the dialogue window returned, select Create a 4D
Multivolume.
3.
Once the volumes are loaded into the workspace, select

the appended multivolume (Figure 1).
4.
Open the DTI module (Apps > DTI), the module will open
to the Config tab (figure 2).
5.
Analyze will attempt to automatically load the gradient

directions. If the gradient directions are not automatically
loaded, click the Load Gradient Directions button and
select a text file with the gradient directions already logged.
6.
The data may require a flip along an axis.
7.
Select the Map Processing tab.
8.
Set a threshold so the background noise is set to white,

any voxels displayed in white will not have map values
computed (figure 3). Click Compute DTI Maps.
Figure 1
Figure 2
Figure 3
154

9.
Exercise 63
After the DTI Maps have been computed, select File > Save DTI
Maps. In the window returned, set the Destination to Analyze
Workspace and click Save Volume.
10. All the DTI Maps will be output to the Analyze workspace.
11. To define a region of interest, select the FA map and the EVCM.
Open the Region of Interest module (Measure > Region of
Interest).
12. By moving the slice slider bar, select a slice that contains a region
of interest. In this example, we will define the corpus callosum.
13. To begin defining, select the Auto Trace tool and set a seed point
within the corpus callosum. A doubled ended threshold bar will be
returned in the ROI window.
14. For this example, we set the Minimum Threshold to 143 and a
Maximum Threshold of 237. Click Apply to define this trace as an
object.
15. Next, we will move to the next slice and set another object for the
corpus callosum. Click to set a seed point within the region, and the
threshold previously set should be automatically populated.
16. Click Apply to create a second object.
17. Now that there are multiple objects defined, save the object map
(File > Save Object Map).
Figure 4
155
Exercise 63
18. Return to the DTI module and click on the Fiber Tracking tab. Click
the Load Object Map button. Select the object map from the last
section, and click Open. The two objects defined in the last section
will be displayed.
19. Click the Compute Fibers button. Once the computation is
complete, click the Display Fibers button.
20. In the display window, the fiber bundles are displayed (figure 5). You
will see the fibers displayed in the object color they were assigned
in the Region of Interest module. To zoom in or out on fiber bundles,
hold the middle mouse button while moving the mouse forwards
and backwards.
21. To rotate the fiber bundles, hold the left mouse button and move in
the direction you wish to rotate.
22. To move the bundles within the window, hold the right mouse
button and drag the bundles around the window.
23. To change the opacity of the image data, use the Opacity slider bar
just below the window containing the fiber bundles.
24. Now under the Boolean Operator, select AND. Click Display
Fibers. This operation will just show the fibers that are connected to
Object 1 AND Object 2. The metrics of these fibers can be logged
by clicking Log Displayed Fiber Metrics.
25. You can save these metrics out by clicking Save in the window
returned. These metrics can then be imported into an excel
spreadsheet.
Figure 5
156
T2 Projection
Exercise 64
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 prior 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.
Load the MRI_T2.avw data set from the $:\BIR\images\

2.
Open the T2 Projection add-on (Apps > T2 Projection).
3.
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.
4.
Click Show Forward, until Slice 15 is displayed.
5.
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.
6.
Similarly, the Echo Time (TE) can be adjusted by selecting a value

from the TE (msec) drop-down menu. Select 110.
7.
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.
8.
Close all windows associated with the T2 Projection module before

Figure 1
157
Volume Metrics
Exercise 65
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.
Load the MRI_3D_Head.avw and the MRI_3D_Brain.avw data

sets from the $:\BIR\images\TutorialData directory.
2.
With both volumes selected, open the Volume Metrics module

(Apps > Volume Metrics). The first volume selected is the input
volume, the second volume is the comparison volume.
3.
To calculate all of the statistics for a specific metric option, select

the Metric Type, then click the Calculate Metrics button. The
metrics are calculated and displayed next to each Similarity Value.
4.
To log the metrics in a log file, click on the Log Metrics button.
5.
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.
6.
Click Done to close the log screen.
Figure 2
Figure 1
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Analyze 12.

1999-2014 AnalyzeDirect, Inc.

Analyze 12.0 Training Guide

Volume Render: High Def Volume Rendering......................... 50

Analyze 12.0 Training Guide

Installing Tutorial Data

In order to work through the Essential Training Guide exercises

Button Reference: Displays PowerBar button or tool button

Insert the Analyze Resources CD into your computer.

Open Analyze 12.0 and choose Help > Tutorials.

Click Install Tutorial Data at the bottom of the Tutorials

In the window returned, specify the path to the tutorial data,

Analyze 12.0 Training Guide

Open the DICOM Tool (File > DICOM Tool).

Loading Data into Analyze

Analyze 12.0 Training Guide

Right Mouse Button Menu

Main Analyze Window Quick Keys

Edit Header: Modify the header information of a selected data set

Analyze 12.0 Training Guide

Resources: The Resource Monitor assists in maintaining

The Help menu provides access to several important Analyze

PowerBar Editor: the PowerBar Editor is an option that

Tutorials: Tutorial exercises covering some of the main

Options: The Options item allows you to switch on and off

AppDefaults Editor: The AppDefaults Editor provides

Analyze 12.0 Training Guide

Online Support: Provides a direct link to the AnalyzeDirect

PowerBar Editor - Customizing PowerBars

Analyze 12.0 Training Guide

Analyze 12.0: Essential Training Guide

Loading Data into Analyze

Analyze 12.0 Training Guide

DICOM Tool: Quick Configuration

Open the DICOM Tool (File > DICOM Tool).

The Create New Image Database window (Figure 1) allows you to

The Local Database Name will default to SystemName_PortNumber;

On your systems local disk create a folder called AnalyzeDB

Analyze 12.0 Training Guide

DICOM Tool: Quick Configuration

Once the database has been created a dialog box will be

10. To import DICOM data into the DICOM Tool right-click

Analyze 12.0 Training Guide

DICOM Tool: Advanced

Open the DICOM Tool (File > DICOM Tool).

Specification of the Database Name and Directory

The Local Database Name will default to SystemName_PortNumber; change the

Analyze 12.0 Training Guide

DICOM Tool: Advanced

Specification of a DICOM Receiver (optional)

The Configure DICOM Receiver option allows you to configure a

DICOM Receiver configuration requires three key pieces of information:

Analyze 12.0 Training Guide

DICOM Tool: Advanced

Specification of a Database Server (optional)

The Configure Database Server option allows you to configure an optional

Analyze 12.0 Training Guide

It is recommend using a closely related

DICOM Tool: Advanced

Specification of the Source of Initial Images (optional)