user manual - Circle Cardiovascular Imaging Inc.

user manual - Circle Cardiovascular Imaging Inc.
cvi42 / cmr42/ ct42
Version 5.3
USER MANUAL
1
cvi42
cmr42
ct42
USER MANUAL
Aug 09 2016
2
Regulatory Information
Manufactured by
Circle Cardiovascular Imaging Inc.
250, 815 - 8th Avenue SW
Calgary, AB, T2P 3P2
Telephone:
1 (403) 338-1870
Fax:
1 (403) 338 1895
Australia:
cmr42 only
ARTG Certificate No.: 177785
Sponsor:
Market Access Australia Pty Lt
PO Box 1019,
WAHROONGA, NSW, 2076
European Union
cmr42 only
0086
http://www.circlecvi.com
cmr42 is qualified as a class IIa medical device. It
complies with the requirements of the European
Medical Device Directive 93/42/EEC.
EC
Canada
cmr42: Health Canada device license number:
78347
ct42: Health Canada device license number: 87520
REP
EU Authorized Representative
Philipp Barckow Dipl. MedInf.
Ravenweg 9
14163 Berlin
Germany
United States of America
cmr42 :US FDA 510K number: K082628
ct42
:US FDA 510K number: K111373
cvi42
:US FDA 510K number: K141480
© Copyright 2016 Circle Cardiovascular Imaging Inc.
cmr42 & cvi42 is a registered trademark of Circle International Corporation in Canada and/or other countries.
The information contained herein is subject to change without notice. The only warranties for Circle products
and services are set forth in the express warranty statements accompanying such products and services.
Nothing herein should be constructed as constituting an additional warranty. Circle shall not be liable for
technical or editorial errors or omissions contained herein.
3
TABLE OF CONTENTS
1 About .................................................................................................................................................. 1
2 Getting Started .............................................................................................................................. 11
3 Set Up ................................................................................................................................................ 16
4 Working with Multiple Monitors ............................................................................................ 22
5 Viewing ............................................................................................................................................ 26
6 Contour Drawing, Labeling and Measurement Tools ...................................................... 41
7 Values Reported by cmr42 and cvi42 (Clinical Report) ..................................................... 48
8 Patient List ...................................................................................................................................... 54
9 Patient Data .................................................................................................................................... 65
10 Report Module ............................................................................................................................ 68
11 Series Overview .......................................................................................................................... 76
12 Study Viewer Module................................................................................................................ 82
13 4D Viewer ..................................................................................................................................... 85
14 Multiplanar Reformatting....................................................................................................... 99
15 Vessel Module (Auto plaque).............................................................................................. 115
16 Calcium Scoring ....................................................................................................................... 132
17 Aortic Valve ............................................................................................................................... 135
18 LV/RV Function Modules ..................................................................................................... 146
19 Tissue Characterization Module**.................................................................................... 169
20 T2* Module ................................................................................................................................ 183
21 T2 Mapping ............................................................................................................................... 187
22 T1 Mapping and ECV quantification ................................................................................. 192
23 First Pass Perfusion Module ............................................................................................... 203
24 Flow Module ............................................................................................................................. 211
25 Main Menu, Preferences and Configuration .................................................................. 217
26 Technical Support .................................................................................................................. 229
4
1 About
1.1
System Requirements
2
1.1.1
cvi42
Requirements1
Standalone and Client System
1.1.2
cvi42
Enterprise Server System Requirements v5.3
1.1.3
cmr42 Standalone
1.1.4
cmr42 Enterprise Server System Requirements v5.3
3
1.1.5
ct42 Standalone and Client System Requirements1 v5.3
4
1.1.6
ct42 Enterprise Server System Requirements v5.3
4
and Client System
Requirements1
v5.3
2
2
v5.3
3
1.2
Regulatory Information
5
1.3
Basic Components and Indication for Use
5
1.4
Abbreviations and Conventions
9
1
ABOUT
1.1
System Requirements
1.1.1
cvi42 Standalone and Client System Requirements1 v5.3
Requirement
Minimum Requirements
Recommended Requirements
Operating
Windows 7 64-bit2 /
Windows 10 64-bit2 /
System
Mac OS X 10.9
Mac OS X 10.11
Network (LAN)
100BaseT
1000BaseT
Network (WAN)
10Mbps Downstream
1000Mbps Downstream
for client
2.5Mbps Upstream
100Mbps Upstream
Display
1280x800 Resolution at 24-bit color
1920x1080 Resolution or higher 3
Processor
Intel Core 2 Duo at 2.2 GHz
Intel i7 2.2 GHz or greater
Video Card
nVidia or AMD Dedicated GPU
nVidia Dedicated GPU
MR
CT
MR
CT
System RAM
4 GB
8 GB
8 GB
16 GB
Video RAM
1 GB
1 GB
2 GB
4 GB
Systems without dedicated graphics4
Processor /
Graphics
Intel i7 with HD 3000 integrated Graphics5
3D/4D dataset viewing capability varies based on series size and amount of available RAM and VRAM. A system capable of viewing 3D
is automatically capable of viewing 2D images.
2 Windows 8.1, and Windows 10 are supported. Windows 8.0 and Vista are not supported at this time.
3 Multiple screens are supported up to 2560 x 1600 at 24-bit color. Landscape orientation preferred.
4 May affect the performance such as longer response time. It is strongly recommended to use a system with dedicated graphics card,
preferably nVidia GPU.
5 Intel HD 520/530 Video (Skylake) with Windows 10 not supported (with current drivers as of Feb 5, 2016)
1
1.1.2
cvi42 Enterprise Server System Requirements v5.3
Requirement
Minimum Requirements
Recommended Requirements
Operating
Windows Server 2012 R2
System
Windows Server 2008 R2
Mac OS X 10.9
Network (LAN)
100BaseT
1000BaseT
Network (WAN)
25Mbps Upstream
1000Mbps Upstream
for server
5Mbps Downstream
100Mbps Downstream
Display
24-bit color
24-bit color
Processor
Intel Core 2 Duo at 2.2 GHz
Intel i7/Xeon 2.2 GHz or greater
System RAM
4 GB (MR or CT)
4 GB (MR) or 8 GB (CT)
Storage space
1 TB Hard Drive6
2 TB RAID 1+0, 5,6,or SAN6
6Adjust
Mac OS X 10.11
by study size, number of studies to retain prior to archival, etc. SSD drives are preferred.
2
ABOUT
1.1.3
cmr42 Standalone and Client System Requirements1 v5.3
Requirement
Minimum Requirements
Recommended Requirements
Operating
System
Windows 7 64-bit2 or
Windows 10 64-bit2 or
Mac OS X 10.9
Mac OS X 10.11
Network (LAN)
100BaseT
1000BaseT
Network (WAN)
for client
10Mbps Downstream
1000Mbps Downstream
2.5Mbps Upstream
100Mbps Upstream
Display
1280x800 Resolution at 24-bit color
1920x1080 Resolution or higher3
Processor
Intel Core 2 Duo at 2.2 GHz
Intel i7 2.2 GHz or greater
Video Card
nVidia or AMD Dedicated GPU
nVidia Dedicated GPU
System RAM
4 GB
8 GB
Video RAM
1 GB
2 GB
Systems without dedicated graphics
Processor /
4
Intel i7 with HD 3000 integrated Graphics5
Graphics
3D/4D dataset viewing capability varies based on series size and amount of available RAM and VRAM. A system capable of viewing 3D is
automatically capable of viewing 2D images.
2 Windows 8.1 is supported and Windows 8.0 and Vista are not supported at this time.
3 Multiple screens are supported up to 2560 x 1600 at 24-bit color. Landscape orientation preferred.
4 May affect the performance such as longer response time. It is strongly recommended to use a system with dedicated graphics card,
preferably nVidia GPU.
5 Intel HD 520/530 Video (Skylake) with Windows 10 not supported (with current drivers as of Feb 5, 2016)
1
1.1.4
cmr42 Enterprise Server System Requirements v5.3
Requirement
Minimum Requirements
Recommended Requirements
Operating
System
Windows Server 2008 R2
Mac OS X 10.9
Windows Server 2012 R2
Network (LAN)
100BaseT
1000BaseT
Network (WAN)
for server
25Mbps Upstream
1000Mbps Upstream
5Mbps Downstream
100Mbps Downstream
Display
24-bit color
24-bit color
Processor
Intel Core 2 Duo at 2.2 GHz
Intel i7/Xeon 2.2 GHz or greater
System RAM
4 GB
4 GB
Storage space
6Adjust
1 TB Hard Drive
6
Mac OS X 10.11
2 TB RAID 1+0, 5,6,or SAN6
by study size, number of studies to retain prior to archival, etc. SSD drives are preferred.
3
ABOUT
1.1.5
ct42 Standalone and Client System Requirements1 v5.3
Requirement
Minimum Requirements
Recommended Requirements
Operating
System
Windows 7 64 bit2 or
Windows 10 64–bit2 or
Mac OS X 10.9
Mac OS X 10.11
Network (LAN)
100BaseT
1000BaseT
Network (WAN)
for client
10Mbps Downstream
1000Mbps Downstream
2.5Mbps Upstream
100Mbps Upstream
Display
1280x800 Resolution at 24-bit color
1920x1080 Resolution or higher 3
Processor
Intel Core 2 Duo at 2.2 GHz
Intel i7 2.2 GHz or greater
Video Card
nVidia or AMD Dedicated GPU
nVidia Dedicated GPU
System RAM
8 GB
16 GB
Video RAM
1 GB
4 GB
Systems without dedicated graphics
Processor /
4
Intel i7 with HD 3000 integrated Graphics5
Graphics
3D/4D dataset viewing capability varies based on series size and amount of available RAM and VRAM. A system capable of viewing 3D
is automatically capable of viewing 2D images.
2 Windows 8.1 is supported and Windows 8.0 and Vista are not supported at this time.
3 Multiple screens are supported up to 2560 x 1600 at 24-bit color. Landscape orientation preferred.
4 May affect the performance such as longer response time. It is strongly recommended to use a system with dedicated graphics card,
preferably nVidia GPU.
5 Intel HD 520/530 Video (Skylake) with Windows 10 not supported (with current drivers as of Feb 5, 2016)
1
1.1.6
ct42 Enterprise Server System Requirements v5.3
Requirement
Minimum Requirements
Recommended Requirements
Operating
System
Windows Server 2008 R2
Mac OS X 10.9
Windows Server 2012 R2
Network (LAN)
100BaseT
1000BaseT
Network (WAN)
25Mbps Upstream
1000Mbps Upstream
for server
5Mbps Downstream
100Mbps Downstream
Display
24-bit color
24-bit color
Processor
Intel Core 2 Duo at 2.2 GHz
Intel i7/Xeon 2.2 GHz or greater
System RAM
4 GB
8 GB
Storage space
6
1 TB Hard Drive
6
Mac OS X 10.11
2 TB RAID 1+0, 5,6, or SAN6
Adjust by study size, number of studies to retain prior to archival, etc. SSD drives are preferred.
4
ABOUT
1.2
Regulatory Information
AGENCY
cmr42
ct42
cvi42
US FDA 510K #
K082628
K111373
K141480
Europe CE Certificate #
CE 539277
Pending
Pending
Health Canada Device License #
78347
87520
K93385
Australia TGA ARTG #
177785
Pending
Pending
Brasilian ANIVSA
South Korea KFDA
1.3
094337/14-1
14-1334
Pending
Pending
Basic Components and Indication for Use
cvi42 is intended to be used for viewing, post-processing and quantitative evaluation of cardiovascular
magnetic resonance (MR) and computed tomography (CT)* images in a Digital Imaging and Communications
in Medicine (DICOM) Standard format.
Module: Patient List

Browse and filter database

Import and Export of Cardiac MR Images in DICOM format

Anonymization
Module: Patient Data

View Patient related DICOM Header information

Edit patient biometrical data and history

Choose BSA calculation method

View collected images for Case Review
Module: Report

View clinical and scientific report

Send and/or save report
Module: Series Overview

View all images/series in an overview

Filter for specific images/sequences

Series Composer to rearrange or combine series and to delete or add images, slices or phases
Module: Viewer

Custom viewing in up to 12 viewer frames
5
ABOUT

Basic measurements like length, area and SI

Option to view two scans side-by-side
Module 4D Viewer

DVR, MIP and Surface rendering rendering

Dataset clipping, cutting and cropping

Internal and external view

Segmentation via " volume growing tool" based on 3D threshold segmentation

Segmentation for the heart, coronary and vessel tree, left atrium and ventricle and segmentation (CT
only*)

Single LV segmentation including calculation of ESV, EDV, SF, EF (CT only*)

Movie export in multiple formats (AVI, QuickTime)

Secondary DICOM capture saving options include rotation images and cines
Module Multiplanar Reformatting

3D data resampling in any oblique plane

Customizable interface with the option of three MPR viewers and a 4D reference view.

Thick and thin slab rendering

Synchronized zoom, windowing, slab thickness

Multiple preset views designed for cardiac and vascular imaging

Create secondary DICOM captures as cine or stack of any view

Automatic generation of a short axis stack, including long axis reference of CT images* for LV function
assessment

Volume navigation and/or vessel segmentation can be done directly on the 4D reference image

Free form rotation option allows to navigate through the volume in all directions

A report panel will provide predefined measurement profiles and allows for reporting of measurements
and respective images. Measurements and MPR locations will be saved and can easily be reviewed
Module: Vessel (Autoplaque)

The Vessel module workflow includes sub modules for Creating and Editing and Analyzing of vessel
segmentations

The Create section provides automatic coronary tree, aorta and femoral artery segmentation option

In addition it provides an auto-segment TAVI option, that includes aorta/subclavian/femoral
segmentation, aortic valve and annulus plane detection

Optionally vessel segmentation and/or extension of automatic detected vessels can be done via seedpoints or a key-points tool to plot the centerline curve via control points directly.

Vessel displays include projected, stretched and straightened CPR views as well as multiple cross
sectional views

Artifact-free viewing option

Immersive view option
6
ABOUT

Animated centerline fly-through

Automatic contour detection for vessel lumen and wall

Automatic min/max/average diameter as well as stenosis percentage calculation of the vessel lumen

Contours will be saved automatically

Multiple export options include recording of fly through videos

Centerlines can be restored and saved from workspaces

A report panel will provide predefined vessel lists and profiles and allows for reporting of images and
respective centerlines. Measurements and MPR locations will be saved and can easily be reviewed

Autoplaque is part of the Analysis sub-module and performs an automated plaque analysis providing a
color overlay and a report panel displaying all plaque measurements
Module: Biplanar/Triplanar LAX

Global LV function in 2 or 3 planes

Atrial Volumetry (area length)
Module: Multiple Long LAX

Global LV function

Time resolved LV volume curves
Module: Short Axis 3D

Global and regional LV function analysis including polar map display

Global RV function assessment

Atrial volumetry (disc summation technique)

Color coded 3/4D contour model
Module: Perfusion

Semi quantitative Perfusion analysis of rest and stress images

Qualitative Perfusion analysis compared to LGdE and Function images

Polar Map display
Module: Tissue Characterisation

Late Gd Enhancement analysis (viability)

T2 analysis (edema)

Early Gd Enhancement (inflammation)

Color coded 3D mesh model

Polar Map display
Module: T2*
7
ABOUT

Analysis of gradient echo sequences for the assessment of myocardial iron overload; Color coded overlay
and graphical display of decay curve.
Module T2 mapping

global and segmental T2 times

T2 and R2 map with customizable color LUT
Module: T1 mapping

Assessment of native and post contrast T1 Relaxation times

T1, T1*and R2 maps with customizable color LUT and polar map display

Assessment of ECV % per slice and segment including polar map display and map generation with
customizable color LUT
Module: Flow Analysis

Color-coded flow display with semi-automatic contour detection, synchronization and forwarding

Option to perform flow analysis on ROI´s of different series and derive values such as flow difference,
sum and ratio.

Graphical Display of flow rate and flow velocity (mean/max/min)

Background and Phantom correction options

Automatic calculations include volumes, velocities, regurgitant fraction and mean/max pressure gradient
Module: Calcium Scoring (cvi42 and ct42 only*)

Quantification of calcium load in coronary arteries

Automatic calculation of Agatston score, incl. risk classification and percentile ranking based on age and
gender

Threshold and Correction factor can be customized
Module Aortic Valve

Pre-procedural planning of transcatheter aortic valve replacement.

Assessment of the access path for catheter selection and guidance

Measurement of the aortic annulus for device sizing

Ancillary measurements such as the distance between the coronary ostia and the annulus to avoid
obstruction

Device simulation
Reporting

All analyses (and screenshots) in one report

Clinical and scientific reports

Export reports in multiple formats (PDF, ODF, TXT, XML or DICOM)
8
ABOUT
It shall be used by qualified medical professionals, experienced in examining and evaluating cardiovascular
MR images, for the purpose of obtaining diagnostic information as part of a comprehensive diagnostic
decision-making process. cvi42 /cmr42 is a software application that can be used as a stand-alone product or in
a networked environment.
The target population for the cvi42 /cmr42 is not restricted, however the image acquisition by a cardiac
magnetic resonance scanner may limit the use of the device for certain sectors of the general public.
WARNING:
Quantitative analysis is dependent on the quality and correctness of the image source data.
WARNING:
**The Tissue Characterization and Perfusion modules are not available in the USA since the FDA
does not approve the use of contrast agents for cardiac MR procedures. A non-diagnostic version of
cvi42/cmr42 , intended to be used only for scientific research is available upon request.
*Analysis of Computed Tomography (CT) images is not available in Europe for clinical purpose. A
non-diagnostic version intended to be used only for scientific research is available upon request.
1.4
Measurement Accuracy
All the measurements in the software application are direct transfer of the original DICOM data acquired as a
result of image acquisition process. The expected error for the on-screen measurements will be limited to sub
pixel matrix size, which divides up each pixel of the input image into a set of sub pixels, i.e.
Original Pixel
4 x 4 sub pixel matrix
Depending on the original pixel dimensions and the number of sub pixels used, the accuracy of our
measurements will be limited to each sub pixel dimension.
For example, given an original CT or MR image with an isotropic pixel dimension of 0.4 mm and a sub pixel
matrix size of 4 x 4, the length (min/max/average diameter) accuracy will be limited to ±0.05 mm. The accuracy
for area and volume will be dependent on the size and complexity of shape, in addition to the sub pixel matrix
9
ABOUT
size. For example, a 4 pixel diameter circle with isotropic pixel dimension of 0.4 mm and 1 x 1 sub pixel matrix
will have an accuracy of ±0.96 mm2.
1.5
Abbreviations and Conventions
References to buttons or icons and modules are written in italic.
If the selection of a menu or function, requires multiple clicks, it will be notated as follows: E.g. Configuration
> Contours > Rounded SAX Endocardial Contours (which explains how to get to the selection of using rounded
contours for the automatic contour detection)
Tooltips, names of menus and icons are written the same as in the interface, e.g. the button for the Short axis
3D volume module is described as Short3D
CMR
Cardiovascular imaging
EGER
Early Gadolinium Enhancement Ratio
dc
Double click
EGE
Early Gadolinium Enhancement
LMB
Left mouse button
lc
Left click
LGE
Late Gadolinium Enhancement
LV
Left ventricle
MB
Mouse button
MMB
Middle mouse button
RMB
Right mouse button
rc
Right click
ROI
Region of interest
TC
Tissue Characterization
SAX
Short axis
10
GETTING STARTED
2 Getting Started
2.1
Installation
12
2.2
Request and/or Add License (if prompted)
12
2.3
Load Images
14
2.4
Analysis
14
2.4.1
Recommended Contouring Options
14
2.4.1.1
Semiautomatic Endo and Epicardial Contours for Phases or an Entire Stack in SAX
14
2.4.1.2
Manually Drawn Endocardial Contours and/or Contour Correction
15
2.4.1.3
Manually Drawn Epicardial Contours
15
11
GETTING STARTED
2.1
Installation
Running cvi42 /cmr42 on a local server

Download from the website

Run installer application

Open the client (cvi42 or cmr42)

Client Login
Connect to the local server. You will find the server.app (Mac) or server.exe (Windows) in the same folder as
the cvi42 Client .app (or .exe)
Default Server Setup Connection settings:

Name: “Local Server"

Server Address: 127.0.0.1

Server Port: 49696
Default UserId and Password:

username: admin

password: password
The first time you run cvi42/cmr42 to your local server and/or if you move or rename the path to the server,
you may be asked to locate the cvi42/cmr42 server .app or .exe on Windows
Depending on how fast the computer is you may need to repeat step 4 and re-enter your name and password
and press Login.
2.2
Request and/or Add License (if prompted)
Clicking the "Request" button opens a dialog
12
GETTING STARTED
Machine ID: All cmr42 and cvi42 licenses are tied to an individual workstation, which is identified by this
number that is calculated from the hardware of the workstation it runs on. To avoid licensing problems, prior
to running the "Request License" dialog, please turn off or remove any hardware from your machine that is
not permanently turned on or connected to your machine during cmr42/cvi42 usage.
After you have entered your information you can proceed by two options:

Send: If you have an e-mail client configured on your workstation, you can click the "Send" button in
order to e-mail the information to the Circle CVI Sales Department

Export: You can export the information to a file by clicking the "Export" button in order to transfer it to
another machine and send it to the Circle CVI Sales Department.
An E-mail with a license file attached will be send to you. Save the file on the desktop and re-open the
licenses window. There are two options:
a) Import: Import the license from the desktop
b) Add: Open the license file and copy /paste into the license string window
If the license has been added successfully the application will open the Image Database, ready to import
studies.
Note: cvi42 will still show the old license expiry date after a new license has been installed.
As soon as the expiry date has elapsed, the new license will automatically take over.
Alternatively:
Manually remove the license files / lines that are superseded by the newly installed license
Restart the server
13
GETTING STARTED
2.3
Load Images
Click on the Import Images button and select the image file on the local system, the network or
CD/DVD.
After the import is completed, the study will be added to the Main DB tab.
One LMB click loads the study in the preview window. Double LMB click opens the study in the Series
Overview
From here choose your series and drag it in the analysis module
2.4
Analysis
Before starting the evaluation, make sure all patient data required to calculate relevant values are present.
You can review the data in the Patient Data module.
In most cases analysis requires the definition of the heart contour or a region of interest (ROI). Therefore
cmr42 and cvi42 provide different sets of contouring tools, to be found in the top toolbar.
Hovering with the mouse over the tools will provide a description.
A LMB click selects the tool.
Icons with a star perform semiautomatic contour detection
Icons with a little arrow provide additional options.
To deselect tools either pick a different tool or with the LMB click somewhere in the background of the
analysis window.
In most cases, when there is a long axis reference image, you are required to determine your analysis
range
. Select the tool in the left bottom corner of the reference window and with two clicks you
define the mitral valve plane, placing a third point in the apex determines the length of the LV.
2.4.1
Recommended Contouring Options
2.4.1.1
Semiautomatic Endo and Epicardial Contours for Phases or an Entire Stack in SAX
Draw LAX LV Extent (see above)
Draw an endo- and epicardial reference contour
a)
Program your button to detect a phase: Open drop down menu, drag the cursor to the desired
function (Detect Epi/Endo Contours current Phase) and release LMB. To perform the detection, click
the button again. Correct contours: select contour with a double click and redraw
or
14
GETTING STARTED
b)
Program your button to perform "stack detection": Open drop down menu, drag the cursor to
Detect Epi/Endo Contours Stack, release LMB. The detection mode has now changed, indicated by the
two arrows (in reference to the grid pointing in phase and slice direction). LMB click will perform the
detection.
2.4.1.2
Manually Drawn Endocardial Contours and/or Contour Correction
Activate Threshold Contours mode
Pick the endocardial contour tool;
Move the cursor into the LV cavity, press LMB and drag up/down and left/right, to find the best match
with the endocardial border.
When you are done, click Freehand Draw Contours
2.4.1.3
Manually Drawn Epicardial Contours
First activate Click Draw Contours
Next, select epicardial contour and with the LMB
Place points along the epicardial border
A double click completes the contour.
When you are done, click the pencil
again to leave the mode
15
SET UP & CUSTOMIZATION
3 Set Up
3.1
How to Define a Protocol
17
3.2
Protocol Examples
19
3.3
Customize Tools and Working Modules
20
16
SET UP & CUSTOMIZATION
The definition of protocols allows for setting up a workflow according to
standardized image acquisition protocols. This can be done for several clinical
indications and they can be named accordingly.
Once this has been done you can hide the protocol list
(Display on Mouse
Hovering) and switch to the next module with the arrows
located on the
top left corner.
In addition to being faster, it provides guidance for inexperienced user.
3.1
How to Define a Protocol
Generate a new protocol:
1
Open the drop-down menu next to Protocol selection
2
Choose New and type in the protocol name. Hitting the return key will enter the
new name and clear the list.
3
Go to Add and select your modules.
Rearrange modules via by drag and drop
Rename a module with a double LMB click on the name (e.g. change "Tissue Characterization" into
"Infarct")
Delete a module with the Delete button (bottom right)
Tip for setting up multiple protocols at once: Save some time by duplicating and renaming lists.
Go to the menu click Duplicate,
Next Rename.
Type in a new name and click enter-key,
Add, delete, rearrange or rename modules.
Publish your protocol: Mark protocols that shall be visible to other users on the same server as "Public"
Automate protocol selection: If you are using standardized image aquisition protocols, you can link
your cvi42 protocol to the scanning protocol. Open a standard e.g. AMI sequence, set up a post-processing
protocol, open the menu and choose "typical". The next time you open an AMI sequence that exact
protocol with all the defined presets will pop up.
Reset typical studies: This removes all recorded study characteristics for the respective protocol and
allows to start selecting typical studies from scratch.
17
SET UP & CUSTOMIZATION
18
SET UP & CUSTOMIZATION
3.2
Protocol Examples
Myocardial Perfusion and Viability
Series Overview
Viewer
Patient Data
Short 3D
Perfusion
Tissue Characterization
C-M-P: Cardiomyopathy/Myocarditis/Pericardium:
Series Overview
Patient Data
Viewer
Short 3D or Multiple Long LAX
Tissue characterization
Valvular
Series Overview
Viewer
Patient Data
Short 3D or Multiple Long LAX
Flow
19
SET UP & CUSTOMIZATION
3.3
Customize Tools and Working Modules
cvi42/cmr42 offers a wide range of functionality and tools. In the clinical routine not everything is needed, thus
toolsets, window frames reserved for specific evaluations and certain functionality can be turned on or off. In
addition you are able to set your preferred thresholds and analysis options, like e.g. greyzone analysis.
The following modules don't provide interface customization: Patient Data, Report, Series Overview, 4D
viewer,
Customize the Interface
1.
In the protocol list select the module you would like to customize
2.
Click on the wrench (bottom)
3.
Everything that is now highlighted in green and has a little circular off button in the
right lower corner of the frame can be turned on or off. You can hide single buttons or entire groups of
buttons. They will be hidden in all your protocols
4.
Hovering with the mouse over the buttons will display a tool tip
5.
De-activated functionality is highlighted by a purple frame
6.
To reactivate click on the X
7.
To return to default click
8.
Save your selection by clicking the wrench again.
For activating or deactivating more functions (e.g. include exclude papillaries) or to customize settings (e.g.
metric vs. imperial units), please go to Preferences.
20
SET UP & CUSTOMIZATION
Display options like

Exclude Papillaries

Show Cross View

LV volume curve

Reference

View Regional Function and

Mitral Valve Plane correction
will be availble in the Context Menu, when disabled in the Protocol
21
SET UP & CUSTOMIZATION
4 Working with Multiple Monitors
4.1
Set up your displays
23
4.2
Activate multiple screen functionality
23
4.3
Locating the main screen
23
4.4
Choose a module for the other screen
24
4.5
How to handle protocol and thumbnail panel in a multi monitor set-up
25
22
SET UP & CUSTOMIZATION
4.1
Set up your displays
In your Windows settings open up your
display controls, arrange your monitors and
determine your main monitor.
4.2
Activate multiple screen functionality
In cvi42, go to the Preferences>Appearance
>Startup View and check Use Multiple screens
click ok
Quit cvi42 and restart the application
4.3
Locating the main screen
The main screen is the only screen that displays the following icons:
Move current module to screen x icon will be shown on the bottom right corner of the
Patient List module
23
SET UP & CUSTOMIZATION
Patient List module icon in the top tool bar
Main screen
Second screen
4.4
Choose a module for the other screen
There are 2 ways to switch to a different module (default Viewer Module) on the second screen
On the second screen: simply use the arrow keys on the top toolbar
On the home screen:
Select the module you would like to push to
the second screen and click the button in the
lower right corner Move current module to
screen no. x
24
SET UP & CUSTOMIZATION
4.5
How to handle protocol and thumbnail panel in a multi monitor set-up
When working with multiple screens, the panes
will always follow your mouse cursor.
If you want them fixed on a specific monitor, use
the pin on the bottom of the pane.
25
VIEWER CONTROLS
5 Viewing
5.1
View Ports - Overview
27
5.1.1
Viewer Overlays, Annotations
28
5.1.2
Sequence Parameter
28
5.2
Image Editing, Viewer Controls
30
5.2.1
Panning
30
5.2.2
Windowing
30
5.2.3
Main Viewer Controls Table
31
5.2.4
Shortcut and modifier keys
32
5.2.5
Context Menu Table
33
5.3
Additional Viewing
36
5.3.1
Floating Viewer
36
5.3.2
Reference Viewer
37
5.3.3
4D Visualization Viewer
38
5.3.3.1
5.4
Mesh Model Options
Compare Two Studies
39
40
26
VIEWER CONTROLS
There are 3 dedicated viewer modules
Series-Overview module
Viewer module
4D viewer including
(For a detailed description please refer to the respective module chapter)
Next to the main viewer frames within the modules, there are additional frames embedded that allow for
optimal assessment by displaying different aspects and/or orientations
Reference frames
4D Visualization frames
Floating viewer
Multiview display option
(For more detail, please refer to the respective chapter below)
You will start your assessment by loading an image into the viewer
5.1
View Ports - Overview
Each module provides viewer frames for image post-processing.
The frames are tagged and prepared for specific image sets (e.g. T2-weighted images).
27
VIEWER CONTROLS
Result Frame
Thumbnails
Frame
Add-on viewer
Analysis Frame
Reference Frame
Slice/Phase Grid Orientation
5.1.1
3D Mesh Model
Viewer Overlays, Annotations
Overlays consist of information retrieved from the DICOM Header, on-screen tools and contours.
You can remove all overlays e.g. for screenshots, via context menu (opens with a RMB click in the viewer
frame)
5.1.2
Sequence Parameter
Sequence Parameter settings are found in the Preferences/Viewer/ DICOM annotations
If checked DICOM Annotations will be visible on all images
If unchecked, they are hidden, but can still be retrieved with a LMB click in the left bottom corner of
the image frame. Parameters will be displayed for 3 seconds.
More parameters are available in Image Database/Extended View
To increase font size, go to Preferences/Appearance/Font
28
VIEWER CONTROLS
DICOM Header
Navigation Buttons
Target Point
Postion Tags
Sequence Parameter
Start/Stop Cine
Pencil Box
Cines will be displayed in real time speed
By pressing the “S” key during cine display the speed shall be reduced to half of the real time speed.
29
VIEWER CONTROLS
5.2
Image Editing, Viewer Controls
5.2.1
Panning
Center your image with the LMB held.
All signal intensities within the frame border (= frame input area) will be included into signal intensity
calculation. By default the Contour Detection Connect to View is activated in the Preferences, which means
the frame input area automatically adjusts with the zoom.
Zoom in to your region of interest (ROI) using the scroll wheel.
5.2.2
Windowing
Mouse: The mouse allows for direct window adjustments
While holding the shift-key, click and drag the LMB (up/down and left/right)

Clicking the MMB of a 3-button mouse will auto-window
Context menu: Allows to apply or to save custom presets

Windowing Presets and Auto-Windowing options can be found in the context menu.

Keyboard short-cut keys for presets are: 1, 2, 3, 0

To change the default Windowing Preset and/or to add a custom windowing preset choose Edit from the
Window… menu:
A newly defined Window will be added to the Window… menu
Toolbar: Synchronizes window settings within the module
The Sync Window button
will automatically sync the window settings to the other frames
Preferences: Changes apply to all modules
Change the default setting in the Preferences/Viewer menu (preset is 8%).
30
VIEWER CONTROLS
5.2.3
Main Viewer Controls Table
ICON
FUNCTION
Windowing
Panning
MOUSE CLICKS
ALTERNATIVE
Window: push mouse wheel
Windowing presets: keyboard
and drag
keys 1-2-3-0
Auto adjust: double click MMB
Windowing presets: context menu
Holding shift-key+LMB and
Define your own preset via Edit in
drag
the context menu
Hold LMB down and pan
Move cursor to the right frame
border until symbol appears; LMB
Zooming
Scroll mouse wheel
drag up/down
Context menu: Image/Auto adjust
Zoom
Cine mode
Navigation
LMB click
Open on-screen navigation
buttons
Keyboard arrow keys
Scroll
through
Hold the shift key and scroll
Customize your mouse wheel:
phases/slices
the mouse wheel
Preferences/Viewer/Mouse Wheel
and series
function
31
VIEWER CONTROLS
5.2.4
Shortcut and modifier keys
COMMAND KEY COMBINATIONS
WINDOWS
MAC
Undo
Control + Z
⌘+Z
Redo
Control + Y
⌘+Y
Delete Contour
Control + X
⌘+X
Delete All Contours
Control + Del
⌘+⌫
Delete Contour (slice)
Control + D
⌘+D
Delete All Contours (slice)
Control + M
⌘+M
Delete Contour (phase)
Control + O
⌘+O
Delete all Contours (phase)
Control + P
⌘+P
Hide contours
Shift
Shift
Select a contour & jump to the next contour
Tab
Tab
Contours On/Off
Control + Shift + C
⌂+⌘+C
Copy Contour
Control + C
⌘+C
Copy All Contours
Control + A
⌘+A
Paste
Control + V
⌘+V
Forward Contour (slice)
Control + F
⌘+F
Forward All Contours (slice)
Control + E
⌘+E
Smooth contour
Control + S
⌘+S
Round contour
Control + L
⌘+L
Add to Case Review
Control + R
⌘+R
Default Window (set in the preferences)
Control + W
⌘+W
Auto Windowing (type I)
1
1
Auto Windowing (type II)
2
2
Auto Windowing (type III)
3
3
Auto Windowing (Min Max)
0
0
Change mouse wheel from zoom to phase
Shift
Shift
navigate.
Hide
cmr42
Control + H
⌘+H
Hide others
⌥Control + H
⌥⌘ + H
Click-Draw Contours
c + LMB click
c+ LMB click
Threshold segmentation contour definition
Alt + LMB drag
Alt + drag
Drag Contours
d + LMB click
d + LMB click
Push Contours
p + LMB click
p + LMB click
Contour reposition (all at once)
Control + LMB drag
⌘ + LMB drag
View all images of a series next to each other
space bar
space bar
Full Screen
⌘F11
(fn) ⌘F11
Refresh study list
⌘F5
(fn) ⌘F5
Preferences
Control + " ,"
⌘+ " ,"
Quit
Control + Q
⌘+Q
press
press
Contour refinement (
)
32
VIEWER CONTROLS
5.2.5
Context Menu Table
The context menu allows you to make changes to the active viewer frame.
CONTEXT MENU
COMMAND
DESCRIPTION
Undo
⌘Z
Deletes last action e.g. last drawn contour
Redo
⌘Y
Retrieves deleted action
Copy Contour
⌘C
Copies a selected contour
Paste Contour(s)
⌘V
Pastes previously copied contours
Delete Contour
⌘X
Deletes a selected contour (double click)
Copy All Contours
⌘A
Copies all contours that are drawn on the
selected image
Forward Contour (Slice)
⌘F
Forwards a selected contours across all phases
Forward All Contours (Slice)
⌘E
Forwards all contours of a selected slice across
all phases
Delete All Contours
⌘⌫
Deletes all contours in the active frame
Delete Contour (Slice)
⌘D
Deletes a selected contour in all phases per slice
Deletes All Contours (Slice)
⌘M
Deletes all contours in one slice across all phases
Delete Contour (Phase)
⌘O
Deletes a contour in all slices of a selected phase
Delete All Contours (Phase)
⌘P
Deletes all contours in all slices of a selected
phase
Copy/Forward
Delete
Delete Contour (Series)
Deletes a selected contour within a series
Delete All Contours (Series)
Deletes all contour of the selected series
Contours
Smooth Contour
⌘S
Smoothes a shivery contour
Round Contour
⌘L
Contour will assume a round shape
Derive Cardiac Contours
Existing contours in short axis can be retrieved
in other series
Derive Cardiac Contours Phase
Existing contours in short axis can be derived for
an entire phase
Forms - Tools for planimetry
Freehand
Line
Box
Circle
Annotate
Annotation Text
Type in text
Annotation Arrow
Point out a structure with an arrow
33
VIEWER CONTROLS
Annotation Arrowhead
Point out a structure with an arrowhead
Annotation Circle
Point out a structure by encircling it
Closed Contour Rotation1
Adjust a selected contour for heart twisting
Display Contours
⇧⌘C
Hide or display drawn contours
Display Text Annotations
Removes all overlays from the image
Display On Screen Navigation
Shows navigation arrows
Windowing Preset
⌘W
Auto windowing
1
2
3
Ignoring outliers, the system automatically
Windowing
AutoWindowingImage Type I
AutoWindowingImage Type II
AutoWindowingImage Type III
provides you with an optimized setting for
window contrast
Calculates the optimal windowing by taking all
AutoWindowing MinMax
0
(minimal and maximal) grayscale values into
account
AutoWindowingImageRegion
4
AutoWindowingImageRegion
MinMax
5
See auto windowing, but only calculated for
display window
Auto windowing min/max but only calculated
for display window
Edit
Add Current Window
Adds a custom window preset to the menu
Remove Windows
Allows to remove one or all custom presets
Current Window Default
Sets the window as a default for the chosen
image type
Reset Default Window
Reset All Default Windows
If there are multiple defaults they will be reset
Export As
Export Image
Opens a window that allows the user to save the
active frame to a different location
Export Image Multiview
Exports the images in a multiview format and
displays them all at once side-by-side
Copy Image To Clipboard
Copies the image and allows the user to paste it
into any other application
Export Cine Current Slice
Exports the cine of a selected slice to a new file
as AVI movie
Export Movie All Slices Multi
View
Exports all slices and phases of a selected cine as
one movie file (AVI)
34
VIEWER CONTROLS
Separates the slices of a cine and exports them
as a sequential stack of movie files (AVI)
Export Movie All Slices
Stacked
Add Current Series To Case Review
AddFrameToReport
⌘R
Adds a complete series to the case review in the
Patient-Data module
Adds the active frame to the report
Image
Rotate Image
Allows the user to rotate the image e.g. for better
comparison
Reset Image Rotation
Resets previous rotations
Interpolate Image
Shows the image with its raw data
Invert Image
If checked, the image will be displayed with
inverted grayscales (negative image)
Display Overlay
Displays existing color-coded overlays e.g. LE
Display Cursor Signal Intensity
Display of SI in according to the cursor position
Use Open GL
Optimization for video cards that increases
performance
AutoAdjustZoom
Optimizes the zoom
Display & Localizer
Display Localizer
Turns localizer in the reference window on/off
Display Localizer Cut Line
Display of a cut line
Display Localizer Box
Localizer is checked this will display a box
Display Current Localizer Box
Histogram
Display Image Histogram
Display Contour Histogram
Other
Display Additional DICOM Tags
Turns on/off sequence parameter
Display Pos Tags
Displays position tags
Display Scale
Displays scale located on the right middle frame
border
Display Window
Displays window width (contrast) and window
center (window level, brightness) located in the
left bottom corner
Display Cine Tags
Clear Frame
Removes image from frame
Show DICOM Dump
Shows complete DICOM header information
Note: Changes only apply to the active frame; general settings have to be changed in the Preference Menu
35
VIEWER CONTROLS
Closed Contour Rotation1:
Contours can be corrected for ventricular twist motion by a simple
rotation of the contour set.
Click on the contour that has to be rotated,
Open the context menu with a right mouse click
Grab the red dot on the contour
Rotate the contour
5.3
Additional Viewing
5.3.1
Floating Viewer
Located underneath the thumbnail panel is an additional
detachable viewer, that can be changed in size and that will stay
on the screen even when switching to a different module.
cross reference
undock
expand
Expand/Collapse Viewer: Opens an additional
viewer frame. Select an image via drag-and-drop from the
thumbnail panel
resize
Undock/Dock Viewer: Creates a floating
viewer
Provides a cross reference
By default the slice location of the main viewer frame is synchronized with the slice location of the floating
viewer.
In addition you can Show/Hide a Cross Reference in the floating viewer
36
VIEWER CONTROLS
To disable the synchronization go to the Preferences/Viewer and turn of Synchronize Slice Location
5.3.2
Reference Viewer
Reference Viewer requires an orthogonal plane to display the slice orientation of the main viewer frame. In
addition, it allows for defining the range of slices to be included into the analysis by marking the basal and
apical edges of the anatomical long axis.
37
VIEWING
5.3.3
4D Visualization Viewer
Modules with 4D Visualisation frames
Short3D
Tissue Characterization
Perfusion
T2*
T1
Note:
No mesh model will be displayed, when images are not
parallel or have variable slice distances.
CONTEXT MENU MESH MODEL
Reset View
SHORTCUT
⌘R
Follow Module Selection
Display Volume Frame
Display All Overlay
O
Export as file...
Export Image
Export Image Multiview
Copy Image to Clipboard
Export Video Rotation
Export Video Cine
Save as DICOM Secondary Capture…
Save Single Image
⌘
Save Rotation Images
⌘
Save Cine Images
⌘
Save Cine Rotation Images
⌘
38
VIEWING
5.3.3.1
Mesh Model Options
MESH MODEL Options
Choose a set of
contours to create a
3D Model
Choose the analysis
to visualize, or
simply click on the
corresponding
polar map
D - on/off endocardial
Choose which
contour
contour to display
E - on/off endocardial
contour
Switch to a
Q - on/off endo wireframe
wireframe display
W - on/off epi wireframe
Display color
overlay for LGdE
and T2
1-3 select a plane:
Select the image
planes are numbered
plane to scroll
according to the order they
through
have been loaded
Click to pan the
model
39
VIEWING
5.4
Compare Two Studies
cvi42 and cmr42 allow for the comparison of two studies side by side, even of two different modalities.
Load the first study (double-click)
Go back to the Patient List and load (double-click) a second study from the patient list while holding
the shift key. (Repeating this process will substitute the second study)
In the Series Overview Module, both studies will be shown side by side.
In the Viewer Module click on the Primary Study tab above the thumbnails and select your images for
viewing
Go to the Secondary Study tab and make your selection. Images from the secondary study are
highlighted with an thicker frame
In the 4D Viewer you can load either the primary or the secondary study
Analyses are only allowed for primary studies
40
POST-PROCESSING
6 Contour Drawing, Labeling and Measurement Tools
6.1
Measurement tools
6.1.1
Manual Contouring
42
43
6.1.1.1
Free-Hand Drawing
43
6.1.1.2
Free-Hand Drawing Using a Selected Drawing Mode (e.g. by setting points)
43
6.1.2
Semiautomatic Contour Detection
44
6.1.3
Automatic Contour Detection
44
6.1.4
Contour Review
45
6.1.5
Contour Correction
45
6.1.5.1
Tips for a rapid review
45
6.1.6
Contour Propagation
45
6.1.7
Contour Saving
46
6.1.8
Contour Deletion
46
6.1.9
Add the Analysis to the Report
46
41
POST-PROCESSING
Selected contour:
highlighted with a white square in the
centre
Pencil Box
Pencil Box
Drawing tools are located in the top toolbar or the on-screen pencil box and in the context menu.
In addition, the context menu provides multiple options for contour editing
and display, export and more.
Tooltip: All buttons show a brief description on mouse hover.
You can label contours or the respective anatomical structure via context
menu.
An overview as well as a short description of all toolbar buttons is provided in
the chapter "Toolbar Buttons".
Tools that seem to be missing might be deactivated: Go to the Protocol panel, select the module and go into
Edit mode by clicking the wrench and check if they are turned off.
6.1
Measurement tools
There are 2 tools that can be customized in the Configuration or Preferences/Viewer
1.
An angle measurement tool: By default the angle measurement will use angles within 180
degrees. Unchecked it will provide all angles. It will pick the smaller or larger angel depending on the
order you set the 3 measurement points (from left to right it will measure the smaller angle and vice
versa)
2.
Perimeter tool: By default the Calculate Ellipse Perimeter will measure perimeter and area of a
drawn contour and in addition it will estimate a strict elliptical perimeter including it's area .
42
POST-PROCESSING
6.1.1
Manual Contouring
The toolbar is sorted into tool-sets:
for the left heart chambers;
the right heart chambers;
Buttons with a little white triangle indicate, that there are more options provided: Click and hold the
LMB for displaying more options. To select, drag the cursor to the desired function and release the mouse
button
6.1.1.1
1.
2.
3.
4.
Free-Hand Drawing
Select a tool with a LMB click.
To draw, click and hold the left mouse button.
To switch to another tool, simply click on the new tool.
To drop the tool, double click LMB anywhere within the frame (to change settings to leave draw mode
after drawing, go to Preferences/Viewer). Alternatively LMB click on the Leave draw mode icon
the toolbar
6.1.1.2
in
Free-Hand Drawing Using a Selected Drawing Mode (e.g. by setting points)
Start with selecting the contouring mode,
Select the contour (e.g. endocardial ) you would like
to draw.
Drawing Mode Options:
Click-Draw-Contour: sets a series of points for edge definition. This mode is a great option when you have
limited contrast, e.g. epicardial contours.
Modifier Key: "c"
Threshold segmentation: allows to define borders by dragging with
the LMB downwards and sideways until you have found the threshold
that best defines your border. A great contour detection mode for
close contours that have distinct contrast. (e.g. endocardial and vessel
contours ).
Modifier Key: "alt"
43
POST-PROCESSING
Nudge Contour: allows to drag part of the contour in a defined direction. The section of the contour that
will be affected by dragging will be depicted by a thicker contour line. This area can be mini-/maximized
using arrow keys on the keyboard.
Modifier Key: "d" for drag
Push Contour: Shape the contour by pushing the circle. The circle becomes larger the further away you
are from the contour when engaging the contouring mode. Alternatively you can use the arrow keys on
the keyboard to in-/decrease the size.
Modifier Key: "p" for push
Click the contouring mode button or the freehand mode to exit the way of drawing. Instead of entering and
exiting the mode by clicking the buttons, hold down the modifier keys while contouring.
6.1.2
Semiautomatic Contour Detection
This will perform a automatic detection for either endo- (left and right ventricle) or epicardial contours
1.
Target your area of analysis (LV or RV) by centering the small yellow circle (target point) in the
respective chamber cavity
2.
Click the button ones to apply a contour detection
3.
Click and hold to adjust
6.1.3
Automatic Contour Detection
The automatic contour detection is specific to the LV function assessment in a short axis stack and allows for
performing a contour detection for a group of images. Please refer to the respective chapter.
44
POST-PROCESSING
6.1.4
Contour Review
There are multiple ways to review the quality of your edge detection:
The 4D Viewer will instantly provide a 3D model of your contours.
Display all slices in a tile view by clicking the spacebar.
Use the shift-key to toggle contours.
Check contours of all relevant images, by using the on-screen navigation buttons or the arrow keys.
Check by viewing a cine loop (double-click on the
film-icon).
In case you have contours in all phases, use the LV
volume curve or the LV myocardial mass curve to
detect misplaced contours.
6.1.5
Contour Correction
This function is meant to be used in case certain sequences systematically require contour
adjustment.
Adjust the contours by turning the adjustment wheel.
Saving the setting allows to apply the calibration to other series, using the series description and/or the
sequence name as an identifier.
Use any of the desribed manual contouring options described above.
If you change a contour manually and you click the automatic
contour detection again, the manual contour will be preserved.
You can change that behaviour in Preferences>Contour
6.1.5.1
Tips for a rapid review
Holding the "shift"-key hides contours and allows checking the borders.
Refine the contour by moving the cursor over the contour and pushing the RMB.
Key- combination command + L rounds a contour (e.g. vessels in the Flow module)
Key- combination command + S, smoothens out a wiggly contour
6.1.6
Contour Propagation
You can forward a contour via Context Menu/Contours/Forward (All) Contours (slice) or via shortcut ⌘F
This will copy the contour across all phases within a slice. You may need to manually adjust the contours.
45
POST-PROCESSING
6.1.7
Contour Saving
Contours are saved automatically. You have the option to save a second
workspace via workspace menu in the main menu bar.
A simple drag and drop of the image to the thumbnail panel will save it as a
screenshot (DICOM secondary capture)
(Please refer to the Main Menu>Workspace chapter)
6.1.8
Contour Deletion
Shortcut ⌘X deletes a selected contour.
More options can be found in the context menu (RMB click)
6.1.9
Add the Analysis to the Report
Measurements will be displayed either on-screen at the bottom of the viewer frame or in a reporting
window
Measurements change simultaneously with your drawing
Add the measurements of the reporting frame to the report by clicking on the Add to Report
button
Add an image to your report via context menu (right mouse click and left click on Add Frame To Report)
See more detailed information in the module Chapters
Note: A warning message will be displayed in the results frame (and the exported reports), if

Only one phase has been evaluated,

The number of evaluated slices differ between systole and diastole,

Less than 3 slices are used for calculations.
At the readers discretion, warning messages can be turned off. They will re-appear after contour alteration
46
POST-PROCESSING
WARNING: Automatic Contour Detection
The automatic contour detection provides an initial assumption of contour
definitions. It is the responsibility of the user to verify and correct the results.
47
ANALYSIS INPUT/OUTPUT
7 Values Reported by cmr42 and cvi42 (Clinical Report)
7.1
Left Ventricular Function.................................................................................................................. 49
7.2
Right Ventricular Function............................................................................................................... 49
7.3
Atrial Volumetry .................................................................................................................................. 50
7.4
Late Gd Enhancement......................................................................................................................... 50
7.5
T2 Signal Intensity Analysis ............................................................................................................. 50
7.6
T1 Early Gd Enhancement ................................................................................................................ 51
7.7
Perfusion................................................................................................................................................. 51
7.8
T2* ............................................................................................................................................................. 51
7.9
T1mapping ............................................................................................................................................. 52
7.10
Flow Analysis ...................................................................................................................................... 52
7.11
Auto Plaque ......................................................................................................................................... 52
48
ANALYSIS INPUT/OUTPUT
More values will be found in the scientific report.
PARAMETER
UNIT
REMARK
LV EDV
(ml)
End diastolic volume
LV ESV
(ml)
End systolic volume
LV SV
(ml)
Stroke volume
LV EF
(%)
Ejection fraction
LV EDV/H
(ml/cm)
End diastolic volume indexed to height
LV ESV/H
(ml/cm)
End systolic volume, indexed to height
LV SV/H
(ml/cm)
Stroke volume, indexed to height
LV EDV/BSA
(ml/m2)
End diastolic volume indexed to body surface area
LV ESV/BSA
(ml/m2)
End systolic volume, indexed to body surface area
LV SV/BSA
(ml/m2)
Stroke volume, indexed to body surface area
LV CO
(l/min)
Cardiac output
LV CI
(ml/min/m2)
Cardiac index
LV MyoMass (diast)
(g)
Myocardial mass (diastolic)
LV MyoMass (syst)
(g)
Myocardial mass (systolic)
LV PapMass
(g)
Papillary mass
LV MyoMass/H (diast)
(g/cm)
Myocardial mass, indexed to height (diastolic)
LV MyoMass/H (syst)
(g/cm)
Myocardial mass, indexed to height (systolic)
LV MyoMass/BSA (diast)
(g/m2)
Myocardial mass, indexed to body surface area
(diastolic)
LV MyoMass/BSA (syst)
(g/m2)
Myocardial mass, indexed to body surface area
(systolic)
Peak Diastolic Wall Thickness (scientific
report)
(mm)
Peak Ejection Rate (scientific report)
(ml/s)
Requires contours in all slices and phases
Peak Filling Rate (scientific report)
(ml/s)
Requires contours in all slices and phases
RV EDV
(ml)
End diastolic volume
RV ESV
(ml)
End systolic volume
RV SV
(ml)
Stroke volume
RV EF
(%)
Ejection fraction
RV EDV/H
(ml/cm)
End diastolic volume indexed to height
RV ESV/H
(ml/cm)
End systolic volume, indexed to height
7.1
7.2
Left Ventricular Function
Right Ventricular Function
49
ANALYSIS INPUT/OUTPUT
RV SV/H
(ml/cm)
Stroke volume, indexed to height
RV EDV/BSA
(ml/m2)
End diastolic volume indexed to body surface area
RV ESV/BSA
(ml/m2)
End systolic volume, indexed to body surface area
RV SV/BSA
(ml/m2)
Stroke volume, indexed to body surface area
RV CO
(l/min)
Cardiac output
RV CI
(ml/min/m2)
Cardiac index
RV MyoMass (diast)
(g)
Myocardial mass (diastolic)
RV MyoMass (syst)
(g)
Myocardial mass (systolic)
RV PapMass
(g)
Papillary mass
RV MyoMass/H (diast)
(g/cm)
Myocardial mass, indexed to height (diastolic)
RV MyoMass/H (syst)
(g/cm)
Myocardial mass, indexed to height (systolic)
RV MyoMass/BSA (diast)
(g/m2)
Myocardial mass, indexed to body surface area
(diastolic)
(g/m2)
Myocardial mass, indexed to body surface area
(systolic)
EDV (left and right atrium)
(ml)
ESV (left and right atrium)
(ml)
Disc summation (Short 3D Module) and area lenght
technique (Bi-, Tri-Planar Module)
Myocardial Volume
(ml)
Myocardial volume
Myocardial Mass
(g)
Myocardial mass (g)
Total Enhanced Volume
(ml)
Total enhanced volume
Total Enhanced Mass
(mg)
Total enhanced mass
No Reflow Volume
(ml)
No reflow volume
No Reflow Mass
(g)
No reflow mass
Enhanced Volume/Mass (relative)
(%)
Enhanced volume related to myocardial mass as
calculated in the TC module
1) LV MyoMass/BSA (syst)
7.3
7.4
Atrial Volumetry
Late Gd Enhancement
Enhanced Volume/Mass (rel SAX mean
diast/syst)
Enhanced volume related to myocardial mass as
calculated in the short 3D Module
Salvaged area at risk
(ml)
Manually excluded Volume
(ml)
Manually excluded Volume/Mass
(%)
Greyzone volume
ml
Greyzone mass
g
Greyzone Volume/Mass (rel)
%
7.5
T2 enhanced volume - LGdE enhanced volume
T2 Signal Intensity Analysis
Myocardial Volume
(ml)
Myocardial volume
Myocardial Mass
(g)
Myocardial mass (g)
Total Enhanced Volume
(ml)
Total enhanced volume
Total Enhanced Mass
(mg)
Total enhanced mass
50
ANALYSIS INPUT/OUTPUT
No Reflow Volume
(ml)
No reflow volume
No Reflow Mass
(g)
No reflow mass
Enhanced Volume/Mass (relative)
(%)
Enhanced volume related to myocardial mass
Salvaged area at risk
(ml)
Manually excluded Volume
(ml)
Manually excluded Volume/Mass (rel)
(%)
T2 Signal Intensity Ratio
Total Ratio
SI myocardium/SI skeletal muscle
Per slice:
T2 SI Ratio
Myocardial SI + SD
Skeletal Muscle SI + SD
7.6
T1 Early Gd Enhancement
Myocardial Early Enhancement
(%)
EGER
Mean SI and standard deviation in T1
Early Gadolinium Enhancement ratio:
myocardial enhancement/skeletal
muscle enhancement
Per slice, pre and post CA
EGER
(%)
Myocardial Enhancement
Myocardial SI enhancement
Myocardial SI + SD
Myocardial SI + standard deviation
Skeletal Muscle SI + SD
Skeletal muscle SI + standard deviation
7.7
Perfusion
For Rest and Stress:
Baseline SI
Max SI
Time to max SI
Time to 50% max SI
Time between 20% and 80% max SI
Maximum upward slope
The user has the possibility to specify the number of
graph points used for this.
Perfusion Index (PI)
Upslope (tissue)/Upslope (LV)
Myocardial Perfusion Reserve Index
(MPRI)
(PI (stress)/PI (rest)
7.8
T2*
T2* Relaxation time
(m/s)
R2 value
7.9
T2 mapping
Global and Regional Segmental T2 time
R2
Estimation of accuracy (coefficient of determination)
value
(ms)
Estimation of accuracy (coefficient of determination)
51
ANALYSIS INPUT/OUTPUT
7.10 T1mapping
Global and regional and segmental T1 time
(ms)
R2 value
ECV per slice and segment
Estimation of accuracy (coefficient of determination)
(%)
7.11 Flow Analysis
Total Forward Volume (TFV)
ml
positive + negative velocities = positive value (above xaxis)
Total Backward Volume (TBV)
ml
positive + negative velocities = negative value (below xaxis)
Total Volume
ml
TFV + TBV
Net positive Volume
ml
only positive velocities (above x-axis)
Net Negative Volume
ml
only negative velocities (below x-axis)
Regurgitation Fraction
%
Volume/min
ml/min
Volume/min effective
ml/min
Heart rate
bpm
Maximum pressure gradient
mmHg
Mean pressure gradient
mmHg
Maximum velocity
cm/s
Maximum mean velocity
cm/s
Minimum velocity
cm/s
Maximum Flow
ml/s
Minimum Flow
ml/s
Inside Ruler Volume
ml
Outside Ruler Volume
ml
The phase with the maximum velocity out of all
calculated mean (per phase) velocities
Comparison of two flow studies (Qp/Qs)
Difference total volume (Flow 1-Flow 2)
ml
Difference volume/min (Flow 1-Flow 2)
ml/min
Ratio Total Volume (Flow1/Flow2)
Ratio Total Volume (Flow2/Flow1)
Ratio vol/min (Flow1/Flow2)
Ratio vol/min (Flow2/Flow1)
7.12 Auto Plaque
NCP Volume
(mm3)
CP volume
(mm3)
Total Plaque Volume
(mm3)
Low-density NCP Volume
(mm3)
NCP Perc
(%)
52
ANALYSIS INPUT/OUTPUT
Low-density NCP Perc.
(%)
NCP Burden
(%)
CP Burden
(%)
Total Plaque Burden
(%)
Low-density NCP Burden
(%)
Dm Stenosis (Vessel Taper)
(%)
Minimal Luminal Area
(mm3)
Mean Ref. Dist. Stenosis
(%)
Area Stenosis
(%)
Remodeling Index
(FU)
Contrast Density Drop
(%)
NCP X-sections
CP X-sections
Total X-sections
Plaque lenght
(mm)
Proximal Dm.
(mm)
Distal Dm.
(mm)
Max. Stenosis Dm.
(mm)
NCP Threshold
(HU)
Peak Threshold
(HU)
CP Threshold
(HU)
53
PATIENT DATA MODULE
Modules
8 Patient List
8.1
Study List
56
8.1.1
Series List
56
8.1.2
Image List 57
8.2
Study Import
57
8.3
Study Filter
58
8.4
Study Export
59
8.5
Delete Study or Series
60
8.6
Sort your Studies by Applying a Tag
60
8.7
Anonymize Studies
61
8.8
"View" Buttons
64
8.9
Rebuild Database
64
54
PATIENT DATA MODULE
All images will be imported into the main database.
The number of studies contained in your database is displayed next to the date filter at the bottom
It is possible to browse the database and look at images, including cines, and sequence parameter
without loading a study.
A right click on the study line opens a menu

Export study

Anonymize study

Load with Automatic sorting

Send Study to XYX (DICOM Node)

Log...
In case the study has been tagged, the tags will be listed in the menu as well
Study List
Preview
Series List
Image List
Thumbnails
Image Database: Extended view, showing the level of information without loading
55
PATIENT DATA MODULE
A double LMB click opens the study and displays it in a new module, called Series Overview.
8.1
Study List
Green dots indicate a "new study", this study has not been loaded yet.
White highlights the study currently loaded.
Select the attributes that will be displayed in the header line:
RMB click on the column header provides a context menu that allows to choose a study attribute and hide
or unhide the selected column
Sort the columns alphabetically with a click on the attribute in the study-list header. The sorting will be
stored and will be appplied at the next start up.
Sorting: left mouse drag
8.1.1
Select attributes: right mouse click
Series List
Click on the button Extended View at the bottom left will open the series and image level. Here you
find series and sequence related data. A RMB click on the series header row opens a menu from which the displayed
parameter can be chosen. LMB Click on a series line to:

display respective image parameters in the image level (section below)

display the images of that series in the thumbnail section to the right. The selected
image will be framed in green.
56
PATIENT DATA MODULE
RMB click on a series allows to export, remove and send a series
Clicking on the View Preview button on the bottom right of the operation
panel will open/close a preview frame on top of the thumbnail panel,
displaying the first picture of the selected series.
Click on View Preview Cine starts a cine in the Preview window
8.1.2
Image List The image level displays values related to the image of a selected series.
A RMB click on the series header row opens a menu from which the displayed
parameter can be chosen. Click on an image line will frame the corresponding image in the thumbnail panel
in orange and displays the corresponding image in the Preview frame.
8.2
Study Import
Import images from a folder on the computer:
1. Click on Import Images
2. Browse the computer for the images and click to activate
3. Click on “choose”
4. The status bar on the bottom left shows the progress of the download
Import DICOM files as a command line attribute:
cmr42 and cvi42 allow the definition of a list of absolute file paths or directories to DICOM files as a
command line attribute. These images will be loaded from the file system after the startup of the
software. In case of an existing process, these files will be loaded by the existing cmr 42 instance
Find your study:
1.
In the Patient List files are sorted according to the date. Unread files are marked by a green dot
2.
Use the filter options on the bottom of the screen (magnifying glass)
3.
Use the Query filter to retrieve a study from a remote DICOM server (e.g. PACS)
57
PATIENT DATA MODULE
8.3
Study Filter
A customizable filter is located at the left bottom corner. A RMB click on the
magifying glass opens a drop down menu, that will provide filter options
Date filter, again a RMB click opens a menu to filter for

Birth Date

Study Date

Import Date
A Query Filter to search a connected DICOM node.
In order to use the Query/Retrieve functionality, the option Enable Storage SCP in the Preferences,
must be enabled.
Click on the respective server button on the bottom right, underneath the thumbnails.
LMB-click on Preview next to the server buttons to switch back to the thumbnail panel
58
PATIENT DATA MODULE
Query Filter: The Study Date filter can be set to auto. This way you will always be presented with the
choosen setting. E.g. Always filter for patients of the recent 7 days.
8.4
Study Export
A right mouse button click on the study opens the menu that will allow
to export, anonymize or send a study:
Export Study: opens a browser to determine the destination
DICOM file set writer:
Activate 'Write DICOMDIR' in the Preferences>Image Database menu.
cmr42 and cvi42 will now export studies in a directory that contains, in
addition to the DICOM objects, a DICOMDIR file.
59
PATIENT DATA MODULE
Send Study to...: If you are embedded in a network the DICOM nods will be listed in the menu or
underneath the thumnail panel.
8.5
Delete Study or Series
Delete an entire study: Click on the study, (a study that is currently open can not be deleted! Go to the
Workspace menu and close study) and click the delete button on the bottom of the screen.
Remove a single series: In Extended View, select the series from the series list , right-click on the series
and select Remove Series
8.6
Sort your Studies by Applying a Tag
Instead of creating sub-databases you are able provide one or multiple tags to a study.
All available tags are listed above the patient list.
To create a new tag click "+"
In the Create New Tag Menu provide a name and assign a user to the tag.
60
PATIENT DATA MODULE
There are 3 ways to assign a tag to a patient

Drag the applicable tag on the highlighted line of the patient study

Drag the patient study on the tag

RMC on the patient name opens a menu that allows to check and apply
an existing tag
To remove a tag from a study, open the context menu and uncheck.
To delete a tag, RMB click on the tag and select
To review assigned users hover over the tag (tag name is "Linda"
assigned role "Technichian")
To filter for multiple tags, hold down the command key and select as many as you wish
8.7
Anonymize Studies
Anonymization is conforming to the DICOM standard. However, depending the requirements, you have the
option to disable certain attributes. (Preferences>Anonymization).
On all accounts the DICOM attribute Patient Address will be removed.
All available tracings will be included into the anonymization procedure; DICOM Secondary Captures will be
re-created.
61
PATIENT DATA MODULE
1.
Customize anonymization: Set the attributes in Preferences/Anonymisation by dragging the attributes
that you wish to keep into the right column.
2.
RMB click on the Patient study in your database to open a context menu
3.
Click on Anonymize
4.
Provide an identifier
5.
Click ok
6.
The old study will be kept, the anonymized study will be appended to your patient list
Anonymizing multiple studies at once (Batch Anonymization):
1.
Go to Preferences/Anonymization and check Batch Anonymization
2.
Multiple studies can now be selected from the image database (holding the shift key selects continuous
studies, cmd/ctrl selects multiple non sequential studies).
3.
LMB click on Anonymize opens a dialog: provide a name.
4.
Anonymized studies will be labeled with the name provided (e.g Snow Trial) and a number will be
assigned
62
PATIENT DATA MODULE
5.
Track anonymization: You will find a list of your anoymized studies in the folder
cvi42/ServerLogs/logAcces.txt.
Open the file in Text Edit and search for the Identifier (e.g Snow Trail 2014):
Mc Carthy - Snow Trial 2014 -001
Mayer - Snow Trial 2014 -002...
When using the option Remove Private Tags a warning will be displayed in case velocity encoded images
are about to be removed (applies GE and Philips).
Caution: For clinical trial purposes anonymization has to be validated by the readers/core lab)
WARNING: Anonymize
The Anonymization/Pseudanonymization of DICOM data sets removes all data that are selected. In
addition to the DICOM information, cmr42 removes another subset of DICOM tags with private
information. The end user must decide whether this level of removal satisfies the local
regulations/policies of the institute.
63
PATIENT DATA MODULE
8.8
"View" Buttons
I hope ited View: displays series and image information
View Preview: A Preview Window above the thumbnails will open
LMB click on the pencil box in the left bottom corner will provide tools for simple measurements.
View Preview Cine: allows to play a cine loop in the Preview window
8.9
Rebuild Database
In case the database seems to be corrupt it has to be rebuild. Therefore the system will re-read the content of
the sub database folder into the cmr42-image database.
You have to have administrator rights to rebuild. In the Preferences>Server Admin>Rebuild Database you will
find the following option
Update Image File Path - This option rebuilds paths to the images in the cvi42 database without having to
perform a full database rebuild. Typically used when images are not displaying due to migration of existing
images and/or migration of the cvi42 database to a different drive or machine.
Import Orphaned Workspaces - This option rebuilds the linkage between user workspaces and studies. If
there are workspace files that the cvi42sqldb does not know about in the /ProgramData/cvi42/users folders
(in each user's workspace folder) then the association is rebuilt, without having to perform a full database
rebuild. Typically used when workspace associations have been broken due to migration of the
database/workspaces to a different drive or machine.
Full Database Rebuild - Complete rebuild of the cvi42 database. Includes rebuild of the workspace associations
and updating the image data file paths. This option can take a long time to complete, as it needs to re-read
every image in the database. Use with caution, as cvi42 will not be available during this time. Before starting a
full database rebuild, we recommend to use the Go Offline button to place the cvi42 server in an "offline" state
so that client connections are not permitted during the rebuild process.
64
PATIENT DATA MODULE
9 Patient Data
9.1
View DICOM Header Information .................................................................................................. 66
9.2
Enter Patient Data ............................................................................................................................... 66
9.2.1
Enter Patient Related Comments ............................................................................................................ 67
9.2.2
Create a Case Review Presentation ........................................................................................................ 67
65
PATIENT DATA MODULE
Patient-Data Module: Editing patient data and annotations, and creating a case review report
9.1
View DICOM Header Information
DICOM Frame on the top left, displays DICOM Header information
WARNING: Patient Data
The displayed study/patient data is initially derived from the DICOM information if available. Note that
editing these values affect the calculations of all modules. It is the responsibility of the user to verify
these data before releasing final results.
9.2
Enter Patient Data
The User Edit Frame allows you to enter patient related data, which are necessary for calculation,
documentation and reporting.
You have the option to change the units from metric to imperial. Go to Preferences/Appearance/Patient Data
Metric. Settings will be updated as soon as you load the next patient.
66
PATIENT DATA MODULE
Note: The software retrieves the heart rate from the first image of a series. Please check for probability and
make sure the correct heart rate is entered, before you tick the “use this heart rate for calculation” box.
A heart rate over 250 bpm will not be displayed. The value remains at 250 bpm.
9.2.1
Enter Patient Related Comments
The Comments Frame allows you to type in comments for internal purposes.
9.2.2
Create a Case Review Presentation
The Case Review Frame displays the images, which had previously been selected for a case review.
Select an Image for Case Review: Select your image for review via context menu Add Current Series to
Case Review or ⌘R.
Change the Order of the Images: Select an image and click on the arrow buttons underneath or simply
drag and drop the image to the desired position.
Present Your Case Review

If the study is already open: Go to Overview and select Case Review in the Filter.

If you would like to present the case at a later time point: Before you leave cmr 42, go to the
configuration/Series Overview and check Case Review. The next time you open the study, the Study
Overview windows will display the previously selected Case Review Images
67
REPORT MODULE
10 Report Module
10.1
The Clinical Report
69
10.2
Review the Scientific Report
70
10.3
Edit the Report
70
10.4
Customize the Header and Generate Canned Text
71
10.4.1
Writing the Text File
72
10.4.2
Create canned Text (Example)
72
10.4.3
Adding a Logo
73
10.4.4
Add Your Phrase to the Report
73
10.5
Save and Export the Report
74
10.5.1
Save and Export the Clinical Report
74
10.5.2
Save and Export the Scientific Report
74
10.5.3
Export the Scientific Report into Excel or Numbers.
75
68
REPORT MODULE
10.1 The Clinical Report
1. In the Analysis modules click the Add to Report button
. This will add measurements,
images, and polar maps to the report.
The
command in the Context Menu allows adding additional images.
To review report additions, navigate to the Report module.
You will find a report panel next to the protocol pane. cvi/cmr42 automatically generate a Clinical and
a Scientific Report.
Click on the line, e.g. Late
Enhancement to view the report.
To remove a certain part, do a RMB
click on , e.g. Late Enhancement the
and select
To remove warning messages from
the report, go back to the analysis
module and check the box in the
report window:
69
REPORT MODULE
10.2 Review the Scientific Report
For scientific purposes, cvi/cmr42 has the option to display all calculated values (e.g. each SI per phase).
For further analysis the scientific report can easily be transferred into a spreadsheet. See below: export the
scientific report
10.3 Edit the Report
Clicking on the Summary in the left panel will display the editing frames for the:
Header frame
Patient related data
Findings frame
Summary frame (if you are not in Full Screen mode, you need to scroll to get to it)
Text Module frame
cvi/cmr42 automatically retrieves the patient related data from the DICOM Header as well as from the PatientData module where the patient specific data is entered.
70
REPORT MODULE
10.4 Customize the Header and Generate Canned Text
cmr42/cvi42 provides the option to customize the header and to define 'pre-canned' text modules.
71
REPORT MODULE
10.4.1 Writing the Text File
Create a text file (see example below)
Save it with the suffix ".conf"
Copy the file (e.g. "cvi42ReportText.conf") into the Documents/cvi42 (or cmr42) folder
Restart the software
10.4.2 Create canned Text (Example)
Indentations and empty lines will be ignored.
The first "tag" will be your name/affiliation/institution
Type [InstitutionName] in rectangular brackets in the first line
Next line will be your free text: Institution name and address
[/InstitutionName] ends the command
Standard phrases (example):
Type [LV function] in rectangular brackets in the first line
Next line will be your free text: e.g. Left ventricle not enlarged, no hypertrophy
[/LV function] ends the command
[InstitutionName]
Sunshine General Hospital
Success Rd
Somewherenice, 2013
[/InstitutionName]
[Standard phrases for reports]
[LV function]
Left ventricle not enlarged (EDV ml/cm, ESV ml/cm), no hypertrophy (LV mass g/cm) with normal/globally
mildly/moderately/severely reduced left ventricular systolic function; regional mild hypokinesis/moderate
hypokinesis/severe hypokinesis/akinesis/dyskinesis in the basal/mid/apical
anterior/lateral/posterior/inferior/inferoseptal/anteroseptal region / without regional wall motion
abnormalities; Ejection fraction normal/mildly impaired/moderately impaired (45 to 55%)/severely
impaired, % (triplanar evaluation).
[/LV function]
[/Standard phrases for reports]
[Standard phrases for report summaries]
[LV function]
Normal LV function
72
REPORT MODULE
Normal LV function with regional wall motion abnormality
Impaired LV function with global hypokinesis
Impaired LV function with basal/midventricular/apical
anterior/lateral/posterior/inferior/septal/anteroseptal hypokinesis
Severely impaired LV function with global hypokinesis
[/LV function]
[/Standard phrases for report summaries]
Repeat for other modules in the same way.
[First Pass Perfusion]
text
[/First Pass Perfusion]
After restarting, a window will appear with the text modules next to the save and export buttons.
10.4.3 Adding a Logo

The filename has to have the extension ".png" .

Depending on which side of the report the logo should be placed, add "Right" or "Left" to the name e.g. :
RockyMountainHospitalLogoLeft.png

The file has to be copied into the cvi42 folder within the documents folder.

Restart the software
10.4.4 Add Your Phrase to the Report
To select a phrase, select an editing window (Findings or Summary box) with a left mouse click.
From the menu, select the Text Module. The complete text will be shown in the right window. Click Add
To preview the report: go to Print Clinical Report/PDF/Preview
73
REPORT MODULE
10.5
Save and Export the Report
Unlike the tracings, reports will not be saved automatically in the patient study. Closing the study will result
in loosing previously added analyses, text editions in the Findings and the Summary frame.
To save the report, either save it as a separate file to the desired location or take a DICOM Secondary Capture.
The secondary capture will be added to the image series and will reside within the study for future review.
On the bottom of the reporting panel there are several options to save, print and export reports.
10.5.1 Save and Export the Clinical Report
Clicking on the Save Clinical Report button provides the following
options:
Saving it in an open text format allows to make changes.
10.5.2 Save and Export the Scientific Report
Clicking on the button on the bottom left, lets the user save the scientific reports in different formats
74
REPORT MODULE
10.5.3 Export the Scientific Report into Excel or Numbers.
The Report can be copy-pasted into Excel (Microsoft) or Numbers (Mac).
To transfer the analysis into Numbers, simply copy and paste the measurements into Numbers.
To transfer the report into Excel, one extra step is required otherwise all numbers will be pasted into one
column:
a) Copy the Report
b) Open Excel
c) In Excel go to the Edit menu
d) Choose Paste Special
e)
A dialog will open, choose Text
75
SERIES OVERVIEW MODULE
11 Series Overview
11.1
Series-Overview configuration .................................................................................................. 77
11.2
Features .............................................................................................................................................. 77
How to open a series in one of the analysis module ................................................................................................78
How to use a multiview window as an add-on viewer in other modules ......................................................78
11.3
Series Composer .............................................................................................................................. 80
76
SERIES OVERVIEW MODULE
Intended use:
Get a quick, in-depth overview of sequences and images
Choosing the right image/ series for evaluation.
Series Composer sub-unit allows for recomposing studies
11.1 Series-Overview configuration
Settings for the Series Overview can be changed in the Preference>Series Overview
11.2 Features
Synchronization options (toolbar)

Zoom

Windowing: series that shall be synched have to be selected first. Press the command key while
selecting with a LMB click
Display options (toolbar)

Slide Show Mode: Will always present the first image of the series use the on-screen navigatin buttons to
move to the next slice/phase or series
Multiview Mode: opens a series and displays all images next to each other (Short-cut-key: spacebar).
The Multiview layout can be added to the report via context menu (Add Frame To Report)
Cines are tagged with this symbol
.
By default cines start as soon as you move the mouse over the image. To stop the cine, click on the icon.
Stacks will always display the first image of that series.
Click on the spacebar will open the stack and display all images in a multi-view fashion (see below
Multiview) . Click again to go back
77
SERIES OVERVIEW MODULE
Double-click on the image will display it in the Viewer module
A filter is located at the bottom right of the toolbar
How to open a series in one of the analysis module
Select the series
Drag and drop it into one of the modules in the module pane or
Open the context menu with a RMB click and select the module from here or
Go to the toolbar and use the module selection button or
Open the analysis module and drag and drop the series from the thumbnail
How to use a multiview window as an add-on viewer in other modules
A Multiview display shows all images of a selected series in a new window. The window can be undocked
and shifted
Select a series with a left mouse click.
To open up the series either use the Multiview button (if present) or simply click the spacebar of
your keyboard to open the selected series.
The window can be undocked and resized. It will now stay on screen even if you change modules.
Contours in the Multiview can be altered. With the short-cut-keys you can even engage a certain drawing
mode (threshold segmentation="alt" or click-draw="c").
78
SERIES OVERVIEW MODULE
grab the window
detach
undock and take along
scroll to the next phase or series
play cine and change frame rate
resize window
79
SERIES OVERVIEW MODULE
11.3 Series Composer
The Series composer allows to generate new manually composed series
Browser
Composer
New series
Select series via
mouse drag
Drag a series to the Browser, choose slices or phases and drag them into the composer:
Click on the slice or phase number to select all. To select a row of images press the the control key; or for
multiple individual images the command key, while selecting via left mouse click.
A complete series can be dragged directly to the composer
For sequence information (e.g. trigger time or slice location) hover over an
image.
In the Composer select the phase/slice or series and use the context menu to
remove, insert or sort images
Click Apply to assemble the newly composed series. The lower window provides a showcase for
newly composed series.
A newly composed series will automatically be appended to the list of series. Manually composed
series can be identified by their tag (e.g. 28 (manual 9/1/1)
80
SERIES OVERVIEW MODULE
Plausibility check: cmr/cvi42 performs a plausibility check before it assembles a new series.
Composition refused if the following check fails:
1. all images have the same frame of reference
2. for stacks containing velocity encoded images:
 series has exactly two slices,

both slices have the same slice location,

both slices have the same acquisition time,

only images in the first slice are velocity encoded.

both slices have the same number of phases,

trigger times in every phase is equal between both slices,

all images have the same orientation normal.
 Warnings will be shown if one of the following checks fails:
1. same number of phases in each slice
2. parallel slices or slices with a central rotation axis
3. for parallel stacks:
1. equal slice distances,
2. sort order from basal to apical.
3.
In some cases, the user is offered the choice to continue or to ignore the warning. It is at the users discretion
to accept.
81
STUDY VIEWER MODULE
12 Study Viewer Module
12.1 Change the number of view ports ............................................................................................................... 83
12.2 Optimize Image Viewing ................................................................................................................................ 83
82
STUDY VIEWER MODULE
12.1 Change the number of view ports
The study viewer offers different layout views from 2 to 12 view ports.
12.2 Optimize Image Viewing
Images can be synchronized for cines, zooming and windowing.
Cines will be displayed in real time speed. By pressing the “S” key during cine display the speed shall be reduced to
half of the real time speed.
In addition there are cross reference displays, contouring and annotation options.
A context menu that opens with a right mouse click, allows for more features including multiple Display and Export
options.

Image menu
83
STUDY VIEWER MODULE
Display menu
84
4D VIEWER
13 4D Viewer
13.1
Edit ......................................................................................................................................................... 87
13.1.1
4D Viewer Control Features (Table) ................................................................................................... 87
13.1.2
4D Viewer Specific Context Menu ........................................... Error! Bookmark not defined.
13.1.3
Rendering Options...................................................................................................................................... 90
13.1.4
Segmentation Options (CT only) .......................................................................................................... 91
How to perform automatic segmentation ......................................................................................................................91
How to adjust an automatic segmentation .....................................................................................................................91
13.1.5
Manual Segmentation ............................................................................................................................... 92
How to use clipping and cropping......................................................................................................................................92
How to create a custom Background MIP .......................................................................................................................92
How to use the growing tool .................................................................................................................................................93
13.2
Color....................................................................................................................................................... 95
How to Save and Export 3D/4D Rendered Images .....................................................................................................98
85
4D VIEWER
This viewer is designed to analyze 3D and 4D data such as MR and CT (cvi42 only) angiography.
The Preferences offer several 4D Viewer configuration options
Voxel Precision: If you encounter problems
loading large series due to limited VRAM on
the graphics card, you can decrease the
spatial resolution of the displayed volume
from 16 bits to 8 bits. Changes require
reloading of the series.
Note: A change in voxel precision may affect
apparent image quality.
3D Segmentation: set which of the
segmentation options will be performed
automatically upon loading a CT data set
The 4D Viewer module provides 2 sub-modules: Edit and Color
86
4D VIEWER
13.1 Edit
Drag a 3D, 4D or stacked 2D image data set into the viewer frame.
Note: The image will be rejected and a warning will be displayed if slices
are not parallel
have different slice thickness
contain DICOM secondary captured images
have an inconsistent phase count for each slice (time-resolved data sets)
contain invalid or inconsistent image parameters (i.e. width/height, pixel spacing, image orientation
patient, slice thickness, or slice locations
13.1.1 4D Viewer Control Features (Table)
4D VIEWER SPECIFIC COMMANDS
SYMBOL
WINDOWS
MAC
H
H
Y
Y
+/-
+/-
(S)
(I)
(A)
(P)
(L)
(R)
(S)
(I)
(A)
(P)
(L)
(R)
High Quality (bottom left)
Applying a shorter sampling distance while ray casting allows for
capturing finer details within the volumetric data.
Spin
control speed with the fps wheel in the top tool bar
Windowing
a) Use the LMB and the shift key to window.
b) 3 button mouse: press the MMB and move the mouse to fine tune
grayscale settings.
c) Alternatively change window width and center using the histogram
Zooming
Use the mouse wheel to zoom in (scroll down) or out (scroll up)
Phase/Slice Navigation
Open the navigation bar to use the on screen widgets
Panning
Move the cursor over the icon and drag
Rotation
When in clipping or cutting mode, use the 'Rotate Volume' icon.
With the left mouse held, you can rotate the image in all directions.
The center of the view port will be the center of rotation.
Aspect
Navigator: clicking on the navigator in the bottom left corner
switches to different aspects
Clipping the Volume
87
4D VIEWER
When activated, the clip tool displays cones. Grab a cone with
the left mouse button to clip the volume in orthogonal
directions. The process does not affect the actual 3D data, so
the visible volume can be reset at any time.
Axial
C
Cylindrical
C
View
C
Free Form Cut
Ctrl+D
⌘D
Free Form Crop
Shift+Ctrl+D
⌘ D
To open the tool-pop-up, move the cursor to the box in the topmiddle of the viewer frame.
You have the option between Free hand drawing and ClickDraw
3D Threshold growing: move the mouse over your ROI and
drag downwards. (sideways will increase the threshold)
Ctrl+G
Reset View: Resets to default pan/zoom/orientation. (keeps
segmentation and clipping)
Ctrl+E
Reset clipping: resets segmentation and clipping
⌘E
(⌘Z)
Pane opens during cut/crop or threshold segmentation:
Undo: refers to the last step
Revert: resets segmentation (keeps zoom, orientation and
clipping)
Clipping options:
Axial
Cylindrical
View Clip
88
4D VIEWER
Context Menu 4D View Ports
Reset View
⌘Y
Display Volume Frame
⌘F
Display Drawing Tools Popup
Display all Overlay
O
Segmentation
Heart
Coronary Vessel
Left Ventricle
Left Atrium
Coronary Tree (1-Click)
Vessel Tree (1-Click)
Left Ventricle (1-Click)
Aorta (1-Click)
Femoral Artery (1-Click)
Windowing Preset
⌘W
Windowing... ( MR)
Type I
Type II
Type III
Vessel
Min-Max
1
2
3
4
0
Windowing...(CT)
CTA
CT Heart
CT Lung
CT Bone
CT Soft Tissue
Auto Windowing Image Type Min - Max
5
6
7
8
9
0
Export as file...
Export Image
Settings for: Size and format (jpeg, tiff....)
Export Image Multiview
1.
Format (jpeg, png,...) and size


Format (mov.Quicktime,avi)
Copy Image to Clipboard
Export Video Rotation
Export Video Cine
Settings for: Format and Size, Video Speed
Save as DICOM Secondary Capture
Save Single Image
⌘1
Save Rotation Images
⌘2
Save Cine Images
⌘3
Save Cine Rotation Images
⌘4
Unload Volume
Settings for: No. of Images, Rotation Angle
Settings for: No. of Images, Rotation Angle
Clears the frame
89
4D VIEWER
13.1.2 Rendering Options
Select a rendering option from the side-panel
Direct Volume Rendering (DVR)
This technique can be effective at depicting arteries and veins even when these
structures are adjacent.
Maximum Intensity Projection (MIP)
The MIP connects pixels with maximal signal of the blood vessels in three
dimensions, providing an angiogram that can be viewed from any projection.
Angio Rendering:
Surface Rendering:
This technique is mainly used to visualize complex anatomical details.
Background MIP
A fusion between DVR and MIP rendering
Set Background Mask allows for creating a custom Background MIP (can be done
in DVR)
Internal/External View*
* When the volume is clipped or showing a segmented region of interest (e.g. Auto
LA Segmentation), switching to the internal view may display empty content.
Adjust window width/level or switch off segmentation from the context menu,
segmentation option.
90
4D VIEWER
13.1.3
Segmentation Options (CT only)
How to perform automatic segmentation
Select the option from the toolbar Auto menu (CT only)

Heart Segmentation

Left Ventricle Segmentation: For SV and EF run a segmentation in every slice. The following values
will be calculated: EDV (ml), ESV (ml), SV (ml), EF (%)

Left Ventricle (1- Click)

Left Atrium Segmentation
For single -click segmentation, choose the option from the menu (toolbar or context menu), and click
on the respective structure in the volume.
4D viewer context menu with segmentation options
How to adjust an automatic segmentation
Select the Segmentation Controls from the context menu under Segmentation/Segmentation Controls.
Adjust the contrast or volumes by rotating the contrast/volume dial either way: Turning to the right
increases, and to the left decreases contrast/volume area.
Click on Apply, which will re-segment e.g. coronary or LV using the new contrast/volume area setting.
This setting will be remembered. Therefore re-running segmentation will always produce the same
result. If you want to do the segmentation all over again, Reset the segmentation controls and re-run .
91
4D VIEWER
13.1.4 Manual Segmentation
The toolbar offers cutting cropping and growing tools.
How to use clipping and cropping
Select the tool from the tool bar and select a drawing mode from the tool pop-up menu
(default=freehand).
Cut: Drag the mouse cursor to encircle structures you would like to remove
Crop: Drag the mouse cursor to encircle things you would like to keep
To rotate
or pan
the volume while in clipping mode move the mouse over the icons and
drag
How to create a custom Background MIP
A cvi42 specific feature allows the displaying of a segmented structure with a MIP background.
In addition, the background MIP allows continuous growth of the segmented structure e.g. vessels after
segmentation.
In DVR create an image that you would like to use as background MIP via auto-segmentation, growing,
clipping or cutting.
Save the segmentation by clicking Set as Background Mask in the DVR drop down menu.
Now carry on to segment your structures of interest, e.g. vessels. As soon as you click keep the
structure will be displayed isolated with the surrounding clipped away.
Go back to the DVR drop down menu and select Background MIP. This will add the previously saved
MIP and will allow for further vessel growing.
92
4D VIEWER
How to use the growing tool
1
Grow will open a clipping menu next to the color schemes.
2 Move the cursor over the region of interest. A black dot will indicate the
software has detected a structure that can be segmented. A red square will
appear over a structure that has already been segmented.
3 Dragging the cursor downwards will define the region of interest according to
the SI threshold.
4 Dragging the cursor sideways will increase the threshold, taking more SI into
account.
5 The clipping menu to the right allows for the following options:

Define a structure and click Delete (D): click the button several times to continuously delete the
surrounding structures.

Define a structure and click Keep (K): this will isolate the vessel, removing all other structures.
93
4D VIEWER

To continue with the segmentation, add a Background MIP (B) (see above)
Continue segmentation and click Add
In addition you can undo/redo/exit/unclip all
94
4D VIEWER
13.2 Color
Opacity and Brightness: In DVR mode, move the slider or use up/down arrows.
Lighting: In DVR mode different lighting scenarios are available. Changing the lighting modifies the
appearance of surfaces and textures and allows for better definition of certain structures.
Increasing the opacity will lead to a stronger impact of the lighting adjustment on the image.

Ambient Light: simulates surrounding light

Diffuse Light: light that reflects into all directions.

Specular Light: simulates the light reflection on the surface depending on the vantage point.

Shininess: increases the highlights.
Color Schemes: cmr42 and cvi42 provide 6 predefined color schemes (vascular 1-6) and 2 custom
schemes
To save a custom scheme, use the save button in the top tool bar.
95
4D VIEWER
Advanced Transfer functions

Histogram: Within the Signal Intensity Histogram the window range is displayed as a purple shaded area.
The vertical red line marks the signal intensity value at zero.
The window is separated into three horizontal regions, which are shaded slightly differently. The upper
horizontal region is divided into a 3 sections.
1. Top: Dragging the left or right sections on the top of the shaded area allows adjustment of the window
boundaries (i.e. minimum and maximum); dragging the middle section expands or minimizes the entire
window
2. Middel: The middle horizontal section: Dragging up/down changes the window width; left/right changes
the window center
3. Bottom horizontal section, changes the window center

Opacity curves and color palettes: The transfer function maps SI values to a 4-component color lookup
table (i.e. red, green, blue, and alpha) for color-coding of DVR images.
1. Add/Remove: the plus and minus button on the top right lets you add/remove transfer functions. By
default pushing the '+' button will display a triangular opacity curve with white color palette
2.
Clicking on one of the opacity curves in the selection on the top left (above the graph) substitutes
the current opacity curve with the selected preset
3.
4.
Switch between curves: click on the left/right arrow
Invert opacity curves in interior views.
96
4D VIEWER
Color Palette
There are 2 types of color palettes

Global: A global palette applying a color to a specific signal intensity value, thus representing a specific
texture. If Global is checked, moving the window center will only change the opacity curve not the color.

Local: window-center adjustment will reposition the attached color palette, thus changing color and
opacity

Setting the Color Palette
The Color mixer provides a pre-defined color palette. The preset will be positioned relatively to the active
window.

Add a color: double-click in the palette and choose a color from the palette
Mac

Windows
Remove a color: Move the cursor in the palette and with the LMB drag over the bar that you would like to
delete;

Reposition color bar: Grab and drag the bar with the LMB

Change the color of existing color bars: double click on the bar and choose a new color from the palette
Note for Windows Vista and Windows 7 users:
97
4D VIEWER
Using anything other than the Windows Aero Color Scheme might result in images partially refreshed after
certain actions (e.g. after closing context menu, dialogs, and minimizing other windows on top of cmr 42/cvi42).
How to Save and Export 3D/4D Rendered Images
The easiest way to save an image is creating a secondary DICOM capture by dragging it to the thumbnail
panel:
Workspace>Save Workspace will remember all clipping, rotation and the segmentation
More options for saving and exporting are provided in the context menu
98
MULTIPLANAR REFORMATTING (MPR)
14 Multiplanar Reformatting
14.1
Double Oblique
100
14.1.1
Toolbar
101
14.1.2
MPR Control feature
101
14.1.3
MPR Viewer Controls
103
14.1.4
MPR Context Menus
105
14.1.5
Reporting and saving of image captures and measurements
107
How to set up or alter a measurement profiles (groups)
108
How to save and restore and clear measurements
108
How to add multiple MPR frame sets to the report
109
14.1.6
Export/Save MPR Images and videos
14.1.6.1
Toolbar options
How to generate a short axis stack and a long axis reference:
14.1.6.2
14.2
The context menu options
"Navigation" tab
110
110
110
112
113
99
MULTIPLANAR REFORMATTING (MPR)
The Multi-planar reformatting (MPR) technique reconstructs a slice in any position and orientation through
the 3D Volume. It can reconstruct the axial images into coronal, sagittal and oblique anatomical planes but
also it can specify a plane off an oblique image.
The MPR Module provides 2 tabs:
Double Oblique
Free Form Navigation
14.1 Double Oblique
By default there are 4 view ports
Colors of the cross-hairs correspond to the orientation framed in the same color.
The short-cut <M> hides the cutting lines
Axial view (top right blue frame)
Coronal view (bottom left, red frame)
Sagital view (bottom right, yellow frame)
3D reference view (MIP, Surface or Direct Volume Rendering)
MPR Options (bottom left of the interface)
o
o
o
Change the layout
Set Synchronization
Set Reset
.
100
MULTIPLANAR REFORMATTING (MPR)
14.1.1 Toolbar
Reset volume resets clipping and segmentation and zoom and defaults back to the original
volume.
Reslice will save multi-slice images as DICOM or DICOM capture (screenshot). Choose between
parallel or rotationl slicing (see below)
Links the 4D view with the MPR orientation
Pan MPR; Toggles between panning and scrolling
Save layout view. You have the option to Save a DICOM secondary capture or to export the view
as a file (see below: Export/Save MPR Images and videos)
Add to Report (multi frame) allows to add multiple sets of corresponding MPR frames including
mesurements, comments and annotations)
14.1.2 MPR Control feature
Switching Between Viewer Frames
A single LMB click at the top-left corner in one of the 3 viewers brings the view port into focus.
A LMB click anywhere else in the view port will additionally reposition the MPR-center
Panning the MPR centre:
Figure 4: Panning the MPR center
101
MULTIPLANAR REFORMATTING (MPR)
Moving the center point will move the entire image plane through the 3D data
A single left click on the image in the MPR viewer repositions the MPR center.
Adjust the Slab-Thickness:
Slab-thickness handle (colored squares next to cutting line):
Moving the little square up and down next to the MPR plane cross-reference lines allows you to
change the slab thickness
Zero slab thickness depicts thin-slab MPR. Positive thickness uses thick-slab volume rendering. The
slab volume will be displayed in the cross-reference viewer frame.
Slab-thickness scroll bar (see screenshot):
Dragging the scroll bar with LMB increases/decreases the slab thickness using the smallest amount of
data increment available for the loaded volume.
LMB double-click on the scroll bar opens up the Adjust Slab Thickness dialog. The slab thickness can
be entered in mm or set by the multiplicity of the originally acquired DICOM slice thickness.
slabthickness
rotate
102
MULTIPLANAR REFORMATTING (MPR)
Maximize View
Move the mouse cursor to the right top corner until 2 opposing triangles appear, click LMB
14.1.3 MPR Viewer Controls
MPR VIEWER CONTROL FEATURE
FUNCTIONALITY
DESCRIPTION
BUTTONS
MPR display option (bottom left of the interface)
Hide Overlay (G)
Removes tags and overlays
MPR Options
Customize:
- Layout
- Synchronisation
- Reset MPR button
How to adjust/save the Layout
Save Layout View as…
Portrait Layout
Preferences
Switch Layout View
Button on the bottom left of the interface
How to navigate through the 4 D Volume
Adjust Animation Speed
Frame Rate
Rotating the plane
Rotating the colored triangle (e.g. yellow)
located next to the cutting lines will rotate the
respective colored plane (sagittal plane)
around the MPR center
Toggle Slice
Navigation/Panning
To toggle the LMB dragging-behavior
between panning and slice navigation
 Click on the icon
 Click on the slice navigation slider, a
highlighted slider indicates slice navigation
Slice Navigation in panning
mode
 Navigation panel: drag the top, slice
navigation slider (next to the arrows)
 Short cut-key: hold ⌘ (ctrl. (PC), command
(Mac)) and drag
 Preferences/Mouse Wheel Function: change
to
 slice navigation
103
MULTIPLANAR REFORMATTING (MPR)
Enlarge View Frame
 move the cursor to the top right corner
until two opposing triangles appear, do a
left mouse click. Go back via "Back to Main
View' in the top tool bar.
Show Rotation Circle
Rotating the little circle at one o´clock, will
rotate the image in all 3 view ports
Rotating the big circle, rotates the image in
the frame
Orthogonalize Planes
Displays an orthogonal view to selected
orientation
Lock Plane orientation
Locks orientation (respective cutting line
becomes dotted) and will not follow
adjustment in other planes
Rotate View
Rotate Left 90
Rotate right 90
Rotate 190
Flip Horizontal
Flip Vertical
Preset Views
Axial View
Coronal View
Sagittal View
Cranial LAO View
Lateral View
Caudal RAO View
Short Axis View (CT Only)
Long Axis View (CT Only)
Custom View
Slab thickness
 a. Drag the square located next to the
colored cutting lines.
 b. Navigation buttons: bottom slider (below
arrows): drag or double click on the slider
for numeric setting
 c. Keyboard shortcut:
Shift + Ctrl (command)+Mouse Drag
up/down
Slab-thickness can be read in the DICOM tag
(STh)
Panning the MPR center in
MPR view
Click on your region of interest or drag the
cross in the center of the plane
Relocating the MPR center in
the 4D viewer
Single LMB click on the visible surface of the
3D volumetric display
Enlarge View
Click space bar
104
MULTIPLANAR REFORMATTING (MPR)
14.1.4 MPR Context Menus
CONTEXT MENU FOR MPR VIEWER FRAMES
MAIN MENU
Display Text Annotations
Display On-Screen
Navigation
Display MPR Cross
Reference
Display Slab Reference
Windowing Preset
Windowing
SUB MENU
Toggles on-screen buttons
M
Toggles the cutting lines
Toggles the slab-thickness squares next to
the cutting lines
⌘W
1
2
3
4
0
5
6
7
8
9
0
Export as file…
For MR:
Type I
Type II
Type III
Vessel
Min-Max
Edit...
For CT:
CTA
CT Heart
CT Lung
CT Bone
CT Soft Tissue
AutoWindowingImage MinMax
Edit...
Export Image
Export Image Multiview
CopyImageToClipboard
ExportCineCurrentSlice
ExportMovieAllSlicesMultiview
Export Movie All Slices Stacked
Save as DICOM
SUB MENU
⌘1
⌘2
⌘3
⌘4
⌘1
⌘2
⌘3
⌘4
Edit:
Add current Window
Remove Windows
Current Window Default
Reset Default Window
Reset All Default Windows
Exports images and displays
them in a multiview format
(next to each other)
Exports a cine of the current
slice
Exports all slices and displays
them as cines in a multi-view
format
Exports cines and displays them
in a slide-show fashion
Save Single Image
Save Multi-Slice Images
Save Cine Images
Save Cine Multi-Slice Images
Save Single Image (Secondary Capture)
Save Multi Slice Image (Secondary Capture)
Save Cine Images (Secondary Capture)
Save Cine Multi-Slice Images (Secondary
Capture)
Add Frame to Report
105
MULTIPLANAR REFORMATTING (MPR)
CONTEXT MENY OF THE 3D REFERENCE FRAME
MAIN MENU
⌘R
View
F1
F2
F3
Rendering
H
B
Color Schemes...
Spin Volume
Display Volume Frame
Display all Overlay
Display MPR Reference
Clipping...
1-6
9,0
Y
F
O
M
⌘E
C

V
M
⌘D
⌘D
⌘G
Segmentation
SUB MENU
Reset
Internal View
Endoluminal View
Link MPR Rotation
DVR
MIP
Angio
Surface
High Quality
Background
Set Background
Vascular
Custom 1 -2
Unclip All
Axial Clip Plane
Cylindrical Clip
View Clip Plane
MPR Clip Plane
Freehand Cut
Freehand Crop
3D Threshold Growing
Heart
Coronary Tree
Left Ventricle
Left Atrium
Coronary Tree
Vessel Tree (1-Click)
Left Ventricle (1-Click)
Aorta (1-Click)
Femoral Artery (1-Click)
Segmentation Controls
Windowing Preset ⌘W
Windowing MR
Windowing CT
1
2
3
4
5
6
0
5
6
7
8
AutoWindowingImage TypeI
AutoWindowingImage TypeII
AutoWindowingImage TypeIII
AutoWindowingImage MinMax
AutoWindowingImageRegion
AutoWindowingImageRegion MinMax
Edit...
CTA
CT Heart
CT Lung
CT Bone
106
MULTIPLANAR REFORMATTING (MPR)
9
0
Export as file…
Save as DICOM…
⌘1
⌘2
⌘3
⌘4
CT Soft Tissue
AutoWindowingImage MinMax
Export Image
Export Image Multiview: Exports images and displays them in a
multiview format (next to each other)
Copy Image to Clipboard
Export Video Rotation: Exports a cine and displays it as a rotating
volume (Quick Time Photo-JPEG/H.264, AVI)
Export Video Cine (Quick Time Photo-JPEG/H.264, AVI)
Save Single Image (Secondary Capture)
Save Rotation Image2 (Secondary Capture)
Save Cine Images (Secondary Capture)
Save Cine Rotation Images (Secondary Capture)
Unload Volume
14.1.5 Reporting and saving of image captures and measurements
A report panel allows for saving measurements including image captures.
The panel to the right consists of 2 drop down menus:
One menu (gear wheel) allows for defining measurement profiles, lists of values,
that will be assessed on a regular basis and can be linked to a workflow protocol
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MULTIPLANAR REFORMATTING (MPR)
The other menu allows for selecting predefined lists
How to set up or alter a measurement profiles (groups)
To create a new, duplicate, rename or delete an existing group click the gear icon next to groups.
For a new list select New, type a name in the window and click Enter
To add an item to the list, go to the bottom of the panel, type a new label and click (+).
To remove an item, select and click (-).
Save all to protocol will save all the vessel groups into the current workflow protocol (e.g. Default
(CT))
How to save and restore and clear measurements
Select the item in the group you are about to measure. E.g. Ascending Aorta DM.
Use the measurement tools in the toolbox of the respective MPR viewport.*
If you wish you can label a contour in the image for future reference via context
menu/contour labels
Clicking Fill (hot-key F4) will fill in the measurement and record MPR location
including double-oblique images. Alternatively you can simply drag and drop
an image from the MPR viewer
To remove image captures and related measurements from an item, click clear
Review will load a selected item into the viewer, recalling saved MPR locations
You can add the measurements to the report. The clinical report
comprises a report with all custom measurements and associated MPR cross
sectional images. In addition you can save a DICOM workspace that will save all
your images and captures.
*Tipp: maximize the view via pressing the spacebar.
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MULTIPLANAR REFORMATTING (MPR)
How to add multiple MPR frame sets to the report
To report a measurement with an appropriate identifier, the contour for this measurement has to be
labeled: in the analysis frame activate the contour and open the context menu. Select Contour Labels.
Labels will be remembered and compiled into a list in the contour label menu
In the toolbar click the Add to Report (Multi Frame) button
Provide a description
In the Frame page select the frames for the report. Optionally provide a comment.
In the Measurement page items can be annotated.
Go to the Report module to find your measurements for reporting.
Check Use List as My Workflow to save the list for futures reference. In your next patient study the list
of values or items will be preset. The set of frames will be linked to an item by simply selecting it in
the list.
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MULTIPLANAR REFORMATTING (MPR)
14.1.6 Export/Save MPR Images and videos
14.1.6.1 Toolbar options
To save the layout view, click the camera icon and
select your output. You have the option to Save a DICOM
secondary capture or to export the view as a file
Reslice will save multi-slice images as DICOM or
DICOM capture (screenshot). Chose between parallel or rotationl slicing
How to generate a short axis stack and a long axis reference:
a) Click LV automatically creates a 4 CV, 2CV and SAO orientation
b) Double click the view port to change to the desired reference slice
c) Select the Slice Thickness (e.g. 7mm) and Gap (e.g. 3 mm)
d) Set Forward/Backward slices and make sure to cover the entire LV.
e) Check With Ref. Images to generate a reference image in LAO
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MULTIPLANAR REFORMATTING (MPR)
The stack will be appended to the thumbnail panel and could be used for LV function assessment
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MULTIPLANAR REFORMATTING (MPR)
14.1.6.2 The context menu options
Export Image
Export Image Multiview
Export Image/Video in Multi View
You can export either a parallel stack (Parallel option) or images rotated along the y-axis of the selected
frame (Rotational option).
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MULTIPLANAR REFORMATTING (MPR)
The color of the frame corresponds with the orientation you are about to export (here red: the images will be
exported in a coronal view.)
In Parallel multi-slice option, you can modify or limit the number of forward/backward navigation slices,
i.e. moving the target MPR image plane along the view direction by clicking on the up/down navigation
arrows.
In the target frame, adjustment of the slab thickness affects the number of the exported slices.
Slice gap could be specified to reduce the number of slices created.
In Rotational multi-slice option, you can specify either the number of slices or the incremental angle of
rotation*: clicking on the up/down navigation arrows rotates the target MPR plane by the specified angle
of rotation, the other parameter will be automatically calculated.
Example: if the incremental angle of rotation is 15 degrees, the plane is rotated about the y-axis of the
plane by 15 degrees increment and the image is obtained with 15, 30, 45, … degrees rotation with respect
to the original image.
Number of slices * incremental rotation angle= 180 degrees, e.g. 10 slices * 18 degrees = 180 degrees
14.2 "Navigation" tab
Select the MPR viewer that you would like to move into the Navigation sub-module and click the button. Or
drag and drop the viewer on the button
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MULTIPLANAR REFORMATTING (MPR)
Panning: LMB drag outside the circle
Free form navigation: drag within the circle.
Hold the centre of rotation during free-form navigation :
Click the "+" at around 11 o'clock or use the modifier key "Shift"
Slice scrolling: toggle between scrolling and free-form navigation by clicking on the slice navigation
slider.
Use CTRL/Command key to allow accelerated slice navigation.
When in slice scrolling mode, you can still freely navigate initiating your mouse drag in the shaded area,
of the circle.
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VESSELMODULE
15 Vessel Module (Auto plaque)
15.1
Create tab
15.1.1
Segmentation Options
15.1.1.1
117
117
How to perform one-click, semi-automatic vessel segmentation
118
Manual segmentation
118
How to create a centreline via "threshold-growing"
118
How to create a centreline via keypoints
119
How to create a centreline via seed-points
119
How to connect 2 vessel segments
120
How to do multiphase vessel segmentation
121
Edit
How to edit the centreline
15.3
117
How to perform automatic vessel segmentation:
15.1.1.2
15.2
Automatic Segmentation Options
116
Analyze tab
15.3.1
Interface
121
122
123
124
How to perform a stenosis assessment
128
How to perform Plaque Analysis
130
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VESSELMODULE
CPR workflow includes sub modules for creating and editing of vessel segmentations as well as analysis
windows for lumen measurements and coronary artery or valve stenosis assessment.
Auto-plaque assessment requires a separate license.
15.1 Create tab
The Create sub-module provides
Automatic and manual segmentation options
Analysis viewer with NPR navigation for optimal vessel delineation
3D reference viewer
Reporting pane with predefined vessel groups and options to create new or customized vessel reports
Reset view will reset zoom, panning and orientation
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VESSELMODULE
15.1.1 Segmentation Options
Choose between automated segmentation and options that require the definition of a centerline:
by placing start and end seed-points
via 3D region growing
and traceing a centreline manually by placing spline control points
This button will delete all centerlines
15.1.1.1 Automatic Segmentation Options
Autosegmentation Menu
The following fully automatic segmentation options are available via drop-down menu
Coronary Vessels
Aorta
Femoral Artery
Subclavian Artery
Aorta+Femoralis+Subclavian
The following semi automatic (one-click) segmentation options are available via drop-down menu
Coronary Vessels (1-Click): in case fully automatic failes, e.g. due to coronary anomaly
Vessel Tree (1-Click)
Aorta (1-Click)
Femoral Artery (1-Click)
On-screen Options:
In addition, the 3D reference viewport provides buttons for quick access to the most common segmentation
options
How to perform automatic vessel segmentation:
Select an option from the menu.
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VESSELMODULE
For a (1-Click) option, select the vessel in the 3D volume (see below).
The segmented vessels will automatically be displayed, labeled and saved in the report panel in Auto
Result
If you are not satisfied with the segmentation, select the respective vessel in the group and click clear.
You can now use any of the available methods to redo the vessel segmentation
How to perform one-click, semi-automatic vessel segmentation
Select the option from the menu and click on the respective blood vessel in the volume. The centerline
will be automatically extracted.
15.1.1.2 Manual segmentation
How to create a centreline via "threshold-growing"
3
1
2
4
5
In the report panel, select the vessel you are about to segment from the list or define a new item or
group
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VESSELMODULE
(see above: 16.2. Reporting and saving of image captures and measurements).
Determine the size of the blood vessel: Select either Small Vessel to preserve details of fine turning
arteries like the coronaries or Large Vessel to allow quick detection of the ascending/descending
aorta or femoral arteries where details are less of a concern. The system will automatically switch to
Large Vessel if Small Vessel was selected and no ideal path can be detected.
Pick up the 3D Region Growing tool from the toolbar.
Place the cursor over the vessel and drag downwards to extend the vessel, or sideways to extend the
SI threshold
When you are done, click Extract Centerline (E) in the report panel
How to create a centreline via keypoints
A manual method, where a 3D spline curve is drawn with control points. It can be used to draw a
centerline in any structure of interest, i.e. aorta, LV, spine, etc..
Note: The recommended minimum resolution for coronary segmentation is 512 x 512.
How to create a centreline via seed-points
Select the vessel from one of the predefined vessel groups or define a new group/vessel (see chapter
16.2).
Start with selecting Start-End from the toolbar.
Place a seed at the origin of the vessel.
Scroll through the volume and define the end of the vessel with a second seed point. It is possible to
set multiple seed points along the way.
Reposition the MPR center or pan the image back into the center by dragging the image outside the
NPR circle.
Rotate Views and Preset Views offer predefined viewing options.
New Segment allows for coping with stepping artifacts or complete occlusion.
Two segments, that are part of the same vessel and can be viewed together as
one stitched line in CPR viewer (see below).
The blood vessel will be displayed in red in both, the analysis viewer and the
4D reference viewer.
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VESSELMODULE
On-screen buttons for heart and coronary tree segmentation allow to quickly switching between the 2
options.
The centerline will be saved automatically including orthogonal views.
Save Layout view allows to export or to take a secondary capture of the layout. More options
are available in the context menu
Switch to the Edit or Analyze tab for further processing
How to connect 2 vessel segments
In the Create tab clear an existing
centerline, if applicable.
Place a seed and define the
first segment.
Click New Segment in the panel to the
right
Segment the next segment of the same
vessel by placing start and end seed points.
Go to the Edit tab to connect the centerlines, you will see two
segments stitched together. The missing intersection is not indicated.
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Click on the Connect button, this will connect the two segments
together, interpolating what's between the two.
How to do multiphase vessel segmentation
For plaque and stenosis assessment in dynamic cine angiography, the Multiphase Centerline
feature allows for the generation of multiple centerlines of the same coronary artery. Activate the
button (bottom left of the screen)
Create a centerline,
Move to the next phase, make sure you have selected the correct vessel in the Vessel List and create
the next centerline. Repeat for all applicable phases.
Alternatively use the button in the toolbar and forward the centerline to the remaining phases.
.
15.2
Edit
The sub-module provides a straightened CPR view with panning synchronized to the dual CP views
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VESSELMODULE
How to edit the centreline
Select a vessel from the group
To move to a different orientation or display option, use the on-screen buttons:
/
Rotate View /Render Mode (Projected (F1), Stretched (F2)
Click on Draw and simply redraw the
line. To switch to a different drawing mode,
click on the tool pop-up
/
Smooth/Flip centerline tool
The Connect tool joins multiple centerlines into one
Go to the top toolbar (Save Layout-View) or the context menu for saving and exporting options
Switch to the Analyze sub-module for further analysis
Target Zone (The Zone Between Two Brackets):
Reduce Artifacts

Dragging the image through the target zone pans and automatically
rotates the vessel in a way that reduces mirroring artifacts.

When in Draw Centerline mode, you can engage this function by
dragging the outside shaded area of the bracket. Alternatively use the
modifier key "alt"
Panning

Outside the target zone you pan.
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VESSELMODULE

When in Draw Centerline mode panning is locked, you can engage this function by dragging the white line
within the bracket
Rotate

Dragging the image inside the brackets you rotate.

When in Draw Centerline mode, you can engage this function by
dragging the inside shaded area of the bracket.
15.3
Analyze tab
This tab allows to assess stenosis in % and to perform measurements like min/max diameter as well as the
area of the vessel lumen in mm2.
Auto-Plaques* will assess plaque volume and composition as well as the remodeling index.
*requires a separate licence
Warning:
The use of the Auto-Plaque is not FDA approved and is for non-clinical, scientific use only.
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15.3.1 Interface
Analysis
Reference
Report
Marker
Browse/Stenosis
Orthogonal views of selected marker
Analysis viewer to offers a straightened view and and two different viewing displays: Browse and
Stenosis mode .

Switch to a projected or stretched view
Browse
Stenosis
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VESSELMODULE
Browse mode is designed for visual assessment. A scrollable centerline marker shows 5 cross-sectional
images of the vessel. Dragging the yellow square allows for adjusting the distance
between markers
In Stenosis mode you can choose between 1 and 2 reference marker
Centerline Graph displays min./max./average lumen diameter,
lumen area and tortuosity. It will automatically detect the minimum
and maximum point along the centerline graphs.
Lumen: Clicking on the lumen title will bring up a dropdown menu allowing the
user to switch between the different centerline graphs.
cut off
Options item in the dropdown menu allows the user to define the increments (in
mm) for each angle measurement in the tortuosity graph.
Dragging the yellow handle allows to set a cut off, such that
anything above/below the set threshold for lumen and/or that
exceeds the cutoff threshold for tortuosity will be highlighted.
(e.g. for catheter selection (1 Fr = 0.33mm)). Double clicking on
the yellow handle brings up a dialog where the user can specify
a precise cutoff threshold (in mm or degree).
Note: The stenosis graph is calculated based on auto contour detection for each cross-sectional image along
selected vessel centerline. Each image series may require different SI threshold. Please adjust auto lumen
threshold in the threshold tuner to update the stenosis graph accordingly.
The ruler measures the distance between vessel markers along the
centerline
Reference viewer:
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VESSELMODULE
Switch between different views with the on-screen buttons (heart, vessel, endoluminal)
Endoluminal view. To move slowly through the vessel, drag the
stenosis marker in the CPR viewer. Clicking the Play button, will display a
fly through animation of the vessel.
This view can be exported via Context Menu>Export>Export Video
Immersion.
A context menu offers, viewing, rendering, saving, export and more
options
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VESSELMODULE
Report panel:
Vessel
Stenosis
Captures
Plaque
The report panel has three (four with Auto-Plaque) tabs:
Vessel list
Stenosis measurements (see below)
Captures with predefined lists for TAVI planning and z-scores as well as options for custom
measurements
Auto-Plaque : requires a separate licenses and is for non-clinical use only.
3 MPR viewer provide orthogonal views of a selected vessel display (in this example it reflects the
stenosis marker point)
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VESSELMODULE
How to perform a stenosis assessment
3
4
7
8
2
6
5.1
1
3
5.2
5.1- 5.3
5.3
Select the vessel from the list or simply click on the vessel in the 3D reference viewer
Switch to the Stenosis mode and set the number of reference marker
Place the marker via mouse drag, or use the Leison tool from the top toolbar to define an
analysis range: Pick up the tool (LMB-click), go to the CPR viewer and drag the shaded area over the
leison. The upper limit will define the proximal reference, the lower the distal reference.
Activate the automatic vessel Lumen contour detection button
Successively select the reference images and check the respective MPR images for correct orientation.
Measurements will be done automatically
In the report panel click on Stenosis to view the analysis
To make adjustments to the contours you can use the Auto-Contour Threshold Tuner and lower
or increase the threshold.
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VESSELMODULE
Alternatively you can simply double-click the contour, pick one of the contouring options from the
tool-pop-up and redraw or use one of the contour tools from the toolbox (left lower corner of the MPR
viewer).
Threshold adjustment
Manual contour correction
Add to Report after each vessel assessment, it composes a report using values displayed in the
currently selected report tab
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VESSELMODULE
How to perform Plaque Analysis
2
3
4
5
7
6
Load the study into the Vessel module.
Perform auto coronary segmentation in the Create tab
Go into Analyze tab and define the Lesion range by dragging the shaded area over the leison.
To provide a blood pool reference for the automatic threshold
function, click the Aorta Seed in the toolbar and check or define the
aorta seed in the same slice as the LM. It will remember the center of
the circle as the aorta seed point.
Click on auto plaque.
The plaque will be color coded and your report is available in the
Plaque tab of the reporting panel
Add to Report composes a report using the values displayed in
NPR seed window
the report tab.
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Troubleshooting:
3D/4D module cannot be enabled even though the computer has a video card that meets the minimum system
requirements (nVidia 520M GT):
Some laptops (Mac 15", 17", HP, Dell with nVidia) have integrated graphics cards to help save battery life and
dedicated GPU's for Games. Always make sure the dedicated graphics card (GPU) is turned ON and that the
video drivers (windows) are up to date.
Settings for the GPU can usually be enabled in the control panel for the Display or Energy Saver settings.
131
CA SCORING
16 Calcium Scoring
16.1
Toolbar
How to do Calcium Scoring
133
133
132
CA SCORING
Calcium scoring is a method to quantify the plaque load of the coronary arteries.
Post processing for Calcium Scoring requires the detection of calcium and assignment to a coronary
16.1 Toolbar
The toolbar provides 4 buttons to identify Calcium in the different coronary arteries.
The following Region Of-Interest buttons should be selected to depict calcification
Left Main Artery (LM)
Left Anterior Descending Artery (LAD)
Left Circumflex Artery (CX)
Right Coronary Artery (RCA)
Ca Mass calibration factor: Using a phantom with calcium inserts of known mass allows for determination of a
calibration factor for different MDCT scan protocols.
How to do Calcium Scoring

Open the on screen navigation buttons or use your
keyboard arrow keys to scroll through the slices.

Toggle the Overlay Display and scroll through
the volume

When you have detected Ca, select the respective
coronary ROI-button and simply click in the calcified
area.


To re-do the region selection, click again
To re-set all region selections use the Reset
Selection button in the toolbar

To assign calcification to two different
coronaries:

split the lesion with the Ca Scoring Selection Contour ,

select the first matching ROI (e.g. LM) and click into the respective section,

then select the second ROI (e.g. LAD) and click into the other part of the lesion

Add the analysis to your report.
Set the Threshold (default 130) (on the bottom of the reporting panel, underneath the Percentiles)..
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CA SCORING
The calibration factor will be retrieved from the DICOM header or can be entered manually (calibration
factors are specific to scanner, protocol and patient weight)
Volume, Mass and Agatston Score and Agatston Classification determined automatically.
To determine the Percentiles of the patients Agaston Score per coronary, select the ethnic group
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AORTIC VALVE
17 Aortic Valve
17.1
Calculated values............................................................................................................................. 136
17.2
Landmark page ............................................................................................................................... 137
17.2.1
17.3
Annulus page .................................................................................................................................... 139
17.3.1
17.4
How to define the cusp insertion points ........................................................................................ 138
How to measure the aortic annulus ................................................................................................. 139
Ancillary Page................................................................................................................................... 141
17.4.1
How to measure the ostium height .................................................................................................. 141
17.4.2
How to measure the sinus of valsalva ............................................................................................. 141
17.4.3
How to measure the sino-tubular Junction ................................................................................... 142
17.4.4
How to report calcification and additional findings .................................................................. 142
17.4.5
How to add multiple frames and measurements to the report ............................................ 142
17.4.6
How to simulate a device ...................................................................................................................... 143
17.5
Fluoro page........................................................................................................................................ 143
17.5.1
How to identify angulation for fluoroscopy .................................................................................. 143
17.6
Acess page .......................................................................................................................................... 144
17.7
References ......................................................................................................................................... 145
135
AORTIC VALVE
Intended Use
cvi42 – The Aortic Valve modul offers a structured workflow for pre-procedural planning of transcatheter
aortic valve replacement. Accurate measurements of the access path, the aortic annulus, the left ventricular
outflow tract (LVOT) and ancillary measurements such as the distance between the coronary ostia and the
annulus allow for accurate device type and sizing.
17.1 Calculated values
For multiple phases:








Perimeter (mm)
Annulus Area (mm2)
Minimum Diameter (mm)
Maximum Diameter (mm)
Perimeter Derived Diameter (mm)
Area Derived Diameter (mm)
Ellipse Perimeter (mm)
Ellipse Area (mm2)
Ancillary Measurements:
 Ostium height
 Custom measurements
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AORTIC VALVE
Landmark page
The annulus page is designed to identify the annulus plane by defining the cusp insertion points.
According to the recommendations for measurement of aortic annulus dimensions 1 , systolic measurements
(30% of the R-R-cycle) may be preferable to diastolic measurements of aortic annulus size.
The software however allows definition of the basal ring in multiple phases. Landmarks and measurements
will be saved per phase and it is possible to easily switch between the phases in each page.
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AORTIC VALVE
17.1.1 How to define the cusp insertion points
In case you have a multiphase data set, start with selecting the appropriate phase.
Display the annulus plane in the Annulus view port.
Optionally generate a centerline along the Aorta and the LVOT, cutting
through the valve plane.

Activate the Edit Centerline button and set points.
 Deactivate the Edit Centerline button.
 Scrolling in the axial view will now follow the centerline.

allows to delete a centreline
Define the insertion site of each cusp as landmarks for the annulus plane
1.
For a step by step approach
please refer to Achenbach S.,
Determination of the Aortic
Annulus Plane in CT Imaging2
Allows to reset the view
Select a cusp in the Point of Interest pane, move the MPR center in the Annulus view port to the cusp
insertion point and click Define.
To correct, simply click Define again.
Go to the next phase and repeat. You can easily switch back and forth
between the phases by clicking on the phase line or using the arrow
keys.
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AORTIC VALVE
17.2 Annulus page
17.2.1 How to measure the aortic annulus
1.
Measurements will be performed in the annulus view frame.
2.
Optionally maximize the frame for better viewing.. Use the Back to Main View button in the
toolbar to get back.
Choose between different measurement tools:
3.
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AORTIC VALVE
LV Endo- and Epicardial Contour
Tools for manual contouring
Smooth Annulus Contour
Freehand
Round Annulus contour
Contour will be smoothed
Line Contour
Length in mm (LMC, drag and release)
Maximum Length
Minimum Length
Freehand Contour (On/Off)
Area in cm2 and SI
By default the angle measurement will use
Angle Measurement
angles within 180 degrees. Unchecked in the
Preferences it will provide all angles.
By default the Calculate Ellipse Perimeter will
Perimeter control points
measure perimeter and area of a drawn
contour. In addition it will estimate a strict
elliptical perimeter including it's area
Erase annulus contour
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AORTIC VALVE
17.3 Ancillary Page
17.3.1 How to measure the ostium height
Display the ostium in the Double-Oblique frame.
Activate the Ostium Height contour
Drop a point at the height of the otium with a left mouse click. A line measurement perpendicular to
the annulus plane will be performed automatically
Add to Report: Select frame and measurements and provide comments and annotations (s.b)
17.3.2 How to measure the sinus of valsalva
In the oblique axial image display the sinus
Pick up the line contour to measure the diameter
(push the left mouse button, drag and release)
Add to Report: Select frame and measurements and
provide annotations (s.b)
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AORTIC VALVE
17.3.3 How to measure the sino-tubular Junction
Display the junction in the oblique long axis images
Measure the diameter and use the round annulus
contour tool, which will provide min/max diameter
as well as the area
Add to Report: Select frame and measurements and
provide annotations (s.b)
17.3.4 How to report calcification and additional findings
Calcification is associated with a 3-fold increase in vascular complication. Report if calcification is
circumferential or nearly circumferential and/or located at vessel bifurcations along the access path
If a native data set is available a calcium score can be assessed in the Calcium Scoring Module.
In addition, the left ventricle should be evaluated for the presence of thrombi.
17.3.5 How to add multiple frames and measurements to the report
To report a measurement with an appropriate identifier, the contour for this measurement has to be
labeled: in the analysis frame activate the contour and open the context menu. Select Contour Labels.
Labels will be remembered and compiled into a list in the contour label menu
In the toolbar click the Add to report button
Provide a description
In the Frame page select the frames for the report. Optionally provide a comment.
In the Measurement page items can be annotated.
Go to the Report module to find your measurements for reporting.
Check Use List as My Workflow to save the list for futures reference. In your next patient study the list
of values or items will be preset. The set of frames will be linked to an item by simply selecting it in
the list.
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AORTIC VALVE
17.3.6 How to simulate a device
Click the button
Choose a shape
Use the off set to move it up or down
Adjust height and diameter
17.4 Fluoro page
17.4.1 How to identify angulation for fluoroscopy
Scrolling along the optimal viewing curve allows to display the
angels in the synchronized 4D and MPR viewers.
There are preset angles that will be reported
Add custom angles by opening the lock angles in the angulation
pane.
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AORTIC VALVE
17.5 Acess page
If a transapical access route is planned, the position of the LV apex relative to the chest wall and alignment of
the LV axis with LV outflow tract (OT) orientation should be assessed and recorded.
In the long axis double oblique view drag the yellow dot along the preferred access.
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AORTIC VALVE
17.6 References
1S.
Achenbach et al. SCCT expert consensus document on computed tomography imaging before transcatheter aortic valve
implantation (TAVI)/transcatheter aortic valve replacement (TAVR) . Journal of Cardiovascular Computed Tomography
(2012) 6, 366–380.
2Achenbach
S, Schuhbäck A, Min JK, Leipsic J. Determination of the Aortic Annulus Plane in CT Imaging—A Step-by-Step
Approach. JCMG. Journal of the American College of Cardiology; 2013 Feb 1;6(2):275–8.
3Jabbour
A, Ismail TF, Moat N, et al. Multimodality Imaging in Transcatheter Aortic Valve Implantation and Post-Procedural
Aortic Regurgitation: Comparison Among Cardiovascular Magnetic Resonance, Cardiac Computed Tomography, and
Echocardiography. J Am Coll Cardiol. 2011;58(21):2165-2173. doi:10.1016/j.jacc.2011.09.010.
4 Jeroen
J. Bax et al. Open issues in transcatheter aortic valve implantation. Part 1: patient selection and treatment strategy for
transcatheter aortic valve implantation. 1,*, . Eur Heart J (2014) 35 (38: 2627 - 22638
5Holmes
DR, Jr., Mack MJ, Kaul S, et al. 2012 ACCF/AATS/SCAI/STS Expert Consensus Document on Transcatheter Aortic
Valve Replacement. J Am Coll Cardiol. 2012;59(13):1200-1254. doi:10.1016/j.jacc.2012.01.001.
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
18 LV/RV Function Modules
18.1
Bi/Triplanar Module
18.1.1
LV Function Analysis
How to do bi-triplanar LV function and volume analysis
18.1.2
Atrial Volumetry
How to do atrial volumetry in one or two planes
18.2
Multiple Long LAX Module
How to do LV function with multiple radial long axis
18.2.1
18.3
Ventricular volume/mass over time
Short 3D Module
18.3.1
Short 3D Interface
148
149
149
150
150
151
152
154
155
155
18.3.1.1
Customize the interface:
156
18.3.1.2
Thumbnail Grid
156
18.3.2
Global LV function and volume analysis
How to do LV segmentation
18.3.2.1
Automatic Segmentation
How to do automatic LV segmentation
18.3.2.2
Manual Definition of Systole and/or Diastole for LV and/or RV
How to manually define systole and diastole
158
158
158
158
160
160
18.3.2.3
Mitral Valve Plane Correction
161
18.3.2.4
Exclude Atrial Volume
161
18.3.2.5
Papillary Muscles
161
18.3.2.6
Ventricular Volume/Mass Over Time
162
18.3.3
Regional Wall Analysis
How to do wall motion analysis
18.3.4
RV function and volume analysis
163
163
165
How to do manual RV segmentation
166
How to do automatic RV segmentation
167
18.3.5
Atrial volumetry
How to do atrial volumetry in short or long axis orientation
168
168
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
The following approaches are available:
Left ventricle:
2-chamber, 4-chamber and short axis view. (see Module Bi/triplanar LAX)
Multiple radial long axis planes. (see Module Multiple Long LAX)
Parallel SAX stack (see Module Short 3D)
Right ventricle:
Parallel SAX stack (see Module Short 3D)
Parallel LAX stack (see Module Short 3D)
Atria:
Bi/Triplanar : (see Module Bi/triplanar LAX)
Parallel LAX stack (see Module Short 3D)
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
18.1 Bi/Triplanar Module
Intended use:
LV function analysis biplanar in 2CV and 4CV or triplanar by adding a short axis view.
Atrial volumetry in one or 2 planes
WARNING: Bi/Triplanar
For the calculations, the diastolic and systolic phase are assumed to be in the same phase of the
cardiac cycle in all three views. The volume calculation is done per phase. The smallest volume is
assumed to be the systolic volume and the largest volume is assumed to be the diastolic volume. In
case a volume can be calculated for one phase only, ESV and EDV will be displayed as equal and no
calculations will be performed for derived parameters such as ejection fraction.
Endocardial contours must always be on the inside of the epicardial contour, cmr42 does not check
for that.
Calculations in cmr42 are performed based on the current state of contour definition and image
selection. For every change the calculations are updated immediately. It is the responsibility of the
user to decide whether the stage of contour definitions reflects the intended measurement task
before releasing final results.
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
18.1.1 LV Function Analysis
How to do bi-triplanar LV function and volume analysis
Drag and drop the series (2CV, 4CV, SAX) from the thumbnail panel into their respective frames and
adjust viewer properties
Select the slice and phase by using the navigation buttons or the arrow keys on your keyboard
Automatic endocardial edge detection requires the definition of the LV extent:

pick up the LAX LV Extent tool and set two points defining the mitral valve plane, and a third point in the
apex to define the length of the ventricle.

As soon as the apex point has been set, the endocardial contour will be detected automatically. Correct if
necessary.
Draw an epicardial contour
Propagate endo- and epicardial contours: Click on the Segment Myocardial Contours LAX in Slice
button.
Repeat for both phases
Add analysis to Report
.
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
18.1.2 Atrial Volumetry
How to do atrial volumetry in one or two planes
Mono or bi-plane area-length method
You have to define ventricular endsystole first, using the LV extent contour
button.
Next, select the Left or Right
Atrium Contour button and delineate the
atrium: start at the valve, trace the atrial
the border and finish at the valve plane.
The valve plane will be determined
automatically. The yellow dot in the valve
plane can be dragged to adjust the contour
for the shape of the valve.
Add analysis to Report
.
Trouble Shooting
Despite drawn contours there are no results calculated:
Systole has not been determined (see step 1. above)!
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
18.2 Multiple Long LAX Module
Intended use: LV function volume and mass analysis.
WARNING: Multiple Long
The input for multiple long calculations requires a multi-slice series with long axis slices that are acquired
along a central rotation axis. cmr42 and cvi42 check for the presence of these requirements, although it allows
some variance to avoid small aberrations being rejected from the analysis. It is the responsibility of the user
to verify the cutting line of the slices and decide whether the variance in the rotation axis is acceptable.
Depending on the shape of the left ventricle the method in use might not be suitable for all evaluations (e.g.
severe regional wall motion abnormalities), it is the user’s responsibility to verify the suitability of the selected
method.
Endocardial contours must always be within (i.e. on the luminal side of) the epicardial contour, cmr42 does not
check for that.
The volume calculation is performed for every phase. The smallest volume is assumed to be the systolic
volume and the largest volume is assumed to be the diastolic volume. If the volume can only be calculated for
one phase, ESV and EDV will be displayed as equal and no further calculations are done.
Missing contours are interpolated, if possible.
Calculations are performed based on the current state of contour definition and image selections. For every
change in this state the calculations are updated immediately. It is the responsibility of the user to verify that
the contours reflect the desired measurements before releasing final results.
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
Drag the red dot to
correct for mitral valve
plane
"V" Schematic View
RMB click on phase or slice number will
display a DELETE menu
How to do LV function with multiple radial long axis
Drag the radial long axis series from the thumbnail panel into the respective frame and adjust viewer
properties. A perpendicular short axis cine series (if available) will automatically be displayed in the
reference window. The currently active slice is highlighted in yellow.
For a better orientation switch to a schematic view of the study display grid: Clicking on the “V” in the
left top corner switches to a schematic view to help you find the right slice and phase
Select the slice and phase by using the navigation buttons or the arrow keys on your keyboard. Start
and stop a cine loop by clicking on the film icon.
Endocardial Contour:
Start with the definition of the LV extent:
Pick up the LAX LV Extent tool and set two points defining the mitral valve plane and a third point in
the apex to define the length of the ventricle.
As soon as the apex point has been set, the endocardial contour will be detected automatically.
Correct if necessary.
Draw an epicardial contour
manually or
Semiautomatic
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
To forward a contour use the toolbar button Segment Myocardial Contours LAX in Slice button.
Repeat for all slices
Systole and diastole will be indicated by the letters "S" and "D" next to the phase number in the grid.
Contour adjustment:
Scroll through the phases and slices and correct where required.

If necessary correct for the angulation of the mitral valve plane by clicking and dragging the red dot to
adjust it to the mitral valve.

Using the tab-key allows to switch between contours.

The shift-key hides contours and allows to check borders.

A click in the grid on the slice-number column or the phase-number row opens a delete menu
Add analysis to Report
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LV FUNCTION ANALYSIS –MULTIPLE LONG MODULE
Warning messages:
A warning message will be displayed in the results frame (and the exported reports) when:

only one phase has been evaluated,

the number of evaluated slices differs between systole and diastole

less than 3 slices are used for calculations
Note:
It is at the user’s discretion to disregard warning messages by checking the box underneath the analysis
report window, next to Disable Warning Message. As soon as there are alterations to the analysis the
warnings will be re-activated
18.2.1 Ventricular volume/mass over time
Define endocardial and epicardial contours in all phases and slices and click LV volume curve
Peak Ejection and Filling Rate and Peak Wall Thickness can be found in the scientific report
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SHORT 3D MODULE
18.3 Short 3D Module
Intended use:
Using the disc-summation technique this module is able to analyze a stack of parallel images in long or short
axis orientations
Global and regional LV function and volume analysis
Global RV function analysis
Atrial volumetry
WARNING: SA 3D
The volume calculation is done for phases. The smallest volume is assumed to be in systole and the
largest volume is assumed to represent diastole. In case a volume can only be calculated in one phase,
ESV and EDV will be displayed as equal and no further calculations are done.
Missing contours are interpolated, if possible.
Calculations are performed based on the current state of contour definition and image selections. For
every change in this state the calculations are updated immediately. It is the responsibility of the user
to verify that the contours reflect the desired measurements before releasing final results.
18.3.1 Short 3D Interface
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SHORT 3D MODULE
18.3.1.1 Customize the interface:
The module is quite comprehensive and sections that are not part of your clinical routine can easily be hidden
in the interface.
In the protocol pane click on wrench "Edit Protocol".
Here is what you can customize:

View ports like the thumbnail grid or reference viewer

Tool sets or buttons for e.g. RV volumetry or the features for extended LV function analysis (View
Regional Function, View LV volume curve)

Options menu, offering the following feature
- Manually define diastole and systole.
- Use Basal and Apical Gap for Volume Calculation: This applies to a stack with a defined gap. Checked,
the software will add half of the gap to the slice thickness of apical and basal slice
Save your settings
The protocol pane and the thumnail panel can be hidden by clicking on the icon on the left
and
right
bottom corner. They can still be accessed by hovering the mouse over the very left and right frame border.
18.3.1.2 Thumbnail Grid
The thumbnail grid represents images of all slices and phases that are contained in a parallel stack.
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SHORT 3D MODULE
Optionally, the display can be changed to a schematic view click the "V"
Switch display
RMB click on phase
number
RMB click on slice
number
Option to manually define
Diastole and Systole
Right mouse button click on a phase number opens a menu
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SHORT 3D MODULE

to delete contours

to manually define systole and diastole. That requires to check the respective box in the option menu

to save a secondary DICOM capture of systole and diastole
Right mouse button click on a slice number or a table cell will open a Delete menu for the respective slice
or image.
18.3.2 Global LV function and volume analysis
How to do LV segmentation
Drag short axis series into the analysis frame.
A perpendicular long axis cine series (if available) will be automatically displayed in the reference
window, highlighting the selected slice in yellow. Starting version 5.3.0, an uneven phase count will be
accepted.
Scroll through the phases and identify diastole and systole
For border delineation select a contouring tool
use the semi-automatic options for endo
,
and epicard.
as well as a contouring mode
or
(please refer to the chapter
Contouring Drawing and Labeling)
Switching to a schematic view in the thumbnail grid (click on the “v”), provides a better overview of
existing contours. In addition it allows for deleting certain contours (RMB click). Current images are
framed in green.
To move to the next slice, use the on-screen navigation buttons or the arrow keys on your keyboard,
or click on the respective image in the grid.
Repeat for all applicable slices
18.3.2.1 Automatic Segmentation
Specific to the Short 3D module is the automatic contour detection that will perform a contour detection for a
group of images.
How to do automatic LV segmentation
Centre your LV, so that the yellow target point is in the middle of the left ventricle.
Program the automatic contour detection button: The button is located in the top toolbar. It can
be programmed to perform edge detection for multiple slices/phases or the entire stack at once.
A RMB click opens a menu:
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SHORT 3D MODULE
Detect endo, epi or both contours for the current phase
Detect endo, epi or both contours for the current slice
Detect endo, epi or both contours for the entire stack
Drag the mouse to the desired option and release the button.
The image of the icon will change according to the selected function.
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SHORT 3D MODULE
Define your analysis range:
If your stack has slices beyond the left ventricle, they
have to be excluded for the automatic LV
1
segmentation.
In the reference frame, open the pencil box and select
3
the LAX LV Extent contour.
Using the navigation buttons, select end-systole.
The LAX LV Extent contour tool allows to set 3 points
1
2
(= 3 LMB clicks):
The first two points define the mitral valve plane and the third point has to be placed at the apex (subepicardial). Make sure the blue base line is in close proximity to the first, basal slice.
Slices/images that will be excluded from analysis are highlighted in grey in the thumbnail grid (see image
above)
Repeat for end-diastole.
Alternatively, use the Forward the LAX range contour (top toolbar).This will propagate the slice
selection to all phases. Start the cine loop to check the registration. To correct, double-click on the blue tbar and adjust the points
Draw a reference contour for diastole and systole: Before you click the automated edge detection it is
recommended to provide a reference contour for the endo- and epicardial borders in a midventricular slice.
Trigger edge detection: LMB click on the automatic contour detection button will trigger the edge
detection
The software will pick the the phase with the largest (diastole) and the smallest volume (systole) and mark
them with the letters "S" and "D" next to the phase number in the grid.
18.3.2.2 Manual Definition of Systole and/or Diastole for LV and/or RV
In case you would like to change the automatically detected phase for systole and diastole (largest and
smallest LV volume) you can do the following:
How to manually define systole and diastole
In the Option menu, check Manual Definition of Diastole and Systole
If you can't see an Option menu, click the wrench in the protocol pane and switch on the display.
Select the phase, then RMB click on the phase-number
LMB click on Systole/Diastole to overwrite the automatic selection
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SHORT 3D MODULE
Note: The setting for Manual Definition of Diastole and Systole will be remembered and no calculation
will be processed unless you manually define diastole and systole. If this is not intended for all your
analyses, uncheck this option after you are done!
18.3.2.3 Mitral Valve Plane Correction
Visually: Identify the most basal slice of the left ventricle and/or the outflow tract:
Start cine by clicking on the film icon in the analysis window and watch cine in the reference window
(carefully control the slice position in systole to avoid accidental inclusion of left atrial volume).
Mitral valve plane correction button: LMB Click on the icon will display two more reference
windows.
Using the CrossReference display, define the
plane in two orthogonal
orientations.
A correction will automatically
be calculated.
18.3.2.4 Exclude Atrial Volume
Use the exclude area tool to exclude atrial volume in mitral plane.
18.3.2.5 Papillary Muscles
By default, the automatic contour detection will include papillary muscles in
mass calculations and exclude them from the lumen.
Exclude Papillary Muscles

Per Image:
To exclude papillaries and trabecular structures in the current
image use the Exclude Papillars tool.
An orange contour displays the endocardial contour without papillars.

For all Images:
Change your settings to exclude papillary and trabecular structures
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In the Preferences/Contour menu:
Check "Use Rounded Endocardial Contour". Using automated edge detection, the software will apply a
rounded contour, cutting off trabecular structures and/or papillaries.
De-select Detect papillary muscle contours to turn off the detection of papillaries within the LV lumen
(pink contour)
Include Papillary Muscles

Manually in each image
To include papillary muscles in the current image use the SA
papillary muscle contour tool. The LV mass calculations will add
them to the mass and subtract them from LV volume.
A warning line in red will be added to your report in case less
than 3 slices have been used for calculating the volume of the
papillary muscles.

For all images using automated (and thresholding) segmentation methods
To include papillary muscles, not connected to the compact wall, go to the Preferences/Contour and check
Detect papillary muscle contours.
18.3.2.6 Ventricular Volume/Mass Over Time
If you have endocardial and epicardial contours in all phases, you have
the option to view a LV volume curve.
A click on the volume curve button will display a
graph next to the study display frame.
A warning message will be displayed in the results frame (and the
exported reports) if:

only one phase was evaluated,
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SHORT 3D MODULE

the number of evaluated slices differs between systole and diastole, or

less than 3 slices are used for calculations.
Peak Ejection Rate and Filling Rate and Peak wall thickness will be reported in the Scientific Report
(Report Module)
18.3.3 Regional Wall Analysis
Myocardial thinning and wall motion abnormalities are important indicator for suspected impaired function.
(myocardium < 4 mm is unlikely to be viable).
Peak diastolic wall thickness will be reported in the scientific report
How to do wall motion analysis
Define the analysis range: Define length of anatomical long axis using the LA LV Extent
Contour button. (see above)
The purpose of this contour is
a.) to select the slices that shall be included into the analysis and
b.) to assure displayed polar maps reflect the entire left ventricle. Polar Maps will display a grey ring if
o
slices do not cover the entire ventricle or
o
the gap between slices is too large for interpolation
o
there are missing contours in existing slices
Define reference points for the segmentation: In the analysis window select a midventricular slice and set the points at the anterior and inferior insertion of the RV.
The two reference points define the septum, whereas
the septal part will be accounted as one third of the
total circumference.
The points will automatically be forwarded.
Note: The segmentation points don't have to be
adjusted in the remaining images.
Reference Points
To move the point within the image, grab and shift it.
To re-do the entire phase or stack, delete the point
(Context menu: Delete…/DeleteContour Series) and
reposition.
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SHORT 3D MODULE
Display Polar Map: To view the polar maps click the View Regional Function button
Define Segmentation:

Chords: Range between 2 and 100 chords. (segments will be counted clockwise)

AHA segmentation: Volumes per AHA segment will be reported in the Scientific Report
AHA segments and corresponding
territories (segments are defined
counter-clockwise)
Using chords, segments are defined
clockwise. Hovering over the segment will
display the respective value (they are
reported in the scientific report).
Choose the value you would like to display in a Polar Map

Wall Thickening

Wall Motion

Wall Thickness for Diastole and Systole
Note: max. wall thickness is reported in the scientific report
LMB Click on the polar map will synchronize 4D Visualization and display the parameter
RMB click allows to export the polar map
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SHORT 3D MODULE
Wall thickening (%), Wall Motion (mm)
Wall Thickness (mm) for Diastole and Systole
18.3.4 RV function and volume analysis
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SHORT 3D MODULE
How to do manual RV segmentation
Verify that the right ventricle is in the center of the frame by panning the image, so that the yellow
seed point is in the center of the RV.
To determine the tricuspid valve plane open the 3 reference viewer and drag the applicable images
into the frames.
Select the LAX RV Extent tool and define the plane as well as the length of the RV.
Turn on the cross-reference lines for better orientation. Clicking one of the reference windows
will highlight the respective plane in yellow in the analysis viewer. Vice versa, the slices will be
highlighted in yellow in the reference viewer.
Select phase and images for evaluation using the navigation buttons or run the cine by clicking on the
film icon.
To be able to view a cine during evaluation, use the floating viewer (see chapter 6)
Contours can be drawn and or corrected freehand (default) or by using a specific drawing mode e.g.
Click-Draw mode or Threshold Segmentation (preferred if you have good contrast) mode
Tip:
Draw a rough endocardial contour, sparing the septum.
Next, use the Segment RV Endocardium to grow the contour towards the endocardial edge (press
and hold)
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SHORT 3D MODULE
Exclude papillary muscles from the volume: go to Preferences>Contours> Detect Papillary Muscle
Contours. This setting will affect all automatic and semiautomatic edge detection.
To include papillaries for each image individually, use RV Papillary muscle Contour.
For mass calculation, draw an
epicardial RV contour: You will
find the contour button for the RV
epicardial contour by clicking on
the white arrow.
Repeat for all slices you want to include in the analysis.
Add analysis to Report
.
Note: Make sure to always use the same technique, either in or exclude papillaries and/or delineate
trabecle. Left and right SV should match! Follow-up results done with a different contouring technique
can mimic deterioration!
How to do automatic RV segmentation
Verify that the right ventricle is in the center of the frame by panning the image, so that the yellow
seed point is in the center of the RV.
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SHORT 3D MODULE
For automatic endocardial RV detection, make sure you have defined the tricuspid valve plane in
systole and diastole
Set the automatic RV contour detection button to the desired option:
Provide a reference contour in systole and diastole.
Release the button to run the contour detection.
Click space-bar key on your keyboard to get a multi-view display
Click RV volume curve for a time resolved volume analysis
Double-click a contour for correction. Do a right mouse-click to open a contextual contour menu.
Click the Add to Report button
18.3.5 Atrial volumetry
How to do atrial volumetry in short or long axis orientation
Drag a stack of parallel images, long or short axis, into the analysis frame.
The atrial volumes will be reported for LV systole and diastole and therefore require the definition for the
LV endsystolic and enddiastolic phase.
If there is no LV analysis applicable, you can manually define the phases. Please refer to the chapter
"Manual Definition of Systole and/or Diastole for LV and/or RV".
Click on the SAX Left Atrium Contour tool to trace the border of the left atrium.
use the SAX right Atrium Contour tool for the right atrium.
The software will report ESV, and EDV for the right and left atrium
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TISSUE CHARACTERIZATION
19 Tissue Characterization Module**
19.1
Global Late Enhancement and T2 Imaging ............................................................................ 170
19.1.1
Analysis of LGE and T2 Images .......................................................................................................... 171
19.1.1.1
Customizing the Module to Your Needs ...................................................................................................... 171
How to do scar and edema analysis in ischemic disease ...................................................................................... 171
19.1.1.2
Myocardial Reference and Threshold Settings ........................................................................................ 172
How to do edema analysis in non-ischemic disease ............................................................................................... 175
19.1.1.3
Areas with 'No Reflow' (Add Myocardium to the Enhanced Volume) .......................................... 176
19.1.1.4
Greyzone Analysis................................................................................................................................................. 176
19.1.1.5
Salvaged Area at Risk .......................................................................................................................................... 177
19.2
Regional LGE and T2 analysis and assessment of transmurality .................................. 177
How to do segmental scar and edema analysis ......................................................................................................... 178
How to assess transmurality ............................................................................................................................................. 178
How to display a greyzone polar map ........................................................................................................................... 179
19.2.1
19.3
Analysis of Phase Sensitive Sequences (PSIR) ............................................................................. 180
Early Enhancement Analysis....................................................................................................... 180
How to do contour definition in Early Enhancement images ............................................................................. 180
169
TISSUE CHARACTERIZATION
cmr42 and cvi42 provide four adjustable viewer frames for determining various tissue characteristics by CMR
methods (Late Gd Enhancement=LGE; T2-weighted CMR; Early Gd Enhancement=EGE).
The viewer layout is customizable, depending on your protocol (please refer to the chapter “Set Up/Customize
Tools and Working Modules”)
19.1 Global Late Enhancement and T2 Imaging
LGE is a T1 sensitive imaging technique that depicts contrast agent that diffuses freely in interstitial space.
The distribution volume of contrast agent in damaged or dead tissue, around 10 min after application, is
increased in acute and chronic MI, as well as in areas of fibrosis due to other pathology such as myocarditis or
cardiomyopathy.
T2 weighted, black blood images have a strong fluid weighting, with no signal from the blood. This method
has become established to diagnose edema that occurs in inflammatory conditions, such as myocarditis or
acute myocardial infarction.
Next to cine and stress perfusion imaging, LGE and T2 imaging are the most important methods for the
assessment of viability
Imaging starts around 10 min after contrast application.
Postprocessing for the analysis of LGE and T2 weighted images images include:
The definition of endo- and epicardial borders,
The definition of healthy myocardium as an area of reference
The definition of a threshold to depict signal enhancement
The definition of microvasular obstruction
Setting a threshold for peri- infarct “greyzones” .
Segmentation to generate a Polar Map View
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TISSUE CHARACTERIZATION
19.1.1 Analysis of LGE and T2 Images
19.1.1.1 Customizing the Module to Your Needs
The module allows assessment of multiple tissue characteristics. Not all of them are used in the clinical
routine.
Here is what you can customize:
Turn on/off view ports
Select tool sets or buttons
Select additional analysis such as greyzone
Turn on/off an option menu
Set your preferred threshold algorithm
How to do scar and edema analysis in ischemic disease
Drag and drop series into the frames marked “Late Enhancement” and “T2” respectively.
Derive existing contours via Context Menu/Contours/Derive Cardiac Contours. Correct if needed. If no
contours are present, synchronize contour drawing, and draw endocardial and epicardial contours
for each slice
Synchronize Contours (button in the top toolbar): Provided that T2 and LGE images have the
same slice location contours will automatically be copied to the other frame. You can refresh the contour
synchronization by altering the contour slightly.
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TISSUE CHARACTERIZATION
Choose a threshold algorithm and define a reference if needed. (see below for more detail 21.1.1.3).
Toggle the Overlay Display to display a color overlay for scar and edema. (For T2 ratio please see
below 21.1.1.4)
Use the Exclude Enhancement contour in case of e.g. artifacts.
Quantify MVO (see below for more information)
Click on Display Result to view the analysis
Add measurements to report by clicking the Add to Report button
.
In the Preferences/Reporting menu, you can choose if you would like to display (default) or hide the
threshold contours on your report images.
LGE and T2 weighted image: Contours are synchronized; Color overlay depicts scar
(yellow) and edema (blue)
19.1.1.2 Myocardial Reference and Threshold Settings
Except for choosing Autothreshold, or the Manual settings, where you use the histogram to determine the
threshold, you have to draw a myocardial reference ROI in every slice.
The threshold will automatically be applied to all slices, except for the Manual per Slice setting.
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TISSUE CHARACTERIZATION
Preferred thresholds for LGE are

Infarct 5 SD over remote myocardium

Inflammatory diseases 2-3 SD over remote myocardium

Hypertrophic CM 6SD over remote myocardium
Preferred threshold for T2 imaging:

2 SD over remote myocardium
Preferred threshold for Greyzone analysis:

2-3 SD over remote myocardium (SD for the greyzone has to be below the SD for fibrosis)
Drop Down Menu options are:

mean +2 to +10 x SD

mean -2 to -10 x SD

FullWidthHalfMax

AutoThreshold

Manual per Slice: threshold will be set manually, using the histogram for each slice separately

Manual

Enhancement ROI
To enable more threshold options, go to the Option menu at the bottom of your screen.
Automatic thresholding:
Autothreshold does not require to define an area of reference, this will be done automatically. It uses the
OTSU algorithm. This algorithm finds the point that best differentiates remote from enhanced
myocardium.
Standard Deviations
The drop Down Menu provides SD from +2 to 5 (+10 in the extended Option) and -2 to -5 ( -10)
From the toolbar select either the SAX Myocardial Reference tool and define a region of visually
healthy myocardium or
You can use your defined myocardial reference for all slices by checking Use Reference ROIs from Nearest
Slice in the option menu.
use the Segment Reference ROIs button to automatically detect remote and enhanced myocardium
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TISSUE CHARACTERIZATION
Note:
Using the Segment Reference ROI button will provide 2 contours:
blue = is the myocardial reference, when you are working with a defined threshold.
pink = is the myocardial reference, when you are working with the Full Width Half Max, which requires a
reference in the enhanced area. This does not segment scar
Autothreshold
mean+5xSD,
mean+5xSD,
FullWidthHalfMax requires to define a ROI within the brightest area
of the enhanced myocardium.
For Manual threshold settings toggle the Histogram Display
(toolbar) and move the slider. The threshold to best differentiate remote from enhanced myocardium lies
between the bell-curves of the lowest and highest signalintensities
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TISSUE CHARACTERIZATION
Manual per Slice setting requires to set the threshold for each slice separately
Enhancement ROI: This contour allows to directly delineate the enhancement
on the base of visual assessment.
Use the SAX Enhanced Area Reference contour tool and trace the
enhancement in every slice.
How to do edema analysis in non-ischemic disease
In non-ischemic heart disease edema as well as scarring does not adhere to perfusion territories and will be
found in a more diffuse pattern. In this case, a skeletal muscle reference will be defined outside the heart
muscle (e.g. m. serratus anterior) instead the myocardial reference and a T2 ration will be calculated.
Select the Skeletal Muscle Contour tool and draw a contour within skeletal muscle. The global
signal intensity ratio will be quantified by dividing the myocardial signal intensity by that of the
skeletal muscle, with a ratio value of > 2 is typically indicating edema.
The percentage as well as the SI ratio will be reported on the right bottom corner of the frame.
Tip to verify skeletal reference position
An image acquired with an SSFP sequence or T1-weighted image may be used to verify the correct
position of the contour within the skeletal muscle. You can drag and drop such an image into the floating
frame.
Activate the T2 Ratio Overlay.
The color will depict a ratio between 1.2
(yellow/green transition) and 2.0 (green/blue
transition)
Repeat for all slices.
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TISSUE CHARACTERIZATION
WARNING: Automatic Contour Detection
The expected input for the volume calculation in this module is a series containing parallel slice in the
short axis direction.
Endocardial contours must always be inside the epicardial contour. cmr42 and cvi42 do not check for
that.
In case of missing contours in one slice linear interpolation is done if possible.
Module calculations in cmr42 are in generally done based on the current state of contour definition and
image selections. For every change in this state, the calculations are updated immediately. It is the
responsibility of the user to decide whether the stage of contour definitions reflects the desired
measurement task before releasing final results.
19.1.1.3 Areas with 'No Reflow' (Add Myocardium to the Enhanced Volume)
To quantify a 'No Reflow Area’ (depicting MVO - micro vascular obstruction), use the
No Reflow Contour button.
The no-reflow areaThe contour doesn't have to be exact, roughly draw a contour around
the region with low signal. Within the contour, (only) the areas with low SI will be added to
the late enhancement region.
Trouble-shooting: No-reflow area is not added to the calculation.
The reason might be that either there is no-reflow or you choose the manual thresholding
and your threshold is set to "0".
19.1.1.4 Greyzone Analysis
Infarct border regions reflect a mixture of fibrosis and viable myocardium and has been associated with
increased susceptibility to ventricular arrhythmias.
Greyzone Analysis calculates the volume/area of the peri-infarct area with intermediate signal intensity
providing the following threshold options:

Threshold: 2xSD + mean SI to 5xSD + mean SI of remote myocardial area

Threshold: 10% max SI to 40% max SI of enhanced myocardial area

Threshold: peak SI of remote myocardial area
The grey zone will automatically be displayed in a color overlay
The upper threshold is given by the threshold for the core region.
Note: Areas within MVO that have the same SI as the greyzone will be displayed as such.
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TISSUE CHARACTERIZATION
19.1.1.5 Salvaged Area at Risk
The salvaged area of risk will be measured as therapy control after
intervention. Using the results of LGE and T2 segmentation, calculation will
be done automatically by subtracting scar from edema volumes.
You will find the quantified area at risk in the result pane (click on the
Display Result button).
Note:
It will not be calculated in case

slice locations are not matching

number of slices are not matching

there is a difference of myocardial volumes > 10%
19.2 Regional LGE and T2 analysis and assessment of transmurality
Click to view
Select Parameter and Segmentation
Toggle Polar Map
button.
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TISSUE CHARACTERIZATION
How to do segmental scar and edema analysis
Set Segmentation points: Position at the anterior and inferior insertion point of the RV
ventricle in a mid-ventricular slice. It will automatically be forwarded to all other slices and phases.
To move the point within the image, grab and move it. To redo the entire stack, delete and re-draw the
point.
Define length of anatomical long axis using the LAX Extent contour button
.
The purpose of this contour is to
a) select the slices that shall be included into the analysis
b) ensure displayed polar maps reflect the entire left ventricle
In end-systole draw a line between the mitral valve plane and the left ventricular apex.
Slices beyond the range will not be included in the Polar Maps.
Segments will be greyed out in case
slices don´t cover the entire ventricle
the gap between slices is to big for interpolation
there is input missing for that particular slices (check contours, reference ROIs, segmentaion points)
Select Parameter from Drop Down Menu
Relative Enhanced Area: The enhanced area can be divided into a user-defined number of segments
(range 3-100).
AHA segment model can be applied by checking the "Display AHA Segments" box. The result is displayed
as the ratio non-enhanced/enhanced area
How to assess transmurality
Repeat step 1-2
Select one of the following from the drop down list

Maximum Transmurality: the maximal transmural extent of segments with late enhancement will be
calculated for 100 segments only (it will not be reported in an AHA-segmentation display since segments
are too large and mav eraged percentages would not provide an accurate picture)
To view a percentage transmurality select one of the display options below and set the transmurality
percentage using the arrow keys to the right.

Transmurality offset
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TISSUE CHARACTERIZATION
Enable Extended Options

Maximum Transmurality (endo): Filters for segments where, late enhancement originates subendocardial.

Transmurality (endo) offset: applying an offest of e.g. 75% (default) will display all segments that have a
transmurality >75% in black, and segments with a tranmurality <75% in green
How to display a greyzone polar map
Repeat step 1-2
Select Relative Greyzone from the menu (make sure you
have defined a threshold for the greyzone and activated
the analysis option)
Enhanced Area
Maximum Transmurality
Maximum Transmurality (endo)
25% Transmurality (offset)
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TISSUE CHARACTERIZATION
19.2.1 Analysis of Phase Sensitive Sequences (PSIR)
Phase-sensitive image reconstruction results in reduced need for precise choice of TI and more consistent
image quality. But there are less greyscale values and results might differ between magnitude and psir.
McAlindon E, Pufulete M, Lawton C, Angelini GD, Bucciarelli-Ducci C. Quantification of infarct size and myocardium at risk:
evaluation of different techniques and its implications. European heart journal cardiovascular Imaging. 2015;16(7):738–746.
In phase sensitive images the histogram is shifted towards higher signal intensities. For proper analysis the SI
have to be normalized to the Myocardium.
If the Checkbox is not available, go to Edit in your protocol pane and click on the little “x” on the right.
Activate in Phase
Sensitive images
19.3 Early Enhancement Analysis
The early enhancement method uses T1 weighted images where image acquisition starts immediately after
contrast application
Indications for Early Enhancement Imaging amongst others are

Inflammation (hyperemea)

Microvascular Obstruction

Intracardiac Thrombus
How to do contour definition in Early Enhancement images
Draw endocardial and epicardial contours in T1 pre and post contrast images.
Define a skeletal reference
Repeat for all slices.
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TISSUE CHARACTERIZATION
In case of bad image quality, you can still assess the Early Gadolinium Enhancement Ration (EGER)
by using the Myocardial Contour tool
To View analysis results click the Display Result button
.
A global signal intensity ratio (EGER) of myocardium over skeletal muscle > 4 or an absolut myocardial
enhancement > 45% is consistent with myocarditis
Add measurements to report using the Add to Report button
.
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T2* MODULE
20 T2* Module
20.1
Assessment of T2* Times
20.1.1.1
Customizing the module to your needs
How to do T2* Analysis
20.1.2
Options Menu
184
184
184
186
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T2* MODULE
Intended use:
Cardiac involvement in siderotic cardiomyopathies can cause arrhythmia and/or congestive heart failure and
indicates a poor prognosis. The module allows for the analysis of T2* values for disease monitoring and
guiding chelation therapy
20.1 Assessment of T2* Times
20.1.1.1 Customizing the module to your needs
To adapt the module to your requirements click the wrench (Edit protocol) in the Protocol pane. Here is what
you can customize:

Tool sets

Color map options

Decay curve settings
After customization save your settings!
How to do T2* Analysis
For global T2* times, draw an endocardial and an epicardial contour for the assessment
of global T2* values
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T2* MODULE
Draw a ROI contour in the septal wall for regional T2* values
Forward contours to other images within the series.
Check contour in every image and correct if necessary (turn off the Forward Contours button)
T2* values will immediately be displayed, as well as the
absolute iron content (1.5 Tesla only).
Normal :
52+16 ms
Reduced :
cutoff: 20 ms
Severe :
<10 ms
Anderson LJ, Holden S, Davies B, Prescott E, Charrier CC, Bunce NH,, Firmin DN, Wonke B, Porter J, Walker
JM, Pennell DJ. Cardiovascular: T2-star (T2*) magnetic resonance for the early diagnosis of myocardial iron
overload. Eur Heart J 2001;22:2171–2179.
T2* decay curves will immediately be displayed, choose a fitting algorithm (non linear=default) from
the context menu.
Toggle color map on
Choosing a lower threshold for the R2 and a higher error
tolerance for T2* will include more pixel into the
colormap.
Create DICOM Map
T2/T2*
Color
0 - 10
Dark red
0 – 25 ms
Red
25 – 40 ms
Yellow
40 – 55 ms
Green
55 - 80 ms
Blue
80 ms and above
Blue
Optional map output for pixelwise fitting in
grayscale. In addition to the grayscale map a R2 map will be created. You will find both maps combined in
one series. The will be appended to your thumbnails.
Reference: Taigang He, Peter D. Gatehouse, Paul Kirk, Raad H. Mohiaddin, Dudley J. Pennell and David N. Firmin
Myocardial T*2 Measurement in Iron-Overloaded Thalassemia: An Ex Vivo Study to Investigate Optimal Methods
of Quantification Magnetic Resonance in Medicine 60:350–356 (2008)
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T2* MODULE
20.1.2 Options Menu
Error Threshold Options

Exclude R2: The coefficient of determination indicates the strength of the correlation between the curve
fitting logarithm and the data points (default is 0.7). R2 should be > 0.99

Max Error: Adjusting the error tolerance changes the allowed maximum error of the T2* times, for which
the result of the fitting should be displayed (default 100%) When the T2* map is generated, any pixels
that have higher than the allowed accuracy, or higher than the error threshold selected, will be set to a
value of zero.
Fitting Options

Nonlinear (default)

Linear

Linear Weighted
Fitting Correction methods

Truncation (default): Uses the mean value of the background noise (purple contour) as a reference and
truncates all data below that value. The truncation model was shown to produce more reproducible and
accurate T*2 measurements.

Baseline subtraction: noise is directly subtracted from each echo time image.

Three parameter fit: an offset is added to the curve fitting equation to account for noise and artifacts.
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21 T2 Mapping
21.1
T2 Measurements ........................................................................................................................... 188
How to do a T2 analysis ....................................................................................................................................................... 188
21.1.1
T2 Options menu ...................................................................................................................................... 189
21.1.2
Motion Correction.................................................................................................................................... 189
How to apply a motion correction T2 series .............................................................................................................. 189
21.2
T2 Map ................................................................................................................................................ 190
How to analyze T2 maps ..................................................................................................................................................... 191
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T2 MAPPING MODULE
T2 mapping quantifies T2 of tissue, which directly reflects free water content and thus is a very accurate tool
for identifying myocardial edema, overcoming limitations of standard T2-weighted imaging (susceptibility to
motion artifacts, inconsistent image quality among scanner models).
The module consists of two pages
T2 Measurements: that allow for the assessment of T2 times
T2 Map: and the analysis of a T2 map.
21.1 T2 Measurements
How to do a T2 analysis
Segment the myocardium for global T2* values. Forward the contours via context menu.
Select one of the ROI contours for the assessment of a specific region of interest. The ROI can be
forwarded with the Forward contour button
Global and regional T2 times will be calculated immediately.
The decay curve will be displayed. A right mouse click in the graph allows to change the display or to
export the graph
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T2 MAPPING MODULE
Add calculations to your report.
21.1.1 T2 Options menu
Error Threshold Options

Exclude R2: The coefficient of determination indicates the strength of the correlation between the curve
fitting logarithm and the data points (default is 0.7). R2 should be > 0.99

Max Error: Adjusting the error tolerance changes the allowed maximum error of the T2 times, for which
the result of the fitting should be displayed (default 100%) When the T2 map is generated, any pixels that
have higher than the allowed accuracy, or higher than the error threshold selected, will be set to a value
of zero.
Fitting Options

Nonlinear (default)

Linear

Linear Weighted
Fitting Correction methods

Truncation (default): Uses the mean value of the background noise (purple contour) as a reference and
truncates all data below that value.

Baseline subtraction: Noise is directly subtracted from each echo time image.

Offset: An offset is added to the curve fitting equation to account for noise and artifacts.
Create T2 map upon loading: Automate DICOM map generation by checking the box for Create map
upon loading. Save this step to your protocol.
21.1.2 Motion Correction
How to apply a motion correction to T2 series
Make sure you have endo- and epicardial contours in all images.
Set the Segmentation point.
Select the image with the best contrast and enter the phase that you would like to use for the
registration.
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T2 MAPPING MODULE
Click the registration button: The new series will be
created and automatically loaded into the
respective frames. You will find the new series in the thumbnail panel under “Reg NativePh#
.[original series description]”. The contours of the reference phase will be forwarded to all registered
images.
If you decide to use a different phase for registration, reload the original series and repeat steps 1-4.
Note: The registration works for points that are on or inside the contours; the image outside of the
contours
may appear warped or distorted after registration. This is expected, and users should not use any outer
regions for analysis. 21.2 T2 Map
The module consists of 2 viewports: the upper one for the T2 map, the lower one for the R 2 map.
To the right you will find the polar map and the window for the long axis reference.
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T2 MAPPING MODULE
How to analyze T2 maps
Drag and drop the map from the thumbnail panel into the respective window.
Drag a long axis reference into the reference window and define the extent of the left ventricle: Set 3
points. Two define the base, one defines the apex and define the long axis extent.
Derive existing contours from the T2 measurement via context menu>Derive Contours Phase.
Alternatively, draw new contours.
Set a segmentation reference point.
To add the polar map to report42 export the image via context menu and import into report. 42
.The values can be found in the scientific report.
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T1 MAPPING MODULE
22 T1 Mapping and ECV quantification
22.1
Module layout ................................................................................................................................... 193
22.2
T1 Analysis (native and post contrast) ................................................................................... 194
How to load various sequences ........................................................................................................................................ 194
How to do global or regional T1 analysis..................................................................................................................... 194
22.3
Motion Correction for ECV map generation .......................................................................... 195
How to do Intensity Based Registration ....................................................................................................................... 196
How to do Feature Based Registration ......................................................................................................................... 196
22.4
T1 Map Analysis............................................................................................................................... 197
22.4.1
T1* maps ..................................................................................................................................................... 198
How to analyse the T1 map ................................................................................................................................................ 198
22.5
ECV and lambda quantification (λ) ........................................................................................... 200
How to do segmental ECV and lambda quantification ........................................................................................... 201
22.6
T1 mapping Troubleshooting ..................................................................................................... 202
Note: Due to a lack of standardization, this module is for research only.
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T1 MAPPING MODULE
22.1 Module layout
Analysis options are organized in pages
T1 Native: T1 values and recovery curve
for global and/or regional myocardium
T1 CA: s.a. post contrast
T1 Map Native: T1 and R2 maps and a segmental polar map display (1-100 or AHA)
T1 CA: s.a. post contrast
ECV/λ: Polar maps and global/per slice ECV and partition coefficient (λ) quantification.
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T1 MAPPING MODULE
22.2 T1 Analysis (native and post contrast)
How to load various sequences
Since the algorithm for the calculation of T1 times differs from sequence to sequence, it is important
that your data set matches the chosen algorithm.
Choose from the menu at the bottom of the screen
Select the series from the thumbnail panel. Hovering over the thumbnail will provide a series
description. Drag it into the analysis window.
If the series is rejected, it could have been due to one of the following reasons:

The last image of the series actually is a scanner generated map (Siemens). Solution: In the option menu,
check the box for Skip Last Slice Image

In the DICOM header the TI time is encoded in the field for the Trigger Time (Philips). Solution: In the
option menu, check the box for Use Trigger Time as Inversion Time

During anonymization the information for TI has been stripped and you get a warning message "TI times
are equal." Go to the patient list module and in the Extended view check if the information for the TI can
be found under either TI or Image Comments (Siemens). If possible, try to re-anonymize the data,
preserving the TI information.
Note: Some recent Siemens sequences use a correction or scaling factor for the calculation of T1 times. In
this case, there might be a deviation between Siemens and cvi42 calculated T1 times.
You will find the scaling factor in your Siemens documentation; otherwise consult your Siemens
representative. In the Option menu (where you selected the sequence) you can enter the correction factor.
This will eliminate any deviation. Alternatively, use Siemens-generated maps.
How to do global or regional T1 analysis
For global T1 values, draw endocardial and an epicardial contours. Forward the contours
via context menu Forward All Contours Slice (short-cut: ⌘E/ctrl E)
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T1 MAPPING MODULE
For regional analysis, select one of the ROI contours. This contour can be forwarded via toolbar
button
Repeat for all slices.
Global, regional T1 Relaxation times and R2-values will be
shown in the result frame.
The T1 recovery curve will be presented in the frame below.
RBM click in the graph opens a Context Menu
You can adjust the error and threshold and the curve
fitting in the options (see options).
Create DICOM map. Make sure you have set R2, , Max. Error
and the Noise Limit appropriately.
Click the button in the toolbar.
In addition to the grayscale map a R2 map will be created. You will find both maps, combined in one
series, appended to your thumbnails.
Automate DICOM map generation: In the option menu, check the box
for Create map upon loading and save this step to your protocol.
For the post-contrast series, contours can be derived via context menu: The command Derive
Contours>Derive Contours Cardiac Phase, will derive previously drawn contours for all slices.
Add evaluation (images, values and graph) to the report
22.3 Motion Correction for ECV map generation
195
T1 MAPPING MODULE
Intensity-based registration is to be used with already motion corrected images and will register between preand post-contrast series. If you don't have motion corrected series, move to Feature-based registration.
Feature-based registration registers all images (pre- and post-contrast) to a selected image in the native
series. Therefore, it is required to have contours in both the pre- and post-contrast series as well as in all
slices.
Go to the respective pages and select the motion correction of your choice.
How to do Intensity Based Registration
Identify motion corrected series in the thumbnail panel.
Drag the series into the respective pages: T1 Native/T1 CA.
Although the algorithm does not require any contours, it is recommended to draw contours on the
chosen reference phase for a visual evaluation of the registration performance.
Choose a phase that has good contrast between endo- and epicardial contour as well as between
surrounding tissues in both the native and post contrast series. Avoid images with bright intensities
in the outer regions (areas of fat, air regions, etc.). In the Registration Options enter the chosen registration phases:

Adjust Native Registration Phase for the image selected in the
native series to be the reference image.

Select CA Registration Phase for the image selected in the post
contrast series, to be registered with the reference image.
Click the registration button.
The registration registers the CA Series to the Native Series. Because the series are already motion
corrected - and it is assumed that the native series aligns well throughout the phases - only one new
series distinguish the registration phases that were selected as follows: “Reg NativePh# CaPh#
[original series description].” If contours were drawn on the Native Registration Phase, they will be forwarded to the new registered
CA series. If the registration worked well, contours should line up with the new images.
If contours do not match well, or if you notice the endo/epi contours have an abnormal shape, try the
registration again with another Native and/or CA registration phase. Reload the initial series before
applying image registration again.
How to do Feature Based Registration
This registration can be used on motion and non-motion corrected series. It registers every phase in both
the native and post-contrast series to a chosen reference image in the native series.
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T1 MAPPING MODULE
Make sure you have accurately drawn the endo- and epicardial contours, as well as a segmentation
point in all images, in pre- and post-contrast series. Due to motion, contours across the phases may
not be exactly the same.
Select a reference image in the native series with the best contrast and enter the
phase into Native Registration Phase.
Click the registration button: Two new registered series will be
created and automatically
loaded into the respective frames. You will find the new series in the thumbnail panel under “Reg
NativePh# [original series description].” The contours of the reference phase will be forwarded to all
registered images.
If you decide to use a different phase for registration, reload the original series and repeat steps 1-4.
Note: The registration works for points that are on or inside the contours; the image outside of the
contours
may appear warped or distorted after registration. This is expected, and users should not use any outer
regions for analysis. 22.4 T1 Map Analysis
You can either create a map in cvi42 or you can use the map that has been created by the scanner software.
Some vendors append the map to their series. In this case, you have to remove it in the Series
Overview>Compose page Module, or you create a new one.
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T1 MAPPING MODULE
22.4.1 T1* maps
T1* maps will be automatically extracted from Molli, shMolli and Molli Oxford sequences.
T1* maps may offer a more accurate estimation of blood pool T1.
Bhuva AN, Treibel TA, Bulluck H, Simpson J, Manisty C, Moon J. Precision and reproducibility of blood T1 estimation:
implications of T1 star on ECV calculation. J Cardiovasc Magn Reson. BioMed Central Ltd; 2015 Feb 3;17(Suppl 1):P4.
How to analyse the T1 map
Drag the map from the thumbnail panel to the analysis window.
Alternatively, you can check the box for Create T1 Map upon loading
In the option menu adjust the Noise Limit
Draw or derive contours for a segmental analysis
Draw a blood-pool contour for ECV or λ maps.
For a color coded display, select a color map from the drop down menu or create your own LUT (see
below: How to create a color Look-Up-Table)
For a segmental polar map display, place an anterior and inferior SAX Reference point.
Define the left ventricular extent in the reference window. This is an important feature for quality
control and will assure that the segments and slices displayed in the polar map truly reflect the
198
T1 MAPPING MODULE
number and location of slices. In case the slice gap is too large or a slice or contour is missing, the
software will display a grey ring. The same will happen if the distance between the first acquired slice
and the base is too large to be recognized as - or truly reflect the basal slice.
In the polar map frame, the number of segments per ring can be customized or you can switch to a 16segment AHA model.
To exclude zero values (non-signals) you can set an off-set by checking Exclude Zero Values for Map
Measurements.
Add evaluations (images, values and graph) to the report
.
Repeat for post-contrast maps.
How to customize the color look up table
The LUT Selection menu offers a DICOM LUT (if present) as well as a predefined T1 Native map.
To create a table that better highlights specific or out-of range T1 values, based on your own data, for
different field strengths or sequences, you have the option to create several custom color look-up tables.
Click the (+) or (-) to add/delete a color table. Click the wrench to alter an existing table.
To assign a color to a T1 value, start with typing a value (T1 time) in the box.
Choose a color model: RGB or HSV (Red-Green-Blue table, or a cylindrical-coordinate color point
representation, called Hue-Saturation-Value look-up-table.)
Select a color from an existing palette.
To define a custom colors, click on a white box under Custom Color. Select a color and click Add to
Custom Color. Adjust the selection with the options to the right (for HSV the Hue is limited to 255).
To apply the color to the value click Add Value/Color.
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T1 MAPPING MODULE
Repeat for all values that you would like to display.
To remove a color from a value, select from the table on the left and click Remove Selected Value.
When you are finished, provide a description to the LUT.
Add the LUT to the protocol.
Save the protocol if you wish to use the LUT for all future series.
Add evaluation (images, values and graph) to the report
Note:
For encoding purposes, HSV values are expressed in values ranging from 0-255 instead of percentages
(0-100%) or degree (0-359°). Therefore when trying to translate HSV to RGB using an color
conversion app the values might be different
22.5 ECV and lambda quantification (λ)
ECV is a measure of interstitial space that is derived from the partition coefficient, reflecting the distribution
of contrast agent between blood and myocardium, corrected for the hematocrit (minus volume fraction of
erythrocytes).
Partition Coefficient : λ = ΔR1myocardium/ΔR1blood (where R1=1/T1)
ECV= λ *(1−hematocrit)
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T1 MAPPING MODULE
An accurate estimation of ECV requires contrast equilibrium between blood and myocardium and must be
achieved prior to image acquisition (aprox. 8.5 minutes post contrast injection*).
*Lee JJ, Liu S, Nacif MS, et al. Myocardial T1 and extracellular volume fraction mapping at 3 tesla. J Cardiovasc Magn Reson 2011;13:75.
How to do segmental ECV and lambda quantification
Make sure you have contours, segmentation points and a blood-pool contour in all slices in both T1
map. Native and T1Map CA. The blood pool contour can be drawn either in the T1 or the T1* map (see
above).
Enter the hematocrit for the ECV quantification.
Add an ECV map.
For a polar map display, make sure you have defined the long axis
extent in the reference frame of the T1 Map Native and T1 Map CA
page.
Add evaluation (images, values and graph) to the report
Normal Values
D. Dabir et al., Reference values for healthy human myocardium using a T1 mapping methodology: results from
the International T1 Multicenter cardiovascular magnetic resonance study. Journal of Cardiovascular Magnetic
Resonance 2014, 16:69 doi:10.1186/s12968-014-0069-x
MOLLI
1.5 T (msec)
3T (msec)
native T1
950 ± 21
1052 ± 23
λ
0.44 ± 0.06
0.44 ± 0.07
ECV
0.25 ± 0.04
0.26 ± 0.04
Piechnik et al.. Normal variation of magnetic resonance T1 relaxation times in the human population at 1.5T using ShMOLLI.
J Cardiovasc Magn Reson. 2013; 15:13.
ShMOLLI
1.5 T (msec)
native T1
962 ± 25
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T1 MAPPING MODULE
22.6 T1 mapping Troubleshooting
The dataset can not be loaded
Check in the Option menu if you have selected the correct dataset
For some sequences, the trigger time is entered in the inversion time field (e.g. some Philips or
Siemens sequences). Check Use Trigger Time as Inversion time
If a map is appended to the series, it can't be loaded. Check skip last slice image
There a grey ring in the polar map:
Check that you have contours and a segmental reference point in each slice
Check that you have defined the LV extend
Check if the slices truly cover the entire LV or the anticipated region: e.g. first slice is too far away
from the mitral valve plane to actually reflect the base.
No ECV map output: check that you have a blood-pool contour defined in the native and post-CA map
Reference Paper:
Moon JC, Messroghli DR, Kellman P, Piechnik SK, Robson MD, Ugander M, Gatehouse PD, Arai AE, Friedrich MG, Neubauer S,
Schulz-Menger J, Schelbert EB. Myocardial T1 mapping and extracellular volume quantification: a Society for Cardiovascular
Magnetic Resonance (SCMR) and CMR Working Group of the European Society of Cardiology consensus statement. J
Cardiovasc Magn Reson. 2013 Oct 14;15(1):92. doi: 10.1186/1532-429X-15-9
C. Jellis and D. Kwon. Myocardial T1 mapping: modalities and clinical applications. Cardiovascular Diagnosis and Therapy.
202
FIRST PASS PERFUSION
23 First Pass Perfusion Module
23.1
"Multi View" Compare Rest and Stress Perfusion ............................................................... 204
How to do a visual perfusion analysis ........................................................................................................................... 205
23.2
"Edit Contour", semi quantitative analysis ............................................................................ 205
How to do Semi-Quantitative Perfusion Analysis .................................................................................................... 206
23.2.1
Option Menu .............................................................................................................................................. 208
How to analyze the perfusion curves ............................................................................................................................ 208
23.3
"Analysis", segmental analysis ................................................................................................... 209
How to do a regional perfusion analysis ...................................................................................................................... 210
23.3.1
Perfusion Analysis Troubleshooting ................................................................................................ 210
203
FIRST PASS PERFUSION
The Perfusion module consists of 3 pages

Multi View: Compare rest and stress perfusion with scar images and wall motion kinetics

Edit Contour: Semi-quantitative analysis

Analysis: Polar Maps
23.1 "Multi View" Compare Rest and Stress Perfusion
turn contours off, set frame rate
Rest
synchronize frames
Stress
Function
LGE
Visual Analysis of Rest and Stress Series
To hide a slice, click the grey bar above the slice.
Hide slice
204
FIRST PASS PERFUSION
How to do a visual perfusion analysis
Adjust window and zoom for rest and stress series.
To set the frame rate use the wheel in the toolbar
Turn existing contours off (toolbar button)
Synchronize the frames for rest and stress by using the slider

If applicable drag Late Enhancement and Function images into their respective frames for comparison
Add the Floating Viewer for more viewing options
23.2 "Edit Contour", semi quantitative analysis
205
FIRST PASS PERFUSION
To adapt the module to your requirements click the wrench button in the protocol pane.
Select specific buttons and tool sets
Switch on/or off the Option menu (see below)
How to do Semi-Quantitative Perfusion Analysis
Drag the appropriate series in the Rest and Stress frame and adjust viewer properties.
Select a phase with good contrast and draw endo- and epicardial contours
Draw endo- and epicardial contours. To copy and paste contours from rest to stress series via context
menu
Draw a Blood Pool contour, (input function) in the brightest, most
homogeneous area of the blood pool.
Check Use Bloodpool Contour in the Options (underneath the graph). In case the option Search for
Basal Bloodpool Contour is checked, the software will only use the most basal blood pool contour for
calculation purposes.
Set the anterior and inferior segmentation reference points at the insertion of the RV to the
epicardial border of the LV.
Contour Propagation: Forward all contours, including blood pool contour and segmentation
point to the remaining phases.
Check and adjust contours for each phase within the analysis range. Use the align contour
button to correct for breathing motion
To manually shift all contours at once: press and hold the command (⌘) key and shift the contours with
the LMB.
Choose AHA segmentation or a number of custom segments per slice or from
the Options/Segments menu (see below).
Optionally apply an Offset:
206
FIRST PASS PERFUSION
Endo: Modifies the region for evaluation by moving the endocardial border contour towards the
epicardial border (0 - 50%)
Epi: Modifies the region for evaluation by moving the epicardial border
towards the endocardial border. (range 0 - 50%)
Analysis of myocardial layers: Use the menu in the Options to generate curves of eno-, mid-, and
epicardial layers.
Define the analysis range (contrast inflow during first pass) by moving the left and right slider at the
bottom of the graph, or by using the context menu while scrolling through the phases. This will also
limit the frames in the 'Multi View' to the defined range.
Apply baseline correction via context menu (RMC in the graph)
For a special region of interest, there are 4 additional contours in the top
tool bar. To view the curve, check the respective ROI in the Option menu
Repeat for all slices and add results to the report
The following will be added to the clinical report:

the calculated values for each segment and each slice,

the polar maps as specified below

the first phase frame of each slice as a sample image.
The following will be added to the scientific report:

the calculated values for each slice and each segment,

for each slice, each segment, and each phase: the average, maximum, minimum, and median signal
intensity, the standard deviation thereof, and the area of the region (segment or cavum).
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FIRST PASS PERFUSION
23.2.1 Option Menu
Endo/Epi: Exclude sub-endocardial and/or sub-epicardial layers
Fit points Choose the number of points that will define the slope
Skip Images: you can exclude images from the from baseline
Segments: Choose between custom segments (up to 100) or AHA segmentation
Blood Pool contour: Checked, it requires to define a blood pool contour
Basal Blood Pool Contour: The software only uses the most basal blood pool contour
Check a box to view the perfusion curve of a drwan ROI
How to analyze the perfusion curves
To switch to an enlarged view, go to the context menu and check Enlarged View
Move the mouse cursor over the icon to view the curve of the
respective segment.
The context menu offers several display options:

Display standard deviation.

Spline interpolation: Smoothes the graph.

Display shadow line: A line will indicate the previous line position
while modifying the analysis range.

Display data points.
208
FIRST PASS PERFUSION

Display Baseline: The software calculates and displays a pre-contrast signal intensity baseline (depends
on slider setting) for each segment. The Option menu provides a preference that excludes images from
the baseline calculation (Skip Images) Display Time to Max/ Time to 50%Max:

Maximum slope: The local slope will be determined from a linear regression fit applied to the adjacent
graph points. The number of graph points used can be can be specified Option>Fit Points

Display for each segment, SI maximum and 50% of the maximum

Display Time 20 to 80%Max: This will display the time elapsed between 20 % and 80% of the maximal
signal intensity
Note: Lines may not be displayed if the input data does not contain 20, 50 or 80% max criteria for the
Perfusion Graph. Try applying a baseline correction.

Apply baseline correction (Rel% -bl): All SI values are expressed as a percentage of the baseline value. The
baseline value is given as the mean SI of all SI values (excluding the first image) before the arrival of the
contrast agent in the left ventricle.

Apply baseline correction (Diff-bl): All SI values are expressed as the difference to the baseline value. The
baseline value is given as the mean SI of all SI values (excluding the first image) before the arrival of the
contrast agent in the left ventricle

Exit the Enlarged View via context menu (uncheck)
23.3 "Analysis", segmental analysis
209
FIRST PASS PERFUSION
How to do a regional perfusion analysis
Define length of anatomical long axis using the LAX LV Extent Contour button In end-systole draw a
line between the mitral valve plane and the left ventricular apex. Slices beyond the range will not be
included in the Polar Maps.
The purpose of this contour is to ensure displayed polar maps reflect the entire left ventricle.
cmr/cvi42 will display grey segments in case :

slices do not cover the entire ventricle

the gap between slices is too big for interpolation

there are missing contours in existing slices
Select a parameter from the drop down list:

Max Slope: Maximum Signal Intensity increase over time (SI/sec)

Time To 50% Max: Time elapsed between onset of contrast inflow and reaching 50 % of the maximum
signal intensity (sec).

Time To Max: Time elapsed between onset of contrast inflow and reaching the maximum signal
intensity. (sec)

Time 20%to80%: time elapsed between 20% and 80% of SI maximum

MaxSI: Maximal Signal intensities (SI)

Myocardial Perfusion Reserve Index (dividing the upslopes of the time-intensity curves at stress and
rest)
Apply a baseline correction
Baseline Difference: (SI_corrected = SI -SI_baseline)
Baseline Relation: (SI_corrected = SI/SI_baseline * 100)
23.3.1 Perfusion Analysis Troubleshooting

In anonymized studies the perfusion curve only has 2 data points: Some vendor sequences the timing
information is part of the Aquisition Date and should not be removed during anonymization.
The polar map displays grey rings: According to the defined extent of the left ventricle the software was
not able to find a true apical or basal slice. Or the slice gap is to large to be interpolated.
210
FLOW
24 Flow Module
24.1
Reported values ............................................................................................................................... 212
24.2
Flow quantification ........................................................................................................................ 213
How to do a Flow Analysis.................................................................................................................................................. 213
24.3
Comparison of Two Different Flow Series (Qp/QS) ............................................................ 215
How to assess (Qp/QS) ........................................................................................................................................................ 215
24.4
Invert Results ................................................................................................................................... 216
24.5
Sample Size Volume for Maximum and Minimum Velocity Calculation ...................... 216
24.6
Flow Profile ....................................................................................................................................... 216
WARNING: Flow
For the analysis of velocity encoded images the utilization of vendor specific DICOM information is required. If
this information is missing or not readable, the particular series will be rejected as a non-valid flow study.
Measurements in series of velocity encoded images should only be done in sequences that validated for those
measurements. Due to different options for the file encoding of different vendors an initial validation for the
used imaging pipeline is strongly recommended.
211
FLOW
Flow analysis (Only through plane velocity encoding)
24.1 Reported values
Flow Analysis
Total Forward Volume (TFV)
ml
positive + negative velocities = positive value (above
x-axis)
Total Backward Volume (TBV)
ml
positive + negative velocities = negative value
(below x-axis)
Total Volume
ml
TFV + TBV
Net positive Volume
ml
only positive velocities (above x-axis)
Net Negative Volume
ml
only negative velocities (below x-axis)
Regurgitation Fraction
%
ratio between total backward and total forward
volume.
Volume/min
ml/min
Volume/min effective
ml/min
Heart rate
bpm
Maximum pressure gradient
mmHg
Mean pressure gradient
mmHg
Maximum velocity
cm/s
Minimum velocity
cm/s
Maximum Mean velocity
cm/sec
Maximum Flow
ml/s
Minimum Flow
ml/s
Inside Ruler Volume
ml
Using the ruler in the diagram, you can restrict the
analysis to a certain range of the cardiac cycle.
Outside Ruler Volume
ml
Volume that is outside the defined range
Value of the phase with the highest mean velocity
212
FLOW
24.2 Flow quantification
Postprocessing of velocity encoded images requires
Definition of vessel contour in all phases
Application of Background correction
To adapt the module to your requirements click the Edit button in the protocol pane.
Toggel on/off the option to compare to series
Select display options for the flow curves
Display the Options to use rounded contours
Check/uncheck the option to use a phatom correction
How to do a Flow Analysis
Drag the Phase series into the top left analysis frame, the corresponding Magnitude image will be
displayed automatically in the right viewer window.
For color encoding click on the Toggle Flow Overlay button.
To reduce noise, the threshold color overlay can be adjusted; by default it
is 15%:
Adjust the viewer frame properties and select a reference image with good contrast and some darker
pixels.
213
FLOW
Define the vessel border, e. g. using the Threshold Segmentation mode
Forwarding the contour . The automatic contour detection will grow the contour towards the
vessel borders based on the information from all phases. It also forwards the contours to all phases.
Correct the contour: Scroll through phases to ensure the contours are correct.
Define the Anatomical Region: Either choose a custom term or pick from
the drop down menu, that opens right next to the ROI contour.
Apply Baseline correction:
To incorporate a background correction into your calculations

start by selecting the Background Correction button and drawing a BC contour in an area with no flow
(turn on the color overlay and run the cine loop to check for flow)

Forward this contour to all phases with key combination ⌘F (also to be found in the Context menu/Copy
Forward....). Do not use the Forward Flow Contour button since it will also grow the
contour.

Apply the Baseline Correction to your measurement by selecting BC ROI from the
Correction drop down menu

To view the BC-curve, check the respective box underneath the graph. All displayed values
now incorporate the background correction.
Phantom corrections, check Use Phantom Correction and drag the image into the respective window,
Graphical Display

To view the diagram go to the graph window (lower left hand
side) and check the box associated with the ROI.

A right mouse click in the graph opens a context menu, that offers several
display options and an option to export the flow curves.

Clicking on the menu button 'DisplayedValue' will open a drop down menu
that allows to look at different parameter:
-
Flow displays the flow m/s over time within the selected ROI
Velocity (mean) displays the mean velocity within the selected ROI
Velocity Env. displays both the maximum velocity and minimum
velocity.
ROI Area displays the area (mm2) of the selected ROI.
ROI Net Positive Flow forward flow data corrected for inaccuracies
caused by turbulent flow within the slice.
ROI Net Negative Flow
ROI Positive Velocity Area
ROI Negative Velocity Area
214
FLOW
Add to report. Flow assessments of different series have to be added individually to the report.
24.3 Comparison of Two Different Flow Series (Qp/QS)
This function provides an option to perform flow analysis on ROI´s of different series and derive values such
as flow difference, sum and ratio. Ideal for phantom corrections, to assess shunt volumes and more
Select ROI
How to assess (Qp/QS)
Perform analysis of Flow Series 1 and Flow Series 2. Define the Anatomical Region by providing a
name to your ROI.
For easier reference select 2 different colors, e.g. red ROI1 contour for Series 1 and green ROI2
contour for Series 2.
Switch to the Comparison window and select the anatomical regions
Add to Report
215
FLOW
24.4 Invert Results
In case of unexpected flow encoding directions, you have the option to invert the input for all calculations
(multiplied by -1). Checked it will be used for every report.
24.5 Sample Size Volume for Maximum and Minimum Velocity Calculation
The minimum and maximum velocity calculations are based on an average value of a
determined sample volume. The size of the sample volume can be selected with the drop
down menu in the lower panel.
Pixel matrix selection: The choices range from sub-pixel up to 4x4 pixel matrices. The size
and location is graphically reflected in the phase image, by the red (maximum) and blue
(minimum) squares displayed within the selected ROI. The velocity displayed in the graph is the average SI
from within the square. Note that as you change the size of the sample volume, the location of the min and
max may also change.
1x1 Pixel
4x4 Pixel
24.6 Flow Profile
Select the Flow Line Profile tool
and draw a line across the vessel. To view your analysis, check the
appropriate box in the ROI Selection menu.
216
25 Main Menu, Preferences and Configuration
25.1
Preferences ....................................................................................................................................... 218
25.1.1
Appearance................................................................................................................................................. 218
25.1.2
Viewer........................................................................................................................................................... 219
25.1.3
Image Database......................................................................................................................................... 221
25.1.4
Anonymization Settings ........................................................................................................................ 221
25.1.5
Series Overview Setting ........................................................................................................................ 221
25.1.6
Reporting..................................................................................................................................................... 222
25.1.7
Settings for Contours, Matrix Size and Standard Deviation ................................................... 223
25.1.8
4D Viewer.................................................................................................................................................... 224
25.1.9
Tissue Tracking............................................................................... Error! Bookmark not defined.
25.1.10
Network .................................................................................................................................................... 224
25.1.11
License ....................................................................................................................................................... 226
25.1.12
Server Admin .......................................................................................................................................... 226
25.1.13
LDAP Admin ............................................................................................................................................ 226
25.2
Workspace Menu............................................................................................................................. 227
25.3
Protocol .............................................................................................................................................. 228
25.4
View Menu ......................................................................................................................................... 228
25.5
Tools .................................................................................................................................................... 228
25.6
Help ...................................................................................................................................................... 228
217
PREFERENCES AND CONFIGURATION
25.1 Preferences
The main menu bar is located at the top of the screen. Here you will find your "Preferences"
PC
MAC
To activate the changes you have to reload the study
25.1.1 Appearance
Font: Pick the style (default: Lucia Grande). Changes take effect immediatly.
Applies to text displayed in the viewer, reports and diagrams.
Apple Options: Retina Display

Startup View: cmr42 and cvi42 have the capability to work with several screens for an optimized
workflow.
Start Full Screen: default = turned off

Use Multiple Screens (default = turned on): Enables the system to work with two screens (see chapter Set
Up)

Select your preferred setting and restart the software. (See chapter 5.3 Working with multiple screens)
Window Frameless (Second Screen): default = turned on; text will be omitted

Start Module: Determines the default module that opens upon program start up. Options are:
Viewer

Series Overview (default)

4D Viewer

Patient Data Metric: applies to Patient Data module(weight and height).
Metric Units (default)

Imperial Units: If changed in the settings to imperial, both units will be shown.
218
PREFERENCES AND CONFIGURATION
Screen Report: changes to a bright report window background
25.1.2 Viewer

Contour Drawing Settings
Stay in contouring mode: Double click will not drop a primary selected tool allowing the user to draw a
second, third etc. contour.

Exit contour mode: As soon as the left mouse button is released the tool will quit.

Enable Drawing Mode Pop-up: Will display a toolbox for drawing modes like Click-Draw or Threshold
Segmentation

Use angle within 180 degrees: The default for angel measurement is 360 degrees and depending on the
direction, you set your points (form left to right or vice versa) it will pick the larger or smaller angel. This
option checked it will only measure up to 180 degree

Calculate Ellipse Perimeter: checked the tool will give 2 measurements. The perimeter of the drawn
contour and for an elliptical shape
Contour Display: Changes the width of the contourline between 1-2-3 pixels
Window/Zoom/Panning Forwarding Policy
The policies determine if windowing, zooming or panning will be applied to:

Series (default)

Slice

Image

Zooming/Panning Settings:
Smart Forwarding policy (enabled by default): Settings will only be forwarded if images are parallel
and/or have the same FOV respectively.

In some cases where the images are not parallel, (e.g. multiple long axis series) it doesn't make sense to
automatically forward the viewer settings.

Adjust Zoom To View Size: Adjusts the image size to fit the frame (enabled by default)
Cine Synchronization: Sync by time is the default option
219
PREFERENCES AND CONFIGURATION
Cine Playback, All Dropped Frames: Check, if frames cannot be displayed in time
Default Zoom Factor: Displays all prospective images by default with the chosen zoom factor
Default Window:
Changes the default window settings given by percentage histogram offset.
E.g. Images are constantly to dark, set the default to a higher value to display brighter images.
The off set ranges from 0-40 %; the default setting is 8%.
The DICOM option will retrieve the window information from the DICOM header.
Mouse Wheel Function:
Changes the wheel functionality from zooming to phase or slice navigation.

While Phase Navigation is enabled the user has the option to zoom by dragging the cursor to the right
frame border until the zoom symbol appears
; click on the symbol with the left mouse button, hold
and shift up and down.

If Zooming is selected, the user can switch to Phase Navigation temporarily by holding the shift-key while
scrolling

Zoom to mouse: checked it will take the cursor position as a zoom center.
Autosave Workspace:
Customize the interval for automatic workspace saving

DICOM Annotation
Display Additional DICOM Annotations: When checked it will display DICOM tags (TD,TR, TE....). To
activate, reload study!

Display DICOM Annotations in Multiview: Applies to the multiview layout (tile-display of all slices) that can
be entered via spacebar click or by clicking the Multiview button in the Viewer Modules
Display DICOM LUT : checked a color look up table defined in the DICOM header will be used for the
display in the viewer
Floating Viewer
Checked by default. This functionality synchronizes the slice location of the series loaded into the
Floating Viewer with the slice location of the series in the main viewer frame. When scrolling through the
series, the images in the floating viewer will follow accordingly.
Context Menu:
Checked by default. If this feature is selected it is still possible to retrieve the full menu with a short-cutkey combination ⌘+RMB.
220
PREFERENCES AND CONFIGURATION
25.1.3 Image Database
Export Options
Write DICOMDIR: Checked, the "Export Images " button in the Image Database will export studies in a
directory that contains an additional DICOMDIR file.
Study Sorting: allows to accept unordered stacks (Siemens only): cvi42 will allow to import stacks that are
divided into different series and are unsorted. Slices will be automatically sorted into correct order,
thereby preventing consecutive sorting issues with other series.
Performance Options:

Image Cache Size Limit: Loaded voxel data will be cached in memory. The size of the memory cache is
configurable by the user. Default size: 256 MB.

In case of performance options try to increase the cache size.

Smart Image Loading: cvi42/cmr42 uses a smart predictive loading to ensure a smooth image handling for
the user. However in some cases this can cause unstable conditions. When this rare problem occurs, the
user can try to turn off the “smart image loading” option.
25.1.4 Anonymization Settings
Anonymize Options: Select the attributes desired to keep during anonymization by dragging them to the
right column (Don’t Anonymize).
Note: In some perfusion sequences the timing information is part of the Acquisition Date and you will not
be able to display a perfusion curve if this is anonymized.
Private Tags:
When checked, it removes patient and vendor specific proprietary data (private DICOM tags). Using the
option Remove Private Tags will prompt a warning in case velocity encoded images are about to be
removed (applies GE and Philips)
Batch Anonymization:
Allows for anonymizing multiple studies at the same time. Please refer to Image Database Module
/Anonymization.
25.1.5 Series Overview Setting
Changes apply after reloading.
Startup View:
By default, the Series Overview module displays all images and series comprised in the study.

Slide Show: Presents the study in a slide-show fashion

Case Review: Will only display images that have previously been selected for a case review
221
PREFERENCES AND CONFIGURATION
Study Preview:
These setting relate to the cine loops and image stacks

Auto Start Cine on Mouse Move: Hovering over cine will automatically run the cine (checked by default)

Auto Start All Cine will start cines as soon as the module is open

Show Navigation Buttons will display on screen buttons to navigate through series, slices, and phases

Open Series Selection in Viewer on Double Click: A double click on an image or a series will display the
selection in the Viewer module

Slide Show:

Show Progress Bar: Displays a progress bar on the bottom right of the slide frame, indicating the number
of current series/total number of series

Auto Start Cine: Cine starts as soon as the slide show mode is entered
25.1.6 Reporting
The Reporting menu relates to the report module and allows defining/changing the settings for DICOM report
saving functionality
DICOM Export Options
The Save DICOM Report button in the Report module by default creates an image of all previously added
text reports (analysis).
To add images the following options are provided:

Create Additional Images: Checked it will automatically create and save secondary captures of all polar
maps, diagrams, and reference windows.

Create Selected Images: Images that have previously been added to the report will be captured and
automatically saved.

Create Series Images: Images with contours will be captured and automatically saved

Create Monochrome Images Only: In order to save memory space images can be saved in black and white.

Secondary Capture Image Storage SOP: Exiting DICOM storage behavior (Multi Frame Secondary Capture
SOP class) can be switched to a different class.
Report Image Export Options
Hides or displays threshold contours in the images added to the report.
Report Server:
Set the following parameter:

Server Type: report42 or generic

Server URL

Username

Password
Number of Decimals:
222
PREFERENCES AND CONFIGURATION
Depending on the module, the user can individually choose the number of decimals displayed.

Screen: refers to reporting windows in modules

Scientific: the scientific report

Viewer: refers to values that are displayed on the image in the Viewer
25.1.7 Settings for Contours, Matrix Size and Standard Deviation
Sub Pixel Matrix Size: Changes the spatial resolution of the contour drawing (default: 4x4).
Note:
The higher the resolution, the longer the processing time. With a high resolution and low processing capacity,
the system might seem to be unresponsive.
Signal Intensity Standard Deviation: Changes the sensitivity of the SD calculation.

Use Sub-pixel Weighted SD (default = checked): The user has the option to determine if the complete
pixel or, if checked, a sub-pixel will be counted into the standard deviation. A normal curve of SI
distribution is assumed here.

Use biased SD: Lets the user choose between a normal and biased distribution of Signal Intensities
(default = unchecked).
Contour Detection

Contour Detection Connect to View (Reload the study to apply settings):
Unchecked, a yellow frame will be visible around the area of analysis for contour detection (you may
have to zoom out to see it). It is possible to change the frame size by clicking on the frame and dragging
the yellow corner dots. Grabbing the center square allows for panning the frame.
When checked (default), the analysis frame border becomes identical with viewer frame border. To
change the area of analysis, the image has to be panned or zoomed.

Preserve Manually Drawn Contours: Contours that have manually been drawn or corrected will not be
overwritten by the automatic contour detection

Use Contour Detection Dragging: Applies to the drag contour tool. When checked, the dragging behavior
changes and will perform a contour detection while dragging.
Rounded SAX Endocardial Contour
By applying a rounded endocardial contour when using automated contour detection, papillary muscles
and trabecular structures will be cut off, thus excluded from myocardial volume.
Papillary Muscle Detection
checked, papillary muscles for right and/or left ventricle will be detected and added to the myocardial
mass, when using the automated contour detection. Images will display a purple papillary muscle contour
within the LV cavity where papillary had been detected.
223
PREFERENCES AND CONFIGURATION
SAX chord generation:
By default the centerline method is used to perform segmentation. In some cases, e.g. atypical anatomy,
the software is not able the generate cords. By checking the box it is possible to switch to a different
approach for segmentation, where the center point will be determined for each slice individually.
25.1.8 4D Viewer
Voxel Precision can be changed between 8 and 16 bit. By default, 16 bit precision is being used in order to
retain the original data precision. However, if the video memory is limited, 8 bit precision could be
selected temporarily to lower the amount of video memory usage.
Note:
In case the original data contains a higher precision than 8 bit and 8 bit precision is selected, the original data
is down-sampled to fit the 8 bit memory boundary and some details could be lost.
Rendering (4D Viewer/MPR Viewer): The Rendering Acceleration option could be used to speed up
rendering during rotation/manipulation/editing. No Acceleration will result in high quality rendering (if
the graphics card is fast). Higher settings will decrease rendering quality to achieve faster rendering
speed.

Use Full Quality Rendering (requires a fast graphic card)

Empty Space Optimization: if a 3D rendered volume only has a small visible mask or anatomic structure,
the rendering algorithm will only load the visible structure into video memory and skip the remaining
empty volume. This is designed for performance improvement and speeds up the rendering. Example: If
we are only visualizing the coronary arteries in a large volumetric CT with a resolution of 512x512x500,
only the coronary artery voxels will be loaded in memory instead of the entire volume since most of the
volume is empty.

Video Memory Saving Mode for Cine Volumes
3D Segmentation (CT images only)
Regarding automatic segmentation upon loading you have the choice between heart, coronary tree or left
ventricle segmentation
Viewers:

Enable 4D Mesh Visualization: When unchecked, no 3D/4D mesh model will be created.

Portrait Layout: check if preferred
25.1.9 Network
The Network Window Tab allows you to define entities for DICOM communication. In order to connect to
another entity, the DICOM communication system needs to know the exact

AE Title
224
PREFERENCES AND CONFIGURATION

IP Address

Port Number
WARNING: DICOM Networking
The DICOM communication interfaces do not use encryption or user authentication. It is the user’s
responsibility to use these communications abilities only in a secure environment.
You have to define your own (provider) name = AE title. By default it is “CVI42”.
This selected name has to
be provided to the other entity you wish to communicate with.
Network Settings

AE title: Define your provider name. By default it is “CVI42”.
This selected name has to be provided to
the other entity you wish to communicate with.

Store SCP Port
- A port number has to be defined. Provide that number to the entity you wish to
communicate with.

Database update interval - By default every 30 seconds the system updates the image database.
Network Options

Enable Storage SCP - Automatic Image Receiving: Checked: DICOM listener is active and able to receive
images automatically.

Enable Q/R SCP – Allows for DICOM Query/Retrieve.

Accept Unknown AE Titles – Allows push from any SCP.

Enable Low Level Debug Log – Turns on Debug logging.
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PREFERENCES AND CONFIGURATION
Remote DICOM Notes: configure where, who and what to send
25.1.10 License
(see also Chapter 4.1 Request a License)
License status:
If the license is valid it notes: x valid licences available.
If the license is expired it notes: No valid license available.
Available license:
The following information of all available licenses is shown here:

Product

Start date

Expiry date

Maintenance Expiry

License holder

Status

Count

Machine ID

License File
To Import, Add or Request a license please refer to Chapter Request and/or Add License
25.1.11 Server Admin
Allows for configuration of user accounts
25.1.12 LDAP Admin
The LDAP Admin Tab allows you to define settings used for connecting on to AD/LDAP server.
These settings will allow users to be authenticated against existing AD/LDAP server when logging into cvi 42.
cvi42 needs to know the following information:
1.
2.
3.
4.
5.
6.
AD/LDAP server’s hostname or IP address
Whether the connection is over TLS/SSL
AD/LDAP’s domain
Base distinguish name
Username attribute
Additional criteria (optional)

Primary Server – A primary server has to be defined. Provide a hostname of the AD/LDAP server for user
authentication.
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PREFERENCES AND CONFIGURATION

Secondary Server – This entry is optional, it serves as a backup server to connect when the primary server
is unavailable.

Use TLS/SSL to connect – If this option is checked, all communication with AD/LDAP server will be
performed over TLS/SSL.
Account Info for Initial Bind

Username – This is the field used for entering the username along with a domain of the AD/LDAP server
giving administrators the ability to test the AD/LDAP connection. The domain specified here will allow
other users logging into cvi42 to be authenticated using AD/LDAP.

Password – User credentials used for testing user authentication against AD/LDAP server.

Anonymous connection: check name – A button the administrator clicks on to check the authenticity of the
given user credentials against the AD/LDAP server.
AD/LDAP Specific Information

Base Distinguished Name – This defines the location (or forest) of the directory to search when
performing an AD/LDAP query.

Username Attribute – A AD/LDAP attribute used when searching for a user on the AD/LDAP server. For
example, sAMAccountName is often used when looking up users on Active Directory servers. Or uid for
LDAP servers.

Advanced – Allows you to specify additional criteria to use when searching for a user on the AD/LDAP
server. In particular this allows you to specify additional permission a user must have in order to gain
access to cvi42. For example, a user must be a member of the cvi42 group in order to log into cvi42.
25.2 Workspace Menu
By default, drawn contours are automatically saved and will be reloaded when the patient study is reopened.
In addition, the user has the option to:
Load Workspace: Loads a workspace that has been previously stored in a location other than the default
location. (“Save Workspace As” option)
Save Workspace: Saves a newly created or updated workspace in the default location
Save Workspace As: Saves the workspace to a different location
Load Workspace DICOM: Loads a workspace that has been previously created as a DICOM Secondary
Capture
Save Workspace DICOM: Saves the current workspace as a DICOM Secondary Capture and appends it as
an image to the series
Import Workspace: Imports a workspace from a local file system
Export Workspace: Exports a workspace from a local file system
Reset Workspace: Deletes all drawn contours in the current patient study
Close Study
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PREFERENCES AND CONFIGURATION
25.3 Protocol
This menu item lists the default protocol in the protocol pane and all the other protocols that have been
generated.
In addition, it is possible to:
Load Protocols From Server
Load Protocols To Server
Import protocol definitions from a local XML file
Save protocol definitions to a local XML file
25.4 View Menu
Full Screen: Extends or diminishes screen view <command/crl F11>
Hide Status Bar: Hides the status bar that displays the progress of an image import
Show Application Log: Displays an application log, which might be used for system checks and error
logging
Refresh Study List <F5>
The software generally tries to refresh the list as necessary, but for times when the list does not seem
updated it may be necessary to choose "refresh study list" from the menu.
Examples of when refresh study list may be necessary:

After importing studies from disk

After importing studies from PACS

When expecting studies to be received from scanner

While user A is currently logged in, and user B has just finished importing a study (and shared it), user A
may need to refresh to see it.

Anytime the study list may look incorrect
25.5 Tools
Login to server
Disconnect from server
Change Password
25.6 Help
Manual
Video Tutorials
Release Notes
Downloads
228
26 Technical Support
For technical questions please contact our team by phone or e-mail:
North America
Circle Cardiovascular Imaging Inc.
250, 815 - 8th Avenue, SW
Calgary, AB
Canada, T2P 3P2
P: +1 403 338 1870
F: +1 403 338 1895
Europe
Circle Cardiovascular Imaging B.V.
Obriglaan 15
1852 KA Heiloo
The Netherlands
Europe Support Phone: + 31 (0)20 893 2381
Report a problem:
[email protected]
Website:
www.circlecvi.com
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