Vascular Research Tools 5 - Medical Imaging Applications LLC · Vascular Research Tools 5 Documentation Medical Imaging Applications, LLC °c Medical Imaging Applications, LLC July

Vascular Research Tools 5

Documentation

Medical Imaging Applications, LLC

c© Medical Imaging Applications, LLC

July 15, 2006

Contents

1 The Family of Vascular Research Tools 7

1.1 Image Format Compatibility 10

1.2 FDA Approval 10

1.3 Year 2000 Compliance 10

1.4 How to Contact Medical Imaging Applications, LLC 10

2 Installation of Vascular Research Tools 12

2.1 Vascular Tools System Requirements 12

2.2 Vascular Tools Installation Steps 12

2.3 Vascular Tools Installation Notes 13

2.4 Installed components 14

2.5 Uninstalling Vascular Tools 15

2.6 Vascular Tools Upgrade 15

3 Brachial Analyzer for Research 16

3.1 Running Brachial Analyzer 16

3.2 Demo of Brachial Analyzer 17

3.3 Getting Familiar with Brachial Analyzer 17

3.3.1 Tool Bar – Description of Main Control Buttons 18

3.3.2 Menu Bar – Description of Menu Items 22

3.3.3 Function Panels – Controlling the Analysis Processes 24

3.3.4 Separate Process-Specific Windows 25

3.4 Brachial Ultrasound Analysis using Brachial Analyzer 30

3.5 Tutorial 30

3.5.1 Example Data 30

3.5.2 Tutorial 1: Working with an existing .sdy study file 31

3.5.3 Tutorial 2: Creating a new .sdy file, working with anew ultrasound image sequence 33

3.5.4 Tutorial 3: Manual editing of the automatically iden-tified borders 35

3.6 Brachial Ultrasound Analysis – Detailed Description of Pro-cessing Steps 37

3.6.1 Brachial Ultrasound Data Input 37

2

Contents 3

3.6.2 Pixel Size Calibration 383.6.3 Training 393.6.4 Border Detection in the Entire Sequence 463.6.5 Border Detection Quality Control; Review of the Re-

sults 473.6.6 How to Use Border Reviewing and Quality Control;

Human Intervention and Manual Editing 503.6.7 Report 573.6.8 Generating and Saving Reports 633.6.9 Saving Results 63

3.7 Troubleshooting 65

4 Doppler Flow Analyzer for Research 674.1 Running Doppler Flow Analyzer 674.2 Demo of Doppler Flow Analyzer 684.3 Getting Familiar with Doppler Flow Analyzer 69

4.3.1 Tool Bar – Description of Main Control Buttons 694.3.2 Menu Bar – Description of Menu Items 704.3.3 Function Panels – Controlling the Flow Analysis Pro-

cesses 704.3.4 Separate Process-Specific Windows 71

4.4 Flow Ultrasound Analysis using Doppler Flow Analyzer 724.4.1 Doppler Flow Velocity Image Sequences 734.4.2 Invoking Flow Analysis Function Panel 734.4.3 Calibration 734.4.4 Definition of the ROI 744.4.5 Flow Analysis – Doppler Waveform Envelope Detec-

tion in an EKG-gated sequence 754.4.6 Editing 754.4.7 Exporting Results 764.4.8 Display Customization 76


5 Carotid Analyzer for Research 785.1 Running Carotid Analyzer 785.2 Demo of Carotid Analyzer 795.3 Getting Familiar with Carotid Analyzer 79

5.3.1 Tool Bar – Description of Main Control Buttons 805.3.2 Menu Bar – Description of Menu Items 845.3.3 Function Panels – Controlling the Analysis Processes 865.3.4 Separate Process-Specific Windows 87

5.4 Carotid Ultrasound Analysis using Carotid Analyzer 915.5 Tutorial 91

4 Contents

5.5.1 Example Data 91

5.5.2 Tutorial 1: Working with an existing .sdy study file 92

5.5.3 Tutorial 2: Creating a new .sdy file, working with anew ultrasound image sequence 94

5.5.4 Tutorial 3: Manual editing of the automatically iden-tified borders 97

5.6 Carotid Ultrasound Analysis – Detailed Description of Pro-cessing Steps 100

5.6.1 Carotid Ultrasound Data Input 100

5.6.2 Pixel Size Calibration 101

5.6.3 Training 102

5.6.4 Border Detection in the Entire Sequence 106

5.6.5 Review of the Results 107

5.6.6 Operator Intervention and Interactive Editing 109

5.6.7 Report 111

5.6.8 Generating and Saving Reports 117

5.6.9 Saving Results 117

5.7 Carotid Plaque Analysis 119

5.7.1 Carotid Ultrasound Image Data, ROI Definition, Bor-der Detection 120

5.7.2 Echogenicity Calibration 120

5.7.3 Plaque Identification 120

5.7.4 Plaque Editing 121

5.7.5 Reporting Results 121

5.8 Carotid Distensibility and Compliance 122

5.8.1 Carotid Ultrasound Image Data, ROI Definition, Bor-der Detection 123

5.8.2 Input of Blood Pressure Values 124

5.8.3 Definition of the Image subsequence 124

5.8.4 Reporting Results 126


6 Subject Manager 128

6.1 Running Subject Manager 128

6.2 Getting Familiar with Subject Manager 128

6.2.1 Description of Main Control Buttons 129

6.2.2 Study Status Information 131

6.3 Example Usage 131

6.4 Creating a SUBJECT File from DICOMDIR File 131

6.5 Creating a SUBJECT File from Image Files located in a Sin-gle Directory 133

6.6 Comprehensive Subject-Specific Reports 135

Contents 5


7 Vascular Converter 137

7.1 Need for Conversion 137

7.2 Running Vascular Converter 138

7.3 Getting Familiar with Vascular Converter 138



7.3.3 Function Panels – Controlling the Conversion Processes141

7.3.4 Separate Process-Specific Windows 141

7.4 Vascular Ultrasound Conversion using Vascular Converter 144

7.4.1 Supported image formats 144

7.4.2 Opening Existing Third-Party Image Data Files 145

7.4.3 Calibration 149

7.4.4 Specification of the initial frame of the measurementsequence 149

7.4.5 Sub-sequence Specification 149

7.4.6 Conversion 150

7.4.7 Specification of the Measurement Condition 150

7.4.8 Filling Required Data Fields, Saving Study File 150


8 Analyzing DICOM Data 152

8.1 Using Vascular DICOM Module – Overview 152

8.1.1 DICOM Data Input 153

8.1.2 DICOM Clip Data Input - No DICOMDIR 154

8.1.3 Saving Study File when Working with DICOM ImageData 155

8.1.4 Opening a Previously Analyzed DICOM Sequence 155

8.2 Data Management Recommendations when Working with DI-COM Image Data 155


9 Analyzing HP-DSR (Philips Sonos) Data 157

9.1 General Issues 157

9.2 Running Vascular Converter HP-DSR – Specifics 157


10 Vascular Imager 159

10.1 Running Vascular Imager 159

10.2 Getting Familiar with Vascular Imager 160



6 Contents

10.2.3 Function Panel – Controlling the Image Acquisition 16210.3 Image Acquisition 162

10.3.1 Factors Influencing Performance of Vascular Imager 16310.3.2 Proper Setting of the Windows Environment to Reach

Full Performance 16310.3.3 Number of Frames that can be Acquired 16310.3.4 Timed Image Acquisition 16410.3.5 Triggered Image Acquisition 16510.3.6 Manual Image Acquisition 16610.3.7 Vascular EKG Gating Module 16610.3.8 Triggering Options 16710.3.9 Saving the Acquired Image Sequence 168

10.4 Vascular Imager in Real-Time Acquisition 16910.4.1 Display of Reference Image 17010.4.2 Pre-Acquisition Study Information Input 17110.4.3 Four-click Operation to Acquire Baseline and Defla-

tion Sequences 17110.5 Troubleshooting 173

11 Vascular EKG-Gating Module 17611.1 EKG-gated image acquisition using HP Sonos ultrasound ma-

chines 17711.2 EKG-gated image acquisition using Toshiba ultrasound ma-

chines 17811.3 Troubleshooting 178

12 References 181

CHAPTER 1

The Family of Vascular Research Tools

The software family of Vascular Research Tools allows comprehensive as-sessment of brachial and carotid arterial function. FDA-approved versionof the described software is described in Chapter 1.2. The programs areWindows 95, Windows 98, Windows Me, Windows NT, Windows 2000, andWindows XP compatible. The Vascular Research Tools (shortly, VascularTools) consist of the following modules:

• Brachial Analyzer for ResearchBrachial Analyzer for Research (shortly, Brachial Analyzer) is a programenvironment for highly automated analysis of brachial ultrasound im-ages and image sequences. Brachial Analyzer uses an automated methodfor near and far wall border detection and vessel diameter measurementin brachial ultrasound image sequences. The method automaticallylearns properties of the analyzed vessel in one frame of the sequencethat is analyzed under operator’s supervision. The vessel propertiesare reflected in the cost function used in a graph-search-based borderdetection. To improve the automated method’s accuracy and repro-ducibility, several automated quality control steps are incorporated.Brachial Analyzer creates an output data file with study informationand can export it in several selectable formats.

• Carotid Analyzer for ResearchCarotid Analyzer for Research (shortly, Carotid Analyzer) is a programenvironment for highly automated analysis of carotid ultrasound im-ages and image sequences. Carotid Analyzer uses an automated methodfor near and/or far wall border and near and/or far intima borderdetection and vessel diameter as well as intima-media thickness mea-surement in carotid ultrasound image sequences. When analyzing a se-quence of images of the same vessel location, the method automaticallylearns properties of the analyzed vessel in one frame of the sequencethat is analyzed under operator’s supervision. The vessel propertiesare reflected in the cost function used in a graph-search-based borderdetection. Carotid Analyzer creates an output data file with measured

7

8 CHAPTER 1 The Family of Vascular Research Tools

vessel diameters and other accompanying information in several se-lectable formats.

• Doppler Flow Analyzer for ResearchDoppler Flow Analyzer for Research (shortly, Doppler Flow Analyzer)is a program environment for highly automated analysis of Dopplerflow images and EKG-gated Doppler flow image sequences. DopplerFlow Analyzer is a separate module functionally embedded within theBrachial Analyzer. Doppler Flow Analyzer uses an automated methodfor detection of Doppler flow velocity waveform envelopes and conse-quent measurement of the maximum flow velocity in the cardiac cycle,and the flow velocity integral over the cardiac cycle. Doppler Flow Ana-lyzer creates an output data file with measured flow velocity and otheraccompanying information in several selectable formats.

• Vascular ImagerVascular Imager is a program environment for continuous acquisitionof image data sequences as well as individual image frames. In com-bination with image data from some of the ultrasound machines (e.g.,Toshiba 140, HP Sonos), ECG-triggered image acquisition is possiblewhen grabbing the images directly from the machine’s video outputor using videotape. Vascular Imager creates an image data file in theVascular Tools data format. Vascular Imager is a software tool requir-ing Matrox frame grabber to be installed on your PC. As an add-onhardware option, a complete hardware/software image acquisition so-lution is available from Medical Imaging Applications, LLC as VascularImager and Frame Grabber. If an entire system is needed, complete HighPerformance Vascular Analysis Integrated Systems are offered in severalperformance configurations as described below.

• Vascular Imager and Frame GrabberVascular Imager and Frame Grabber includes the Vascular Imager bun-dled with Matrox frame grabber in a complete package for those need-ing image digitization but already having adequate computer equip-ment.

• Vascular ConverterVascular Converter is a program environment for image data conversionfrom several data formats created by third-party frame grabbers. Vas-cular Converter includes customization for your site to work with yourimage data sets. Vascular Converter is not designed to convert imagedata from a general DICOM format, DICOM data can be analyzedusing Vascular DICOM Module of the Brachial Analyzer.

9

• Vascular DICOM ModuleVascular DICOM Module is a module for DICOM image data input intoVascular Tools. Vascular DICOM module is not a separate program ofthe family of Vascular Tools, rather it is a data input module facili-tating to directly analyze DICOM data without the need to performa separate data conversion step. Consequently, no separate DICOMConverter application is needed to work with DICOM data.

• Vascular EKG-Gating ModuleVascular EKG Gating Module is an R-wave signal conditioning moduleallowing direct EKG-gated digitization from the ultrasound machine aswell as from videotape-recorded brachial ultrasound image sequences.

In addition to these software products, several configurations of completesystems for Vascular Ultrasound Analysis are available from Medical ImagingApplications, LLC.

• High Performance Vascular Analysis Integrated SystemThis workstation represents an integrated and complete solution forhighly automated analysis of brachial ultrasound images and imagesequences stored on videotape.

Software components:

– Brachial and/or Carotid Analyzer

– Vascular Imager

– Vascular DICOM Module

– Windows 2000/XP operating system

Hardware components:

– Pentium IV system with sufficient disk storage, large monitor,keyboard, mouse, CD ROM, floppy drive, Matrox frame grabber,network card

• Top Performance Vascular Analysis Integrated SystemThis workstation represents a more powerful version of the integratedand complete solution for highly automated analysis of brachial ul-trasound images and image sequences stored on videotape describedabove. Its brachial and/or carotid analysis software as well as thecomprehensive support are identical to those described in the packagedescribed above. System hardware offers top performance availableamong the Windows computers at the time of delivery and provides atwo-monitor display setup.

10 CHAPTER 1 The Family of Vascular Research Tools

• Additional ConfigurationsMany other configurations are available, e.g., configurations with noframe grabber to interface with fully digital DICOM or HP-DSR basedsystems, specifically configured brachial analysis or carotid analysisworkstations, etc.

Exact technical specifications of the integrated systems change in responseto the continuous progress in the area of computer hardware available onthe market.

1.1 Image Format Compatibility

Vascular Tools components and Vascular Workstations are compatible witha wide variety of image data formats including DICOM, HP-DSR, CRI,JPG, BMP and others. The input image data may be directly readablein the Vascular Tool components, e.g. those produced by Vascular Imagerimage digitization package for videotape-originating ultrasound images, ora compatible format is produced by Brachial Converter modules that canconvert most of the existing image data formats into the Vascular Tools dataformat.)

1.2 FDA Approval

The software or hardware tools from the Vascular Research Tools Familyare not FDA approved and can only be utilized for investigational use.

However, a subset of the research suite marketed under the name VascularTools 5 is FDA approved for clinical use. Please, contact MIA for additionalinformation or visit www.mia-llc.com.

1.3 Year 2000 Compliance

The Vascular Tool Family programs for vascular diameter measurementworked flawlessly through the Year 2000 date change.

Vascular Tools do not use the date information of any kind in identifyingthe vessel wall borders and measuring the vessel diameters, neither do theyinterpret or manipulate any date information.

Vascular Tools, however, assume no assurance of any kind about thecomputer platform or any other third party applications running on thatplatform.

1.4 How to Contact Medical Imaging Applications, LLC

• E-mail:[email protected]

• URL:http://www.mia-llc.com/

1.4 How to Contact Medical Imaging Applications, LLC 11

• Fax:(319) 688-5296

• Phone:(319) 358-1529

• Regular Mail:Medical Imaging Applications, LLC832 Forest Hill Dr.Coralville IA, 52241USA

CHAPTER 2

Installation of Vascular Research Tools

The Vascular Research Tools (shortly, Vascular Tools) installation uses thecurrent software industry standard. You will find the installation processfamiliar and friendly. Whenever you have any questions or concerns, pleasecontact Medical Imaging Applications, LLC.

The installation information provided here describes standard installa-tion procedures. If your installation set was customized to fit your specialneeds, please refer to the specific installation attachments describing how toinstall all necessary components.

2.1 Vascular Tools System Requirements

Before the installation, please check the minimum installation require-ments:

1. Pentium III or Pentium IV processor (Pentium class processor is notrequired but it is highly recommended).

2. Windows 95, 98, Me, NT, 2000, or XP operating system.

3. At least 50 MB free space on your hard drive.

4. XGA (1024x768) or higher resolution. (You can easily find out thesesettings from the [Control Panel → Display → Settings], change thesettings if necessary).

5. At least 256 MB of memory is recommended to analyze image se-quences with more than 100 frames/sequence.

6. CD-ROM drive – the installation is shipped on CD-ROMs.

2.2 Vascular Tools Installation Steps

When upgrading from version 3.x to version 4.x, please unin-stall the Brachial Tools residing on your system before the VascularTools installation is performed. See Section 2.5 for details.

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2.3 Vascular Tools Installation Notes 13

1. Close all running applications (for example, Word, Excel, Netscape,Internet Explorer).

2. Insert the installation CD into your CD-ROM drive.

3. The installation will start automatically. If not, please ...

• Invoke the main Windows 95/98/Me/NT/2000/XP Menu by click-

ing button. Go to [Run] and type inside of the dialogbox:

D:\Disk1\setup

IMPORTANT NOTE: If your CD-ROM drive is not labeled“D”, under the “My Computer” window, change “D” to the ap-propriate label.

• Alternatively, you can explore the installation CD-ROM diskusing the Windows Explorer and double click on the Setup iconthere.

4. Read the next section below containing important Installation Notes.

5. Follow the on-screen instructions to finish the installation.

2.3 Vascular Tools Installation Notes

• The application serial number is included with the installation CD.The correct serial number is required to install the software, as well asto obtain subsequent technical support.

• It is required to install the application in the installation default foldersince all accompanying material refers to this default destination.

• At the end of the installation, you may be asked to reboot the system.If asked, please do so to ensure the necessary update and cleanup. Ifyou have a new computer or recently installed some new software fromMicrosoft, you may not be asked to reboot.

After the installation and possibly rebooting the computer, you can find thenew Vascular Tools menu item in the Programs menu, MIA Vascular Toolssubmenu item, e.g.:

14 CHAPTER 2 Installation of Vascular Research Tools

The contents of the MIA Vascular Tools menu differs for each shipment. Allshipped applications of the Vascular Tools family are shown under the MIAVascular Tools menu.

2.4 Installed components

You don’t need to read this section in order to install the Vascular Tools.This section provides some in-depth information about what the installationprocess adds to your computer.

The default destination of the Vascular Tools installation is:

C:\Program Files\MIA-LLC\Vascular Tools

Several directories are created there:

\bin\

contains all Vascular Tools applications,

\Samples\

contains few short example image data sets and example study files (ad-ditional example images and study files are located on the CD ROM andare not copied during installation due to their large size of hundreds ofmegabytes, see Section 3.5 and Section 5.5 for details),

\Help\

contains an electronic copy of this manual and some other documents.

2.5 Uninstalling Vascular Tools 15

2.5 Uninstalling Vascular Tools

Uninstalling the Vascular Tools is even simpler than its installation.

1. Close all running applications INCLUDING the Vascular Tools appli-cations.

2. Go to [Start menu → Control panel → Add/Remove Programs].

3. If the Vascular Tools item is on the list, you can select it and uninstallit by clicking the [Add/remove] button. If it is not on the list, it iseither not installed yet, or has already been uninstalled.

4. Depending on your computer situation, you may be asked whether youwant to keep some files. Please keep all the files. The reason youare asked is that the Windows system failed to determine if any otherapplication needs the files that were also a part of the Vascular Toolsapplication. When the Windows system can figure it out by itself, youare not asked.

2.6 Vascular Tools Upgrade

When upgrading from version 3.x to any higher version, please unin-stall the Brachial Tools residing on your system before the Vascular Toolsinstallation is performed. See Section 2.5 for details.

For upgrades from version 4.x to higher versions, there is no need touninstall Vascular Tools before you can install a new one. Newer VascularTools Family applications (with the same or higher version numbers) can beinstalled to replace the existing one.

It is not recommended to install an older version when you already havea newer version installed. Please consult Medical Imaging Applications, LLCin such a situation.

CHAPTER 3

Brachial Analyzer for Research

Brachial Analyzer for Research (shortly, Brachial Analyzer, Fig. 3.1) is a Win-dows 95, Windows 98, Windows Me, Windows NT, Windows 2000, and Win-dows XP compatible program environment for highly automated analysis ofbrachial ultrasound images and image sequences.

Brachial Analyzer uses an automated method for near and far wall borderdetection and vessel diameter measurement in brachial ultrasound image se-quences. The method automatically learns properties of the analyzed vesselin one frame of the sequence that is analyzed under operator’s supervision.The vessel properties are reflected in the cost function used in a graph-search-based border detection [1]. To improve the automated method’s accuracyand reproducibility, several automated quality control steps are incorpo-rated. Brachial Analyzer creates an output data file with measured vesseldiameters and other accompanying information in several selectable formats.

Previous, less sophisticated versions of the method have been used forresearch purposes since 1997 [2–5].

3.1 Running Brachial Analyzer

To run Brachial Analyzer:

1. Invoke the main Windows 95/98/Me/NT/2000/XP Menu

by clicking button.

2. Select Programs → MIA Vascular Tools.

3. Select Brachial Analyzer.

To exit from Brachial Analyzer:

1. Save your work [File → Save/Save As]

2. Exit [File → Exit] or click the upper right corner of the Brachial Ana-lyzer window.

16

3.2 Demo of Brachial Analyzer 17

Menu bar Tool bar Function panel Image Status bar

Figure 3.1: Main Brachial Analyzer window.

3.2 Demo of Brachial Analyzer

Brachial Analyzer is a complex software package. Several image sequencesand prepared demonstration analysis case studies are included with yourinstallation. A small number of images and image sequences is copied to yourhard drive. Several other image sequences are located on the InstallationCD, each with a complete analysis study file generated using our BrachialAnalyzer software.

Section 3.5 contains step-by-step demonstration of basic functionalitiesof the Brachial Analyzer.

3.3 Getting Familiar with Brachial Analyzer

The Brachial Analyzer is a complex program with a number of interactiveand automated steps that have to be performed to complete the analysis of

18 CHAPTER 3 Brachial Analyzer for Research

brachial ultrasound image sequences.

Due to its complex nature, this section presents an overview of themain process control blocks from the user’s viewpoint. This section willidentify the main parts of the application window as well as the functionblocks.

In Fig. 3.1, you can identify the following window partitions:

• Menu Bar

• Tool Bar

• Function Panel

• Image

• Status Bar

The first three are depicted in Fig. 3.2. Note that while the first two (MenuBar, Tool Bar) do not change, the Function Panel appearance and contentchange according to the currently performed function. Similarly, the StatusBar content changes to reflect the current status of the analysis, it frequentlycontains analysis results associated with the currently displayed image frame.The subject name information – when available – is continuously availablein the bottom right corner of the status bar.

Some processes also open additional windows that allow process-specificinteractions.

The tools (control buttons) and menus are described in Sections 3.3.1and 3.3.2. In Section 3.3.3, we list all possible appearances of the Func-tion Panel and briefly describe their individual functionality. Section 3.3.4introduces separate process-specific windows that pop-up in response to in-dividual process control steps.

It is recommended that you scan through the following paragraphs de-spite the fact that during the first reading you most likely will not acquirefull understanding of the functionality of individual controls. The first read-ing is important for you to be able to follow the Tutorials and more detaileddescription in the later sections. In any case, after you finish reading theentire manual, it may be a good idea to return to the following sections andread through this part again with a deeper understanding.

3.3.1 Tool Bar – Description of Main Control Buttons

In Fig. 3.2 and the following paragraphs, please familiarize yourself withall basic control buttons and menus. All of them will be frequently referencedthroughout this chapter.


Figure 3.2: Controls of the main Brachial Analyzer window – Menubar, Tool-bar, and Function Panel.

• . invokes a process window to create a new brachial ultrasoundsequence study.

• . opens existing brachial ultrasound sequence study.

• . saves the current brachial ultrasound sequence study.

• . invokes a Subject Manager window (Chapter 6). Subject in-formation is also available in the Subject subwindow of the Resultswindow.

• . switches to a function panel for border detection training.

• . performs automated analysis of the current frame. It also servesas a flag to allow or disallow automated border detection after click-

ing the review/analyze button or any other button changing the

“current” frame , automated analysis is enabledin its “set” (“down”) position. In other words, as long as this buttonis set, changing the “current” frame always invokes reanalysis of theframe that becomes “current”. This behavior is suspended either af-

ter reaching the last frame of the sequence in the mode, or after

clearing the button to be in its “up” position.


(a) (b) (c)

Figure 3.3: Menu controls: (a) File menu; (b) Edit menu; (c) View menu.

• . switches to a function panel allowing manual corrections or re-analysis of the already identified vessel borders in the current frame.

• . displays or hides the region of interest overlay.

• . displays or hides the determined vessel borders.

• . displays or hides the overlaid text with frame analysis informa-tion.

• . switches borders on and off in a rapid fashion to allow visualassessment of border positioning.

• . opens Analysis Results window.

• . starts sequential review of results or automated analysis, begin-

ning at the current frame; starts automated border detection if isset (“down”).

• . stops sequential review or automated analysis.


(a) (b)

Figure 3.4: Menu controls: (a) Action menu; (b) Help menu.

• . displays the first frame of the image sequence, makes this frame“current”.

• . displays the previous frame of the image sequence, makes thisframe “current”.

• . displays the next frame of the image sequence, makes this frame“current”.

• . displays the last frame of the image sequence, makes this frame“current”.

• . allows frame selection by interac-tively controlling the slider, displays the sequential number of the cur-rently displayed image frame.

• . toggles between repeated display of the sequence in a loopand single display of the image sequence during the review process.


• . specifies frame display speed during the review process.

For each button, a simple help text occurs whenever a mouse cursor is po-sitioned over the button and left with no motion for a short period of time.

3.3.2 Menu Bar – Description of Menu Items

The functionality of the main menu items shown in Figs. 3.3 – 3.4 isbriefly described below. Some of the menus can be invoked by clicking rightmouse button within the image field - in that case, the menu that occurs iscontext-sensitive depending on the analysis status.

• File menu

– New – invokes a process window to create a new brachial ultra-

sound sequence study – identical to clicking .

– Open – opens existing brachial ultrasound sequence study – iden-

tical to clicking .

– Close – closes current brachial ultrasound sequence study withoutexiting from the Brachial Analyzer.

– Save – saves the current brachial ultrasound sequence study –

identical to clicking .

– Save As – saves the current brachial ultrasound sequence studyunder a new name.

– Report – opens a dialog window for saving and printing the resultsreport.

– Properties – opens a window with border and ROI display pa-rameters and other options. Display options can also be modifiedin the Display Options subwindow of the Results window.

– Exit – exits from the Brachial Analyzer, identical to clicking upperright corner button of the main Brachial Analyzer window.

• Edit menu

– Copy and Paste options have no functionality at this time.

– Study information – invokes Study Information window, allowsediting its content.

• View menu


– Toolbar – displays or hides the toolbar with main control buttons.

– Status bar – displays or hides the status information line in thebottom of the main Brachial Analyzer window.

– Refresh – Refreshes the screen if window is not updated for somereason.

– Options – opens a dialog window allowing modification of borderand ROI display parameters and other options.

– Analysis Results – opens Analysis Results window – identical to

clicking .

– Subject Manager – invokes subject management module, see Chap-ter 6 for details. Subject information is also available in the Sub-ject subwindow of the Results window.

• Action menu

– Calibrate – switches to a function panel allowing calibrations ofpixel sizes used in vessel size measurements as well as in bloodflow measurements.

– Train the system – switches to a function panel for border detec-

tion training – identical to clicking .

– Launch automated analysis – Invokes re-analysis of the currentframe.

– Play – starts sequential review of results or automated analysis,beginning at the current frame; starts automated border detection

if is set (“down”).

– Edit - no functionality.

– Edit manual– switches to a function panel allowing manual cor-rections or re-analysis of the already identified vessel borders in

the current frame – identical to clicking .

– Exclude Frames from Analysis – defines a range of image framesthat are not analyzed in the current sequence.

– Reject – rejects current frame from border analysis results.

– Undo Reject – includes current previously rejected frame in bor-der analysis results.

– Clear All Borders / Measurements – deletes all current analysisresults, keeps the ROI location.


– View Results – opens Analysis Results window – identical to click-

ing or selecting Analysis Results in the View menu.

– Subject Manager – invokes subject management module, see Chap-ter 6 for details. Identical to selecting Subject Manager in the Viewmenu.

• Help menu

– Online Manual – invokes the online version of this manual usingAdobe Acrobat.

– On DICOM – provides basic information how to use DICOMimage data.

– About – provides basic information about the Brachial Analyzer.

3.3.3 Function Panels – Controlling the Analysis Processes

The Function Panels change most frequently. Two default panels are:

• Initial Function Panel

• Sequence Navigator Function Panel

In addition to the two default Function Panels, the following Menu items orControl buttons invoke process-specific Function Panels:

• Clicking [Action → Calibrate], invokes Calibration Function Panel:

This Function Panel also opens automatically at the beginning of theanalysis when no pixel size calibration value is available.

• Clicking [Action → Train the System] or invokes the TrainingFunction Panels:Training – stage 1:

After clicking [Proceed] in the previous panel, Training – stage 2 panelappears:


After clicking [Proceed] in the previous panel, Training – stage 3 panelis displayed:

• Clicking [Action → Edit] or invokes Intervention Function Panel:

• Many useful analysis-context-specific help items can be found on theblue “Hints” panel that changes its textual content based on the anal-ysis status

3.3.4 Separate Process-Specific Windows

• Clicking [File → New] or opens a dialog window for entering rel-evant information to create a new study information file:

The Study Information panel includes required fields (in red) and op-tional fields (in black). The required information fields must be filled


before the [Save] button becomes enabled. However, specification ofwhich fields are and which are not required can be customized by theuser. After clicking Options button in the Information Window, adialog window opens allowing the user to select “required” and “op-tional” fields. Note that the fields with user-customizable labels (Sec-tion 3.6.7.1) are always “optional” and cannot become “required”.

This window can also be invoked by clicking [Edit → Study informa-tion] – in that case, study parameters can be interactively edited intheir respective fields.

• Clicking [File → Open] or opens a dialog window for opening anexisting analysis study:

• Clicking [File → Save As] opens a dialog window for saving the per-formed analysis study:



• Clicking [File → Properties], a window appears showing parameters ofborder display.. Display options can also be modified in the DisplayOptions subwindow of the Results window.Border display parameters/Options window:

• Clicking [View → Options], same window opens as specified above(Properties).


• Clicking [View → Analysis Results] or opens a Results window.Note that there are several subwindows available within this window.

• .[Help → Online Manual] opens the electronic version of this manual.

• .[Help → On DICOM] invokes DICOM-related help window.

• .[Help → About] invokes information about Brachial Analyzer, its ver-sion, Medical Imaging Applications, LLC contact address, etc.

• Context Sensitive Help Windows appear in the bottom of the screenbased on the stage of processing. These windows provide hints aboutthe current analysis steps. They can be closed if obstructing the im-age by clicking the [Go away] button. Mode of their appearing can be


completely switched off in two ways – by unclicking [Smart Showing]within the context-sensitive help window, or inside the [View → Op-tions] window. If smart showing is switched off, it can only be switchedon by selecting this option in the [View → Options] window.

3.4 Brachial Ultrasound Analysis using Brachial Analyzer

During a typical analysis of a brachial ultrasound image sequence,the following steps must be performed:

1. Opening of an existing ultrasound image sequence study file or creatinga new one.

2. Pixel size calibration

3. Training of border detection parameters

4. Brachial ultrasound image analysis

5. Review of results

6. Output report generation and saving of results

For the purposes of this manual, a brachial ultrasound image sequenceis a sequence of brachial ultrasound image data that were previously acquiredunder constant image acquisition conditions during which the brachial arteryas well as the imaging transducer were kept in a stable position with no mu-tual motion. Consequently, what is frequently called a brachial ultrasoundflow mediated dilatation study is separated into several brachial ultrasoundimage sequences – usually three sequences can be formed: baseline sequence,inflation sequence, and deflation sequence. Brachial Analyzer can analyzeboth ECG-gated and non-gated brachial ultrasound image sequences.

Analysis of each of these sequences requires to perform all the above-listed steps that will be described in detail. Before we proceed, it may beadvantageous to use the Demo image data sequences included with yourinstallation to get familiar with the basic operations. The next section de-scribes several example analysis sessions.

3.5 Tutorial

The Installation CD includes several example data sets.

3.5.1 Example Data

A number of short sequences of example data sets are included withthe Brachial Analyzer installation. If you followed the standard installationprocedure, their location–filenames are:

3.5 Tutorial 31

C:\Program Files\MIA-LLC\Vascular Tools\Samples\

Brachial\...\Demo-XXX.sdy ,


Brachial\...\Demo-XXX.raw ,

and


Brachial\...\New-XXX.raw

where XXX is an identification number. The .raw files contain ultrasoundimage sequence data and the .sdy files carry all non-image information as-sociated with the brachial ultrasound study including the border detectionresults.

Additional longer, more realistic, and also more challenging example im-age sequences (ECG-gated and non-gated) remain located on the CD andare not copied to the C: drive due to their large size, possibly hundreds ofmegabytes. These additional example files are again named Demo-XXX.raw,Demo-XXX.sdy, and New-XXX.raw and are located in the following directory:

X:\Samples\...

where X: represents the label of your CD ROM disk drive. The tutorialexample analyses may use the CD ROM location but accessingthe CD is slow in general. Therefore, to appreciate the analysisspeed of the Brachial Analyzer, it is highly recommended to copy allexample files in a single directory some place on the local harddisk of your computer. To analyze such sequences, you simply browseyour hard disks to locate an appropriate .sdy file and open it as describedbelow in Tutorial 1. Please run the Brachial Analyzer on these studies togain familiarity with the software.

3.5.2 Tutorial 1: Working with an existing .sdy study file

The first Tutorial will demonstrate basic functionality of the BrachialAnalyzer and will teach you how to review previously completed brachialimage analyses.

1. Open one of the demo files.

(a) Click [File → Open] or button .

(b) Traverse to directory

C:\Program Files\MIA-LLC\Vascular Tools\Samples\Brachial\...

and select one of the Demo-XXX.sdy files.

(c) Click Open and the first frame of the image sequence will occurin the Brachial Analyzer main window.


2. Since you work with an existing and previously analyzed image se-quence, you can directly review the automatically identified vessel bor-ders.

(a) Make sure that button is set (in its “Down” position).

(b) Click [Action → Play] or to review the borders detected inthe entire image sequence.

(c) Set the loop option in and review all analyzed frames

again using . The review will play in a loop mode.

(d) Modify the playback speed by changing the option in ,identify your optimal speed for border review.

3. Review of a specific frame.

(a) Using Sequence Navigator , se-lect and review a specific frame.

(b) Using ROI (region of interest) button , display and hide theROI used for analysis. Note that the near and far border sidesare marked by “N” and “F”.

(c) Toggle the button several time in a quick sequence to seethe overlaid borders display and hide – this is often the best wayhow to assess the correctness of the border detection.

(d) Set the borders to flash on-off repeatedly by clicking the button

. Click again to stop border flashing.

4. Review table of results and the vessel diameter chart. Note that thecurrent frame is marked by an asterisk (*) positioned next to the framenumber in the table of results.

(a) Click [View → Analysis Results] or to open the AnalysisResults window.

(b) In the new window, the lower part shows the measurement table,the upper part shows vessel diameter chart.

(c) Note that the measurement can be performed in millimeters orpixels.

3.5 Tutorial 33

(d) There are several other Quality Control buttons inside of thiswindow that are described in Sections 3.6.5 and 3.6.6.

3.5.3 Tutorial 2: Creating a new .sdy file, working with a newultrasound image sequence

The second Tutorial will teach you how to create a new image sequenceanalysis study and how to analyze the new ultrasound image sequence.

1. Open one of the new, not yet analyzed, image analysis sequences.

(a) Click [File → New] or button .

(b) Fill in all required analysis data fields (marked in RED).

(c) To select image data, traverse to directory

C:\Program Files\MIA-LLC\Vascular Tools\Samples\Brachial\...

and select one of the New-XXX.raw files. Note that the Files-of-type selection choice within this file opening window must specifyRAW files. (Of course, you can open other file types, in such acase, the Files-of-type selection must correspond to your file type).

(d) After all required fields are filled in, the [OK] button in the bottomleft gets enabled, click on it and the first frame of the new imagesequence will occur in the Brachial Analyzer main window.

2. Since this is a new image sequence, no automatically identified vesselborders are available for review.

3. To analyze this new sequence, the border detection method must betrained for this specific data set.

(a) Select a good-quality image frame for training. A good-qualityframe is one that has well-depicted near and far vessel bordersalong the entire vessel segment of interest. It is not necessarilythe first frame of the sequence. Use Sequence Navigator

to find a good quality frame.

(b) Click [Action → Train the system] or button , a training boxwill replace the Sequence Navigator:

(c) Note the line of text below the main control buttons. It says Train-ing step 1 of 3: Define the ROI. In this location, you can frequentlyfind useful hints about how to proceed with the analysis.


(d) Using the mouse, point to the location within the vessel lumenthat is in the middle of your vessel segment of interest and clickthe left mouse button. A region of interest will occur. (If no

ROI occurs, click on the ROI button that displays/hides theROI.)

(e) Using the sizing, moving, rotation buttons, position and size theROI. The following button labels are used: L,s ... Larger/smallerROI size; L,R,U,D ... move ROI Left, Right, Up, Down; C, CC... rotate ROI Clockwise or CounterClockwise. The initial ROIorientation and width do not have to be perfect, the program willoptimize them during the training step. Experiment with the ROIpositioning so that you become familiar with their functionality.You can always start over with the ROI definition after clickingthe Clear button.

(f) The ROI position, size, and orientation can also be defined andmodified by clicking directly on the image in proximity of thecurrent ROI. Clicking inside of the middle circle moves the ROI.Clicking inside the end-circles changes the ROI orientation and/orROI length. Clicking in the proximity of the near-border (N) orfar-border (F) ROI limit modifies the ROI width. You can alsoreposition the ROI using a click-hold-and-drag approach. Exper-iment with the mouse-controlled ROI modifications to becomecomfortable with these ROI definition options.

(g) When satisfied with the ROI, click the Next button. The firststage training will proceed automatically and vessel borders willbe identified within the ROI. Note that the ROI orientation andwidth automatically changes (ROI width changes only if the LockROI button was “cleared”, it is “set” as default. The second-stageFunction Panel appears:

(h) Review the detected borders and follow the instructions given onthe blue Context-sensitive Help Panel – if the entire border issatisfactory, click on the Proceed button. Otherwise, you mayspecify the preferred location of the near or far wall border byclicking the left mouse button on the desired border location (seealso Fig. 3.11).

(i) Alternatively, you can modify the ROI in this step as you didbefore or return to Step 1 of training by clicking the Back to step1 button, modify the ROI, and repeat the training process.

3.5 Tutorial 35

(j) There are more advanced training steps that can be applied toborder detection system training in lower-quality or otherwise dif-ficult images. They will be described later in Section 3.6.3.

(k) The third-stage Function Panel appears:

4. The completed training process displays the borders determined in thecurrent frame used for training. It does not necessarily display theentire length of the border, rather it displays the parts that are con-sidered reliable. The relationship between the reliable length and thetotal length of the border defines the confidence index that is displayedin the lower right corner of the Brachial Analyzer main window. Ifyou agree with the border positioning and if a sufficient portion of theborder length (ROI length) has been displayed, click the Yes, launchautomated analysis button. Otherwise, you can return to Step 1 or Step2 of the training process.

5. The method will automatically analyze the entire sequence, performstandard quality control steps, possibly reject some lower quality frames,and will prepare results for review.

6. Review results as specified in Tutorial 1.

7. Generate a report and save your work. If you have a demo-only versionof the program, the next two steps are disabled.

(a) Generate the sequence analysis study Report by clicking [File →Report] or clicking [Generate Report] button in the Results win-dow, print this report by clicking [Print] button in the Reportwindow.

(b) Save your results by clicking [File → Save/Save As] or button

, this creates a .sdy file. From now on, you will be able to

use [File → Open] or button to access this image sequenceanalysis study.

3.5.4 Tutorial 3: Manual editing of the automatically identifiedborders

The last Tutorial will teach you how to manually edit borders in situa-tions when the automated border detection was not successful.


1. Open a previously analyzed image analysis sequence study as describedin Tutorial 1, Section 3.5.2.

2. Review the borders and select a frame in which you will interactivelyedit the border(s).

3. Start editing by clicking [Action → Edit] or button , an editingbox will replace the Sequence Navigator.

4. Repeatedly click on the correct position of the border and watch theborder being interactively edited as you proceed. Note that in thismode, the entire length of the border is displayed and available forediting. Do not attempt to “trace” the border, rather click repeatedlyat points you want to define as border points. After each click, waitfor the border to be adjusted to reflect your interactive border pointdefinition.

5. Experiment with different settings of the Editing Sensitivity options.The three options (from left to right) increase the length of borderinfluenced by the manual editing, they also influence the distance fromborder within which a manually-defined border point can be placed. Ifthe needed distance exceeds the maximum, it may require a sequenceof two or more clicks to move the border to a desired position. Notethat the modified borders are marked “edited”.

6. If you are unhappy with the result of editing, you may click the [ClearEditing] button and the original automatically determined borders willreappear.

7. To manually edit another frame of the sequence, you may use the“+” and “–” buttons to display image frames without abandoning themanual editing mode.

8. Click the [Finish] button to abandon the manual editing mode.

9. Open the Results window, note that the edited frame is marked by aletter “i” – border editing intervention – in the table of results. (TheResults window can only be opened when not in the manual editingmode.)

10. With the Results window open, one more convenient editing optionis available. Whenever you click on the diameter chart, the imageframe corresponding to the chart location is displayed and the currentnumeric measurement values are provided on the 1st line of the Resultstable (if one of the last 12 frames, the values will not appear on the

3.6 Brachial Ultrasound Analysis – Detailed Description of Processing Steps 37

1st displayed line). Similarly, if you double-click on a row within thediameter table, the corresponding image frame is displayed. Using thisclick-and-display option, it is easy to target image frames that seemincorrectly analyzed according to the diameter context shown in thediameter chart.

11. To leave the manual editing mode at any time, click the [Finish] button.

3.6 Brachial Ultrasound Analysis – Detailed Description of Pro-cessing Steps

3.6.1 Brachial Ultrasound Data Input

An ultrasound sequence study has to be formed and its associated datastructures filled before any subsequent action can be performed. You cancreate a completely new study or you can open a previously-saved studyfrom a study file. Study files have an extension .sdy.

As mentioned in Section 3.5, there are typically two files associated witheach image sequence study – image data file with file extension .raw, .tif,.cri, .jpg, .bmp, or DICOM files and non-image data file containing all otherinformation including the border detection results with file extension .sdy.The image files are created during image acquisition or digitization, e.g., theymay be obtained as an output from Vascular Converter or Vascular Imager (seeChapter 1).

Clearly, two basic modes of operation with brachial ultrasound studiesare typical. The first deals with analyzing of new image sequences, thesecond with reviewing previously analyzed image sequences. These two basicmodes of data input were already described in Tutorials 2 and 1, respectively(Sections 3.5.3, 3.5.2).

Briefly, with the Brachial Analyzer running (Section 3.1), perform one ofthe following steps:

• To create a new study, click [File → New] or . Fill in all requiredinformation fields, the required fields are labeled in RED. To selectthe brachial ultrasound image sequence for the analysis, click the redImage File label on the left or the button with three dots on the rightof the image filename field [...], select your file type (.raw, .tif, .cri, .jpg,.bmp, or DICOM files), then locate and select the input image file withthe corresponding extension.

• To open an existing study, click [File → Open] or . Then select astudy file with the extension .sdy you want to review. Upon opening ofthe study file, the images, all available information, parameters, andanalysis results are loaded automatically.


3.6.2 Pixel Size Calibration

Pixel size calibration Function Panel automatically appears whenever anew (previously not analyzed) brachial ultrasound image sequence is opened.However, if several analyses are performed in a row, the program assumesthat the pixel size does not change and the previously determined pixel sizeis carried over to the next analysis. Alternatively, when the pixel size isknown a priori, the numerical pixel size value can be entered in the StudyInformation window (Section 3.3.4). If a zero (0) value is entered as the Pixelsize in the Study Information window, the previous pixel value is not carriedover and the calibration dialog is invoked. Pixel size calibration can also beinvoked by clicking [Action → Calibrate] during the analysis session. TheFunction Panel looks as follows:

To calibrate the pixel size:

1. Select vertical calibration option.

2. Click with left mouse button on the first calibration marker on the im-age, a cross-in-a-circle will occur in the image. The calibration markersare provided by the ultrasound machine and are part of the image. Youcan reposition the marker by dragging (move mouse with left buttonclicked) until full satisfaction with the cross placement. Positioning thecross properly is crucial to achieve correct measurement calibration.

3. Click with left mouse button on the second calibration marker on theimage. If several markers are present in the image, choose the twomarkers with largest known distance between them, this will maximizethe calibration accuracy. Again, you can reposition the marker bydragging until satisfied with its placement.

4. Using the numeric distance window in the Calibration Function Panel,enter or confirm the known distance value between the two identifiedmarkers.

5. If horizontal calibration is available, select horizontal calibration optionand perform horizontal calibration in the same way. If no horizontalmarkers are available, a square pixel size (same size horizontally andvertically) can be assumed by not calibrating in the horizontal direc-tion.

6. Click the [Finish] button to exit from the calibration process.


Whenever this calibration Function Panel is invoked, it automatically dis-plays the locations of the starting and ending point markers as they weredefined in the previous calibration attempt. Also, the distance value thatappears in the window is identical to that used in the previous calibrationattempt. This behavior is motivated by the observation that calibrationmarkers as well as the distance between them are stable in the images acrossa variety of sequences originating from the same ultrasound machine whenusing the same probe. In such cases, the user simply approves the calibra-tion marker location. Whenever the markers change their position, it is easyto reposition the cross-in-a-circle markers to achieve the highest possiblecalibration accuracy. The existing calibration markers may be deleted byclicking [Start over] button - and calibration then repeated from scratch.

As a result of the calibration process, a pixel size for vessel diametermeasurements is determined. The pixel size values (horizontal and vertical)are provided in the Results window.

3.6.3 Training

It may be for the first time you are meeting with machine learning face-to-face [1]. The border detection training steps that are incorporated inthe Brachial Analyzer are extremely important as they directly influence theborder detection performance. The rationale behind the training steps isbased on the observation that brachial ultrasound responses from the nearand far walls are highly variable across individuals. At the same time, how-ever, they are very stable for the same individual over the period of several-minutes-long brachial ultrasound imaging, as long as the sonographer holdsthe transducer in the same position during the entire study. Since the as-sumption of no probe motion is paramount to the entire concept of flowmediated dilatation measurement, it was incorporated in our method as apriori knowledge. In other words, we expect the border properties not tochange dramatically during the image acquisition and if they do, we con-sider such variations to represent imaging artifacts. At the same time, weare well aware of the fact that the brachial ultrasound images are noisy, thatthe sonographer is practically unable to hold the probe absolutely steadythroughout the entire exam, that the subject itself causes changes in therelative position between the transducer and the brachial artery. Therefore,we have developed and incorporated quality control steps to identify andremove many of such artifacts.

Consequently, our method is designed to learn the border properties froma single good-quality image frame, and the learned border properties arereflected in the border detection process in all remaining images of the se-quence. Then, automated quality control is invoked to identify the artifactsand outliers that unfortunately are always present in today’s brachial ultra-


sound image data sets.Clearly, in such a scenario, it is necessary to select a representative and

good quality image frame for training. Fig. 3.5 demonstrates the importanceof good frame selection for training. When Fig. 3.5a was selected, only asmall portion of the vessel border can be reliably identified. In such a case,the chances that the entire sequence will be reliably analyzed are small sincethe method did not learn sufficiently well the vessel border properties. Fig.3.5b shows a good frame selected for training, note that almost entire borderis successfully identified after training in this step. Consequently, a muchbetter overall performance in this very same sequence can be expected sincethe method was able to learn the border properties appropriately. See alsoSection 3.6.3.

(a) (b)

Figure 3.5: Importance of selecting proper frame for training. (a) Whenselecting this frame of a sequence for training, only 21% of the border is reli-ably identified – consequently, the method cannot learn the border propertiesreliably. (b) Selecting a better training frame, just two frames apart fromthat shown in panel (a), provides 100% of the border length reliably detectedand thus used for training. Clearly, the learning step can extract much moreinformation about the border than in case (a). As a rule of thumb, at least70% confidence index (in lower right corner of the main screen) is recom-mended. If the confidence after training is lower than that, it is recommendedto retrain using one of the methods listed in Sections 3.6.3 – 3.6.3.

In other words, the training frame selection, analysis of the trainingframe, and assessment of border detection success in this training frame aftertraining is completed are performed interactively under the direct supervi-sion of the human operator – interpreter. On the other hand, the analysis ofhundreds of the remaining image frames can be performed without direct su-pervision. The obtained border detection results are further processed usingautomated Quality Control processes and finally reviewed by the interpreter


as described in Section 3.6.5.Recall that the training process consists of three main steps that may be

repeated separately or in their entirety:

1. ROI definition.

2. First-stage border detection and approval.

3. Border detection parameter design and approval of the overall trainingprocess result.

Tutorial 2 went over the individual steps of border detection training inquite some detail. Here, we give a little higher level description of the sameprocess – see Tutorial 2 for practical details if needed.

First of all you need to use the sequence navigator to identify a goodquality frame for the training. To invoke the training, click [Action → Train]

or . The 1st training stage Function Panel provides tools to define anROI. If the ROI has already been defined, it is displayed on the image screen.Note that the near and far border sides are marked by “N” and “F”. TheROI size is indicated below the ROI box as demonstrated in Fig. 3.6. Thissize display can be switched on and off by a switcher in the Border displayparameters/Options window.

Figure 3.6: ROI size display – can be switched on and off in the Optionspanel.

You can modify the ROI position easily by click-and-point or draggingthe mouse left button or clicking the set of buttons on the panel. When anew image sequence is analyzed for which wall borders are not yet available,

the ROI from the previous training is displayed after first clicking thebutton. This feature is designed to facilitate reproducibility of ROI positionwhen baseline/inflation/deflation image sequences of the same subject areanalyzed in an analysis stream.


If, at any time, no ROI is available, an initial one must be defined. Thiscan be done by clicking the left mouse button on the location of the center ofthe ROI. A default, horizontally-oriented ROI is displayed and modificationscan be performed to create an approximate ROI. The final ROI is thendetermined automatically. Figs. 3.7 and 3.8 give an examples of definingan approximate ROI position and show how ROI is automatically adjustedduring the training step. See also Section 3.6.3.

(a) (b)

Figure 3.7: Automated positioning of the ROI if the Lock ROI option in Step 1Training Function Panel is set (default setting). (a) The initial positioningof the ROI may be very approximate. (b) The ROI orientation is adjustedautomatically.

At any time during the ROI definition you can click the [Clear] buttonto start definition of ROI all over again. You can also click [Cancel] to abortthe entire training process.

When you are satisfied with the ROI, click the [Proceed] button. Thesystem automatically detects the first-stage borders, opens 2nd stage train-ing Function Panel, and asks the human observer for 1st stage border ap-proval. In situations when the borders do NOT correspond to the near andfar brachial artery borders as judged by the human operator supervising thetraining process, training has to be repeated with a modified ROI, ROI sizemay be fixed, near and/or far border location can be interactively identi-fied, or training may be performed in another frame. All these options aredescribed below. For now, assume that the 1st stage borders are satisfac-tory. In that case, clicking the [Proceed] approval button invokes a borderfeature acquisition process, training process designs a final border-detectionfunction, and the supervising human operator is again asked to approve theborders resulting from the border detection with this final border detectioncost function. If the borders are approved, the cost function is applied to allframes of the analyzed brachial ultrasound image sequence.


(a) (b)

Figure 3.8: Automated positioning of the ROI if the Lock ROI option inStep 1 Training Function Panel is cleared (ROI size is not locked). (a) Theinitial positioning and size of the ROI may be approximate. (b) The ROIorientation and size are adjusted automatically.

Let’s now discuss the situation that may occur in lower quality images –the situation in which the supervising operator did not approve the detectedborders either after the 1st or the 2nd training stage. In such a case, thefollowing options are available to achieve satisfactory training results andconsequently allow good analysis performance:

1. Repeating training in a modified ROI.

2. Freezing the ROI size.

3. Interactive definition of near and/or far border location.

4. Training in another frame.

5. Changing the robustness of the border detection process.

These options are now described in detail.

Repeating training in a modified ROI

This approach is appropriate in situations when the border after 1ststage of training is incorrectly positioned or the border after 2nd stage oftraining does not have sufficient confidence – the length of the reliable borderis too short (confidence shown in % in the bottom right corner of the mainwindow). In that case, repositioning the ROI along the vessel may improvethe training results. Keep in mind however that the position of the ROImust be appropriate for the entire sequence, not only for the single frameused for training. The modifications of the ROI can be performed in this


2nd stage of training or you can return to Stage 1 training window. Fig. 3.9shows an example of using this approach.

(a) (b)

Figure 3.9: Repeating training in a modified ROI. (a) Situation after 2ndstage of training, border detection confidence is too low. (b) Moving the ROIalong the artery increases the training efficiency, border detection confidenceis much higher.

Freezing the ROI size

Freezing the ROI size is a default selection. Using this option is appro-priate when another strong border is present in the proximity of the near orfar border. In such a case, the automated modification of ROI size duringtraining may cause the identified border to “find” the strong border posi-tioned somewhat outside of the manually identified ROI. While this behaviormakes ROI definition in most cases easy not requiring an exact manual ROIdefinition, it may cause incorrect border identification in situations with astrong parallel border present. An example of such a case and ROI freezingsolution is shown in Fig. 3.10.

Interactive definition of near and/or far border location

The approach of ROI freezing may not be always effective, especiallyin situations when the parallel stronger border is positioned “inside” withrespect to the desired border. This may be the case of strongly visualizedintimal border while the user may want to follow the medial border. Then,it is appropriate to provide an interactive hint to the training process bydefining the location of the desired border in the image. The desired bordermay be identified by one interactively defined point, interactive definitionof this single point may be repeated. Simply click with a left button in thevicinity of a desired border position. The boundary will change its location.


(a) (b) (c)

Figure 3.10: Freezing the ROI. (a) Initial position of the ROI. (b) Situationafter 1st stage of training, incorrect border identified due to existence ofanother strong border in the proximity to the desired border. Consequently,the ROI width increased as a result of the automated ROI size optimization.(c) Result of training with the ROI lock option set, the ROI width did notchange and correct border was determined.

The clicks can be repeated until a desired effect is reached. After each pointdefinition, the borders are automatically re-determined. Once the borderpositioning becomes acceptable, click the [Proceed] button. Otherwise, in-teractively define another required border point; and the borders will berecalculated again.

Note that it may not be possible to identify the border running throughan arbitrary manually identified point. The point identified must be anexpected border point, meaning that it must be located on the border withusual brachial artery wall properties.

Yet another word of caution ... the fact that the modified and repeated1st stage of training did after interaction identify the border at the desiredposition does not necessarily guarantee that the 2nd stage of training willbe able to design an appropriate cost function to determine the desired bor-der reliably in this training frame or the entire sequence. It is important torealize that while there are significant strengths in the graph-search basedborder detection process that result in identification of correct borders mostof the time, there are also inherent limitations that may not allow identifi-cation of the border that you would like to see identified if its properties arenot in agreement with usual properties of brachial artery borders. In such acase, it is recommended to repeat training in another frame of the sequence.

Example of usage of this training process interaction is shown in Fig.3.11.


Training in another frame

This training option is straightforward from the training descriptionstandpoint – the operator selects a better quality or more representativeimage frame of the analyzed sequence and repeats the training in a standardway. See also Fig. 3.5.

Changing the robustness option of the border detection process

The likelihood that a correct border is determined during the automatedprocess is called border detection robustness. This training option allows toselect among the three following border detection behaviors:

• Most accurate

• Intermedium

• Most robust

As the labels suggest, the robustness of the analysis increases from the firstto the third choice. At the same time, robustness increase may (but doesnot have to) be associated with a decrease of accuracy – we observed thisbehavior during validation of the method in artificially generated data, nosimilar assessment is possible in vivo. Therefore, it is recommended that theanalysis is performed with such robustness setting that results in sufficientrobustness while maximizing the accuracy.

Analyzing curved vessels

A switch in Training stage 2 panel allows to distinguish cases when thebrachial artery segment of interest is not straight. Selecting Curved Vesselallows the vessel border to follow non-straight borders.

3.6.4 Border Detection in the Entire Sequence

Upon approval of the training, the system is ready to perform the nextstep – a fully automated analysis of every frame of the sequence. It switchesto the first frame and performs border detection and diameter measurementthroughout the sequence.

No user input is required in this step. However the user can abort the

border detection process at any time for any reason, by clicking but-ton on the tool bar. One of the possible reasons for stopping the analysisprematurely may be frequently repeated detection of incorrect borders. Insuch a case, the method may be retrained or the ROI repositioned. On theother hand, if the borders are incorrectly detected in some frames but theanalysis mostly finds correct borders, this is not a good enough reason forstopping the analysis. Most likely, these artifactual image frames will be


automatically rejected by the Quality Control steps anyway and will have noeffect on the final results.

Overall, the best approach to achieve a minimal number of incorrectlyanalyzed frames throughout the sequence is 1) acquisition of high-qualityultrasound image data, 2) minimization of probe-motion-related artifacts,and 3) appropriate training of the border detection system.

3.6.5 Border Detection Quality Control; Review of the Results

Reviewing the automatically detected borders is an important step onthe way to receive correct data analysis results. As we mentioned earlierand as is widely known, the brachial ultrasound images are noisy and sufferfrom a variety of imaging artifacts.

The result-reviewing steps allow human-observer-evaluation of the bor-der detection and diameter measurement, as well as possible interventions.There are several ways of reviewing the results.

1. Borders and diameters can be reviewed for any specific frame usingthe Sequence Navigator, the diameter measurement and measurementconfidence (in %) is always provided in the lower right corner of themain Brachial Analyzer window.

2. Borders and diameters can be reviewed for the entire sequence using

[Action → Play] menu item or button.

3. Diameter measurements, measurement confidence indices and the ves-sel diameter function over time can be reviewed in the Analysis Results

window after clicking [View → Analysis Results] menu item orbutton. The following measurements are available in the Analysis Re-sults window for each image frame:

• Avg. – Average vessel diameter calculated from reliable portionsof the vessel borders (from those portions shown as border overlapwhen reviewing the borders).

• STD. – Standard deviation of the vessel diameter function, mea-sured in the reliable parts of the border.

• C(%) – Diameter measurement confidence determined as the per-centage of the region of interest length in which the vessel wasconsidered reliable (e.g., if the ROI length is 100 pixels, and ifthe diameter measurement is considered unreliable in 30 pixels,the resulting confidence is 70%).

• Avg. Diameter of the sequence – In addition to the parametersassociated with each frame, average vessel diameter of the entire


sequence is calculated from valid frames for baseline and inflationsequences and displayed within the Results and Report windows(in the upper portion of the Report display, part of the reported‘Condition’ field). No average diameter is calculated for deflationsequences since this information is irrelevant.

• Max. diameter of the sequence / its frame number – this infor-mation can be found immediately below the diameter chart inthe form max diameter@frame number and is given in the selectedunits.

• Other information items associated with the analyzed sequenceare also displayed.

4. For better monitoring of the automated diameter function generationprocess, the user can invoke the Results window and arrange the chartalong with the main image window by clicking [Attach to Main] but-ton within the Results window (the Results window is automatically

aligned whenever it is invoked by clicking ). The diameter func-tion construction can be viewed in real-time together with the framestatus symbols (*/r/e/i/n ... see below). Real-time reviewing is pos-sible whenever the Results window is open during the image sequenceanalysis – at any time, “*” next to the frame number represents thecurrent frame that is displayed in the main window. While this fea-ture is useful, it is computationally demanding and may slow down theanalysis process on slower machines. The slow-down should be barelynoticeable on 600 MHz and faster computers. On slower machines, youmay want to close the Results window when performing the brachialimage sequence analysis.

5. Correspondence between the Results chart and the image frame dis-played can be accomplished using the click-and-display option. When-ever you click on the diameter chart, the image frame corresponding tothe chart location is displayed and the current numeric measurementvalues are provided on the 1st line of the Results table (if one of thelast 12 frames, the values will not appear on the 1st displayed line).Similarly, if you double-click on a row within the diameter table, thecorresponding image frame is displayed. Using this approach, it is easyto target image frames that seem incorrectly analyzed according to thediameter context shown in the diameter chart.

6. Diameter function chart zoom – the user can modify the scale of the

diameter function chart by clicking the buttons . If no furtherscaling up or down is allowed, the corresponding button disappears.


7. At any time of the reviewing process, border display can be switched

on and off by clicking the button or the borders may be set to

flash repeatedly by clicking the button .

The primary goal of the result-reviewing process is to identify those framesthat do not contribute correct quantitative diameter measurement to theoverall analysis of brachial vessel diameter, flow mediated dilatation, com-pliance, etc. The implemented quality control steps are incorporated to helpidentify such frames automatically, label them with a measurement confi-dence index, and possibly exclude them from the final quantitative results.

Note that the brachial ultrasound study is usually performed over a pe-riod of 2 minutes or more. The diameter measurements in adjacent framesare expected to be almost identical and consequently, there is substantialinformation redundancy present in the brachial ultrasound image sequence.Therefore, rejecting some number of image frames from the final data anal-ysis does not adversely affect the measurement accuracy. Similarly, vesseldiameter in a single frame is determined from a large number of local diame-ters measured in all points along the region of interest – typically more than100 diameter measurements are averaged to represent the vessel diameterfor a particular frame. Using the same rationale as above, there is substan-tial information redundancy and therefore it is possible and advantageousto measure the vessel diameter in reliable border portions only.

Therefore, the following major quality control steps are incorporated:

• Quality Control in individual images – this quality control mechanismremoves measurements from unreliable border portions caused by localultrasound dropouts or insufficient quality of the local wall echo usingthe confidence index expressed in % as described above. A confidencethreshold can be input from the user ([Conf. threshold] in the Anal-ysis Results window). If the [Conf. threshold] is non-zero, the systemautomatically excludes all image frames whose confidence is below thethreshold.

• Global Quality Control – this quality control mechanism removes mea-surements from image frames with an unlikely vessel diameter mea-surement with respect to the vessel diameter trend during the entiremeasurement period. Consequently, frames with incorrect diametercaused by sudden transducer motion, by isolated noise frames, etc.can be automatically identified and rejected. A 3rd-order polynomialis fitted to all valid measurements and fitting errors are computed forevery frame. An error threshold with respect to the mean square errorcan be input from the user in the [Trend threshold] box of the Analysis


Results window. The frames with diameter fitting error falling outsidethe allowed error range are automatically excluded.

• Interactive Quality Control – the human interpreter can selectively re-ject any number of consecutive frames or frame intervals by repeatedlyselecting these frames and clicking the [Reject Selected Frames] but-ton. Individual frames can also be rejected during the frame-by-framereviewing button by clicking the menu item [Action → Reject].

• As a result of these Quality Control steps, only those vessel diametersthat were not automatically or excluded interactively or rejected areshown in the table and in the chart. The diameter measurements forthe rejected or excluded frames are left empty and a status symbol isshown next to the frame number indicating the reason – r=rejected bya human, e=excluded by the Quality Control assessment according tothe current threshold criteria. n=not yet analyzed.

3.6.6 How to Use Border Reviewing and Quality Control; HumanIntervention and Manual Editing

The quality control steps are not only providing some confidence values,they can positively influence the overall quality of the final results. There areprobably many ways of using the Quality Control steps to increase reliabilityand correctness of the brachial diameter measurement in long ultrasoundsequences. As the first guiding information, in excellent and good qualityultrasound sequences, setting the confidence threshold [Conf Thr] value to50% or more and the [Trend threshold] value at 1 or less is usually givingvery good results. In such high-quality sequences, the final measure of flowmediated dilatation is usually minimally affected by the selected values in awide range.

In low-quality image sequences, the following reviewing and quality con-trol interaction mechanisms may be both effective and efficient to improvethe overall result:

1. Assess the quality of the diameter function (chart in the Quality Controlsubwindow of the Results window), if necessary, interactively modifythe Trend Threshold value to exclude majority of the outliers – theTrend Threshold value may need to be interactively modified withrespect to the total number of remaining diameters.Important: The trend threshold quality control mechanism is onlyappropriate in long deflation image sequences only. Also, to be keptin mind, the trend-threshold quality control mechanism is designed forECG-gated sequences that do not depict cardiac cycle caused diameterchanges (although even in non-gated sequences this mechanism maybe useful).


2. Assess the quality of the vessel border detection process with respectto the border detection confidence. In many cases, the ConfidenceThreshold value as low as 30% is still providing meaningful diametermeasurement allowing the Trend threshold value to be stricter to keepa high-enough number of non-excluded diameter measurements.

3. Manual rejection of some frames or frame intervals may be appropriateas a response to image intervals of low quality.

4. Exclusion of one or more subsequences of image frames can be usefulin situations when a subsequence or subsequences within the brachialanalysis image sequence contain invalid data – for instance Dopplerblood flow images are recorded within the brachial ultrasound se-quence. One or more such subsequences of consecutive frames maybe defined in a window occurring after clicking [Action → Excludeframes from analysis] or after hitting CTRL-E. The subsequences arethen excluded from any analysis or re-analysis that is performed after

training or invoked by the button. If the analysis was already

started via the button and a subsequence is found that should

be excluded, analysis can be stopped by clicking the button, ex-clusion sequence(s) can be defined, and analysis re-started by clicking

and .

5. Manual editing of detected borders can always be performed if nec-essary as the last option, it is described in Tutorial 3 (Section 3.5.4).

To perform this operation, select [Action → Edit] menu item orbutton, select one of the three editing Sensitivity options, and edit theborders using mouse clicks. Do not attempt to “trace” the border,rather click repeatedly at points you want to define as border points.After each click, wait for the border to be adjusted to reflect your in-teractive border point definition. If you are unhappy with the result ofediting, you may click the [Clear Editing] button and the original auto-matically determined borders will reappear. Click the [Finish] buttonto abandon the manual editing mode. To manually edit another frameof the sequence, you may use the “+” and “–” buttons to display imageframes without abandoning the manual editing mode. Note that theclick-on-chart-and-display option (Section 3.6.5) is also functional inthe manual editing mode. Manually edited frames are marked by “i”(intervention) in the Results window table.


Fig. 3.12 shows an example of the usefulness of Quality Control in brachialultrasound image sequences. It shows the usage of Trend Threshold whenapplied to a long brachial ultrasound deflation sequence suffering from proberotation artifacts. Another example of quality control in a somewhat noisyimage sequence is provided in Fig. 3.14. Fig. 3.15 demonstrates the 3rdorder polynomial fit through the quality-control processed data shown inFig. 3.14d. The maximum diameter for the deflation sequence can be easilyand reliably obtained.


(a) (b)

(c) (d)

Figure 3.11: Interactive definition of far border location. (a) Originalbrachial ultrasound vessel segment. (b) The border identified during 1st stageof training. In this case, modification of the ROI size and freezing does nothelp since the stronger border belongs to the intimal layer closer the ROIcenter and the desired border is the medial layer (This example is not meantto imply that identification of the intimal layer is incorrect.) (c) The arrowdepicts the required border point interactively defined after clicking [No, pointfar border] in the Training step 2 Function Panel. (d) Desired border identi-fied by the repeated 1st stage of training. The border now passes through therequired border point.


25

30

35

40

45

0 20 40 60 80 100 120 140

Cardiac Cycle

Ve

sse

l D

iam

ete

r (p

ixe

l)

Figure 3.12: Quality control example – analysis of a deflation sequence con-taining probe-rotation artifacts. Dashed line shows the diameter functionbefore the automated diameter function quality control. Smaller diameterswere measured from some images where probe rotations occur. The effectwas recognized in the automated diameter function quality control by settingthe Trend Threshold=1. The solid line shows the final diameter function.The thick line is the diameter function showing the non-excluded diameters.The imaging artifact of this sequence is explained in Fig. 3.13.


a)

b)

c)

Figure 3.13: Example of rotations probe motion artifact and the projectedimaging position from three frames in a sequence, vessel diameter changesare observed (arrows): a) Good quality frame. b) Rotational probe motionartifact produces an image with smaller vessel diameter. c) Operator recog-nizes the problem and corrects the imaging position.


(a) (b)

(c) (d)

Figure 3.14: Quality control in a noisy deflation sequence. (a) Measured ves-sel diameter function when not using Quality Control, Confidence Thresh-old = 0%, Trend Threshold = 0. Note the noisy character of the diameterfunction. (b) Using Confidence Threshold as a quality control means, Con-fidence Threshold = 50%, Trend Threshold = 0. Note that one of the noiselocations was successfully removed. (c) Using Trend Threshold as a qualitycontrol means, Confidence Threshold = 0%, Trend Threshold = 1. The flowmediated dilatation can now be more reliably assessed. (d) Using both theConfidence Threshold and Trend Threshold as quality control means, Confi-dence Threshold = 50%, Trend Threshold = 1.


Vessel Diameter (mm)

Cardiac Cycle

Figure 3.15: Flow mediated dilatation assessment using a 3rd-order polyno-mial fit through quality-control processed data. The maximum diameter forthe deflation sequence can be easily and reliably obtained.

3.6.7 Report

All image sequence analysis information and the analysis results arestored in the study file .sdy. For convenient post-processing managementof the results, a formatted Report can be generated by either clicking [File→ Report] or clicking [Generate Report] button in the Results window.

The output file is printable from virtually any editor, includes only ASCIIcharacters, and consists of two groups of data:

• Data that are common to the entire data set occur once in the header.

• Data that change with each frame occur in the body.

The following information fields are included in the Report header. Ifsome of the header information fields do not have values associated withthem, the value fields are left empty. Which fields are and which are notincluded in the Report can be customized as detailed in Section 3.6.7.2.

The header is preceded by a single line containing the text

“BRACHIAL-ANALYZER-REPORT SERIAL #: xxx-xxx-xxxx)”.


• Report-date Date of Report generation.• Subject-ID Subject identifier.• Pat-ID-type Type of Subject-ID identification label.• Study-ID Research project identifier.• Condition Imaging condition – baseline/inflation/deflation/other.• – 2nd column Average diameter in valid frames (for baseline/inflation only).• Gender Subject’s gender.• First-Name Subject’s first name.• Last-Name Subject’s last name.• Date-of-birth Subject’s date of birth.• Imaging-date Date of brachial ultrasound imaging.• Analysis-date Date of computer analysis.• Machine-ID Ultrasound machine identifier.• Probe-ID Ultrasound probe identifier.• Sonographer-ID Sonographer identifier.• Interpreter-ID Computer analyst identifier.• SDY-filename Filename of the .sdy file.• Image-filename Filename of the .raw file.• Pixel-siz-mm/p Pixel size in mm/pixel.• Frame-trained Number of frame used for training.• Frames-total Total number of frames in sequence.• Frames-valid Number of successfully analyzed frames.• Frames-reject Number of rejected frames.• Frames-exclud Number of excluded frames.• Frames-edited Number of manually edited frames.• Frames-notanal Number of frames not analyzed.• Confid-thresh Confidence threshold used for frame exclusion.• Trend-thresh Trend threshold used for frame exclusion.• Trend-MSE-mm Mean square error of the trend fitting function.• Study-type Study type identifier.• Reproduc-round Analysis repetition identifier I.• Reading-number Analysis repetition identifier II.• Code-1 User-specified code I.• Code-2 User-specified code II.• Code-3 User-specified code III.• Code-4 User-specified code IV.• Code-5 User-specified code V.• Code-6 User-specified code VI.• Code-7 User-specified code VII.• Code-8 User-specified code VIII.• Code-9 User-specified code IX.• Code-10 User-specified code X.


All following information fields are included in the Report body, thesevalues are provided for each frame of the sequence, one line of the Reportper image frame, again fixed column width format, 20 ASCII characters percolumn. The body is preceded by a single line containing the text “DATA:”.

• FRAME Sequential frame number within a sequence of analyzed images.• BDIAMM Average vessel diameter in millimeters,

no value given for rejected, excluded or not-analyzed frames.• IDTYPE Type of Subject-ID (same as in header).• PID Subject’s identifier (same as in header).• STYPE Study type (same as in header).• SDATE Imaging date (same as in header).• STIME Time of frame acquisition, millisecond accuracy.• MSEC Time offset of this frame with respect to

the start time of sequence acquisition in milliseconds.• COND Imaging condition (same as in header).• SONOG Sonographer ID (same as in header).• INTERP Interpreter ID (same as in header).• ADATE Analysis date (same as in header).• CODE1 User-specified code I (same as in header).• CODE2 User-specified code II (same as in header).• CODE3 User-specified code III (same as in header).• FCYC Frame within cycle – sequential number of image frame

within a single cardiac cycle if more than one frameper cardiac cycle were acquired.

• QC Result of the analysis and Quality Control– r=rejected/e=excluded/i=intervened(edited)/n=not analyzed.

• BDPX Average vessel diameter in pixels, diameters in pixelsgiven for all analyzed frames (even for those rejected or excluded).

• CONF Confidence threshold value used for Quality Control.• TRND Trend threshold value used for Quality Control.• MINPX Minimum local diameter measured in frame.• MAXPX Maximum local diameter measured in frame.• STDPX Standard deviation of local diameter function in frame.• REPROD Reproducibility round (same as in header).• READNG Reading number (same as in header).

The body is concluded by a single last line containing the text “BRACHIAL-ANALYZER-EOF”.

Note that not all of the indices and identifier values listed above maybe available for your particular implementation. For example, not all imageacquisition devices allow storage of the exact frame acquisition time, notall identifiers are important for your study and therefore are not routinely


entered, etc. The fields not holding any information are left empty. All theinformation indices included in the final report are always stored in the .sdyfile that keeps all information about the analysis parameters and results.Therefore, after any image sequence is analyzed, results stored [File → Save]in a .sdy file, and the Report generated using some Report Fields selection,the .sdy file can be opened at any later time and a new Report file generatedwithout reanalyzing the image sequence.

There are two formats in which the Report file can be stored:

• Excel-compatible format - the file can be directly opened using MSExcel.

• SAS-compatible format – individual fields (columns) of the Report havea fixed width of 20 characters.

After clicking the [Print Summary] button within the Report window, thereport header (summary) can be printed. The entire report is not printedhere since the width of the printed Report exceeds the page width. However,when printing the entire Report is desirable, it can be easily accomplishedby opening the Report.txt file using virtually any text editor and printingfrom inside of the editor. In this case, selecting a non-proportional font (e.g.,Courier) is recommended to keep the columns properly formatted.

Needless to say, several different reports can be generated at any timeand stored under unique file names in text files. The default file name isthe study name with an appended sequence of characters “-Report.txt”. Thedefault location of the Report file is in the directory that contains the currentstudy file.

3.6.7.1 Customization of User-Defined Codes

Starting with Brachial Analyzer version 3.2.6, there are 10 user-customizablecodes that can carry non-standard and/or site-specific information (onlythree non-customizable codes were available in previous versions). See Sec-tion 3.6.7.3 for additional information if you are upgrading from an earlierversion. The first three of these codes occur in the Report header as well asin the Report body. The remaining seven codes only occur in the Reportheader. Default code names (labels) of these user-defined codes are Code-1to Code-10. However, the code labels can be customized to better reflecttheir contents. Code label customization is performed within the Informationwindow (click [Edit → Study Information]). After clicking on any of the 10blue code-labels, the labels can be edited as shown below. The modifiedlabels are stored and used to label the corresponding fields in the Reportheader. Note that the customized code label is NOT stored in the .sdy file.Rather, it is stored as a status of the Brachial Analyzer. Consequently, themost recent codes labels will always be displayed in the Study Information


window. (To be exact, the .sdy file always keeps the values of all 10 codes infields labeled Code-1 to Code-10. The naming of these codes is customizable.However, change of the code name does not change any corresponding valueassociated with the code.)

Note that the user-specified code labels may contain spaces (blanks).These spaces are however stored as underscores due to the need to avoidblanks in the Report.txt files since blanks are used for field separation.

As described earlier (Section 3.3.4), Study Information fields can be spec-ified as required or optional. Note that the fields with user-customizablelabels are always “optional” and cannot become “required”.

3.6.7.2 Report Customization

Whether or not specific information fields are included in the Reportbody can be customized after clicking Customize button within the BrachialAnalyzer Report window.


All Report body fields can be selectively included or excluded from the re-port (note that only the first three user-defined codes are included in theReport body, the remaining seven user-defined codes only occur in the Re-port header). The latest setting is automatically memorized by the BrachialAnalyzer. At least one information field must be selected, if none is selected,all fields are included.

Note that no matter which fields are selected for the Report, all informa-tion is always stored in the .sdy file.

To ensure data integrity for Excel or SAS off-line data analysis, the listof included data fields should be kept consistent for all data sets from thegroup of related image sequences.

3.6.7.3 Consequences of Upgrading from Version 3.2.5 or Earlier

If you use import macros for reading the Report.txt files in statistical orspreadsheet packages, or if you use analysis macros to process the data, youmay need to slightly modify these macros. Upgrading from earlier versionof Brachial Analyzer to version 3.2.6 or higher results in a modification ofthe structure of the exported Report.txt file. Due to adding 10 customizable


codes, the lengths of the header is increased by 7 lines. This change causes noproblems if the resulting Report file is opened in Excel or SAS and furtherprocessing is performed manually. However, if a macro was developed toimport the Report files in the statistical or spreadsheet packages, the macromust be adjusted to properly deal with the additional 7 codes that are nowpresent in the header. Contact the person who developed the original macrothat you are using if problems are encountered.

3.6.8 Generating and Saving Reports

As mentioned above, the Report can be saved in Excel and SAS formats.The exact content of the Report is controlled by the current selection ofreported fields. See Section 3.6.7.2.

Therefore, if a specific field is not selected, it is not included in the Excelor SAS output file. The Report header information and measurements arestored in separate worksheets of the Excel file (Fig. 3.16).

After an Excel report is generated, a window opens asking the userwhether the generated file shall be opened in Microsoft Excel immediately.

3.6.9 Saving Results

All information about the performed analysis session may be saved in asingle study file (.sdy). That includes the name and location of the image file(.raw), the study information as entered in the Create New Study window,the region of interest, detected borders, diameter measurements, etc.

The user-entered information contained in the study file can be modi-fied by clicking [Edit → Study information] and study parameters can beinteractively edited in their respective fields. Naturally, the image sequencefilename cannot be modified. The study information modification feature isalso useful if the operator needs to enter or access any study related com-ments in the Comments field of the .sdy file.

The study file (.sdy) and the image file (.raw) are saved separately, foreasy maintenance and flexibility. For example different analysis sessions canbe performed in the same image file by different observers, using differentregions of interest, etc., and it is therefore not necessary to store large imagedata files in duplicate copies.

Each study file (.sdy) contains information about an analysis session per-formed on one and only one image file. It stores the file name and locationinformation about the image file (.raw). Therefore when you open a study file(.sdy) from within the Brachial Analyzer, the Brachial Analyzer knows whereto find and open the image file (.raw) as long as the file saving conventionswere not violated.

Two file saving conventions are used to specify the file location informa-tion during the study file saving:


Figure 3.16: Excel-compatible Report worksheets.


• If the study file and the image file are located on the same directory,the location information included the image file is not included.

• If the study file and the image file are not in the same directory, theexact directory information of the image file is stored in the study file.

The conventions are intended to serve two common but conflicting datamanagement schemes.

• Scheme I: Both the study file and image file can be moved (simultane-ously) to different directories. For example, archiving to another harddrive or burning to CD-ROMs.

• Scheme II: The directory location of the image file is NEVER changed(e.g., always residing on a CD), but the study files can be moved todifferent directories.

Please keep in mind that you need to select a data management schemeand follow it to ensure reliable data management.

3.7 Troubleshooting

• Problem: Screen does not refresh – e.g., it does not show the dynamicimage movie when played.

Solution: Click on [View → Refresh] to refresh the screen. If thisproblem is frequent, please contact Medical Imaging Applications.

• Problem: The analysis is slower than usually when the Results windowis open and the calculated diameter function is displayed in real time.

Solution: Real-time display of the brachial diameter and the frame sta-tus symbols (*/r/e/i/e) is useful for analysis process monitoring butcomputationally demanding. The slow-down should be barely notice-able on 450 MHz and faster computers. On slower machines, close theResults window when performing the sequence analysis.

• Problem: In image sequences with pronounced intimal layer at the farborder, the first stage training correctly identifies the desired border(e.g., the medial layer) but the second stage border detection identifiesa different well-visible border of the far wall.

Solution: Train in another image frame.

• Problem: The first stage training correctly identifies the desired bor-der but the second stage border detection identifies an incorrect borderthat seems to make little sense.


Solution: The learning process did not correctly resolve the influence ofthe contextual information present in the training frame. This prob-lem is rare but if it appears, it can be frequently solved by a slightmodification (e.g., 1 pixel longer or wider) of the width or length ofthe ROI used for training.

• Problem: The region of interest is not displayed.

Solution: Please make sure that the button is selected.

• Problem: The Brachial Analyzer does not show the resulting borders.


• Problem: The Brachial Analyzer sometimes does not show the resultingborders, the ROI box, and/or the calibration markers.

Solution: This may be caused by an unfortunate selection of colorsused to display borders and lines. To check that, click “Options” fromthe “View” menu, make sure the “Display Colors, Line Styles” tab isselected and make sure the selected colors (shown on the big squares)are visible. Bright colors are preferred for both the ROI and the border.In other words if a black color is selected you will have trouble seeingthe border or ROI on an image. Make changes if necessary and click“OK” or “Apply”.

• Problem: After upgrading to version 3.2.6 or higher, the exported Re-port file is incompatible with my macros to read the Report files inExcel or SAS packages. These macros worked just fine before.

Solution: Read Section 3.6.7.3. A simple customization of your macromay be needed to deal with the user-customizable codes added in ver-sion 3.2.6 and later.

CHAPTER 4

Doppler Flow Analyzer for Research

Doppler Flow Analyzer for Research (shortly, Doppler Flow Analyzer) is aWindows 95, Windows 98, Windows Me, Windows NT, Windows 2000, andWindows XP compatible program environment for highly automated anal-ysis of Doppler flow images and EKG-gated image sequences. Doppler FlowAnalyzer is a separate module functionally embedded within the BrachialAnalyzer (see Chapter 3).

Doppler Flow Analyzer uses an automated method for detection of Dopplerflow velocity waveform envelopes and consequent measurement of the max-imum flow velocity in the cardiac cycle, and the flow velocity integral overthe cardiac cycle.

Doppler Flow Analyzer creates an output data file with measured flowvelocity and other accompanying information in several selectable formats.

Previous, less sophisticated versions of the method have been used forresearch purposes since 1999 [6].

4.1 Running Doppler Flow Analyzer

To run Doppler Flow Analyzer:


by clicking button.


3. Select Brachial Analyzer.

4. Open a single ultrasound image or image sequence containing Dopplerflow velocity signal as described in Chapter 3.

5. Doppler Flow Analyzer functionality can be invoked by selecting Action→ Start Flow Analysis.

To exit from Doppler Flow Analyzer:


67

68 CHAPTER 4 Doppler Flow Analyzer for Research


Figure 4.1: Main Doppler Flow Analyzer window. The envelope is shown inred, the active cycle shown in yellow.

2. Exit [File → Exit] or click the upper right corner of the Brachial Ana-lyzer window.

4.2 Demo of Doppler Flow Analyzer

Doppler Flow Analyzer is a complex software package. Several imagesequences and prepared demonstration analysis case studies are includedwith your installation. A small number of images and image sequences iscopied to your hard drive. Several other image sequences are located on theInstallation CD, each with a complete analysis study file generated using ourDoppler Flow Analyzer software.

4.3 Getting Familiar with Doppler Flow Analyzer 69

4.3 Getting Familiar with Doppler Flow Analyzer

The Doppler Flow Analyzer is a program module embedded within theBrachial Analyzer (see Chapter 3). Due to its complex nature, this sectionpresents an overview of the main process control blocks from the user’sviewpoint. This section will identify the main parts of the application win-dow as well as the function blocks that are specific to the Doppler FlowAnalyzer – see Chapter 3 for a complete description of the Brachial Analyzerfunctionality.


• Menu Bar

• Tool Bar

• Function Panel

• Image

• Status Bar

Note that while the first two (Menu Bar, Tool Bar) do not change, theFunction Panel appearance and content change according to the currentlyperformed function. Similarly, the Status Bar content changes to reflect thecurrent status of the analysis, it may contain analysis results associated withthe currently displayed image frame. The subject name information – whenavailable – is continuously available in the bottom right corner of the statusbar.

The tools (control buttons) and menus are described in Sections 4.3.1 and4.3.2. In Section 4.3.3, we list the appearances of the Function Panel andbriefly describe their individual functionality. Section 4.3.4 introduces sepa-rate process-specific windows that pop-up in response to individual processcontrol steps.


In this section, only Doppler Flow Analyzer specific menu items are pre-sented, all other controls are shared with the Brachial Analyzer described inChapter 3.

• . displays or hides the determined Doppler waveform borders andthe flow-related ROI.



Figure 4.2: Menu controls: Action menu ... all other Menus are shared withthe Brachial Analyzer.


In this section, only Doppler Flow Analyzer specific buttons are presented,all other controls are shared with the Brachial Analyzer described in Chapter3. The functionality of the Action menu items shown in Fig. 4.2 is brieflydescribed below.

• Action menu

– Start Flow Analysis – Opens a flow-analysis function panel – iden-tical to clicking Flow Panel in the Results → Flow Analysis win-dow.

– Edit Flow – switches to a function panel allowing manual correc-tions or re-analysis of the already identified flow envelope bordersin the current frame – identical to clicking Edit Flow in the Results→ Flow Analysis window.

4.3.3 Function Panels – Controlling the Flow Analysis Processes

Several Function Panels exist for the Doppler Flow Analyzer:

4.3 Getting Familiar with Doppler Flow Analyzer 71


• Editing Function Panel

In addition to the two Function Panels mentioned above, the following Func-tion Panel menu items are used to control the Doppler Flow Analyzer func-tionality:

• Clicking [Action → Start Flow Analysis → Define Flow ROI] allowsdefinition of the region of interest within which the flow velocity anal-ysis is performed. This function can also be invoked by clicking FlowPanel in the Results → Flow Analysis window.

• Clicking [Action → Start Flow Analysis → Calibrate Velocity (verti-cal)] allows velocity calibration:

• Clicking [Action → Start Flow Analysis → Calibrate Time (horizon-tal)] allows temporal calibration:

• Clicking [Action → Edit Flow] or [Action → Start Flow Analysis →Edit], or clicking Edit Flow in the Results → Flow Analysis windowinvokes the Editing Panel:

• Many useful analysis-context-specific help items can be found on theblue “Hints” panel that changes its textual content based on the anal-ysis status


• Clicking [View → Analysis Results] or opens a Results window.Note that there are several subwindows available within this window


– Doppler Flow Analyzer results are available after selecting the FlowAnalysis tab in the Results window. The flow analysis results are locatedin the bottom third of the Results window.

4.4 Flow Ultrasound Analysis using Doppler Flow Analyzer

During a typical analysis of an EKG-gated Doppler flow ultrasoundimage sequence, the following steps must be performed:


2. Pixel size calibration – velocity and time.

3. Definition of the region of interest.

4.4 Flow Ultrasound Analysis using Doppler Flow Analyzer 73

4. Flow analysis – velocity envelope detection.

5. Reviewing and – if needed – editing the results.

6. Output report generation and saving of results.

Analysis of Doppler flow sequences requires to perform all the above-listedsteps that will be described in detail.

4.4.1 Doppler Flow Velocity Image Sequences

The Doppler flow velocity image sequences shall be EKG-gated, the en-tire sequence shall be acquired with identical calibration parameters – thesame vertical (velocity) and horizontal (time) scaling must be maintainedthroughout the Doppler image sequence.

The Doppler flow sequences are opened in the same way as described inSection 3.6.1.

4.4.2 Invoking Flow Analysis Function Panel

To start any Doppler Flow analysis, the Doppler Flow Function Panelmust be invoked by selecting [Start Flow Analysis] from the [Action] menu.Alternatively, you may click Flow Panel in the Results → Flow Analysiswindow.

Any frame can be selected either by using the review/analyze button

or any other button changing the “current” frame .Alternatively, a frame can be selected by double-clicking the frame numberthat shall become “current” in the Flow Analysis panel of the Results window.In this panel, the current frame is marked by an asterisk next to the framenumber.

4.4.3 Calibration

Velocity calibration is performed after selecting [Calibrate Velocity (verti-cal)] from the Flow Analysis Panel. For temporal calibration, select [CalibrateTime (horizontal)].


1. Select velocity (vertical) calibration option.




4. Using the numeric velocity window in the Function Panel, enter orconfirm the known velocity difference value between the two identifiedmarkers.

5. Select time (horizontal) calibration option.

6. Click with left mouse button on the first calibration marker on the im-age, a cross-in-a-circle will occur in the image. The calibration mark-ers are provided by the ultrasound machine and are part of the image.Again, you can reposition the marker by dragging (move mouse withleft button clicked) until full satisfaction with the cross placement. Po-sitioning the cross properly is crucial to achieve correct measurementcalibration.


8. Using the numeric time window in the Function Panel, enter or confirmthe known elapsed time value between the two identified markers.


4.4.4 Definition of the ROI

ROI is defined after selecting [Define Flow ROI] from the Flow AnalysisPanel. ROI is defined (or modified) by selecting one corner of the ROIby clicking-and-holding of the left mouse button, and dragging the mousecursor to the desired location defining the ROI. When the ROI shape andsize are as desired, release the left mouse button. The Doppler flow envelopeis immediately detected and outlined. The most recent complete flow cycle(with respect to the time point of the analyzed frame) – the active cycle – isdepicted in yellow. The active cycle is automatically identified as the part ofthe envelope corresponding to the flow of the latest complete cardiac cycle.Since the image sequence consists of EKG-gated cardiac cycles, the detectedcycle actually corresponds to flow of the previous cardiac cycle. The Dopplerflow measurements are performed on the yellow active cycle (see Fig. 4.1).

4.4 Flow Ultrasound Analysis using Doppler Flow Analyzer 75

When the ROI is defined, make sure that the entire width and heightof the Doppler waveform is included in the ROI. If a sequence is analyzed,the ROI must contain the waveform in the entire sequence. Note that it ispossible to define a separate ROI for each frame of a sequence if necessary.

4.4.5 Flow Analysis – Doppler Waveform Envelope Detection inan EKG-gated sequence

Assuming the ROI is defined and the pixel size calibrated, the entireimage sequence can be analyzed by clicking the [Analyze] button in the FlowAnalysis Panel.

4.4.6 Editing

After the automated Doppler flow analysis is complete, the results shouldbe reviewed by an expert operator and edited if needed.

There are three ways of correcting insufficiently accurate measurements:

• Rejecting frames: Frame measurements of the “current” frame can berejected by clicking [Reject] button in the Flow Analysis panel of theResults window. Note that a sequence of measurements can be rejectedby simultaneously selecting several rows of the Flow Analysis panel andclicking [Reject]. The previously rejected frames can be restored ifthey are selected and the [Un-Reject] button is clicked.

• Re-analyzing frames: In many cases, correct analysis can be accom-plished by modifying the ROI of the entire analyzed sequence, or ofa single or a small number of specific trouble-prone frame(s). TheROIs can be modified after selecting [Define Flow ROI] from the FlowAnalysis Panel.

• Interactive editing: Manual editing mode is invoked by clicking [Action→ Edit Flow] or clicking Edit Flow in the Results → Flow Analysiswindow. The previously determined velocity envelope can be modifiedby clicking-and-holding the left mouse button and slowly defining thecorrect envelope with the mouse. Note that only the yellow envelopeof the active cycle is used for the quantitative analysis and thus onlythe envelope of the active cycle needs to be correct. Note also thatthe editing uses a re-analysis approach and thus is not identical tomanual tracing – the active cardiac cycle is automatically detectedeven in the manual editing mode. The sensitivity of manual editingcan be modified by the slider present in the Editing Panel. Interactiveediting is completed by clicking the [Finish] button in the EditingPanel. Clicking the [Reset] button invokes an automated re-analysisof the flow envelope. If the manual editing does not produce desirable


outcome, try to redefine the ROI as described above – the ROI maybe different for each image frame. Alternatively, consider rejecting theframes which are causing the analysis difficulty.

4.4.7 Exporting Results

All image sequence analysis information and the analysis results arestored in the study file .sdy (together with the brachial wall border infor-mation if a split-screen setup is used). For a convenient post-processingmanagement of the results, a formatted Report can be generated by eitherclicking [File → Report] or clicking [Generate Report] button in the Resultswindow. See Section 3.6.7 for details of the Report generation.

For each successfully analyzed frame, three measurements are reportedin the Results window and consequently in the Report: FLOWINT, FLOW-MAX, and FLOWAVG. If these measurements are not available in the Re-port, make sure the FLOWINT, FLOWMAX, and/or FLOWAVG outputfields are selected in the Report customization window (from the Resultswindow, click [Report] and [Customize], then check the desired output fields,see Section 3.6.7.1 for details).

NOTE that all reported flow values are derived from the flowvelocity spectrum envelope and not from the spectrum itself. Con-sequently, the results are based on the maximum detected veloci-ties as a function of time throughout the cardiac cycle. Specifically,the results are NOT based on the analysis of velocity distributionsin the Doppler flow window since this information is not availablein the video image data that are analyzed.

In addition to the Brachial FMD measurements described in Section3.6.7, the following three measurement columns are included:

• FLOWINT Flow velocity integral over the activecardiac cycle (marked in yellowon the analyzed frame), in meters.

• FLOWMAX Flow velocity maximum over the activecardiac cycle (marked in yellowon the analyzed frame), in meters/sec.

• FLOWAVG Flow velocity average over the activecardiac cycle (marked in yellowon the analyzed frame), in meters/sec.

4.4.8 Display Customization

Color of the flow envelope can be modified together with modification ofthe media-adventitia border (M-line) after selcting [Display Options] in theResults window. Color of the ROI can be modified as well.


4.5 Troubleshooting

• Problem: No flow information is visible in the Report window and inthe Excel or SAS report files.

Solution: Make sure the FLOWINT and FLOWMAX output fieldsare selected in the Report customization window (from the Resultswindow, click [Report] and [Customize], then check the desired outputfields).

• Problem: Manual editing does not produce desirable outcome.

Solution: Try to redefine the ROI – ROI may be different for eachimage frame. Alternatively, if a sequence is analyzed, consider rejectingthe frame which is causing the analysis difficulty.

CHAPTER 5

Carotid Analyzer for Research

Carotid Analyzer for Research (shortly, Carotid Analyzer, Fig. 5.1) is a Win-dows 95, Windows 98, Windows Me, Windows NT, Windows 2000, andWindows XP compatible program environment for highly automated anal-ysis of carotid ultrasound images and image sequences.

Carotid Analyzer uses an automated method for near and/or far wallborder and near and/or far intima border detection and vessel diameteras well as intima-media thickness measurement in carotid ultrasound imagesequences. When analyzing a sequence of images of the same vessel location,the method automatically learns properties of the analyzed vessel in oneframe of the sequence that is analyzed under operator’s supervision. Thevessel properties are reflected in the cost function used in a graph-search-based border detection [1]. Carotid Analyzer creates an output data file withmeasured vessel diameters and other accompanying information in severalselectable formats.

5.1 Running Carotid Analyzer

To run Carotid Analyzer:


by clicking button.


3. Select Carotid Analyzer.

To exit from Carotid Analyzer:


2. Exit [File → Exit] or click the upper right corner of the Carotid Analyzerwindow.

78

5.2 Demo of Carotid Analyzer 79


Figure 5.1: Main Carotid Analyzer window.

5.2 Demo of Carotid Analyzer

Carotid Analyzer is a complex software package. Several image sequencesand prepared demonstration analysis case studies are included with yourinstallation. A small number of images and image sequences is copied to yourhard drive. Several other image sequences are located on the InstallationCD, each with a complete analysis study file generated using our CarotidAnalyzer software.

Section 5.5 contains step-by-step demonstration of basic functionalitiesof the Carotid Analyzer.

5.3 Getting Familiar with Carotid Analyzer

The Carotid Analyzer is a complex program with a number of interactiveand automated steps that have to be performed to complete the analysis of

80 CHAPTER 5 Carotid Analyzer for Research

carotid ultrasound image sequences.Due to its complex nature, this section presents an overview of the

main process control blocks from the user’s viewpoint. This section willidentify the main parts of the application window as well as the functionblocks.


• Menu Bar

• Tool Bar

• Function Panel

• Image

• Status Bar

The first three are depicted in Fig. 5.2. Note that while the first two (MenuBar, Tool Bar) do not change, the Function Panel appearance and contentchange according to the currently performed function. Similarly, the StatusBar content changes to reflect the current status of the analysis, it frequentlycontains analysis results associated with the currently displayed image frame.The subject name information – when available – is continuously availablein the bottom right corner of the status bar. Some processes also openadditional windows that allow process-specific interactions.

The tools (control buttons) and menus are described in Sections 5.3.1and 5.3.2. In Section 5.3.3, we list all possible appearances of the Func-tion Panel and briefly describe their individual functionality. Section 5.3.4introduces separate process-specific windows that pop-up in response to in-dividual process control steps.

It is recommended that you scan through the following paragraphs de-spite the fact that during the first reading you most likely will not acquirefull understanding of the functionality of individual controls. The first read-ing is important for you to be able to follow the Tutorials and more detaileddescription in the later sections. In any case, after you finish reading theentire manual, it may be a good idea to return to the following sections andread through this part again with a deeper understanding.


In Fig. 5.2 and the following paragraphs, please familiarize yourself withall basic control buttons and menus. All of them will be frequently referencedthroughout this chapter.

• . invokes a process window to create a new carotid ultrasoundsequence study.

5.3 Getting Familiar with Carotid Analyzer 81

Figure 5.2: Controls of the main Carotid Analyzer window – Menubar, Tool-bar, and Function Panel.

• . opens existing carotid ultrasound sequence study.

• . saves the current carotid ultrasound sequence study.

• . invokes a Subject Manager window (Chapter 6). Subject in-formation is also available in the Subject subwindow of the Resultswindow.

• . switches to a function panel for border detection.

• . performs automated analysis of the current frame. It also servesas a flag to allow or disallow automated border detection after click-

ing the review/analyze button or any other button changing the

“current” frame , automated analysis is enabledin its “set” (“down”) position. In other words, as long as this buttonis set, changing the “current” frame always invokes reanalysis of theframe that becomes “current”. This behavior is suspended either af-

ter reaching the last frame of the sequence in the mode, or after

clearing the button to be in its “up” position.

• . switches to a function panel allowing semi-automated or manualcorrections or re-analysis of the already identified vessel borders in thecurrent frame.


(a) (b) (c)

Figure 5.3: Menu controls: (a) File menu; (b) Edit menu; (c) View menu.

• . displays or hides the region of interest overlay.

• . displays or hides the determined vessel borders.

• . displays or hides the overlaid text with frame analysis informa-tion.

• . switches borders on and off in a rapid fashion to allow visualassessment of border positioning.

• . opens Analysis Results window.

• . starts sequential review of results or automated analysis, begin-

ning at the current frame; starts automated border detection if isset (“down”).

• . stops sequential review or automated analysis.



(a) (b)

Figure 5.4: Menu controls: (a) Action menu; (b) Help menu.





• . toggles between repeated display of the sequence in a loopand single display of the image sequence during the review process.





The functionality of the main menu items shown in Figs. 5.3 – 5.4 isbriefly described below. Some of the menus can be invoked by clicking rightmouse button within the image field - in that case, the menu that occurs iscontext-sensitive depending on the analysis status.

• File menu

– New – invokes a process window to create a new carotid ultra-

sound sequence study – identical to clicking .

– Open – opens existing carotid ultrasound sequence study – iden-

tical to clicking .

– Close – closes current carotid ultrasound sequence study withoutexiting from the Carotid Analyzer.

– Save – saves the current carotid ultrasound sequence study – iden-

tical to clicking .

– Save As – saves the current carotid ultrasound sequence studyunder a new name.

– Report – opens a dialog window for saving and printing the resultsreport.

– Properties – opens a window with border and ROI display pa-rameters and other options. Display options can also be modifiedin the Display Options subwindow of the Results window.

– Exit – exits from the Carotid Analyzer, identical to clicking upperright corner button of the main Carotid Analyzer window.

• Edit menu

– Copy and Paste options have no functionality at this time.

– Study information – invokes Study Information window, allowsediting its content.

• View menu



– Status bar – displays or hides the status information line in thebottom of the main Carotid Analyzer window.


– Options – opens a dialog window allowing modification of borderand ROI display parameters and other options.

– Analysis Results – opens Analysis Results window – identical to

clicking .

– Subject Manager – invokes subject management module, see Chap-ter 6 for details. Subject information is also available in the Sub-ject subwindow of the Results window.

• Action menu


– Train the system – switches to a function panel for border detec-

tion training – identical to clicking .

– Launch automated analysis – Invokes re-analysis of the currentframe.

– Click to Detect - invokes semi-automated editing mode – identical

to clicking .

– Play – starts sequential review of results or automated analysis,beginning at the current frame; starts automated border detection

if is set (“down”).

– Edit – switches to a function panel allowing semi-automated cor-rections or re-analysis of the already identified vessel borders in

the current frame – identical to clicking .

– Edit manual– switches to a function panel allowing manual cor-rections or re-analysis of the already identified vessel borders inthe current frame

– Exclude Frames from Analysis – defines a range of image framesthat are not analyzed in the current sequence.

– Reject – rejects current frame from border analysis results.


– Undo Reject – includes current previously rejected frame in bor-der analysis results.

– Clear All Borders / Measurements – deletes all current analysisresults, keeps the ROI location.

– View Results – opens Analysis Results window – identical to click-

ing or selecting Analysis Results in the View menu.

– View Subject Manager – invokes subject management module,see Chapter 6 for details. Identical to selecting Subject Managerin the View menu.

– Plaque Analysis Panel – opens Plaque Analysis window (Section5.7).

• Help menu

– Online Manual – opens the Vascular Tools Manual.

– On DICOM - provides DICOM-input related information.

– About – provides basic information about the Carotid Analyzer.

5.3.3 Function Panels – Controlling the Analysis Processes

The Function Panels change most frequently. Two default panels are:



In addition to the two default Function Panels, the following Menu items orControl buttons invoke process-specific Function Panels:


This Function Panel also opens automatically at the beginning of theanalysis when no pixel size calibration value is available.

• Clicking [Action → Train the System] or invokes the TrainingFunction Panels:


Training – stage 1:

After clicking [Next] in the previous panel, Review - training step 2panel appears:

After clicking [Proceed] in the previous panel, the analysis completesand – if a sequence is analyzed – all frames are analyzed automatically.

• Clicking [Action → Click-to-Detect] or invokes computer-assistedediting Function Panel:

• Clicking [Action → Plaque Analysis Panel] invokes the interface panelfor plaque region definition and its quantitative analysis (Section 5.7).

• Many useful analysis-context-specific help items can be found on theblue “Hints” panel that changes its textual content based on the anal-ysis status.


• Clicking [File → New] or opens a dialog window for entering rel-evant information to create a new study information file:


The Study Information panel includes required fields (in red) and op-tional fields (in black). The required information fields must be filledbefore the [Save] button becomes enabled. However, specification ofwhich fields are and which are not required can be customized by theuser. After clicking Options button in the Information Window, adialog window opens allowing the user to select “required” and “op-tional” fields. Note that the fields with user-customizable labels (Sec-tion 5.6.7.1) are always “optional” and cannot become “required”.

This window can also be invoked by clicking [Edit → Study informa-tion] – in that case, study parameters can be interactively edited intheir respective fields.

• Clicking [File → Open] or opens a dialog window for opening anexisting analysis study.

• Clicking [File → Save As] opens a dialog window for saving the per-formed analysis study.

• Clicking [File → Properties], a window appears showing parameters ofborder display.. Display options can also be modified in the DisplayOptions subwindow of the Results window.Border display parameters/Options window:


• Clicking [View → Options], same window opens as specified above(Properties).


• Clicking [View → Analysis Results] or opens the Results window.Note that there are several subwindows available within this window.

• .[Help → Online Manual] opens the electronic version of this manual.

• .[Help → On DICOM] invokes DICOM-related help window.

• .[Help → About] invokes information about Carotid Analyzer, its ver-sion, Medical Imaging Applications, LLC contact address, etc.

• Context Sensitive Help Windows appear in the bottom of the screenbased on the stage of processing. These windows provide hints aboutthe current analysis steps. They can be closed if obstructing the im-age by clicking the [Go away] button. Mode of their appearing can becompletely switched off in two ways – by unclicking [Smart Showing]within the context-sensitive help window, or inside the [View → Op-tions] window. If smart showing is switched off, it can only be switchedon by selecting this option in the [View → Options] window.

5.4 Carotid Ultrasound Analysis using Carotid Analyzer 91

5.4 Carotid Ultrasound Analysis using Carotid Analyzer

During a typical analysis of carotid ultrasound images or imagesequences, the following steps must be performed:


2. Pixel size calibration

3. Training of border detection parameters

4. Carotid ultrasound image analysis

5. Review of results

6. Output report generation and saving of results

For the purposes of this manual, a carotid ultrasound image sequenceis a sequence of one or more carotid ultrasound image frames that were pre-viously acquired under constant image acquisition conditions during whichthe carotid artery as well as the imaging transducer were kept in a stable po-sition with no mutual motion. Carotid Analyzer can analyze both ECG-gatedand non-gated carotid ultrasound image sequences.

Analysis of each of these sequences requires to perform all the above-listed steps that will be described in detail. Before we proceed, it may beadvantageous to use the Demo image data sequences included with yourinstallation to get familiar with the basic operations. The next section de-scribes several example analysis sessions.

5.5 Tutorial

The Installation CD includes several example data sets.

5.5.1 Example Data

A number of short sequences of example data sets are included withthe Carotid Analyzer installation. If you followed the standard installationprocedure, their location–filenames are:


Carotid\...\Demo-XXX.sdy ,


Carotid\...\Demo-XXX.raw ,

and

C:\Program Files\Medical Imaging Applications\

Carotid\...\New-XXX.raw


where XXX is an identification number. The .raw files contain ultrasoundimage sequence data and the .sdy files carry all non-image information as-sociated with the carotid ultrasound study including the border detectionresults.

Additional longer, more realistic, and also more challenging example im-age sequences (ECG-gated and non-gated) remain located on the CD andare not copied to the C: drive due to their large size, possibly hundreds ofmegabytes. These additional example files are again named Demo-XXX.raw,Demo-XXX.sdy, and New-XXX.raw and are located in the following directory:

X:\Samples\

where X: represents the label of your CD ROM disk drive. The tutorialexample analyses may use the CD ROM location but accessingthe CD is slow in general. Therefore, to appreciate the analysisspeed of the Carotid Analyzer, it is highly recommended to copy allexample files in a single directory some place on the local harddisk of your computer. To analyze such sequences, you simply browseyour hard disks to locate an appropriate .sdy file and open it as describedbelow in Tutorial 1. Please run the Carotid Analyzer on these studies togain familiarity with the software.

5.5.2 Tutorial 1: Working with an existing .sdy study file

The first Tutorial will demonstrate basic functionality of the Carotid An-alyzer and will teach you how to review previously completed carotid imageanalyses.

1. Open one of the demo files.

(a) Click [File → Open] or button .

(b) Traverse to directory

C:\Program Files\MIA-LLC\Vascular Tools\Samples\Carotid\...

and select one of the Demo-XXX.sdy files.

(c) Click Open and the first frame of the image sequence will occurin the Carotid Analyzer main window.

2. Since you work with an existing and previously analyzed image se-quence, you can directly review the automatically identified vessel bor-ders.

(a) Make sure that button is set (in its “Down” position).

5.5 Tutorial 93

(b) Click [Action → Play] or to review the borders detected inthe entire image sequence.

(c) Set the loop option in and review all analyzed frames

again using . The review will play in a loop mode.

(d) Modify the playback speed by changing the option in ,identify your optimal speed for border review.

3. Review of a specific frame.

(a) Using Sequence Navigator , se-lect and review a specific frame.

(b) Using ROI (region of interest) button , display and hide theROI used for analysis. Note that the near and far border sidesare marked by “N” and “F”.

(c) Toggle the button several time in a quick sequence to seethe overlaid borders display and hide – this is often the best wayhow to assess the correctness of the border detection.

(d) Set the borders to flash on-off repeatedly by clicking the button

. Click again to stop border flashing.

4. Review table of results and the vessel diameter chart and IMT mea-surements.

(a) Click [View → Analysis Results] or to open the AnalysisResults window.

(b) In the new window, the lower part shows the measurement table,the upper part shows vessel diameter chart.

(c) Note that the measurement can be performed in millimeters orpixels.

(d) The current frame is marked by an asterisk (*) positioned nextto the frame number in the table of results.

(e) To switch between vessel diameter and IMT Results windows, usethe pulldown menu selection in the bottom of the Results window.


5.5.3 Tutorial 2: Creating a new .sdy file, working with a newultrasound image sequence

The second Tutorial will teach you how to create a new image sequenceanalysis study and how to analyze the new ultrasound image sequence.

1. Open one of the new, not yet analyzed, image analysis sequences.

(a) Click [File → New] or button .

(b) Fill in all required analysis data fields (marked in RED).

(c) To select image data, click the Select button, traverse to directory

C:\Program Files\MIA-LLC\Vascular Tools\Samples\Carotid\...

and select one of the New-XXX.raw files. Note that the Files-of-type selection choice within this file opening window must specifyRAW files. (Of course, you can open other file types, in such acase, the Files-of-type selection must correspond to your file type).

(d) After all required fields are filled in, the [OK] button in the bottomleft gets enabled, click on it and the first frame of the new imagesequence will occur in the Carotid Analyzer main window.

2. Since this is a new image sequence, no automatically identified vesselborders are available for review.

3. To analyze this new sequence, the border detection method must betrained for this specific data set.

(a) Select a good-quality image frame for training. A good-qualityframe is one that has well-depicted near and far vessel bordersalong the entire vessel segment of interest. It is not necessarilythe first frame of the sequence. Use Sequence Navigator

to find a good quality frame.

(b) Click [Action → Train the system] or button , a training boxwill replace the Sequence Navigator:

(c) Note the line of text below the main control buttons. It saysTraining step 1: Define the ROI. In this location, as well as in theblue area in the bottom of your screen, you can frequently finduseful hints about how to proceed with the analysis.

5.5 Tutorial 95

(d) Using the mouse, point to the location within the vessel lumenthat is in the middle of your vessel segment of interest and clickthe left mouse button. A region of interest will occur. (If no

ROI occurs, click on the ROI button that displays/hides theROI.)

(e) Using the sizing, moving, rotation buttons, position and size theROI. The following button labels are used: L,s ... Larger/smallerROI size; L,R,U,D ... move ROI Left, Right, Up, Down; C, CC... rotate ROI Clockwise or CounterClockwise. The initial ROIorientation and width do not have to be perfect, the program willoptimize them during the training step. Experiment with the ROIpositioning so that you become familiar with their functionality.You can always start over with the ROI definition after clickingthe Clear button.

(f) The ROI position, size, and orientation can also be defined andmodified by clicking directly on the image in proximity of thecurrent ROI. Clicking inside of the middle circle moves the ROI.Clicking inside the end-circles changes the ROI orientation and/orROI length. Clicking in the proximity of the near-border (N) orfar-border (F) ROI limit modifies the ROI width. You can alsoreposition the ROI using a click-hold-and-drag approach. Exper-iment with the mouse-controlled ROI modifications to becomecomfortable with these ROI definition options.

(g) When satisfied with the ROI, click the Next button. The firststage training will proceed automatically and M-line vessel bor-ders will be identified within the ROI. Note that the ROI orien-tation and width automatically changes (ROI width changes onlyif the Lock ROI button was “cleared”, it is “set” as default). Thesecond-stage Function Panel appears:

.

(h) Review the detected borders and follow the instructions given onthe blue “Hints” panel (above).

– if the entire border is satisfactory, click on the Proceed button.Otherwise, you may specify the preferred location of the M-lineborder by clicking the left mouse button on the desired borderlocation. This approach is demonstrated in Fig. 5.5.


(a) (b) (c) (d)

Figure 5.5: Click-to-train determination of preferred M-line locations.(a) ROI - carotid ultrasound vessel segment of interest. (b) The border iden-tified during 1st stage of training, note that I-line was identified for nearborder. The arrow depicts the required border point interactively defined byleft-mouse-button clicking. (c) Border automatically identified in response tothe mouse click. The border now passes through the vicinity of the requiredborder point. The click-to-train border detection can be repeated as manytimes as needed. (d) M-line and I-line borders identified.

(i) Alternatively, you can modify the ROI in this step as you didbefore or return to Step 1 of training by clicking the Back to step1 button, modify the ROI, and repeat the training process.

(j) There are more advanced training steps that can be applied toborder detection system training in lower-quality or otherwise dif-ficult images. They will be described later in Section 5.6.3.

4. The completed training process displays M-line and I-line borders de-termined in the current frame used for training and the method willautomatically analyze the entire sequence if applicable.

5. Review results as specified in Tutorial 1.

6. Generate a report and save your work. If you have a demo-only versionof the program, the next two steps are disabled.

(a) Generate the sequence analysis study Report by clicking [File →Report] or clicking [Generate Report] button in the Results win-dow, print the Report Header by clicking [Print Summary] buttonin the Report window.

(b) Save your results by clicking [File → Save/Save As] or button

, this creates a .sdy file. From now on, you will be able to

5.5 Tutorial 97

use [File → Open] or button to access this image sequenceanalysis study.

5.5.4 Tutorial 3: Manual editing of the automatically identifiedborders

The last Tutorial will teach you how to manually edit borders in situ-ations when the automated border detection was not successful. See alsoSection 5.6.6 for additional details as/if needed.

1. Open a previously analyzed image analysis sequence study as describedin Tutorial 1, Section 5.5.2.

2. Review the borders and select a frame in which you will interactivelyedit the border(s). You will likely need to select a frame in which theborder detection failed - it may be impossible to modify a correctly-detected border using the click-to-detect approach.

3. Start editing by clicking [Action → Click-to-Detect] or button ,an editing box will replace the Sequence Navigator.

4. Select whether you want to modify M-line or I-line borders either bymaking a selection in the Function panel

or by clicking right mouse button inside of the image field.

5. Preferred position of the border can be specified by mouse clicks. Donot attempt to “trace” the border, rather click repeatedly at pointsyou want to define as preferred border points. After each click, waitfor the border to be adjusted to reflect your interactive border pointdefinition. The clicks do not define manually edited borders. Rather,they influence the automated border detection to identify the borderaccording to the image features in the vicinity of the clicked point.

6. If placing a point has no influence on the detected border, do not hes-itate to place additional click(s) at the same location. The influenceof repeat-points is cumulative. The clicked points can be displayed

by checking the switch . Up to 9 clicks are allowedfor each of the four borders. The current number of clicks for a se-lected border is always displayed as part of the click-to-edit information

.


7. If you are unhappy with the result of editing, you may click the [ClearAll] button and the original automatically determined border will reap-pear. Click the [Finish] button to abandon the Click-to-Detect editingmode. To manually edit another frame of the sequence, you may use

the and buttons to display image frames without abandoningthe click-to-detect editing mode.

(a) (b) (c)

Figure 5.6: Click-to-detect editing of I-line borders. (a) Original carotid ul-trasound vessel segment with locally incorrectly identified I-line near and farborders due to ultrasound dropout. (b) Selecting I-line editing and placing 2points in the vicinity of the desired near-wall I-line position corrects the nearborder. The 2 interactively defined click-to-detect points are visible as purplecircles. (c) After placing 3 points in the vicinity of the desired far-wall I-lineposition, the border is semi-automatically corrected. The 3 interactively de-fined click-to-detect points are visible as purple circles. Note the changes ofaverage IMT measurement resulting from the border corrections - near wallIMT changed from average of 0.39 to 0.45 mm, far wall IMT changed from0.35 to 0.42 mm.

8. If you are unhappy with the result of editing, you may click the [ClearAll] button and the original automatically determined border will reap-pear. The [Clear All] button influences the selected border only – toclear editing from all 4 borders, boundaries must be sequentially se-lected and preference points cleared as needed.


10. Open the Results window, note that the quantitative values changedin response to your editing.

5.5 Tutorial 99

11. With the Results window open, one more convenient editing optionis available. Whenever you click on the diameter chart, the imageframe corresponding to the chart location is displayed and the currentnumeric measurement values are provided on the 1st line of the Resultstable (if one of the last 12 frames, the values will not appear on the1st displayed line). Similarly, if you double-click on a row within thediameter table, the corresponding image frame is displayed. Using thisclick-and-display option, it is easy to target image frames that seemincorrectly analyzed according to the diameter context shown in thediameter chart.


13. Fig. 5.6 shows a sequence of click-to-detect I-line border corrections.

14. In case the click-to-detect editing does not produce desirable results, afully manual editing option is also available. Click the Manual buttonin the Click-to-detect control panel. This invokes a manual editingmode.

15. Repeatedly click on the correct position of the border and watch theborder being interactively edited as you proceed. Note that in thismode, the entire length of the border is displayed and available forediting. Do not attempt to “trace” the border, rather click repeatedlyat points you want to define as border points. After each click, waitfor the border to be adjusted to reflect your border point definition.

16. Experiment with different settings of the Editing Sensitivity options.The three options (from left to right) increase the length of borderinfluenced by the manual editing, they also influence the distance fromborder within which a manually-defined border point can be placed. Ifthe needed distance exceeds the maximum, it may require a sequenceof two or more clicks to move the border to a desired position. Notethat the modified borders are marked “edited”.

17. If you are unhappy with the result of editing, you may click the [Reset]button and the original automatically determined borders will reap-pear.

18. To manually edit another frame of the sequence, you may use the‘next/previous frame buttons to display image frames without aban-doning the manual editing mode.

19. Editing M-line or I-line is controlled by the radio-button in the Manual-editing control panel, or by the right mouse button.



21. Open the Results window, note that the edited frame is marked by aletter “i” – border editing intervention – in the table of results. (TheResults window can only be opened when not in the editing mode.)

22. Same as in the click-to-detect mode, whenever you click on the di-ameter chart, the image frame corresponding to the chart location isdisplayed.


5.6 Carotid Ultrasound Analysis – Detailed Description of Pro-cessing Steps

5.6.1 Carotid Ultrasound Data Input

An ultrasound sequence study has to be formed and its associated datastructures filled before any subsequent action can be performed. You cancreate a completely new study or you can open a previously-saved studyfrom a study file. Study files have an extension .sdy.

As mentioned in Section 5.5, there are typically two files associated witheach image sequence study – image data file with file extension .raw, .tif,.cri, .jpg, .bmp, or DICOM files and non-image data file containing all otherinformation including the border detection results with file extension .sdy.The image files are created during image acquisition or digitization, e.g., theymay be obtained as an output from Vascular Converter or Vascular Imager (seeChapter 1).

Clearly, two basic modes of operation with carotid ultrasound studiesare typical. The first deals with analyzing of new image sequences, thesecond with reviewing previously analyzed image sequences. These two basicmodes of data input were already described in Tutorials 2 and 1, respectively(Sections 5.5.3, 5.5.2).

Briefly, with the Carotid Analyzer running (Section 5.1), perform one ofthe following steps:

• To create a new study, click [File → New] or . Fill in all requiredinformation fields, the required fields are labeled in RED. To select thecarotid ultrasound image sequence for the analysis, click the red ImageFile label on the left or the button with three dots on the right of theimage filename field [...], select your file type (.raw, .tif, .cri, .jpg, .bmp,or DICOM files), then locate and select the input image file with thecorresponding extension.

5.6 Carotid Ultrasound Analysis – Detailed Description of Processing Steps 101

• To open an existing study, click [File → Open] or . Then select astudy file with the extension .sdy you want to review. Upon opening ofthe study file, the images, all available information, parameters, andanalysis results are loaded automatically.

5.6.2 Pixel Size Calibration

Pixel size calibration Function Panel automatically appears whenever anew (previously not analyzed) carotid ultrasound image sequence is opened.However, if several analyses are performed in a row, the program assumesthat the pixel size does not change and the previously determined pixel sizeis carried over to the next analysis. Alternatively, when the pixel size isknown a priori, the numerical pixel size value can be entered in the StudyInformation window (Section 5.3.4). If a zero (0) value is entered as the Pixelsize in the Study Information window, the previous pixel value is not carriedover and the calibration dialog is invoked. Pixel size calibration can also beinvoked by clicking [Action → Calibrate] during the analysis session. TheFunction Panel looks as follows:


1. Select vertical calibration option.



4. Using the numeric distance window in the Calibration Function Panel,enter or confirm the known distance value between the two identifiedmarkers.

5. If horizontal calibration is available, select horizontal calibration optionand perform horizontal calibration in the same way. If no horizontalmarkers are available, a square pixel size (same size horizontally and


vertically) can be assumed by not calibrating in the horizontal direc-tion.


Whenever this calibration Function Panel is invoked, it automatically dis-plays the locations of the starting and ending point markers as they weredefined in the previous calibration attempt. Also, the distance value thatappears in the window is identical to that used in the previous calibrationattempt. This behavior is motivated by the observation that calibrationmarkers as well as the distance between them are stable in the images acrossa variety of sequences originating from the same ultrasound machine whenusing the same probe. In such cases, the user simply approves the calibra-tion marker location. Whenever the markers change their position, it is easyto reposition the cross-in-a-circle markers to achieve the highest possiblecalibration accuracy. The existing calibration markers may be deleted byclicking [Start over] button - and calibration then repeated from scratch.

As a result of the calibration process, a pixel size for vessel diametermeasurements is determined. The pixel size values (horizontal and vertical)are provided in the Results window.

5.6.3 Training

It may be for the first time you are meeting with machine learning face-to-face [1]. The border detection training steps that are incorporated inthe Carotid Analyzer are extremely important for analyzing image sequencesas they directly influence the border detection performance. The rationalebehind the training steps is based on the observation that carotid ultrasoundresponses from the near and far walls are highly variable across individuals.At the same time, however, they are very stable for the same individual atthe same location over time.

When analyzing carotid image sequences, our method is designed tolearn the border properties from a single good-quality image frame, andthe learned border properties are reflected in the border detection processin all remaining images of the sequence.

The training process consists of three main steps that may be repeatedseparately or in their entirety:

1. ROI definition.

2. M-line border detection and approval.

3. M-line border detection parameter design (automated) and I-line de-tection.


Tutorial 2 went over the individual steps of border detection training inquite some detail. Here, we give a little higher level description of the sameprocess – see Tutorial 2 for practical details if needed.

First of all you need to use the sequence navigator to identify a goodquality frame for the training - if only one frame will be analyzed, this stepis performed in the single available frame. To invoke the training, click

[Action → Train] or . The 1st training stage Function Panel providestools to define an ROI. If the ROI has already been defined, it is displayedon the image screen. Note that the near and far border sides are marked by“N” and “F”. The ROI size is indicated below the ROI box as demonstratedin Fig. 5.7. This size display can be switched on and off by a switch in theBorder display parameters/Options window.

Figure 5.7: ROI size display – can be switched on and off in the Optionspanel.

You can modify the ROI position easily by click-and-point or draggingthe mouse left button or clicking the set of buttons on the panel. When anew image sequence is analyzed for which wall borders are not yet available,

the ROI from the previous training is displayed after first clicking thebutton. If, at any time, no ROI is available, an initial one must be defined.This can be done by clicking the left mouse button on the location of thecenter of the ROI. A default, horizontally-oriented ROI is displayed andmodifications can be performed to create an approximate ROI. The finalROI is then determined automatically. Figs. 5.8 and 5.9 give an examples ofdefining an approximate ROI position and show how ROI is automaticallyadjusted during the training step.

At any time during the ROI definition you can click the [Clear] buttonto start definition of ROI all over again. You can also click [Cancel] to abortthe entire training process.

When you are satisfied with the ROI, click the [Next] button. The system


(a) (b)

Figure 5.8: Automated positioning of the ROI if the Lock ROI option in Step 1Training Function Panel is set (default setting). (a) The initial positioningof the ROI may be very approximate. (b) The ROI orientation is adjustedautomatically.

automatically detects the M-line borders, opens 2nd stage training FunctionPanel, and asks the human observer for 1st stage M-line border approval.In situations when the borders do NOT correspond to the near and farcarotid artery M-line borders as judged by the human operator supervisingthe training process, simply click with a left button in the vicinity of a de-sired position of the M-line border. The M-line boundary will change itslocation. The clicks can be repeated until a desired effect is reached. Aftereach point definition, the borders are automatically re-determined. Oncethe border positioning becomes acceptable, click the [Proceed] button. Oth-erwise, interactively define another required border point; and the borderswill be recalculated again.

Note that it may not be possible to identify the border running throughan arbitrary manually identified point. The point identified must be anexpected border point, meaning that it must be located on the border withusual carotid artery wall properties.

Yet another word of caution ... the fact that the modified and repeated1st stage of training did after interaction identify the border at the desiredposition does not necessarily guarantee that the 2nd stage of training willbe able to design an appropriate cost function to determine the desired bor-der reliably in this training frame or the entire sequence. It is important torealize that while there are significant strengths in the graph-search basedborder detection process that result in identification of correct borders mostof the time, there are also inherent limitations that may not allow identifi-cation of the border that you would like to see identified if its properties arenot in agreement with usual properties of carotid artery borders. In such a


(a) (b)

Figure 5.9: Automated positioning of the ROI if the Lock ROI option inStep 1 Training Function Panel is cleared (ROI size is not locked). (a) Theinitial positioning and size of the ROI may be approximate. (b) The ROIorientation and size are adjusted automatically.

case, it is recommended to repeat training in another frame of the sequence.

Example of usage of this training process interaction is shown in Fig.5.10.

Training in another frame

If the training frame is not representative of the images of the sequenceor if the training frame is of a low quality, training should be performedin another image frame. This training option is straightforward from thetraining description standpoint – the operator selects a better quality ormore representative image frame of the analyzed sequence and repeats thetraining in a standard way.

Changing the robustness option of the border detection process

The likelihood that a correct border is determined during the automatedprocess is called border detection robustness. This training option allows toselect among the three following border detection behaviors:

• Most accurate

• Intermedium

• Most robust

As the labels suggest, the robustness of the analysis increases from the first tothe third choice. Most robust setting is used as default for carotid analysis.


(a) (b)

(c) (d)

Figure 5.10: Interactive definition of far border location. (a) Original carotidultrasound vessel segment. (b) The border identified during 1st stage of train-ing. (c) The arrow depicts the required border point interactively defined afterclicking in the Training step 2 Function Panel. (d) Desired border identifiedafter interactive identification of preferred boundary point. The border nowpasses through the vicinity of the required border point.

Analyzing curved vessels

A switch in Training stage 2 panel allows to distinguish cases when thecarotid artery segment of interest is not straight. Selecting Curved Vesselallows the vessel border to follow non-straight borders.

5.6.4 Border Detection in the Entire Sequence

Upon approval of the training, the system is ready to perform the nextstep – a fully automated analysis of every frame of the sequence. It switchesto the first frame and performs M-line border detection, M-line to M-linediameter measurement, and IMT measurement for near and far bordersthroughout the sequence.

No user input is required in this step. However the user can abort the


border detection process at any time for any reason, by clicking but-ton on the tool bar. One of the possible reasons for stopping the analysisprematurely may be frequently repeated detection of incorrect borders. Insuch a case, the method may be retrained or the ROI repositioned. Onthe other hand, if the borders are incorrectly detected in some frames butthe analysis mostly finds correct borders, this is not a good enough reasonfor stopping the analysis. If needed, these frames can either be rejectedor semi-automatically corrected using the Click-to-Detect approach (Sectionsec.CA.editing).

Overall, the best approach to achieve a minimal number of incorrectlyanalyzed frames throughout the sequence is 1) acquisition of high-qualityultrasound image data, 2) minimization of probe-motion-related artifacts,and 3) appropriate training of the border detection system.

5.6.5 Review of the Results

Reviewing the automatically detected borders is an important step onthe way to receive correct data analysis results. As we mentioned earlier andas is widely known, the carotid ultrasound images are noisy and may sufferfrom a variety of imaging artifacts.

The result-reviewing steps allow human-observer-evaluation of the bor-der detection and diameter measurement, as well as possible interventions.There are several ways of reviewing the results.

1. Borders and diameters can be reviewed for any specific frame using theSequence Navigator, the IMT measurement is always provided belowthe ROI outline.

2. Borders and diameters can be reviewed for the entire sequence using

[Action → Play] menu item or button.

3. Diameter measurements and the vessel diameter function over timecan be reviewed in the Analysis Results window after clicking [View

→ Analysis Results] menu item or button. The following mea-surements are available in the Analysis Results window for each imageframe:

• Diameter or IMT Results windows can be displayed by selecting“IMT” or ”Diameter” in the pulldown menu in the bottom of theResults window.

4. In the “Diameter” Results window, the following measurements areavailable:


• Avg. – Average vessel diameter.

• STD. – Standard deviation of the vessel diameter function.

• C(%) – not applicable to carotid analyses.

• Avg. Diameter of the sequence – not applicable to carotid analy-ses.

• Max. diameter of the sequence at its frame number – this infor-mation can be found immediately below the diameter chart inthe form max diameter@frame number and is given in the selectedunits.

• Other information items associated with the analyzed sequenceare also displayed.

5. In the “IMT” Results window, the following measurements are avail-able:

• Selection of I-line boundary display.

• Selection of near wall / far wall / both walls analysis mode.

• Near Avg. – near wall IMT average.

• Near Min. – near wall IMT minimum.

• Near Max. – near wall IMT maximum.

• Far Avg. – far wall IMT average.

• Far Min. – far wall IMT minimum.

• Far Max. – far wall IMT maximum.

6. For better monitoring of the automated diameter function generationprocess, the user can invoke the Results window and arrange the chartalong with the main image window by clicking [Attach to Main] but-ton within the Results window (the Results window is automatically

aligned whenever it is invoked by clicking ). The diameter func-tion construction can be viewed in real-time together with the framestatus symbols (*/r/e/i/n ... see below). Real-time reviewing is pos-sible whenever the Results window is open during the image sequenceanalysis – at any time, “*” next to the frame number represents thecurrent frame that is displayed in the main window.

7. Correspondence between the Results chart and the image frame dis-played can be accomplished using the click-and-display option. When-ever you click on the diameter chart, the image frame corresponding tothe chart location is displayed and the current numeric measurementvalues are provided on the 1st line of the Results table (if one of the


last 12 frames, the values will not appear on the 1st displayed line).Similarly, if you double-click on a row within the diameter table, thecorresponding image frame is displayed. Using this approach, it is easyto target image frames that seem incorrectly analyzed according to thediameter context shown in the diameter chart.

8. Diameter function chart zoom – the user can modify the scale of the

diameter function chart by clicking the buttons . If no furtherscaling up or down is allowed, the corresponding button disappears.

9. At any time of the reviewing process, border display can be switched

on and off by clicking the button or the borders may be set to

flash repeatedly by clicking the button .

The primary goal of the result-reviewing process is to identify those framesthat do not contribute correct quantitative diameter measurement to theoverall analysis of carotid vessel diameter, IMT, compliance, etc.

Interactive Quality Control – the human interpreter can selectively rejectany number of consecutive frames or frame intervals by repeatedly selectingthese frames and clicking the [Reject Selected Frames] button. Individualframes can also be rejected during the frame-by-frame reviewing button byclicking the menu item [Action → Reject].

Consequently, only those vessel diameters that were not automaticallyor interactively excluded or rejected are shown in the table and in the chart.The diameter measurements for the rejected or excluded frames are leftempty and a status symbol is shown next to the frame number indicatingthe reason – r=rejected by a human, e=excluded, n=not yet analyzed.

5.6.6 Operator Intervention and Interactive Editing

• Manual rejection of some frames or frame intervals may be appropriateas a response to image sequence intervals of low quality.

• Exclusion of one or more subsequences of image frames can be useful insituations when a subsequence or subsequences within the carotid anal-ysis image sequence contain invalid data – for instance Doppler bloodflow images are recorded within the carotid ultrasound sequence. Oneor more such subsequences of consecutive frames may be defined in awindow occurring after clicking [Action → Exclude frames from analy-sis] or after hitting CTRL-E. Frame selection for exclusion is specifiedin the following dialog window:


The subsequences are then excluded from any analysis or re-analysis

that is performed after training or invoked by the button. If the

analysis was already started via the button and a subsequenceis found that should be excluded, analysis can be stopped by clicking

the button, exclusion sequence(s) can be defined, and analysis

re-started by clicking and .

• Click-to-Detect computer-aided editing of detected borders can alwaysbe performed if necessary, it is described in Tutorial 3 (Section 5.5.4).To perform this operation, select [Action → Click-to-Detect] menu

item or button, select editing of M-lines or I-lines (right mousebutton toggles between these two modes), and edit the borders us-ing mouse clicks. Do not attempt to “trace” the border, rather clickrepeatedly at points you want to define as preferred border points.After each click, wait for the border to be adjusted to reflect yourinteractive border point definition. The clicks do not define manuallyedited borders. Rather, they influence the automated border detectionto identify the border according to the image features in the vicinityof the clicked point. The clicked points can be displayed by setting

the switch . Up to 9 clicks are allowed for each pfthe four borders. If you are unhappy with the result of editing, youmay click the [Clear All] button and the original automatically deter-mined borders will reappear. Click the [Finish] button to abandonthe Click-to-Detect editing mode. To manually edit another frame of

the sequence, you may use the and buttons to display imageframes without abandoning the click-to-detect editing mode. Note thatthe click-on-chart-and-display option (Section 5.6.5) is also functionalin the manual editing mode.

• Fully manual editing. In case the click-to-detect editing does not pro-duce desirable results, a fully manual editing option is available as asecond and ultimate stage of the editing interaction. Select the Manualbutton in the Click-to-detect control panel. This invokes a manual edit-ing mode. Repeatedly click on the correct position of the border andwatch the border being interactively edited as you proceed. Do not


attempt to “trace” the border, rather click repeatedly at points youwant to define as border points. After each click, wait for the border tobe adjusted to reflect your border point definition. If you are unhappywith the result of editing, you may click the [Reset] button and the orig-inal automatically determined borders will reappear. To manually editanother frame of the sequence, you may use the ‘next/previous framebuttons to display image frames without abandoning the manual edit-ing mode. Editing M-line or I-line is controlled by the radio-button inthe Manual-editing control panel, or by the right mouse button. Clickthe [Finish] button to abandon the manual editing mode.

5.6.7 Report

All image sequence analysis information and the analysis results arestored in the study file .sdy (see also Chapter 6). For convenient post-processing management of the results, a formatted Report can be generatedby either clicking [File → Report] or clicking [Generate Report] button inthe Results window.

The output file is printable from virtually any editor, includes only ASCIIcharacters, and consists of two groups of data:

• Data that are common to the entire data set occur once in the header.

• Data that change with each frame occur in the body.

The following information fields are included in the Report header. Ifsome of the header information fields do not have values associated withthem, the value fields are left empty. Which fields are and which are notincluded in the Report can be customized as detailed in Section 5.6.7.2.

The header is preceded by a single line containing the text

“CAROTID-ANALYZER-REPORT SERIAL #: xxx-xxx-xxxx)”.


• Report-date Date of Report generation.• Subject-ID Subject identifier.• Pat-ID-type Type of Subject-ID identification label.• Study-ID Research project identifier.• Condition Imaging condition – common/internal/bifurcation/other.• – 2nd column Average diameter in valid frames (for baseline/inflation only).• Subject-Gender Subject’s gender.• First-Name Subject’s first name.• Last-Name Subject’s last name.• Date-of-birth Subject’s date of birth.• Imaging-date Date of carotid ultrasound imaging.• Analysis-date Date of computer analysis.• Machine-ID Ultrasound machine identifier.• Probe-ID Ultrasound probe identifier.• Sonographer-ID Sonographer identifier.• Interpreter-ID Computer analyst identifier.• SDY-filename Filename of the .sdy file.• Image-filename Filename of the .raw file.• Pixel-siz-mm/p Pixel size in mm/pixel.• Frame-trained Number of frame used for training.• Frames-total Total number of frames in sequence.• Frames-valid Number of successfully analyzed frames.• Frames-reject Number of rejected frames.• Frames-exclud Number of excluded frames.• Frames-edited Number of manually edited frames.• Frames-notanal Number of frames not analyzed.• Confid-thresh Confidence threshold used for frame exclusion.• Trend-thresh Trend threshold used for frame exclusion.• Trend-MSE-mm Mean square error of the trend fitting function.• Study-type Study type identifier.• Reproduc-round Analysis repetition identifier I.• Reading-number Analysis repetition identifier II.• Code-1 User-specified code I.• Code-2 User-specified code II.• Code-3 User-specified code III.• Code-4 User-specified code IV.• Code-5 User-specified code V.• Code-6 User-specified code VI.• Code-7 User-specified code VII.• Code-8 User-specified code VIII.• Code-9 User-specified code IX.• Code-10 User-specified code X.


All following information fields are included in the Report body, thesevalues are provided for each frame of the sequence, one line of the Reportper image frame, again fixed column width format, 20 ASCII characters percolumn. The body is preceded by a single line containing the text “DATA:”.

• FRAME Sequential frame number within a sequence of analyzed images.• BDIAMM Average vessel diameter in millimeters,

no value given for rejected, excluded or not-analyzed frames.• IDTYPE Type of Subject-ID (same as in header).• PID Subject’s identifier (same as in header).• STYPE Study type (same as in header).• SDATE Imaging date (same as in header).• STIME Time of frame acquisition, millisecond accuracy.• MSEC Time offset of this frame with respect to

the start time of sequence acquisition in milliseconds.• COND Imaging condition (same as in header).• SONOG Sonographer ID (same as in header).• INTERP Interpreter ID (same as in header).• ADATE Analysis date (same as in header).• CODE1 User-specified code I (same as in header).• CODE2 User-specified code II (same as in header).• CODE3 User-specified code III (same as in header).• FCYC Frame within cycle – sequential number of image frame

within a single cardiac cycle if more than one frameper cardiac cycle were acquired.

• QC Result of the analysis and Quality Control– r=rejected/e=excluded/i=intervened(edited)/n=not analyzed.

• BDPX Average vessel diameter in pixels, diameters in pixelsgiven for all analyzed frames (even for those rejected or excluded).

• CONF N/A.• TRND N/A.• MINPX Minimum local diameter measured in frame.• MAXPX Maximum local diameter measured in frame.• STDPX Standard deviation of local diameter function in frame.• REPROD Reproducibility round (same as in header).• READNG Reading number (same as in header).• NIMTAVG Average intima=media thickness of near wall.• NIMTMIN Minimum intima=media thickness of near wall.• NIMTMAX Maximum intima=media thickness of near wall.• FIMTAVG Average intima=media thickness of far wall.• FIMTMIN Minimum intima=media thickness of far wall.• FIMTMAX Maximum intima=media thickness of far wall.


The body is concluded by a single last line containing the text “CAROTID-ANALYZER-EOF”.

Note that not all of the indices and identifier values listed above maybe available for your particular implementation. For example, not all imageacquisition devices allow storage of the exact frame acquisition time, notall identifiers are important for your study and therefore are not routinelyentered, etc. The fields not holding any information are left empty. All theinformation indices included in the final report are always stored in the .sdyfile that keeps all information about the analysis parameters and results.Therefore, after any image sequence is analyzed, results stored [File → Save]in a .sdy file, and the Report generated using some Report Fields selection,the .sdy file can be opened at any later time and a new Report file generatedwithout reanalyzing the image sequence.

There are two formats in which the Report file can be stored:

• Excel-compatible format - the file can be directly opened using MSExcel.

• SAS-compatible format – individual fields (columns) of the Report havea fixed width of 20 characters.

After clicking the [Print Summary] button within the Report window, thereport header (summary) can be printed. The entire report is not printedhere since the width of the printed Report exceeds the page width. However,when printing the entire Report is desirable, it can be easily accomplished byopening the Report.txt file using virtually any text editor and printing fromthe editor. In this case, selecting a non-proportional font (e.g., Courier) isrecommended to keep the columns properly formatted.

Needless to say, several different reports can be generated at any timeand stored under unique file names in text files. The default file name isthe study name with an appended sequence of characters “-Report.txt”. Thedefault location of the Report file is in the directory that contains the currentstudy file. Report files can be used as a basis for more advance diameterand IMT charting outputs as shown in Fig. 5.11.

5.6.7.1 Customization of User-Defined Codes

There are 10 user-customizable codes that can carry non-standard and/orsite-specific information. The first three of these codes occur in the Reportheader as well as in the Report body. The remaining seven codes only occurin the Report header. Default code names (labels) of these user-definedcodes are Code-1 to Code-10. However, the code labels can be customizedto better reflect their contents. Code label customization is performed withinthe Information window (click [Edit → Study Information]). After clicking onany of the 10 blue code-labels, the labels can be edited as shown in Fig.


0

1

2

3

4

5

6

7

8

0 1 2 3 4 5 6 7 8 9

M-to-M-line

carotid

artery diameter

Time [s]

Near (yellow)

and far (red)

wall IMT

[mm]

Figure 5.11: Carotid artery diameter and IMT thickness as a function oftime.

5.12. The modified labels are stored and used to label the correspondingfields in the Report header. Note that the customized code label is NOTstored in the .sdy file. Rather, it is stored as a status of the Carotid Analyzer.Consequently, the most recent codes labels will always be displayed in theStudy Information window. (To be exact, the .sdy file always keeps thevalues of all 10 codes in fields labeled Code-1 to Code-10. The naming ofthese codes is customizable. However, change of the code name does notchange any corresponding value associated with the code.)

Note that the user-specified code labels may contain spaces (blanks).These spaces are however stored as underscores due to the need to avoidblanks in the Report.txt files since blanks are used for field separation.

As described earlier (Section 5.3.4), Study Information fields can be spec-ified as required or optional. Note that the fields with user-customizablelabels are always “optional” and cannot become “required”.

5.6.7.2 Report Customization

Whether or not specific information fields are included in the Reportbody can be customized after clicking Customize button within the CarotidAnalyzer Report window (see Fig. 5.13).

All Report body fields can be selectively included or excluded from the


Figure 5.12: Customization of user-defined codes.

Figure 5.13: Report customization window.


report (note that only the first three user-defined codes are included in theReport body, the remaining seven user-defined codes only occur in the Re-port header). The latest setting is automatically memorized by the CarotidAnalyzer. At least one information field must be selected, if none is selected,all fields are included.

Note that no matter which fields are selected for the Report, all informa-tion is always stored in the .sdy file.

To ensure data integrity for Excel or SAS off-line data analysis, the listof included data fields should be kept consistent for all data sets from thegroup of related image sequences.

5.6.8 Generating and Saving Reports

As mentioned above, the Report can be saved in Excel and SAS formats.The exact content of the Report is controlled by the current selection ofreported fields. See Section 5.6.7.2, and Fig. 5.13.

Therefore, if a specific field is not selected, it is not included in theExcel or SAS output file. As described earlier, it is also possible to specifythat only near wall IMT, only far wall IMT, or both wall IMT’s shall bemeasured. This selection is affecting whether or not the respective IMTvalues are or are not present in the Report. However, to maintain integrityof the Reports across images with near/far/both walls analyzed, the fieldsfor these measurements are always present in the Report, with data itemseither filled or not filled. The Report header information and measurementsare stored in separate worksheets of the Excel file (Fig. 5.14).

After an Excel report is generated, a window opens asking the userwhether the generated file shall be opened in Microsoft Excel immediately.

5.6.9 Saving Results

All information about the performed analysis session may be saved in asingle study file (.sdy) (see also Chapter 6). That includes the name andlocation of the image file (.raw), the study information as entered in theCreate New Study window, the region of interest, detected borders, diametermeasurements, etc.

The user-entered information contained in the study file can be modi-fied by clicking [Edit → Study information] and study parameters can beinteractively edited in their respective fields. Naturally, the image sequencefilename cannot be modified. The study information modification feature isalso useful if the operator needs to enter or access any study related com-ments in the Comments field of the .sdy file.

The study file (.sdy) and the image file (.raw) are saved separately, foreasy maintenance and flexibility. For example different analysis sessions canbe performed in the same image file by different observers, using different


Figure 5.14: Excel-compatible Report worksheets.


regions of interest, etc., and it is therefore not necessary to store large imagedata files in duplicate copies.

Each study file (.sdy) contains information about an analysis session per-formed on one and only one image file. It stores the file name and locationinformation about the image file (.raw). Therefore when you open a studyfile (.sdy) from within the Carotid Analyzer, the Carotid Analyzer knows whereto find and open the image file (.raw) as long as the file saving conventionswere not violated.

Two file saving conventions are used to specify the file location informa-tion during the study file saving:

• If the study file and the image file are located on the same directory,the location information included the image file is not included.

• If the study file and the image file are not in the same directory, theexact directory information of the image file is stored in the study file.

The conventions are intended to serve two common but conflicting datamanagement schemes.

• Scheme I: Both the study file and image file can be moved (simultane-ously) to different directories. For example, archiving to another harddrive or burning to CD-ROMs.

• Scheme II: The directory location of the image file is NEVER changed(e.g., always residing on a CD), but the study files can be moved todifferent directories.

Please keep in mind that you need to select a data management schemeand follow it to ensure reliable data management.

5.7 Carotid Plaque Analysis

Similar to the above-described analysis of carotid diameter and IMT, atypical analysis of carotid plaque consists of the following steps:


2. I-border and M-border detection in the region that contains plaque ofinterest.

3. Interactive identification of a blood sample.

4. Interactive identification of an adventitia sample.

5. Interactive identification of plaque.



5.7.1 Carotid Ultrasound Image Data, ROI Definition, BorderDetection

Carotid ultrasound image data are opened and viewed in the same way asdescribed in Section 5.6.1. If the plaque location does not coincide with thelocation suitable for measurement of IMT, a new .sdy file can be generatedby using [File → Save As]. Consequently (or prior to), a new location ofthe ROI can be defined and the M-line and I-line borders determined asdescribed above. Of course, if a sequence is analyzed and plaque of interestis only located in a particular image frame, there is no need to determinethe borders in all frames of the image sequence. Please note that the I-lineis frequently highly variable in the plaque location. Therefore, interactiveediting is frequently needed to determine appropriate I-line location(s). ThePlaque Analysis Panel can be invoked by clicking [Action → Plaque AnalysisPanel].

5.7.2 Echogenicity Calibration

When plaque is analyzed for the first time in a particular image or imagesequence, the echogenicity of blood and adventitia is identified and used forplaque echogenicity normalization.

To minimize the effect of different ultrasound machine gain settings dur-ing image acquisition, a gray level normalization of plaque signal was pro-posed in [7] and since then has been used by several research groups duringmanual plaque echogenicity analyses [8]. The idea is based on manually se-lecting a dark area of blood from the lumen, manually selecting a brightestarea of adventitia along the near or far wall, and deriving a gray level trans-formation function from the gray level median mB of the blood sample andgray level median mA of the adventitia sample so that the range mB...mA

is always mapped to the interval <5,195> after the gray level transform.

To perform calibration, the operator needs to identify a small rectangularregion by clicking-and-dragging the cursor in the area of the vessel lumen.Typical blood appearance shall be sampled. This is followed by clicking-and-dragging the cursor in the area of the vessel adventitia. The brightest portionof the adventitia shall be sampled. The operator is prompted to performthese calibration steps when needed. The blood or adventitia calibrationcan be modified at any time by selecting corresponding action in the PlaqueAnalysis panel – Action pull down submenu. The steps are shown in Fig.5.15a,b.

5.7.3 Plaque Identification

One or more plaques can be identified in the analyzed images – theplaque regions can be interactively identified in any image frames and for anyvessel border (near or far), for which the I-line and M-line borders have been


(a) (b) (c)

Figure 5.15: Calibration of ultrasound echogenicity. (a) Interactive definitionof a typical blood sample. (b) Interactive definition of the brightest adventitiasample. (c) Interactive definition of plaque of interest.

previously determined. This module assumes that the vessel’s long axis isapproximately horizontal on the screen. Plaque is identified by mouse click-and-drag action that defines the left- and right-most limits of the plaque.Any additional plaque can be added by selecting corresponding Add newplaque action in the Plaque Analysis panel – Action pull down submenu.The step is shown in Fig. 5.15c. A virtually unlimited number of plaqueregions can be added.

To exit from the Plaque Analysis panel, click the “Finish” button on thepanel.

5.7.4 Plaque Editing

An already identified plaque region cannot be interactively modified. Itcan, however, be deleted and a new plaque can be identified instead asdescribed in Section 5.7.3.

To select one of the several previously identified plaque regions, openthe Plaque Analysis panel (if not already invoked, click [Action → PlaqueAnalysis Panel]). Any of the identified plaque regions can be selected andhighlighted on screen by selecting from the list of available regions in the“Highlighted” pull-down submenu of the Plaque Analysis panel.

To delete a selected plaque, click the “Delete” button on the right-handside of the Plaque Analysis panel. To exit from the Plaque Analysis panel,click the “Finish” button on the panel.

5.7.5 Reporting Results

The quantitative analysis of plaque regions is shown in the Results win-dow under the Plaque subheading.


The following quantitative indices are determined and reported together withthe plaque region identifier (integer label). The reported measurements in-clude the far/near wall association.

• plaque length

• plaque area

• normalized echogenicity of plaque – average normalized gray value

• standard deviation of the normalized echogenicity of plaque

• median normalized echogenicity of plaque

The individual plaques corresponding to the lines in the Results windowcan be visualized by selecting an appropriate plaque region number in theHighlighted pull-down submenu of the Plaque Analysis panel.

Any of the quantitative measurements reported in the Results windowunder the Plaque subheading can be selected (click and drag) and copied toany other application using the “Copy” button.

The quantitative analysis of plaque regions is also reported in a separatesheet of the Excel-generated Report spreadsheet (see also Section 5.6.8).

5.8 Carotid Distensibility and Compliance

Carotid distensibility and compliance can be determined in carotid im-age sequences, which depict at least one complete cardiac cycle and havesufficiently frequent temporal sampling with respect to the heart rate. As ageneral guidance, 10 frames per second is the minimum frame rate for humandistensibility and compliance measurement. While not an absolute require-ment, distensibility and compliance measurements are most meaningful inthe common carotid artery locations.

The carotid compliance function panel can be invoked by clicking “Com-pliance” tab in the Results window (Fig. 5.16a).

The typical analysis of carotid distensibility and compliance con-sists of the following steps:


(a) (b)

Figure 5.16: Distensibility and compliance analysis. (a) Initial window ap-pearance – locations of the information-entry buttons/subwindows shown.(b) After selection of start/end frames and input of blood pressure parame-ters – the distensibility and compliance indices are calculated. After clickingthe “?” location (marked), equations yielding the calculated indices are pro-vided.


2. I-border and M-border detection in the image sequence or a subse-quence containing at least one complete cardiac cycle.

3. Interactive input of systolic and diastolic blood pressure.

4. Interactive identification of the image sequence interval in which dis-tensibility and compliance are to be assessed.


5.8.1 Carotid Ultrasound Image Data, ROI Definition, BorderDetection

Carotid ultrasound image data are opened, viewed, and analyzed in thesame way as described above.


5.8.2 Input of Blood Pressure Values

Blood pressure in mmHg is typed in the appropriate location of the“Compliance function window” – see Figs. 5.16a,b.

5.8.3 Definition of the Image subsequence

To determine carotid distensibility and/or compliance, near-wall and far-wall M-line borders need to be detected, if necessary edited, and approvedby the operator in a non-gated image sequence. Using the interactive cardiaccycle selection tool on the time/diameter plot, the operator identifies a singlecardiac cycle or several consecutive cardiac cycles in which minimum andmaximum vessel diameters are automatically identified.

To identify the start- and end-frame index defining the subsequence,perform the following steps:

1. Select the frame representing the start frame by clicking on the re-spective location of the diameter chart (you may want to de-selectthe “Mouse on curve to select frame” option) or simply by using theforward/reverse buttons to identify the desired frame.

2. Once you have selected the start frame, click the left button of the “Cy-cle frame Idx” (the “from” button) ... the frame number will appearin the button location.

3. Select the frame representing the end frame by clicking on the respec-tive location of the diameter chart (you may want to de-select the“Mouse on curve to select frame” option) or simply by using th efor-ward/reverse buttons to identify the desired frame. It is required thatat least one location corresponding to systole and one location corre-sponding to diastole is present between the start- and end-frames.

4. Once you have selected the start frame, click the left button of the “Cy-cle frame Idx” (the “from” button) ... the frame number will appearin the button location.

5. If needed, the start- or end-frame identification can be repeated untilsatisfaction.

6. The distensibility and compliance indices appear in the Result window.If blood pressure is not entered, only distensibility indices are provided.

Let the maximum diameter (M-line to M-line) be denoted maxDiamM ,the minimum diameter minDiamM . Frames with the minimum and max-imum M-to-M diameters are automatically marked on the diameter plot.For these frames, lumen diameters are also determined (I-line to I-line) anddenoted minDiamI and maxDiamI, respectively.


Using the operator-entered systolic and diastolic pressures in mmHg,pressure difference ∆P is calculated as the difference between the systolicand diastolic pressures.

The following indices are calculated and reported [9]:

• diameter distensibility – DD [%]

DD =(maxDiamM − minDiamM)

(minDiamM)× 100%

• cross-sectional distensibility – CSD [%]

CSD =π(maxDiamM/2)2 − π(minDiamM/2)2

π(minDiamM/2)2× 100%

• diameter compliance – DC [mm/mmHg]

DC =maxDiamM − minDiamM

∆P

• cross-sectional compliance 1 – CSC1 [mm2/mmHg]

CSC1 =π(maxDiamM/2)2 − π(minDiamM/2)2

∆P

• cross-sectional compliance 2 – CSC2 [1/mmHg]

CSC2 =π(maxDiamM/2)2 − π(minDiamM/2)2

π(minDiamM/2)2∆P

• incremental elastic modulus – IEM [mmHg]

IEM =3{1 + [π(minDiamI/2)2/π(minDiamM/2)2]}

CSC2

All these indices DD, CSD, DC, CSC1, CSC2 and IEM are reported inthe Report – one set of compliance indices is reported per sequence. Theset of compliance indices has frame numbers of the starting and endingframes of the user-identified subsequence of frames associated with them.The definition of the indices can be obtained by clicking the “?” questionmark in the Compliance panel (Fig. 5.16a,b. The calculated indices appearin the Compliance window - see Fig. 5.16b.


5.8.4 Reporting Results

All indices calculated as part of distensibility/compliance measurement,i.e., DD, CSD, DC, CSC1, CSC2 and IEM – as well as the start- and end-frame indices used for calculation and the operator-entered blood pressurevalues – are reported in the “Summary” sheet of the Report – one set ofcompliance indices is reported per sequence. The set of compliance indiceshas frame numbers of the starting and ending frames of the user-identifiedsubsequence of frames associated with them.

5.9 Troubleshooting


Solution: Click on [View → Refresh] to refresh the screen. If thisproblem is frequent, please contact Medical Imaging Applications.

• Problem: The analysis is slower than usually when the Results windowis open and the calculated diameter function is displayed in real time.

Solution: Real-time display of the carotid diameter and the frame sta-tus symbols (*/r/e/i/e) is useful for analysis process monitoring butcomputationally demanding. The slow-down should be barely notice-able on 450 MHz and faster computers. On slower machines, close theResults window when performing the sequence analysis.

• Problem: The first stage training correctly identifies the desired bor-der but the second stage border detection identifies an incorrect borderthat seems to make little sense.

Solution: The learning process did not correctly resolve the influence ofthe contextual information present in the training frame. This prob-lem is rare but if it appears, it can be frequently solved by a slightmodification (e.g., 1 pixel longer or wider) of the width or length ofthe ROI used for training.

• Problem: The region of interest is not displayed.


• Problem: The Carotid Analyzer does not show the resulting borders.


• Problem: The Carotid Analyzer sometimes does not show the resultingborders, the ROI box, and/or the calibration markers.


Solution: This may be caused by an unfortunate selection of colorsused to display borders and lines. To check that, click “Options” fromthe “View” menu, make sure the “Display Colors, Line Styles” tab isselected and make sure the selected colors (shown on the big squares)are visible. Bright colors are preferred for both the ROI and the border.In other words if a black color is selected you will have trouble seeingthe border or ROI on an image. Make changes if necessary and click“OK” or “Apply”.

CHAPTER 6

Subject Manager

Subject Manager (Fig. 6.1) is a Windows 2000 and Windows XP compatibleprogram environment for easier management of multiple image files, imagesequences, and associated .sdy study files for a single subject or a group ofsubjects. The general idea of Subject Manager is to collect the informationabout the multiple image studies and store it in a single subject or .sbjfile. Consequently, Subject Manager is an ideal wrapper allowing to generatesubject-specific Reports based on a collection of subject-specific study (.sdy)files. Many of the Subject Manager functions can also be performed from theSubject Manager subwindow of the Results window.

6.1 Running Subject Manager

Subject Manager may be invoked from either Brachial or Carotid Analyzer after

clicking [View → Subject Manager] or using button . In response, theSubject Manager main window opens as shown in Fig. 6.1. Many of theSubject Manager functions can also be performed from the Subject Managersubwindow of the Results window (Fig. 6.2).Subject Manager can also be invoked from the Subject subwindow of theResults window.To close the large Subject Manager window, invoke the Subject subwindowof the Results window and the main Subject Manager window will disappear.

6.2 Getting Familiar with Subject Manager

Subject Manager creates a subject data file .sbj in the Vascular Tools dataformat.

The Subject Manager contains the following window partitions (Fig. 6.1):

• Tool Bar

• Status Information Area

• Study File Panel

• Maintenance Command Area

128

6.2 Getting Familiar with Subject Manager 129

Figure 6.1: Main Subject Manager window.

• Study Information Area

6.2.1 Description of Main Control Buttons

In Fig. 6.1 and the following paragraphs, please familiarize yourself withall basic control buttons and menus.

• . empties the current contents of the Subject Manager window andmakes the Subject Manager ready for defining content of a new .sbj fileby using the ADD or REMOVE maintenance command buttons.

• . opens a dialog for creating a subject file from a DICOM database,see Section 6.4 for details.

• . opens existing .sbj file, the associated information is displayed inthe Subject Manager window.

130 CHAPTER 6 Subject Manager

Figure 6.2: Main Subject Manager window.

• . saves the information about the subject in an existing .sbj file.

• . saves the information about the subject in a new .sbj file.

• . closes the Subject Manager window and opens the Subject Man-ager subwindow in the Results window of the Analyzer. Once closed,many of the Subject Manager actions can be performed from this sub-window.

• ADD button - allows adding single-image-sequence study (.sdy) files tobe added to the .sbj file.

• REMOVE button – allows removing single-image-sequence study (.sdy)files from the .sbj file.

• OPEN IN CURRENT ANALYZER button - after selecting a .sdy filefrom the Study file panel, the study can be opened in the associatedBrachial or Carotid Analyzer. Study can also be opened by double-clicking on its filename in the Study File Panel. Whenever a studyis selected, its associated information is immediately displayed in theStudy Status Area.

• SUBJECT REPORT button - invokes a dialog window for generatingand optionally saving a subject-specific Report.

6.3 Example Usage 131

6.2.2 Study Status Information

The Subject Manager window contains three areas of study-related infor-mation.

Status of the study currently opened and displayed in the Carotid orBrachial analysis window is given in the Status Information Area.

The Study File Panel provides list of all studies associated with theSubject Manager .sbj file. In this panel, information is available about thesequential study number within the subject file, study file name, informationabout the number of frames in each study, and the color-coded analysis statusof each study. As such, it provides detailed overview of the analysis of allstudies included in the subject file.

The third area containing study-related information is in the bottomthird of the Study Manager window – information about each study selectedin the Study File Panel is provided there. Fig. 6.1 gives an example of asubject file containing 20 studies for which the above-described informationis provided.)

When working with the Study Manager window, the study that is cur-rently open in the Analyzer is identified by an asterisk (*) next to its numberin the left-most column. The study, for which the study-related informationis provided in the bottom third of the Study Manager window is marked bya horizontal colored highlighting.

6.3 Example Usage

Assume that several separate carotid ultrasound images exist for Mr.John Doe. The associated .sdy files are named “IMT TEST-1.sdy”, “IMTTEST-2.sdy”, etc. (Fig. 6.1). These .sdy files can be combined in a single.sbj file. Consequently, all datasets of Mr. John Doe can be treated as asingle entity, the quantitative information from all these study files can becombined and reported in a single report, etc.

In brachial ultrasound image analysis, the .sbj files allow, for example, tokeep together the baseline and deflation image sequences and their associatedanalysis results.

In carotid image analysis, images acquired in several locations - left/right,common/internal/bifurcation, or focusing on near or far wall can be all kepttogether in a single .sbj file.

Many other options exist.

6.4 Creating a SUBJECT File from DICOMDIR File

When working with DICOM data associated with a DICOMDIR file, avery convenient way exists to form SUBJECT files associated with the imagesequences listed in the DICOMDIR file.


After clicking , a “Subject Creation from DICOM” window ap-pears:

DICOMDIR file can be selected after clicking the “Select” button andopening an appropriate DICOMDIR file. Once the DICOMDIR file is opened,the list of the available image sequences populates the Study File Panel.

By default, all image sequences listed in the DICOMDIR are selected andready to be included in the resulting SUBJECT file. Any of the sequencescan be sequentially selected and excluded by clicking the “Exclude SelectedClips” button. The excluded clips (image sequences) are crossed out. Anyof the excluded sequences can be selected and included again.

To generate a SUBJECT file, click the “Subject File Select” button,specify the filename, and Save. It is highly recommended that the SUB-JECT file be created in the same directory as the original DICOMDIR file.The SUBJECT file is populated with “.sdy” files after clicking the “Create”button. If a .sdy file with the same name that is about to be created alreadyexists, the operator is warned and has a choice of keeping or overwriting theexisting file:

6.5 Creating a SUBJECT File from Image Files located in a Single Directory 133

The created SUBJECT file can be used to open and analyze individualimage sequences and generate the comprehensive Subject Report.

NOTE: As a default location, during the later retrieval of the SubjectData – the .sbj file is expected to be in the same directory as the DICOMDIRfile. This location is not required unless the entire structure of DICOM datais moved from one location to another. Since moving data from one place toanother is common, saving the .sbj file in the same directory as the associatedDICOMDIR file is highly recommended.

6.5 Creating a SUBJECT File from Image Files located in a Sin-gle Directory

When working with single-frame or image-sequence data in one of thesupported image formats that are located in a single directory, a very con-venient way exists to form SUBJECT files associated with all of these imagefiles.

After clicking , a “Subject Creation from Image Files” windowappears:


The directory containing the image files can be selected after clicking the“Select” button and identifying an appropriate directory. Once the directoryis opened, the list of the available image files populates the Available FilesPanel:

By default, all images present in the directory are selected and will beincluded in the resulting SUBJECT file. If any of these images are notdesirable, they either shall be removed from the directory prior to runningthis Subject File creation process, or they can be removed later by selecting

6.6 Comprehensive Subject-Specific Reports 135

the non-desirable file and clicking the Remove button.On the right-hand side of the window, information that is common to all

image files existing in the directory can be typed in. For example, assumingall images in a single directory are from the same patient, the patient nameor other identifying information can be entered. Similarly, if all imagesfiles are in a directory containing only images from a specific location, thisinformation can be entered, etc.

To specify a name of the newly created SUBJECT file, click the “SubjectFile Select” button, specify the filename, and Save. It is highly recommendedthat the SUBJECT file be created in the same directory as the originalimage files. The SUBJECT file is populated with “.sdy” files after clickingthe “Create” button. If a .sdy file with the same name that is about to becreated already exists, the operator is warned and has a choice of keeping oroverwriting the existing file:

NOTE: As a default location, during the later retrieval of the SubjectData – the .sbj file is expected to be in the same directory as the imagefiles. This location is not required unless the entire structure of image datais moved from one location to another. Since moving data from one place toanother is common, saving the .sbj file in the same directory as the associatedimage files is highly recommended.

6.6 Comprehensive Subject-Specific Reports

In addition to generating study-specific Reports as described in Sections3.6.7 and 5.6.7, comprehensive reports containing information about andmeasurements from all studies included in the subject file can be generated.

An Excel file with a complete information about all studies included inthe subject file and showing in the Subject Manager is generated by clickingthe GENERATE EXCEL REPORT button. Information and quantitativemeasurements are reported in individual Excel worksheets of a single Excelfile (Fig. 6.3).

The exact content of the Report is controlled by the current selection ofreported fields. See Sections 3.6.7.2, 3.6.8 or 5.6.7.2, 5.6.8 and Figs. 5.13,5.14.

After an Excel report is generated, it can immediately be opened inMicrosoft Excel by clicking text “Click here to open the Excel file” in theStatus area of the Subject Manager.

6.7 Troubleshooting

• No known problems exist at the moment.


Figure 6.3: Excel-compatible Report worksheets – individual worksheets in-clude separate headers and data for each study file organized in a sequentialmanner. The worksheet organization is shown in the bottom of the Excelwindow.

CHAPTER 7

Vascular Converter

Vascular Converter is a Windows 95, Windows 98, Windows Me, WindowsNT, Windows 2000, and Windows XP compatible program environment forimage data conversion from several data formats created by third-partyframe grabbers. NTSC and PAL sized images are supported. The Con-verter is able to convert sequences of raw, bitmap, tiff, or jpeg images (moredetailed specification is given in Section 7.4.1).

Vascular Converter includes customization for your site to work with yourimage data sets. Therefore, the information given below is somewhat generaland the filename extensions of the input data files are not specified since theydepend on the data format of files containing the third-party image data.

Vascular Converter is not designed to convert image data from a generalDICOM format. A separate Vascular DICOM Module serves this purpose (seeChapter 8).

7.1 Need for Conversion

Third party digitizers generate digitize images in some fixed format. Toallow your image data to be analyzed by the Brachial or Carotid Analyzer,the image as well as non-image data must be converted in a Vascular Toolsfriendly format. This process is performed by the Vascular Converter.

Vascular Converter allows the user to create separate sequences for theindividual measurement conditions like baseline, inflation, or deflation. Eachcreated sequence reads the image file or files created by your third partyimage digitization software and – if applicable – it also reads the non-imageinformation contained in one or more associated description files. Afterthe conversion process is completed, a pair of image files is created for eachmeasurement condition, The pair consists of one study file with the extension.sdy that contains all non-image data associated with the converted sequence.It also contains one image file with the extension .raw that contains all imagedata representing the newly converted image sequence. These two files areneeded for the Brachial or Carotid Analyzer to function.

137

138 CHAPTER 7 Vascular Converter

7.2 Running Vascular Converter

To run Vascular Converter:


by clicking button.

2. Select Vascular Tools.

3. Select Vascular Converter.

To exit from Vascular Converter:

1. Save your work [File → Save]

2. Exit [File → Exit] or click the upper right corner of the Vascular Con-verter window.

7.3 Getting Familiar with Vascular Converter

The Vascular Converter uses as an input one or more files containing imagedata and may also input one or more files containing additional vascular-study information.

Similar to the Vascular Analyzer, the Vascular Converter contains the fol-lowing window partitions (Fig. 3.1):

• Menu Bar

• Tool Bar

• Function Panel

• Image

• Status Bar



• . opens a dialog window to specify a new vascular ultrasound imagesequence file and (if applicable) the associated information file.

• . saves the converted vascular ultrasound sequence study – twodata files are created – a file with .sdy extension that contains the non-image study information and a file with .raw extension containing allimage data associated with the image sequence.


Figure 7.1: Controls of the main Vascular Converter window – Menubar,Toolbar, and Function Panel.

• . starts sequential display of image frames of the sequence begin-ning at the current frame.

• . stops sequential display.





• . allows specification of a vascular image sequence - (forbrachial FMD case, the choices are baseline, inflation, deflation, orother).

• . allows specification and display of the frame numberthat contains the initial frame of the image sequence (not necessarilythe first frame to be converted).




• . displays the frame numbers of the first andlast frames of the image subsequence to be converted, by clicking onthese buttons, the first and last frames can be specified as currentlydisplayed frames.



The functionality of the main menu items is briefly described below.

• File menu

– New – opens a dialog window to specify a new vascular ultrasoundimage sequence file and (if applicable) the associated information

file identical to clicking .

– Close – closes current vascular ultrasound conversion session with-out exiting from the Vascular Converter.

– Save – converts and saves the current vascular ultrasound se-quence study according to given first/last frame specifications –

identical to clicking .

– Exit – exits from the Vascular Converter, identical to clicking upperright corner button of the main Vascular Converter window.

• Edit menu

– No functionality at this time.

• View menu


– Status bar – displays or hides the status information line in thebottom of the main Vascular Converter window.


• Action menu



– Play – starts sequential display beginning at the current frame.

• Help menu

– Contents – opens the help window.

– About – provides basic information about the Vascular Converter.

7.3.3 Function Panels – Controlling the Conversion Processes

The Function Panels change according to the selected functionality. Twodefault panels are:



In addition to the two default Function Panels, the following Menu iteminvokes a process-specific Function Panel:



• Clicking [File → New] or opens a dialog window for opening anexisting image data file from a third-party digitization software. Ap-pearance of this window varies, two possibilities are shown below:


• Clicking [File → Save] or invokes conversion into the VascularTools format. First, a confirmation window pops up prompting theuser to review the defined measurement condition (baseline, inflation,deflation, other). This is important since the filename containing theconverted data is affected by the measurement condition choice. Theuser is allowed to make changes as needed. The user can also reviewthe assigned initial, first, and last frame numbers - although thesecannot be changed in this window. If the user is not satisfied with


the frame number assignments, the conversion process can be aborted(by clicking [Abort]). The user is also warned that the conversionprocess once started (by clicking [Continue]) can require several sec-onds to several minutes, depending on the number of image frames,CPU/memory/harddisk/CD-ROM speed, etc. The application willnot respond to the user input during the conversion since the conver-sion process is CPU intensive - it may seem that the application is notresponding, however it is just busy.

After the conversion process is over, a dialog window opens that allowsentering relevant information to create a new study information file:

The Study Information panel may look somewhat differently from theone shown above if additional fields were added or removed as partsyour site-customized implementation.

Note that the information fields that are required for the conversion toproceed are marked in red. These fields must be filled before the con-version process can complete and the [Save] button becomes enabled.The [Cancel] button in this panel has no functionality. The user isstrongly encouraged to complete any initiated conversion process (af-ter the [Continue] button was clicked in the confirmation window asdescribed above) to avoid creation of incomplete files on the hard diskand consequently possible loss of data.


7.4 Vascular Ultrasound Conversion using Vascular Converter

During a typical conversion session, the following steps must be per-formed:

1. Opening of an existing ultrasound image sequence data file and/oropening of an associated description file. The file names and file ex-tensions vary according to the third-party digitization software youuse.

2. Pixel size calibration (optional).

3. Specification of the initial frame of the measurement sequence.

4. Specification of the first and last image frames of the new sub-sequenceto be converted in the Vascular Tools format.

5. Conversion and saving of the newly created image file (.raw) and thestudy file (.sdy).

6. Specification of the measurement condition.

7. Filling in the required non-image data to be included in the associatedstudy file.

For the purposes of this chapter, a vascular ultrasound image sequenceis a sequence of vascular ultrasound image data that were previously acquiredusing a third-party image digitization software. This sequence may contain asingle measurement condition, e.g., may contain only brachial FMD baselineimages, or it may contain a mixture of measurement conditions, e.g., brachialFMD baseline and deflation. Each converted image sequence, however,is only allowed to contain a sub-sequence of a single measurementcondition. Therefore, at least two study files are typically created as a resultof conversion for brachial applications – a baseline sequence (with ”BL”in converted filename) and a deflation sequence (with ”DF” in convertedfilename). These 2-character filename additions are included by default, andif necessary can be modified by user on a per-file basis.

7.4.1 Supported image formats

The following image formats are supported:

• RAW – extension .raw – 8 bit grayscale;

• JPEG - extension .jpg or .jpeg – grayscale or color JPEG images canbe read, color will be converted to grayscale;

• TIFF – extension .tif or .tiff – must be version TIFF 6.0, grayscale,uncompressed, single-plane;


• Bitmap – extension .bmp – Microsoft bitmap, grayscale, uncompressed,no color palette.

One file per image frame is required. The image sequence file names mustconsist of a Prefix, frame number, and a suffix. For example, brachial001.bmp,brachial002.bmp, ..., or BL00234-jones.tif, BL00235-jones.tif, ... are allowedIn the above examples, brachial or BL represent prefixes; 001, 002, 00234,00235 represent frame numbers; and .bmp or -jones.tif represent the suffixes.Details of the file naming structure can be found in Section 7.4.2.3.

7.4.2 Opening Existing Third-Party Image Data Files

An ultrasound sequence study has to be formed and its associated datastructures filled before any subsequent analysis using Brachial or Carotid Ana-lyzer can be performed if image data were digitized using third-party softwareand hardware. A new study .sdy file must be created for each measurementcondition, like baseline, cuff inflation, or cuff deflation.

There are several options of image conversion, please select one of thefollowing several options that applies to your situation.

7.4.2.1 Conversion of files with complete information containedin the associated information file

To open an existing image data file, with the Vascular Converter running,

click [File → New] or . The new file window has the following generalappearance:

Select the file to be opened. The first image frame of the opened imagesequence is displayed, the entire sequence can be reviewed using the controlbuttons or the Sequence Navigator control panel.


7.4.2.2 Conversion of images with incomplete or ambiguous in-formation contained in the associated information file



The information file – if any – can be specified in the ”Infor.txt” Filesubwindow – part of the Step 1 window partition. If the information fileis specified, all image frames can be displayed by clicking the First FrameIndex and Last Frame Index subwindows. If the first and last images selectedbelong to a single sequence, their prefix, first and last frame numbers, andsuffix are displayed in the Filename Composition subwindow. The windowthen looks for example as follows:


At this stage, the operator should confirm the displayed information. Ifthe information does not agree with the desired specification (do not forgetthat we are dealing with a situation in which the Information File containsincomplete or ambiguous information), the first/last frames must be specifiedcorrectly, or the information in the Step 2 window. See the next paragraphfor details of file name composition. To help with the confirmation, theVascular Converter program displays the number of frames found and thenumber of missing frames. The missing frames information is a warninginfo only. If there are some missing frames, the conversion program willsubstitute them with blank frame fields. If the information in the Step 2window part is correct, clicking on the [Accept] button will display the firstframe of the specified sequence and the entire sequence can be reviewed usingthe control buttons or the Sequence Navigator control panel.

7.4.2.3 Conversion of images with no information file




Since there is no information file available, bypass Step 1 leaving all itssubwindows empty. In the Step 2 window part, manually fill in the prefix,first and last frame indices, and suffix of the image sequence. For exam-ple, if the images of the sequence are of the type bitmap and are namedbrachial011.bmp, brachial012.bmp, ..,, brachial258.bmp, the information en-tered will be filled as follows:Prefix = brachialFrames are from the interval 11–258Suffix = .bmp (do not forget the “dot”)Note that the frame numbers can start with any number, note also thatthe number of digits for the frame index is flexible - however fixed for eachsequence.

Another example – files are named BR075Jones0001baseline.tif throughBR075Jones0233baseline.tif. In this case, the information shall be enteredas follows:Prefix = BR075JonesFrames are from the interval 1–233Suffix = baseline.tif

At this stage, the operator should confirm the entered information. Tohelp with the confirmation, the Vascular Converter program displays the num-


ber of frames found and the number of missing frames. The missing framesinformation is a warning info only. If there are some missing frames, theconversion program will substitute them with blank frame fields. If theinformation in the Step 2 window part is correct, clicking on the [Accept]button will display the first frame of the specified sequence and the entire se-quence can be reviewed using the control buttons or the Sequence Navigatorcontrol panel.

7.4.3 Calibration

The optional calibration steps are identical to those described in Section3.6.2. Calibration can be performed either within the Vascular Converter orVascular Analyzer.

7.4.4 Specification of the initial frame of the measurement se-quence

For the deflation sequences (and possibly in other sequences), it is fre-quently important to identify the initial (absolutely first) frame after thechange of the image measurement condition. This frame is not always nec-essarily the first frame of the converted sequence. Assume the followingscenario: Doppler images are on the screen at the moment of cuff deflation,let the frame number corresponding to cuff deflation be, say, 2. The Dopplervelocities are imaged for 10 s. Then the image is switched to display vesseldiameters. Let this switch occur at frame 12. Clearly, it may not be neededto convert the 10 s of Doppler data since they do not contain any diameter-relevant information. Still, it may be useful to keep the information aboutelapsed time after cuff deflation for each converted image frame. In thatcase, it is necessary to specify the frame of deflation, this frame is called theinitial frame of the sequence. This can be done by selecting the frame cor-responding to cuff deflation using the Sequence Navigator control panel, and

then click on the panel . Consequently, the panel changes itscontent from [???] to the current number (in our hypothetical example, itwould become 2.

If the information about absolute timing after some event is not needed,this step can be omitted, In that case, the first frame of the sequence and theinitial frame are identical. The value of the initial frame cannot be greaterthan the value of the first frame of the converted sequence, see next section.

7.4.5 Sub-sequence Specification

Using the Sequence Navigator control panel, identify the first frame of theimage sequence that is to be newly created. Then, click on the left button of

. The frame number of the current frame replaces the


[???] on the ”From” button. Again, using the Sequence Navigator controlpanel, identify the last frame of the image sequence that is to be newly cre-

ated and click on the right button of the . The framenumber of the current frame replaces the [???] on the ”To” button. Thedetermination of the first and/or last frame can be modified by newly iden-tifying a current frame using the Sequence Navigator and clicking on the left

(”From”) or right (”To”) button of . After you aresatisfied with the selection of the first and last frames of the sequence to becreated, start the conversion as described in the next section. The measure-ment condition associated with the converted sub-sequence can be identified

by selecting the measurement condition in the control panel .

7.4.6 Conversion

Click on or [File → Save] invokes the calibration process. While thecalibration is ongoing, a message window is displayed informing about theongoing conversion process that may take several seconds or tens of secondsbased on the speed of your computer.

7.4.7 Specification of the Measurement Condition

To guarantee, that the measurement condition associated with the con-verted sequence is determined, a window requiring the operator to specifythe measurement condition (baseline, inflation, deflation) is displayed afterthe conversion process is invoked.

7.4.8 Filling Required Data Fields, Saving Study File

After the conversion process is completed, a communication window con-taining all non-image parameters associated with the vascular analysis studyis displayed. If any information in required fields is missing, it must be typedin. The required fields are labeled in red. Similarly, all other fields that arenecessary for your study must be filled in. After all required fields are filled,the [Save] button is enabled, and the conversion process can be completedand the converted files saved. However, specification of which fields are andwhich are not required can be customized by the user. After clicking Op-tions button in the Information Window, a dialog window opens allowingthe user to select “required” and “optional” fields. Note that the fields withuser-customizable labels (Section 3.6.7.1) are always “optional” and cannotbecome “required”.

As a default, the saved files will carry the filename identical to that of theoriginal description file or image sequence with a 2-letter identifier added to


distinguish between baseline (BL), inflation (IF), deflation (DF), and other(OT) and the extensions will be .raw for the image sequence file and .sdy forthe study file.

7.5 Troubleshooting

• Problem: When saving a converted file, a message appears Failed tosave the converted file.

Solution: Most likely, you are trying to save the converted file on a CD,or the disk you are saving to is full. Choose another location for yourconverted file using the disk selection functionality within the Save theconverted file to window.


Solution: Click on [View → Refresh] to refresh the screen. If thisproblem is frequent, please contact Medical Imaging Applications, LLC.

• Problem: Vascular Converter is not responding after clicking “Con-tinue” within the confirmation window and before the study informa-tion window pops up.

Solution: This is normal, the application is not crashing. The con-verter behaves this way and the warning has been displayed in theconfirmation window. The application is quite busy performing theconversion – file reading, saving, and data operations that do not al-low to respond to the user input during this period of time. The lengthis dependent on the computer speed and sequence length.

CHAPTER 8

Analyzing DICOM Data

Vascular DICOM Module is a Windows 95, Windows 98, Windows Me, Win-dows NT, Windows 2000, and Windows XP compatible module for DICOMimage data input required by Brachial or Carotid Analyzer. Vascular DICOMmodule is not a separate program of the family of Vascular Tools, rather itis a data input module facilitating to directly analyze DICOM data usingthe Brachial or Carotid Analyzer without the need to perform a separate dataconversion step. Consequently, no separate DICOM Converter applicationprogram is needed to work with DICOM data.

8.1 Using Vascular DICOM Module – Overview

If so equipped, the vascular DICOM module is an integral part of theBrachial or Carotid Analyzer. Therefore, the general strategy of working withthe DICOM data follows that earlier described in the Brachial or CarotidAnalyzer chapter.

When working with a new (previously not analyzed and not saved) vas-

cular ultrasound sequence, the sequence must be opened using the thatinvokes a process window to create a new vascular ultrasound sequence study.All subsequent analysis steps are identical to those previously described inChapter 3 or 5.

To save the analysis results, the operation steps are again identical tothose described in Chapter 3 or 5. DICOM data, however, frequently comeon removable media like magneto-optical (MO) disks or a compact disk (CD).Whenever working with removable media, one must take caution not toremove the medium that is in use. Also, if CDs are used as a storage mediumfor ultrasound data, one has to realize that CDs are typically read-only mediaand thus trying to save the analysis results to a CD will inevitably fail.

When working with a previously analyzed DICOM image sequence, fol-

low the standard procedures outlined in Chapter 3 or 5 – opens existingvascular ultrasound sequence study. Again, if data is stored on a removablemedium, the medium must be inserted in the respective disk drive.

152

8.1 Using Vascular DICOM Module – Overview 153

These main steps will now be described in more detail.

8.1.1 DICOM Data Input

DICOM data from individual image sequences are stored in so calledCLIP files. DICOM data can be acquired in two basic forms – one CLIP fileper sequence or one CLIP file per image frame. For the information abouthow to acquire DICOM image sequences and whether both of the aboveoutlined options are available on your machine, consult the documentationof your ultrasound device. The data handling for the purposes of vascularanalysis is identical for these two approaches.

Nevertheless, there is a minor difference between these two approaches –saving all image frames of a sequence in a single CLIP file is more convenientfrom the data handling standpoint since a single file represents the entiresequence. However, time information is not available for individual framesusing this acquisition protocol. Therefore, whenever time information isrequired for each frame of the image sequence (image frame time stamp), asingle-frame per CLIP image acquisition approach is preferred.

Information about the CLIPs associated with your study can be foundin the DICOMDIR file that is created when acquiring DICOM image data.Nevertheless, the DICOM module is able to understand and open “clip”DICOM image files that are not accompanied with a DICOMDIR file, seeSection 8.1.2. Opening the DICOMDIR and selecting the CLIP is the first

necessary step. After clicking , a Study Information window opens:

Click the Image File label and browse to the directory with the desired file

154 CHAPTER 8 Analyzing DICOM Data

DICOMDIR - the root directory of the DICOM database. Open the DI-COMDIR file and a new information appears within the Study Informationwindow. A sequence of interest can be selected as shown in the followingfigure:

The available information about the imaged subject that was associated withthe image data during image acquisition is automatically filled in the corre-sponding information fields. The remaining required fields must be filled inmanually, required fields are marked in red. The required information fieldsmust be filled before the [Save] button becomes enabled. However, speci-fication of which fields are and which are not required can be customizedby the user. After clicking Options button in the Information Window, adialog window opens allowing the user to select “required” and “optional”fields. Note that the fields with user-customizable labels (Section 3.6.7.1)are always “optional” and cannot become “required”.

After clicking the (enabled) OK button, the image sequence is openedand displayed in the Brachial or Carotid Analyzer window.

8.1.2 DICOM Clip Data Input - No DICOMDIR

The DICOM module is able to deal with DICOM clip files even if the DI-COMDIR file is not supplied with the complete DICOM directory structure.Clip files are files holding the iumage information together with information

about the imaged subject. Single clip files can be opened after clicking .Then, a Study Information window opens (see Section 8.1.1). Click the ImageFile label, select Files of type: DICOM clip and browse to the directory withthe desired DICOM clip file. Open the DICOM clip file and the available

8.2 Data Management Recommendations when Working with DICOM Image Data 155

information about the imaged subject that was associated with the imagedata during image acquisition is automatically filled in the correspondinginformation fields. The remaining required fields must be filled in manually,required fields are marked in red. After filling these fields, the OK but-ton becomes enabled and by clicking it, the image sequence is opened anddisplayed in the Brachial or Carotid Analyzer window.

8.1.3 Saving Study File when Working with DICOM Image Data

The Vascular Tools .sdy study file can be saved in the usual way by clicking

the button. The .sdy file can be saved anywhere on your available disks.The study saves a reference about the location of the DICOM image datathat are associated with the analyzed sequence. For details describing thedata referencing philosophy, see Section 3.6.9 as well as the recommendationsgiven in Section 8.2.

8.1.4 Opening a Previously Analyzed DICOM Sequence

Any previously analyzed DICOM .sdy study file can be opened in a stan-

dard way after clicking button. The DICOM image data files are locatedautomatically and the image sequence (CLIP) is opened. All previouslyavailable information is retrieved from the study file.

If you use the removable medium for DICOM storage, please make surethat the referenced DICOM medium is accessible to the Brachial Analyzerstudy file – in other words, the removable disk must be inserted in the re-spective disk drive. If the Brachial Analyzer .sdy study file was stored alongwith the DICOM files on the same storage medium, data will be alwaysaccessible – this forms the main reason for the data consistency recommen-dations mentioned in Section 8.2.

8.2 Data Management Recommendations when Working withDICOM Image Data

If the DICOM files are stored on a removable medium [MO disk, CD-RW (not CD-Rs), etc.], it is recommended that Brachial or Carotid Analyzer.sdy study file be saved on the SAME medium with the DICOM files. Thisrecommendation is motivated by the resulting higher data consistency, animportant issue in large-volume vascular analysis studies.

When saving the .sdy files, you may create a new directory on the storagemedium to hold the Brachial or Carotid Analyzer study files. You can alsofreely name the study files – e.g., using unique study identifiers.

While not necessary, it is usually easier from the data handling stand-point to store a single subject data and the associated analysis results on asingle removable medium – one MO disk or one CD per subject.

156 CHAPTER 8 Analyzing DICOM Data

8.3 Troubleshooting

• Problem: When saving results, an error message “Study File SavingError” occurs.

Solution: Most likely, you are trying to save a file on a CD, or the diskyou are saving to is full. Choose another location for your file usingthe disk selection functionality within the Save Study File As window.Note however, that saving the .sdy file in a different location from theimage data may cause data consistency problems in the long run. SeeSection 8.2.

• Problem: When opening results, an error message “Image File Error”occurs.

Solution: Most likely, the .sdy file is residing on a hard disk or otheraccessible storage medium, while the referenced DICOMDIR file (itsname is provided in the window with the error message) is not acces-sible. The inaccessibility is most likely due to the fact that the imagedata resides on a removable medium that is not inserted in the respec-tive disk drive. To solve the problem, insert the disk containing thereferenced image data files. To avoid this problem, save the .sdy filestogether with the image data as recommended in Section 8.2.

• Problem: Occasionally, an image frame from the DICOM image se-quence is corrupted and does not carry meaningful image data.

Solution: This data corruption is already present in the DICOM imagedata. Any measurement in such corrupted frame(s) are either auto-matically excluded by the Brachial or Carotid Analyzer quality controlmechanism, or these frames can be rejected manually from the Resultswindow, see also Section 3.6.5.

• Problem: No DICOMDIR file is present but I have DICOM clip filesthat contain the image data.

Solution: Follow steps described in Section 8.1.2.

CHAPTER 9

Analyzing HP-DSR (Philips Sonos) Data

Vascular Converter HP-DSR is a Windows 95, Windows 98, Windows Me,Windows NT, Windows 2000, and Windows XP compatible module for HP-DSR image data conversion required by Vascular Tools The Converter is ableto convert sequences of HP (Philips) Sonos proprietary Tiff images.

9.1 General Issues

See Chapter 7 for general description of vascular conversion.For HP-DSR conversion to run, three HP-distributed files must be present

on your computer (DSR2TIF.EXE, TIFINFO.EXE, and A.MAP) – thesefiles must reside in a path-specified directory (e.g., in C:\WINNT, so thatthese files are found when called from Vascular Converter HP-DSR).

9.2 Running Vascular Converter HP-DSR – Specifics

1. For HP-DSR conversion using Vascular Converter, follow the instruc-tions in Chapter 7 with the specifics listed below.

2. Conversion of files residing on a hard disk or read-write magneto-optical media:

(a) Open Vascular Converter HP-DSR from the START - Programs- MIA Vascular Tools menu

(b) Click File-New and select the corresponding HP-TIF file.

(c) a small window opens informing you about the conversion process,do not close this window.

(d) A (black) window opens informing you about the progress of con-version.

(e) This process is using HP-distributed software that is compatiblewith HP/Philips Sonos machines.

(f) After the conversion is over, the black window disappears and youshould close the small gray window.

(g) Follow on-screen instructions.

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158 CHAPTER 9 Analyzing HP-DSR (Philips Sonos) Data

3. Conversion of files residing on read-only media

(a) Copy the desired files to the hard disk.

(b) Follow the instructions given above.

(c) If you attempt converting the file that resides on the read-onlyMO disk, no black window occurs for an extended period of time,and the Converter seems to freeze (hour-glass cursor stays onscreen). The Converter is not frozen, however the conversionfailed. Copy the files to a hard disk and perform the conversionas needed.

9.3 Troubleshooting

• Problem: When opening an HP-DSR file, no “black window” appearsand the Converter seemingly freezes.

Solution: The Vascular Converter HP-DSR did not find the HP-distributedfiles DSR2TIF.EXE, TIFINFO.EXE, and A.MAP. Make sure thesefiles reside on your machine and that that they are in a path-specifieddirectory. Contact Medical Imaging Applications, LLC if needed.

• Problem: Conversion starts but does not complete properly.

Solution: The problem is likely in a lack of disk space on your medium.Vascular Converter HP-DSR requires substantial temporary space in thesame location where the original HP-DSR file resides.

• Problem: Conversion fails with a message of “Incorrect parameter set-ting”. This is caused by the operating system’s inability to launchHP-distributed files DSR2TIF.EXE and/or TIFINFO.EXE. It may becaused by (rare) Windows setting of the user’s account in which userhas no privilege to run the DSR2TIF or TIFINFO programs from acommand line.

Solution: Modify user’s privileges so that the user is allowed to launchprograms from command line.

• Problem: Conversion fails with a message of “Failed to read the outputfile from DSR2TIF”. This may be (among other reasons) caused by aread-only status of the original TIF file. This happens when the file iscopied to the hard disk from a CD.

Solution: Modify the file status via File Properties so that the file isnot read-only.

CHAPTER 10

Vascular Imager

Vascular Imager is a Windows 95, Windows 98, Windows Me, Windows NTand Windows 2000 compatible program environment for continuous acqui-sition of NTSC or PAL image data sequences as well as individual imageframes. In combination with image data from some of the ultrasound ma-chines (e.g., Toshiba, HP Sonos1), ECG-triggered image acquisition is pos-sible when grabbing the images directly from the machine’s video output orusing videotape. A specialized hardware – Vascular EKG Gating Module –was developed for this purpose (Chapter 11).

Vascular Imager is a software tool requiring Matrox Meteor 2 frame grab-ber to be installed on your PC.

10.1 Running Vascular Imager

Since image digitization is a memory and data traffic demanding application,it is highly recommended that Vascular Imager be the only active applicationwhenever the Vascular Imager is utilized.

To run Vascular Imager:

1. Connect a video source to the BNC connector of the Matrox Meteorframe grabber.

2. Make sure the video source (VCR, ultrasound machine) is switched on(not necessarily running but offering an active video link).

3. Invoke the main Windows 95/98/Me/NT/2000 Menu

by clicking button.

4. Select Vascular Tools.

5. Select Vascular Imager.(Only one copy of Vascular Imager can be invoked at any time.)

To exit from Vascular Imager:

1Toshiba and HP are registered trade marks

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160 CHAPTER 10 Vascular Imager

1. Exit [File → Exit] or click the upper right corner of the Vascular Imagerwindow.

10.2 Getting Familiar with Vascular Imager

Real-time video signal from the ultrasound machine or video recorderdigitized by the Matrox Meteor 2 digitizer is used as the data input to theVascular Imager. If EKG-gated image acquisition is required, a rectangulargating pulse at the TTL level must be connected to the gating input of theMeteor board.

Vascular Imager creates an image data file .raw and the study descriptionfile .sdy in the Vascular Tools data format.

Similar to the Brachial or Carotid Analyzer, the Vascular Imager containsthe following window partitions (Fig. 3.1):

• Menu Bar

• Tool Bar

• Function Panel

• Image

• Status Bar



Figure 10.1: Controls of the main Vascular Imager window – Menubar, Tool-bar, and Function Panel.

• . saves the digitized vascular ultrasound sequence study – two datafiles are created – a file with .sdy extension that contains the non-imagestudy information and a file with .raw extension containing all imagedata associated with the image sequence.

10.2 Getting Familiar with Vascular Imager 161

• . switches between viewing the continuous video from the imagesource and image acquisition. It controls the start or end of image ac-quisition. In Manual Mode, it invokes acquisition of individual framesof the sequence.



The functionality of the main menu items is briefly described below.

• File menu

– Save – saves the digitized vascular ultrasound sequence study –two data files are created – a file with .sdy extension that containsthe non-image study information and a file with .raw extensioncontaining all image data associated with the image sequence. –

identical to clicking . This function disabled in Manual Mode.

– Exit – exits from the Vascular Imager, identical to clicking upperright corner button of the main Vascular Imager window.

• Action menu

– Setup Study (F2) – allows specification of study information be-fore image grabbing.

– Grab Start / Stop (F1) – starts image acquisition.

• View menu

– Reference Image – displays the current image in a new window toserve as a reference image.


– Status Bar – displays or hides the status information line in thebottom of the main Vascular Imager window.

– Current Memory Status – provides info about total and avail-able memory space, the information is displayed in the status barunder the image.

– Options - allows setting duplicate-trigger treatment status.

• Help menu

– About – provides basic information about the Vascular Imager.


10.2.3 Function Panel – Controlling the Image Acquisition

There is one Function Panel containing all image acquisition controls.

• Timer/Trigger/Manual acquisition mode selection (pulldown menu) –acquisition can be performed as timed, triggered, or controlled manu-ally.

• Specification of the number of frames (maximum of 3000 frames, de-pends on the available computer memory).

• Specification of the acquisition length in seconds (so that the totalnumber of frames does not exceed 3000, total number of frames iscalculated as acquisition time in seconds times the number of framesper second).

• Required frequency of frame acquisition (range of 0-15 frames per sec-ond) – this control is only available in the “Timer” acquisition mode.Decimal values including values between zero and one are allowed.

• Estimated heart beat rate – this control is only available in the “Trig-ger” acquisition mode, BPM = beats per minute.

• Brightness control – it is not recommended to modify brightness duringimage acquisition.

• Contrast control – it is not recommended to modify contrast duringimage acquisition.

• Finish Manual Grabbing button – specified end of manual image ac-quisition session (in Manual Mode only).

10.3 Image Acquisition

Once the Vascular Imager is running, a “live” image from the connectedvideo source is displayed. There are three image acquisition modes available:

• Timed acquisition that is controlled by the acquisition time and the(time-based) frequency of acquiring frames.

• Triggered acquisition that is controlled by the occurrence of gatingtriggers resulting in the desired number of frames.

• Manual acquisition that is controlled by the operator, image frames ofa sequence are acquired in response to operator’s commands.

10.3 Image Acquisition 163

10.3.1 Factors Influencing Performance of Vascular Imager

Image digitization is an application that has high demands on the com-puter resources, especially with respect to the on-time availability of CPU,memory, and data bus. Proper setting of the Windows environment isparamount and is discussed in Section 10.3.2. In addition, active Windowsapplications or active network connection may compete for computer re-sources during image acquisition and thus jeopardize frame grabbing perfor-mance.

Therefore, to facilitate the best performance of the Vascular Imager, donot run any other Windows application during image acquisition(not even in an inactive mode). Similarly, the computer used forimage acquisition should not be connected to any network duringframe grabbing.

10.3.2 Proper Setting of the Windows Environment to Reach FullPerformance

The image acquisition performance may vary heavily depending on theprocessor speed, computer platform, memory architecture and the operatingsystem.

Recommended system setting is given below:

• Operating system Windows 2000.

• Pentium III 666MHz or better. AGP or AGP-II architecture.

• Matrox G400 video card.

• Rambus RAM (RDRAM).

• Windows 2000 user running the Imager software belongs to Adminis-trator or Power User group.

Theses settings guarantee a reliable frame rate of up to 15 frames persecond and a total number of frames limited only by memory size. Howeverthese settings are not needed if a consistent frame rate of 15 fps is not strictlyrequired.

10.3.3 Number of Frames that can be Acquired

The number of frames that can be acquired is limited by the amount ofinstalled RAM memory and the operating system used. You need to be run-ning Windows NT or Windows 2000 to reliably acquire image sequences withmore than (about) 500 frames. Windows 95/98/Me operating system wasnot designed to deal with files that are larger than several tens of megabytes.


Acquisition of 3000 image frames (mentioned as the supported maxi-mum) requires 1 gigabyte of computer RAM memory. It is likely that yourcomputer has less memory than that. As a general rule, the maximum num-ber of frames the Vascular Imager can capture equals to:

Number of frames =Total RAM Memory (MB) − OS Memory (MB)

0.3(MB)

The OS memory is used by the Microsoft Windows, about 24MB for Win-dows 95/98, 36MB for NT, and even more for Windows 2000. For example,having 898 MB of RAM memory allows acquisition of about 2800 frames.As another example, 256 MB of RAM allows to capture approximately 700image frames.

10.3.4 Timed Image Acquisition

Timed image acquisition is invoked by selecting Timer Mode from thepulldown menu in the Function Panel. It can be used to acquire up to 3000image frames at the frame rates between 0 and 15 frames per second. (Notethat acquisition of 3000 image frames requires 1 GigaByte of computer RAMmemory.) Decimal values including values between zero and one are allowed.Decimal values less than one allow image acquisition at intervals exceeding1 second. For example, specifying frame rate of 0.2 fps, image frames areacquired at 5 second intervals.

As an example, let us consider acquisition of 500 image frames. For 1 fpsrate, it is possible to acquire the images over the period of up to 500 seconds,higher rate will decrease and lower rate increase the maximum interval offrame grabbing. It means that acquiring 500 frames with the frame rateof 10 fps would cover the time interval of 50 seconds. Similarly, acquiring500 frames with the frame rate of 0.1 fps would cover the time interval of5,000 seconds. Since the three acquisition parameters are inter-dependent,modifying one may result in modifying the others. Therefore, double checkall the three numbers before starting the acquisition to be sure that theacquisition will be performed with the correct parameters.

Image contrast and/or brightness can be modified before the image ac-quisition starts, it is not recommended to modify these parameters duringacquisition.

Clicking the button or using F1 key starts the image acquisition.The camera button stays in the clicked position during the entire image ac-quisition. Image acquisition progress can be monitored in the Status Bar.Also, only the acquired images are displayed – causing the screen update tocorrespond with the prescribed frame rate. Once the prescribed sequenceis acquired, the camera button pops up and the display returns in the con-


tinuous update mode. Simultaneously, the image sequence saving windowappears allowing to save the digitized data.

Image acquisition can be stopped at any time by the second clicking of

the button. If the image acquisition process is interrupted before it iscompleted, the imaged portion of the scheduled sequence is available andcan be saved. This approach can be used if the time length of the desiredsequence is not known in advance – the sequence can be prescribed as longerthan expected and acquisition can be stopped at the desired time point andsaved.

10.3.5 Triggered Image Acquisition

Triggered image acquisition is invoked by selecting Trigger Mode fromthe pulldown menu in the Function Panel. It can be used to acquire up to3000 image frames in response to sensing a corresponding number of triggerpulses. (Note that acquisition of 3000 image frames requires 1 GigaByteof computer RAM memory.) Trigger pulses are negative waves, triggeringoccurs at the negative edge. Consequently, it is impossible to exactly specifythe time duration of trigger-based acquisition. However, if the heart rate isknown, this duration can be estimated by typing a heart rate in the heart-rate window. Again, the three acquisition parameters are inter-dependent,modifying one may result in modifying the others. Therefore, double checkall the three numbers before starting the acquisition to be sure that theacquisition will be performed with the correct parameters. See Section 10.3.8for description of triggering options.


Clicking the button or using the F1 key starts the image acquisition.The camera button stays in the clicked position during the entire imageacquisition. Image acquisition progress can be monitored in the Status Bar.Only the acquired (triggered) images are displayed – causing the screenupdate to correspond with the prescribed frame rate. Once the prescribedsequence is acquired, the camera button pops up and the display returnsin the continuous update mode. Simultaneously, the image sequence savingwindow appears allowing to save the digitized data.

Image acquisition can be stopped at any time by the second clicking of

the button. Note however, that the stop command will not be executedbefore the next trigger comes. Therefore, this approach cannot be used ifthe triggering signal is for whatever reason no longer available. If the imageacquisition process is interrupted before it is completed, the imaged portion


of the scheduled sequence is available and can be saved. This approach canbe used if the frame length of the desired sequence is not known in advance– the sequence can be prescribed as longer than expected and acquisitioncan be stopped at the desired point and saved.

10.3.6 Manual Image Acquisition

Manual image acquisition is invoked by selecting Manual Mode fromthe pulldown menu in the Function Panel. It can be used to acquire avirtually unlimited number of image frames in response to manual commandto digitize a current video frame.

After selecting Manual Mode, a File Saving window opens requestinginput of the image file name. After clicking on the Save button, the ManualMode becomes active. Consequently, one or more frames can be acquired ina sequence after manual commands are given. The manual command can

be given by hitting F1 key or clicking the button. It is necessary to hit

F1 or click for each image frame to be acquired. The progress of imageacquisition (number of frames grabbed) can be monitored in the Status Baras well as in the Function Panel.


Manual image acquisition can be stopped at any time by clicking theFinish Frame Grabbing button in the Function Panel. In response, a windowrequesting input of study information is invoked. Red fields must be filledfor the “Save” button to become enabled (see Section 10.3.9 for details).

Note that the button has no functionality in Manual Mode.After the study information is provided and saved, the Vascular Imager

returns to the Timer Mode.

10.3.7 Vascular EKG Gating Module

The Vascular EKG Gating Module is a specialized hardware module thatenables triggered acquisition of vascular ultrasound images that are accom-panied with a R-wave two-level signal. Most of the current ultrasound ma-chines provide the R-wave pulse output via an output connector. This outputcan be either directly connected with the input of the Vascular EKG GatingModule for on-line image digitization, or connected with one of the inputaudio channels of the recording VCRs. If VCR recording is used, the audiooutput of the VCR is connected to the input of the Vascular EKG GatingModule during videotape playback and digitization. Details can be found inChapter 11.


Figure 10.2: Duplicate triggering setup window.

10.3.8 Triggering Options

Two options are incorporated in the Trigger acquisition mode.

1. Acquiring at every N -th trigger.

2. Ignoring faulty triggers.

Consistent skipping of several triggers can be accomplished by specifyingthe number of triggers to be skipped between the ones to be used (see Fig.10.1).

Another option is to adjust treatment of duplicate triggers. A duplicatetrigger is a quick sequence of two or more trigger pulses. It may happen, e.g.,if the triggering signal is noisy or if triggered acquisition is performed fromvideotape and the original R-wave signals duration was excessively long.This may effectively result in several separate triggers to be generated bythe EKG-gating module (Section 10.3.7). Since no R-wave trigger can occurmore frequently than every cardiac cycle and cardiac cycle length is (at least


approximately) known, it is possible to ignore every trigger occurring afterthe true trigger at interval between 0 and x% of the expected cardiac cyclelength. Setting of the x% value is possible after invoking [View → Options →Trigger Mode Options], see Fig. 10.2. Duplicate triggering can be switchedoff or on. When on, the time interval during which triggers will be ignoredcan be set by the slider. Note that when using an interval greater than about45% of the expected R-to-R-wave time duration, somewhat unpredictablebehavior may result - e.g., the second pulse of the duplicate trigger may beused for triggering and the correct trigger ignored.

In the above paragraph, the R-to-R-wave time duration RRI is definedas

RRI =60

HR

where RRI is in seconds, and heart rate HR denotes number of heart beatsper minute. The HR parameter is input by user when setting up the trig-gered image acquisition (Section 10.3.5).

The duplicate-trigger treatment option should be enabled onlyif duplicate trigger presence is encountered.

10.3.9 Saving the Acquired Image Sequence

After the image acquisition process (timed or triggered) has been com-

pleted, or after clicking [File → Save] or at any time after the acquisitionwas completed, the digitized data can be saved in the Vascular Tools format.After the image data saving process is over, a dialog window opens thatallows entering relevant information to create a new study information file:

10.4 Vascular Imager in Real-Time Acquisition 169

The Study Information panel may look somewhat differently from the oneshown above if additional fields were added or removed as part of your site-customized implementation.

Note that the information fields that are required for the saving to pro-ceed are marked in red. These fields must be filled before the saving processcan complete and the [Save] button becomes enabled. However, specifica-tion of which fields are and which are not required can be customized bythe user. After clicking Options button in the Information Window, a di-alog window opens allowing the user to select “required” and “optional”fields. Note that the fields with user-customizable labels (Section 3.6.7.1)are always “optional” and cannot become “required”. The [Cancel] buttonin this panel has no functionality. The user is strongly encouraged to com-plete any initiated saving process (after the [Save] button was clicked in theFile save window) to avoid creation of incomplete files on the hard disk andconsequently possible loss of data.

The saved .raw and .sdy files are directly readable by the Brachial orCarotid Analyzer.

10.4 Vascular Imager in Real-Time Acquisition

Two features were developed to support real-time vascular ultrasounddigitization – display of a reference image, and pre-acquisition specificationof Vascular Study Information.


10.4.1 Display of Reference Image

During the entire brachial FMD baseline/deflation brachial ultrasoundimage acquisition, it is imperative to image the identical segment of thebrachial artery. To assist the sonographer with holding the identical view,it is possible to record and display a reference image that can be used bythe sonographer for continuous comparison of the acquired image, for properpositioning of the visible landmarks, etc.

The reference image can be acquired at any time as long as the VascularImager is not currently acquiring the image sequence.

To acquire a reference image, click [View → Reference Image] or hit keyF5.

These options are disabled if image sequence is currently being acquired.The reference image is immediately displayed showing the exact acquisitiontime. An example of the reference image window follows:

To acquire another reference image, the current reference image must beclosed by clicking the [x] in the upper right corner of the reference image

10.4 Vascular Imager in Real-Time Acquisition 171

window.

10.4.2 Pre-Acquisition Study Information Input

When acquiring Baseline and Deflation sequences in real time, the sono-grapher has to hold the probe and continuously follow the acquired imagesfor visual feedback. Consequently, it may be difficult to type the StudyInformation text after the Baseline sequence acquisition is completed andbefore the Deflation sequence is acquired.

It may be preferred to type the Baseline Study information before thebaseline image acquisition to avoid any typing between the Baseline andDeflation acquisitions.

To set up a study before any image acquisition, click [Action → SetupStudy] or hit key F2.

A file selection dialog will be displayed asking for the filename and des-tination location of the image file to be acquired. Following the file saveinformation dialog, the Study Information window is displayed and allowsinput of the necessary study data. The fact that a study setup has been

pre-specified is indicated by being displayed in the Function Panel.The sequence acquisition may be performed after this study setup in a

standard way by clicking button or using the F1 key. In such a case,the acquired images and the Study information are saved automatically andthe previously input data are used. A study completion message is displayedin the Status Bar.

If an acquisition is performed without invoking the Setup Study dialogbefore the acquisition, the image file saving and Study Information windowwill be displayed in a standard way after the image grabbing is completed.

10.4.3 Four-click Operation to Acquire Baseline and DeflationSequences

When acquiring the baseline and deflation sequences in real time directlyfrom the ultrasound machine, minimizing the operator interaction is of pri-mary importance. The Trigger Mode acquisition has a default setup thatguarantees that image sequences that may be acquired are long enough even


for fast heart rate. Consequently, each sequence acquisition must be startedAND stopped in the approach described below. However, there is no need totype any acquisition parameters that are otherwise required by the VascularImager.

A recommended procedure that serves this purpose and only requiresfour function-key-hits or four mouse clicks is described below. Additionally,only two of these four clicks/hits are critical. The procedure consists of thefollowing steps:

1. Start the Vascular Imager.

2. Specify the study information parameters for the baseline sequence as

described in Section 10.4.2. As a result, is displayed.

3. Start real-time image acquisition using the ultrasound probe, the liveimages will be appearing on the screen.

4. Adjust the position of the ultrasound probe to image the desired sec-tion of the vessel. If satisfied with the image, hit [F5] function key orclick [View → Reference Image], Section 10.4.1. The reference imagewill appear on the screen, adjust its position not to intervene with thelive image.

5. Change the image acquisition mode to Trigger Mode. Do NOT adjustthe heart rate, seconds, or frame number parameters. Leave in thedefault values showing 180 s of acquisition.

6. You are ready to start the triggered Baseline sequence acquisition. Ifthe probe position has moved, adjust the image so that it matches withthe reference image using the previously visually identified landmarks.

Once satisfied, hit [F1] or click the button. This click is one ofthe two critical ones.

7. After the time that you require for baseline image sequence acquisition

elapsed, hit [F1] or click the button again – this stops the baselineacquisition and saves the baseline image sequence.

8. Now, you have time to go through the cuff inflation stage, still holdingthe image probe in the unchanged position. The Vascular Imager staysin the Trigger Mode and triggered images are being displayed. Again,do NOT adjust the heart rate, seconds, or frame number parameters.Leave in the default values showing 180 s of acquisition.


9. Once it is about time to start acquiring the deflation sequence images,make sure that the probe image position agrees with the reference

image as much as possible. Then, hit [F1] or click the buttonat the time of cuff deflation. This starts the deflation sequence imageacquisition. This is the second critical click.

10. After the time interval elapsed that you require for deflation image

sequence acquisition, hit [F1] or click the button again – thisstops the image acquisition and the Study Information window opens.

11. Fill in the image file name, adjust the sequence information to deflation,and save the sequence by clicking the Save button.

10.5 Troubleshooting

• Problem: After starting Vascular Imager, errors from Hardware MeteorBoard and from Active MIL Controls are reported.

Solution: Only one Vascular Imager can be invoked at any given time.Be sure you do not attempt starting Vascular Imager when anotherversion is already running.

• Problem: Acquisition time or number of frames cannot be entered - asmaller number appears instead.

Solution: The length of sequence exceeds the allowed limits or thememory space available. Decrease the length of the acquired imagesequence to be below the limits specified in Section 10.2.3. If thenumbers are below these limits, and other applications are running,stop the Imager, stop the other applications, and restart the Imager.

• Problem: Vascular Imager does not respond to the application controls.

Solution: End the Vascular Imager application by clicking [File → Exit]or the upper right corner button of the main Vascular Imager window.

• Problem: There is no trigger input and the application is hanging inthe Triggering mode.

Solution: Change the mode to the Timed acquisition by clicking the“Timed” switch. If this cannot be done, end the Vascular Imager appli-cation by clicking [File → Exit] or the upper right corner button of themain Vascular Imager window and correct the lack of triggering signalproblem before restarting the Vascular Imager.


• Problem: EKG-gated triggering is too frequent and acquires imageframes between R-waves – too frequent triggering.

Solution: Triggering signal is incorrect. This may be caused by thesignal itself (contact your EKG system technician) or by the incorrect(too high) voltage level of the triggering signal at the digitization boardtriggering input. In the latter case, adjust (decrease) the gain of thehardware Vascular EKG Gating Module to achieve correct triggering.See also Chapter 11.

• Problem: EKG-gated triggering is not frequent enough and triggeredimage acquisition skips cardiac cycles – too infrequent triggering.

Solution: Triggering signal is incorrect. This may be caused by thesignal itself (contact your EKG system technician) or by the incorrect(too low) voltage level of the triggering signal at the digitization boardtriggering input. In the latter case, adjust (increase) the gain of thehardware Vascular EKG Gating Module to achieve correct triggering.See also Chapter 11.

• Problem: Vascular EKG Gating Module does not provide correct gatingdata while it functioned properly in the past.

Solution: Check the battery of the Vascular EKG Gating Module (redcontrol light on) and replace if necessary. Adjust the gain otherwise.See also Chapter 11.

• Problem:Vascular Imager is not responding after clicking “Save” in thefile saving window and before the study information window pops up.

Solution: This is normal, the application is not crashing. The Imageris quite busy saving the large amount of data. The length is dependenton the computer speed and sequence length.

• Problem:Vascular Imager sometimes requires more time than specifiedto acquire an image frame.

Solution: Image acquisition is a very demanding application. To max-imize the performance, do not run any other Windows applicationduring image acquisition. The computer used for image acquisitionshould not be connected to any network during frame grabbing. SeeSection 10.3.1 for details.

• Problem:Vascular Imager does not let me digitize 3000 frames that arementioned as the maximum in the manual.


Solution: Note that acquisition of 3000 image frames requires 1 giga-byte of computer RAM memory. It is likely that your computer hasless memory than that. As a general rule, the maximum number offrames the Vascular Imager can capture equals to:

Number of frames =Total RAM Memory (MB) − OS Memory (MB)

0.3(MB)

The OS memory is used by the Microsoft Windows, about 24MB forWindows 95/98/Me, 36MB for NT, and even more for Windows 2000.For example, having 256 MB of RAM memory allows acquisition ofabout 700 frames.

• Problem:Vascular Imager does not let me save long image sequences de-spite the fact that I have sufficient amount of RAM memory installed.

Solution: Please, check your operating system. You must be runningWindows NT to be able to handle large-size files reliably. Windows95/98 operating system was not designed to deal with files that arelarger than several tens of megabytes. If you are running Windows 95or 98, upgrade to Windows NT or Windows 2000.

• Problem: When using triggered acquisition, some triggers are missed.

Solution: Make sure the duplicate-triggering option is set as needed(see Section 10.3.8).

CHAPTER 11

Vascular EKG-Gating Module

Vascular EKG Gating Module is an R-wave signal conditioning module al-lowing direct EKG-gated digitization from some ultrasound machines (e.g.,Toshiba, HP Sonos1, and others) as well as from videotape-recorded vascularultrasound image sequences.

The Vascular EKG Gating Module is a specialized hardware module thatenables triggered acquisition of vascular ultrasound images that are accom-panied with a R-wave two-level signal. Most of the current ultrasound ma-chines provide the R-wave pulse output via an output connector. This outputcan be either directly connected with the input of the Vascular EKG GatingModule for on-line image digitization, or connected with one of the inputaudio channels of the recording VCRs. If VCR recording is used, the audiooutput of the VCR is connected to the input of the Vascular EKG GatingModule during videotape playback and digitization.

The Vascular EKG Gating Module is conditioning the signal to representa regular negative wave signal that is used for Meteor 2 frame grabber trig-gering. Since different ultrasound machines and different VCRs output theR-wave signal at different signal levels, the Vascular EKG Gating Module isequipped with a gain control dial. Thus the triggering signal can be ad-justed to agree with the triggering requirements of the Matrox Meteor 2board. Triggering signal is defined as a pulse of the differential voltage be-tween 4.05 V and 9.15 V. The correct gain setting is indicated by a blinkingred light – when a gating signal is present on the input. If the light doesnot blink, increase the gain using the gain dial knob. Similarly, if the lightblinking occurs more frequently than would correspond to the R-wave sig-nal, decrease the gain by adjusting the gain knob. The gain knob setting issensitive to the level of the input signal and consequently sensitive to thetype/make of the VCR or ultrasound machine used. Once the gain settingis adjusted properly, it can be locked in this position by a small lever on theknob.

Vascular EKG Gating Module requires two 9 V batteries to operate. Thebatteries are in a good condition if the red light is on when the EKG Gating

1Toshiba and HP are registered trade marks

176

11.1 EKG-gated image acquisition using HP Sonos ultrasound machines 177

Module is switched on. The battery are inside of the EKG Gating Module andcan be easily replaced. The Vascular EKG Gating Module should beswitched off when not in use to conserve the batteries.

11.1 EKG-gated image acquisition using HP Sonos ultrasoundmachines

HP Sonos ultrasound machines may generate an audio beep with eachR-wave of the EKG signal. These beeps – when generated – are recordedon the videotape. To generate an R-wave beep, the following sequence ofoperations must be performed (the menu sequence may differ on your HPmachines, consult the HP user manual): Select Physio menu → Select R-wave beep on. The Sonos records the beeps in both audio channels (leftand right). Then, EKG-gated image acquisition can be performed usingVascular Imager if the Vascular EKG Gating Module is connected to theplayback VCR.

Figs. 11.1 and 11.2 show the correct wiring for EKG-gated image acqui-sition from the VCR playback. All connecting cables are provided.

VCR

EKG-Gating

Module

Computer

back panel

Matrox

digitizer

Video out

Audio out

In Out

Figure 11.1: Connection of the VCR, Vascular EKG-Gating Module, and PCComputer for EKG-gated image acquisition. The output video signal mustbe connected with the input BNC connector of the Matrox frame grabber.The output audio signal containing R-wave beeps must be connected to theinput of the Vascular EKG-Gating Module, its output must be connected tothe DB-44 connector of the Matrox frame grabber. All connecting cables areprovided. See the next figure for a detailed view of the back panel of theMatrox digitizer.

178 CHAPTER 11 Vascular EKG-Gating Module

Matrox Digitizer back panel - as can be seen on the back panel of the computer

Video connector (BNC)EKG-triggering

connector (DB-44)

Figure 11.2: Back panel of the Matrox digitizer.

11.2 EKG-gated image acquisition using Toshiba ultrasound ma-chines

Toshiba ultrasound machines provide the R-wave signal from an outputconnector on the back of the ultrasound machine. This signal can be directlyconnected to the input of the Vascular EKG-Gating Module and then usedfor direct EKG-gated image acquisition from the ultrasound machine. Thisapproach has an advantage of by-passing the videotape and thus avoiding theimage deterioration inherent to videotape recording. Connection of cablesis shown in Fig. 11.3. Since exact needs for cabling vary in this case, theprovided cable may not perform this connection in your case. Contact yourlocal technician or Toshiba representative.

Alternatively, the R-wave signal can be connected to the audio input ofthe ultrasound machine’s VCR. Consequently, the R-wave signal is recordedon one of the audio tracks of the videotape. This signal is of much loweramplitude than the beeping signal used by the HP Sonos and may not beaudible when the tape is played back. When digitizing the vascular imagesduring tape playback, the VCR must be connected as shown in Figs. 11.1and 11.2. Make sure that the correct audio channel is used on the output aswas used for R-wave recording. All connecting cables are provided.

11.3 Troubleshooting

• Problem: EKG-gated triggering is too frequent and acquires imageframes between R-waves – too frequent triggering.

Solution: Triggering signal is incorrect. This may be caused by the


Ultrasound

machineComputer

back panel

Matrox

digitizer

Video out

R-wave

signal

Figure 11.3: Connection of the Toshiba ultrasound machine and PC Com-puter for EKG-gated image acquisition. The output video signal must beconnected with the input BNC connector of the Matrox frame grabber. Theoutput R-wave signal must be connected to the DB-44 connector of the Ma-trox frame grabber.

signal itself (contact your EKG system technician) or by the incorrect(too high) voltage level of the triggering signal at the digitization boardtriggering input. In the latter case, adjust (decrease) the gain of thehardware EKG Gating Module to achieve correct triggering.

• Problem: EKG-gated triggering is not frequent enough and triggeredimage acquisition skips cardiac cycles – too infrequent triggering.

Solution: Triggering signal is incorrect. This may be caused by thesignal itself (contact your EKG system technician) or by the incorrect(too low) voltage level of the triggering signal at the digitization boardtriggering input. In the latter case, adjust (increase) the gain of thehardware EKG Gating Module to achieve correct triggering.

• Problem: EKG Gating Module does not provide correct gating datausing any setting of the gain.

Solution: Make sure that the audio gating signal is present on thevideotape.

• Problem: EKG Gating Module does not provide correct gating datausing any setting of the gain, the gating signal is on the tape.

Solution: Make sure that the audio setting of the VCR corresponds tothe setting during recording (e.g., Hi-Fi setting).

• Problem: EKG Gating Module does not provide correct gating data

180 CHAPTER 11 Vascular EKG-Gating Module

using any setting of the gain, the gating signal is on the tape.

Solution: Check whether the gating signal from the VCR is presentin the connected channel – reconnect the cable to the other channel ifnecessary (e.g., from left audio to right audio or vice versa).

• Problem: EKG Gating Module does not provide correct gating datawhile it functioned properly in the past. .

Solution: Check the battery of the EKG Gating Module (red controllight on) and replace if necessary. Adjust the gain otherwise.

CHAPTER 12

References

[1] M Sonka, V Hlavac, and R Boyle. Image Processing, Analysis, and Ma-chine Vision. PWS, Pacific Grove, CA, 2nd edition, 1998. (1st editionChapman and Hall, London, 1993).

[2] W. Liang, R L Browning, R M Lauer, and M Sonka. Automated analysisof brachial ultrasound images and image sequences. In Proc. IEEE Engi-neering in Medicine and Biology Society, vol. 19, pages 546–548. IEEE,1997.

[3] M Sonka, W Liang, and R M Lauer. Flow-mediated dilatation in brachialarteries: Computer analysis of ultrasound image sequences. CVD Pre-vention, 1:147–155, 1998.

[4] W Liang, R Browning, R M Lauer, and M Sonka. Automated analysis ofbrachial ultrasound time series. In Proceedings SPIE, Vol. 3337, pages108–118, Bellingham, WA, 1998. SPIE.

[5] W Liang, R M Lauer, and M Sonka. Automated analysis of brachialultrasound image sequences (abstract). Circulation, 98:I–136, 1998.

[6] J. Tschirren, R. M. Lauer, and M. Sonka. Automated analysis of Dopplerultrasound velocity flow diagrams. IEEE Trans. Med. Imaging, 20:1422–1425, 2001.

[7] M M Sabetai, T J Tegos, A N Nicolaides, S Dhanjil, G J Pare, andJ M Stevens. Reproducibility of computer-quantified carotid plaqueechogenicity: can we overcome the subjectivity? Stroke, 31:2189–2196,2000.

[8] B K Lal, R W Hobson, P J Pappas, R Kubicka, M Hameed, E Y Chakh-toura, Z Jamil, F T Padberg, P B Haser, and W N Duran. Pixel dis-tribution analysis of b-mode ultrasound scan images predicts histologicfeatures of atherosclerotic carotid plaques. Journal of Vascular Surgery,35:1210–1217, 2002.

181

182 CHAPTER 12 References

[9] P Tounian, Y Aggoun, B Dubern, V Varille, B Guy-Grand, D Sidi, J PGirardet, and D Bonnet. Presence of increased stiffness of the commoncarotid artery and endothelial dysfunction in severely obese children: Aprospective study. Lancet, 358:1400–1404, 2001.

Index

Address

e-mail, 10

internet, 10

Medical Imaging Applications,LLC, 10

Artifacts

brachial ultrasound, 39

Brachial Analyzer, 7, 16–66

about, 29

border properties, 45

calibration, 38

click-and-display, 37, 48

click-on-chart-and-display, 51

confidence, 43, 47, 51

confidence index, 35, 47, 49

confidence threshold, 49–51

control buttons, 18–22

data input, 37

demo, 17, 31

DICOM

previously analyzed sequence,155

editing, 35, 50–57

manual, 51

example data, 30

function panel, 18

function panels, 24–25

calibration, 24

context-sensitive help, 25

editing, 25

hints, 25

initial, 24

intervention, 25

sequence navigator, 24

training, 24

help

context sensitive, 29

image, 18

interaction

manual, 51

intervention, 35, 50–57

learning, 16, 39

border properties, 16, 39

menu bar, 18, 22–24

menu items, 22–24

new study, 25

open, 26

options, 28

process windows, 25–30

properties, 28

quality control, 40, 47–50

confidence threshold, 49–51

exclusion of subsequence, 51

global, 49

in individual images, 49

interactive, 50

manual rejection, 51

trend threshold, 50, 51

report, 57–62

body, 57, 59

customization, 61

header, 57

saving, 63

user-defined codes, 60

results, 29

labels in Results window, 50

review, 47–57

saving, 63

ROI definition, 41

ROI size, 41

save, 26

183

184 Index

sequence analysis, 46status bar, 18study information, 22, 26, 63tool bar, 18–22training, 33–35, 39–46

curved vessels, 46defining required points, 43,

44first stage, 41freezing ROI, 43, 44in another frame, 40, 43, 46in modified ROI, 43robustness, 43, 46second stage, 41

trend threshold, 50, 51troubleshooting, 65tutorial, 30–37upgrade, 62usage overview, 30vessel diameter measurement,

47

Carotid Analyzer, 7, 78–127about, 90border properties, 104calibration, 101click-and-display, 99, 108click-on-chart-and-display, 110compliance, 122–126control buttons, 80–84data input, 100demo, 79, 92distensibility, 122–126editing, 97, 109–111

click-to-detect, 110manual, 110

example data, 91function panel, 80function panels, 86–87

calibration, 86computer-assisted editing, 87context-sensitive help, 87editing, 87

hints, 87

initial, 86

sequence navigator, 86

training, 86

help

context sensitive, 90

DICOM, 29, 90

Online manual, 29, 90

image, 80

IMT, 7, 78, 93, 106, 109

interaction

click-to-detect, 110

intervention, 97, 109–111

Intima-media thickness, 7, 78

learning, 7, 78, 102

border properties, 7, 78, 102

menu bar, 80, 84–86

menu items, 84–86

new study, 87

open, 88

options, 89

plaque analysis, 119–122

process windows, 87–90

properties, 88

quality control

exclusion of subsequence, 109

interactive, 109

manual rejection, 109

report, 111–117

body, 111, 113

customization, 115

header, 111

saving, 117

user-defined codes, 114

results, 90

labels in Results window, 109

review, 107–111

saving, 117

ROI definition, 102

ROI size, 103

save, 88

sequence analysis, 106

Index 185

status bar, 80study information, 84, 88, 117tool bar, 80–84training, 94–97, 102–105

curved vessels, 106first stage, 102in another frame, 105robustness, 105second stage, 102

troubleshooting, 126tutorial, 91–100usage overview, 91vessel

diameter, 93, 106, 109vessel diameter measurement,

107Compact disk, 152Compliance, 49, 109Cost function, 7, 16, 42, 45, 78,

104

DICOM, 9, 152–156Doppler Flow Analyzer, 8, 67–77

active cycle, 68, 74–76control buttons, 69demo, 68function panel, 69function panels, 70–71

context-sensitive help, 71editing, 71hints, 71initial, 71temporal calibration, 71velocity calibration, 71

image, 69menu bar, 69–70menu items, 70process windows, 71–72results, 72status bar, 69tool bar, 69troubleshooting, 77usage overview, 72–73

FDA approval, 10Flow

velocity, 8, 67Flow mediated dilatation, 30, 39,

49, 50

Graph search, 7, 16, 45, 78, 104

Installation, 12Intima-media thickness, 7, 78

Knowledgea priori, 39

Machine learning, 39, 102Magneto-optical disk, 152

Subject Manager, 128–135DICOM, 131DICOMDIR, 131image files, 133maintenance commands, 128reports

comprehensive , 135study-specific, 135subject-specific, 135

status information, 128study file panel, 128study information, 129tool bar, 128troubleshooting, 135

TroubleshootingBrachial Analyzer, 65Carotid Analyzer, 126Doppler Flow Analyzer, 77Subject Manager, 135Vascular Converter, 151Vascular Converter HP-DSR,

158Vascular DICOM Module, 156Vascular EKG-Gating Module,

178Vascular Imager, 173

186 Index

Vascular ToolsDICOM, 156

Uninstalling, 15

Vascular Analysis Integrated Sys-tems, 9

Vascular Converter, 8, 137–151bitmap, 137, 145calibration, 149control buttons, 138–140conversion, 150function panel, 138function panels, 141

calibration, 141initial, 141sequence navigator, 141

HP-DSR, 157–158troubleshooting, 158

image, 138initial frame specification, 149jpeg, 137, 144menu bar, 138, 140–141menu items, 140–141new, 141new study, 143NTSC, 137opening file, 145PAL, 137Philips Sonos, 157–158process windows, 141–143raw, 137, 144saving study file, 150specification of measurement con-

dition, 150status bar, 138sub-sequence specification, 149tiff, 137, 144, 157tool bar, 138–140troubleshooting, 151usage overview, 144

Vascular DICOM Module, 9, 152–156

clip files with no DICOMDIR,154

data input, 153

missing DICOMDIR, 154

overview, 152

previously analyzed DICOM se-quence, 155

saving results, 155

recommendations, 155

troubleshooting, 156

Vascular EKG-Gating Module, 9,159, 176–180


Vascular Imager, 8, 159–175, 177

control buttons, 160–161

duplicate triggers, 167

function panel, 160, 162

gating, 159, 160

image, 160

image acquisition, 162

manual, 166

saving image sequence, 168

menu bar, 160–161

menu items, 161

new study, 168

NTSC, 159

PAL, 159

performance, 163

pre-acquisition study informa-tion input, 171

real-time acquisition, 169

four-click operation, 171

recommended operating systemsetup, 163

reference image, 170

skipping triggers, 167

status bar, 160

tool bar, 160–161


Vascular imager

image acquisition

timed, 164

Index 187

triggered, 165Vascular Imager and Frame Grab-

ber, 8Vascular Tools

DICOM, 152–156data input, 153saving results, 155

gating, 159, 160installation, 12

installed components, 14notes, 13steps, 12system requirements, 12uninstalling, 15upgrade, 15

system requirements, 12uninstalling, 15upgrade, 15

Vesselcompliance, 49, 109diameter, 7, 8, 16, 32, 46, 47,

49, 78, 93, 107

Year 2000 compliance, 10

Documents

Vascular Research Tools 5 - Medical Imaging Applications LLC · Vascular Research Tools 5 Documentation Medical Imaging Applications, LLC °c Medical Imaging Applications, LLC July