segment ct instructions for use -...
TRANSCRIPT
Segment CTInstructions For Use - English
March 5, 2020
Software platform v3.0 R7908
MEDVISO ABhttp://www.medviso.com
Griffelvagen 3SE-224 67 LundSwedenTel: +46-76-183 6442
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Contents
1 Terms and conditions 11.1 Regulatory status . . . . . . . . . . . . . . . . . . . . . . . . 11.2 Conditions for use . . . . . . . . . . . . . . . . . . . . . . . . 11.3 Indications for use . . . . . . . . . . . . . . . . . . . . . . . . 11.4 Intended patient population . . . . . . . . . . . . . . . . . . . 21.5 Medical indications . . . . . . . . . . . . . . . . . . . . . . . 21.6 Safety Instructions . . . . . . . . . . . . . . . . . . . . . . . . 3
2 Conventions and Abbreviations 52.1 Typographic conventions . . . . . . . . . . . . . . . . . . . . 52.2 Trademarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52.3 Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . 5
3 Getting started 73.1 System requirements . . . . . . . . . . . . . . . . . . . . . . . 73.2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73.3 Add software license code . . . . . . . . . . . . . . . . . . . . 133.4 Starting Segment CT . . . . . . . . . . . . . . . . . . . . . . 133.5 Uninstallation . . . . . . . . . . . . . . . . . . . . . . . . . . 143.6 Software overview . . . . . . . . . . . . . . . . . . . . . . . . 143.7 First time running Segment CT . . . . . . . . . . . . . . . . . 15
3.7.1 Setting preferences . . . . . . . . . . . . . . . . . . . 153.7.2 Setting window positions . . . . . . . . . . . . . . . . 153.7.3 PACS connection . . . . . . . . . . . . . . . . . . . . 15
4 Loading and storing Data - Step by step 174.1 Loading data . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.1.1 Loading data from database . . . . . . . . . . . . . . 17
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CONTENTS
4.1.2 Loading data from PACS . . . . . . . . . . . . . . . . 184.1.3 Loading data from network disc . . . . . . . . . . . . 18
4.2 Storing data . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
5 Image viewing tools 215.1 Viewing options . . . . . . . . . . . . . . . . . . . . . . . . . 215.2 Crop image stack . . . . . . . . . . . . . . . . . . . . . . . . . 215.3 Zoom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215.4 Adjust contrast . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.4.1 Manual adjustment . . . . . . . . . . . . . . . . . . . 215.4.2 Automatic adjustment . . . . . . . . . . . . . . . . . 22
5.5 Measure distance . . . . . . . . . . . . . . . . . . . . . . . . . 225.6 Hide/Show overlay . . . . . . . . . . . . . . . . . . . . . . . . 225.7 Resample image stack . . . . . . . . . . . . . . . . . . . . . . 22
6 Cardiac reconstruction - Step by step 25
7 LV segmentation - Step by step 277.1 Automatic LV segmentation . . . . . . . . . . . . . . . . . . . 277.2 Manual LV segmentation . . . . . . . . . . . . . . . . . . . . 287.3 Erase LV segmentation . . . . . . . . . . . . . . . . . . . . . 287.4 Validation of LV segmentation . . . . . . . . . . . . . . . . . 28
7.4.1 Summary of LV segmentation validation . . . . . . . 28
8 RV segmentation - Step by step 298.1 Manual RV segmentation . . . . . . . . . . . . . . . . . . . . 298.2 Erase RV segmentation . . . . . . . . . . . . . . . . . . . . . 298.3 Validation of RV segmentation . . . . . . . . . . . . . . . . . 29
8.3.1 Summary of RV segmentation validation . . . . . . . 29
9 ROI analysis - Step by step 319.1 Manual ROI analysis . . . . . . . . . . . . . . . . . . . . . . 319.2 Erase ROI segmentation . . . . . . . . . . . . . . . . . . . . . 319.3 Validation of the ROI analysis . . . . . . . . . . . . . . . . . 31
9.3.1 Summary of ROI validation . . . . . . . . . . . . . . 33
10 Bullseye analysis - Step by step 35
11 Report generation - Step by step 37
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1 Terms and conditions
This manual contains Instructions For Use, to safely be able to use SegmentCT.
1.1 Regulatory status
Segment CT bears the CE marking of conformity and is certified accordingto the ISO 13485 standard.
Users are required to investigate the regulatory requirements pertinent totheir country or location prior to using Segment CT. It is in the users re-sponsibility to obey these statues, rules and regulations.
1.2 Conditions for use
• The software may only be used by professionals trained in Cardiac CT.
• The software should be used to read images from CT Scanners. Imagescan be supplied either by CD’s or by using DICOM standard to transferfiles directly from the scanner or PACS systems.
• The user is responsible for installing Segment CT. Medviso provide on-line assistance in the installation process if needed. To install SegmentCT you need to be Administrator on the computer to install on.
• Users should participate in an online training session held by Medvisoprior to use Segment CT. This is provided by Medviso as a part of thesoftware trial process.
1.3 Indications for use
Segment CT is a software that display and analyzes medical images in DICOM-format using images acquired from CT scanners. Segment CT is designedfor review, quantification and reporting of cardiovascular structures usingmulti-slice and multi-frame CT images. Images and associated data analysiscan be stored, communicated, rendered, and displayed within the softwaresystem and transferred bi-directionally to and from PACS system. Segment
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CHAPTER 1. TERMS AND CONDITIONS
CT is intended to use for the patient population and medical indicationsgiven in the Instructions for Use for the device. The data produced by Seg-ment CT is intended to be used to support qualified cardiologist, radiologistor other licensed professional healthcare practitioners for clinical decisionmaking. The device is not intended to give direct medical adviceor treatment suggestions for a patient. It is a support tool thatprovides relevant clinical data as a resource to the clinician.
1.4 Intended patient population
The device can be used on the following patient population
Age From children to adult (radiation inappropriateness versus theclinical need is the limiting age factor)
Weight No limitations. The lower limitations lay in the resolution ofthe CT image and the upper limitations is to fit in the CTscanner
Height No limitations. The lower limitations lay in the resolution ofthe CT image and the upper limitations is to fit in the CTscanner
Health Possible contrast agent contraindications and general inappro-priateness of radiation
Patient state Patient is not user
1.5 Medical indications
The device can be used for the following medical indications
• Provide clinical data by quantifying the following cardiovascular struc-tures in cardiac CT images
– Ventricular volumes and mass
– Areas and distances
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1.6. SAFETY INSTRUCTIONS
1.6 Safety Instructions
The computer where Segment CT is installed should have
• anti-virus protection installed to protect against cyber attacks
• login to access Segment CT to ensure that only accredited users usethe device
• backup on patient data to ensure no data is lost
In the preferences for Segment CT the user can activate user login to thedevice and user logging for the usage of the device.
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2 Conventions andAbbreviations
This chapter describes the typographic conventions in this manual and in theprogram.
2.1 Typographic conventions
A Key A at the keyboard.Ctrl-A Control key. Hold down Ctrl key and A simultaneously.
Icon in toolbar.*.mat Filename extension.C:/Program Folder.File Menu, e.g. File menu.File→Save As Sub menu, e.g. under the File menu the item Save As is found.Close Push/Toggle button in the graphical user interface.} Endocardium Radiobutton in the graphical user interface.� Single frame Checkbox in the graphical user interface.
2.2 Trademarks
Below are some of the trademarks used in this manual.
• Segment CT is a trademark of Medviso AB.
• Segment DICOM Server is a trademark of Medviso AB.
• Sectra PACS is a trademark of Sectra Imtec AB, (http://www.sectra.se).
• Matlab is a trademark of the Mathworks Inc, (http://www.mathworks.com).
2.3 AbbreviationsCT Computed TomographyLV Left VentricleROI Region of InterestRV Right Ventricle
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3 Getting started
3.1 System requirements
• Operating System: 64-bit Windows 10
• Computer with 16 GB of memory or more
• Harddisk with at least 1 GB of available space
• Graphics card supporting both DirectX and OpenGL
• Internet connection for software license management
• Systems with two screens is recommended
• Using SSD disk for reading data is recommended
3.2 Installation
To be able to perform the installation you need to have administrator priv-ileges on the machine. The latest Segment CT version can be downloadedfrom Medviso AB homepage (http://medviso.com/download2/). You needa password to download the software, which you should have received at thetime of purchase. If you have lost the password, please contact [email protected] the Installation file, double click it and follow the instructions inthe figures below.
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CHAPTER 3. GETTING STARTED
Figure 1: Click on Next.
Figure 2: Select Add a shortcut to the desktop. Click on Next.
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3.2. INSTALLATION
For first time installation, Matlab Compiler Runtime (MCR) needs tobe installed according to Figure 3 - 6. For upgrading, continue according toFigure 7.
Figure 3: Click on Next.
Figure 4: Select Yes. Click on Next.
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CHAPTER 3. GETTING STARTED
Figure 5: Click on Install.
Figure 6: Wait for completed process.
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3.2. INSTALLATION
For upgrading, only install Segment CT according to Figure 7 - 8.
Figure 7: Click on Next.
Figure 8: Click on Install.
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CHAPTER 3. GETTING STARTED
For both first time installation and upgrading, continue according to Fig-ure 9.
Figure 9: Wait for completed process.
Figure 10: Click on Finish.
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3.3. ADD SOFTWARE LICENSE CODE
3.3 Add software license code
For new installations you need to add your license code for Segment CT.Add your license code after installation by starting Segment CT and se-lect Generate License under the Help menu in Segment CT. Note thatyou have to run the software as Administrator to be able to add the li-cense code in Segment CT. If you have lost the license code, please [email protected].
3.4 Starting Segment CT
To start the program, double click the file C:/Program Files/Segment CT/Segment
CT.exe, or your shortcut to it. When starting the software, the image in Fig-ure 11 should be displayed. If it is not displayed, then the software is notcorrectly installed.
Figure 11: Startup window for Segment CT.
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CHAPTER 3. GETTING STARTED
3.5 Uninstallation
To uninstall Segment CT, remove all files in the folder C:/Program/Medviso/SegmentCT or C:/Program Files/Medviso/Segment CT. User preferences are storedin the Application Data and the subfolder Segment CT under each useraccount. To uninstall the Matlab Compiler Runtime, use the Windows func-tionality Install or Remove Programs in the control panel menu.
3.6 Software overview
An overview of Segment CT is given in Figure 12. The letters in the figurewill be used as references throughout this manual.
Figure 12: Main graphical user interface. The letters in the figure will beused as references throughout this document.
To learn more about each tool, hold the mouse over the icon in the softwareand a help text will be displayed.
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3.7. FIRST TIME RUNNING SEGMENT CT
3.7 First time running Segment CT
The first time Segment CT is started, it runs a setup process which can takea while, so be patient. To complete the setup, set preferences and windowpositions as described in Sections 3.7.1 and 3.7.2.
3.7.1 Setting preferences
It is recommended to set the preferences of which folders to use to avoidbrowsing each time you want to load or save a file. It is invoked by using the
icon (p). Set Data, Export and CD folders.
3.7.2 Setting window positions
The position of the main window for Segment CT can be set by dragging thewindow to an optional position and size. The size and position will be savedso that next time Segment CT is launched the same position will be used.In case where one have switched to another monitor, Segment CT may moveoutside the screen. In this case you could press Shift-Ctrl-R to reset GUIpositions. This is also available under the File menu (a).
3.7.3 PACS connection
Setting up PACS connection and Segment Server usually requires help fromyour local PACS support, and we recommend that you contact us to setupa telephone / web-based video conference to make this process as smooth aspossible. The Database and PACS connection manual and the Sectra PACSplugin manual is found at Medviso AB homepage(http://medviso.com/products/cmr/resources/). The Sectra PACS pluginmay require additional Microsoft Visual C++ components that can be down-loaded from Medviso AB homepage (http://medviso.com/download2/).
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4 Loading and storing Data -Step by step
4.1 Loading data
To load patient data from the database, follow Section 4.1.1. To load patientdata from PACS, follow Section 4.1.2. To load patient data from networkdisc, follow Section 4.1.3.
4.1.1 Loading data from database
1. Click on the tool (a), Figure 13 is shown.
Figure 13: Graphical patient selector.
2. Select patient.
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CHAPTER 4. LOADING AND STORING DATA - STEP BY STEP
3. Patients can be stored in two formats; DICOM, or Segment CT format.For images in DICOM format, click Select & Load , Figure 14 is shown.For images in Segment CT format click Load all .
4. Select image series to load in Figure 14.
Figure 14: Graphical image series selector.
5. Click on Load .
4.1.2 Loading data from PACS
1. Select Import from PACS in the File menu, Figure 15 is shown.
2. Enter patient or study details and perform search.
3. Select study and series to load.
4. Load the study into Segment CT by select Open files .
4.1.3 Loading data from network disc
1. Select Open from Disc in the File menu, Figure 16 is shown.
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4.1. LOADING DATA
Figure 15: Interface to import image stacks from PACS.
Figure 16: Image stack loading selector.
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CHAPTER 4. LOADING AND STORING DATA - STEP BY STEP
2. Select image stack to load.
3. For DICOM files, select crop size for the image stack and crop theimage.
4. Click on Load Selected File(s) or Folder(s) .
4.2 Storing data
1. To store images including delineation to Patient Database, click on the
tool (b).
2. To store images including delineation to Disc, select Save to Disc in theFile menu (a).
3. To store images including delineation to PACS, select Save to PACS inthe File menu (a).
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5 Image viewing tools
5.1 Viewing options
• Choose panel viewing option by using , , , , , , ,
(c)
• To play a movie of the image stacks, use the tools , (d)
• To synchronize all image stacks, use the tool
• To change between single frame mode or all frames mode, use the tools
,
• To hide the icons and the result panel, use the tools ,
5.2 Crop image stack
1. Click on mode (h).
2. Select the tool (i).
3. Crop an image stack by mark the region in the image stack.
5.3 Zoom
1. Select image stack.
2. Use the tools and (f) to zoom in and zoom out in the imagestack.
5.4 Adjust contrast
5.4.1 Manual adjustment
1. Select image stack.
2. Select the tool (i) under mode (h).
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CHAPTER 5. IMAGE VIEWING TOOLS
3. Adjust the contrast and brightness by right click and drag the mousein the image stack (right-left for contrast and up-down for brightness).
5.4.2 Automatic adjustment
The automatic contrast and brightness adjustment is based on the intensityvalues inside the LV segmentation. If no LV segmentation exist, default HUvalues are used in the adjustment.
• To automatically adjust contrast and brightness in the selected image
stack, select (i) under mode (h).
• To automatically adjust contrast and brightness in all loaded image
stacks, select (i) under mode (h).
5.5 Measure distance
1. Click on mode (h).
2. Select the tool (i).
3. Measure a distance by dragging the mouse from start to end point inthe image stack.
4. To make a curved line, with pressed Shift set points at desired posi-tions on the image.
5.6 Hide/Show overlay
1. Select image stack with any type of overlay.
2. Use the tool to show or hide all overlays like segmentation, text,points, measurements.
5.7 Resample image stack
Select image stack you want resample and choose the following resamplingtype:
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5.7. RESAMPLE IMAGE STACK
• Select Upsample/Downsaple Image (In Plane) under menu Resample im-age stack under menu Image tools to increase/decrease image resolution(in plane).
• Select Upsample/Downsaple Slices under menu Resample image stackunder menu Image tools to increase/decrease number of image slices.
• Select Upsample/Downsaple Temporal under menu Resample image stackunder menu Image tools to increase/decrease number of time frames.
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6 Cardiac reconstruction - Stepby step
To be able to perform automatic segmentation of the left ventricle and rightventricle, as described in 7 and 8, the original transversal CT image stackmust be reconstructed to short-axis image stack.
1. To reconstruct the transversal image stack select LV mode and then the
tool (i). A new interface is open, as shown in Figure 17.
Figure 17: Interface for cardiac reconstruction.
2. Use left mouse click to define LV AV-plane (two blue points). Use rightmouse click to define LV epicadial apex (one red point). Use shift-clickon the mouse to define pulmonary valve (one magenta point).
3. Click on RV Slice and LV Slice to toggle between the slices where youhave placed the RV point and the LV points, respectively.
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CHAPTER 6. CARDIAC RECONSTRUCTION - STEP BY STEP
4. Click on Generate orthogonal image . This generates a orthogonal image,as defined by the dotted red line in the Original image panel.
5. In the orthogonal image, use left mouse click to define LV AV-plane(two blue points) and right mouse click to define LV epicadial apex(one red point).
6. Enter slice thickness for the final generated short-axis image stack.
7. Select if you would like to perform automatic LV segmentation and/orautomatic RV segmentation on the generated short-axis image stack.
8. Click on Generate Short-axis Stack to generate the short-axis image stackto the main Segment CT interface.
9. If you already have been generated a short-axis stack and only wouldlike to store the defined reonstruction points, click on Save Point Positions .
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7 LV segmentation - Step bystep
7.1 Automatic LV segmentation
1. The automatic LV segmentation is applied to a reconstructed short-axis stack, generated by cardiac reconstruction as described in Chapter6. The LV slices to be included in the automatic LV segmentation isdefined by the points entered in the reconstruction process.
2. Start the automatic LV segmentation by select LV mode (h) and select
(i).
3. The segmentation result is presented in the main window where vol-umes curve can be reviewed (k) and the measured LV volumes arepresented, according to Figure 18 (j).
Figure 18: LV analysis result.
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CHAPTER 7. LV SEGMENTATION - STEP BY STEP
4. If needed, correction of the LV segmentation can be performed by using
the following tools: , , , , , , and (i).
7.2 Manual LV segmentation
For manual delineation of the LV, the following tools can be used: ,
, , (i). If the checkbox Single Frame Mode (m) is selected, then theoperation is only applied to the current time frame.
7.3 Erase LV segmentation
To erase the LV segmentation, select Clear All LV Segmentation from LV menu(a).
7.4 Validation of LV segmentation
1. A. Martinsson, A. Gilland, J. Backe, H. Fransson, E. Heiberg, G. En-gstrom, J. G. Smith, E. Ostenfeld, Assessment of ventricular dimen-sions from computed tomography in a prospective cohort study: theSCAPIS Malmo-cohort. EuroEcho Imaging 2018.
7.4.1 Summary of LV segmentation validation
The result in [1] showed a bias between automatic LV segmentation by Seg-ment CT and manual delineation for LVM 10.9 ± 8.5 g and EDV -9.3 ± 5.7mL in a set of 200 patients.
No uncertainty/error information is showed in the software together withthe LV measurements.
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8 RV segmentation - Step bystep
8.1 Manual RV segmentation
For manual delineation of the RV, the following tools can be used: ,
, , (i). If the checkbox Single Frame Mode (m) is selected, then theoperation is only applied to the current time frame.
8.2 Erase RV segmentation
To erase the RV segmentation, select Clear All RV Segmentation from RVmenu (a).
8.3 Validation of RV segmentation
1. E. Heiberg, J. Sjogren, M. Ugander, M. Carlsson, H. Engblom, and H.Arheden, Design and validation of Segment–freely available softwarefor cardiovascular image analysis, BMC Med Imaging 10 p 1, 2010.
8.3.1 Summary of RV segmentation validation
Manual segmentation and measurements for right ventricular volumes areperformed withing the scope of [1].
No uncertainty/error information is showed in the software together withthe RV measurements.
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9 ROI analysis - Step by step
9.1 Manual ROI analysis
1. Click on ROI mode (h).
2. If the checkbox Single Frame Mode (m) is selected, then the operation isonly applied to the current time frame.
3. To place a ROI, use one of the tools (i) or .
4. Scale the ROI with the tool (i).
5. Translate the ROI with the tool (i).
6. Change the ROI segmentation by using the correction tool (i).
7. Select ROIs with Shift-click with the tool (i).
8. Set the label of selected ROIs with the tool (i).
9. Set the color of selected ROIs with the tool (i).
10. Select ROI Analysis from ROI menu to perform ROI analysis accordingto Figure 19 (a).
9.2 Erase ROI segmentation
Delete selected ROIs by selecting Delete Selected ROIs, and all ROIs by se-lecting Clear All ROIs in the ROI menu (a).
9.3 Validation of the ROI analysis
1. E. Heiberg, J. Sjogren, M. Ugander, M. Carlsson, H. Engblom, and H.Arheden, Design and validation of Segment–freely available softwarefor cardiovascular image analysis, BMC Med Imaging 10 p 1, 2010.
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CHAPTER 9. ROI ANALYSIS - STEP BY STEP
Figure 19: ROI analysis GUI.
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9.3. VALIDATION OF THE ROI ANALYSIS
9.3.1 Summary of ROI validation
Manual segmentation and measurements for ROI volumes are performedwithing the scope of [1].
No uncertainty/error information is showed in the software together withthe ROI measurements.
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10 Bullseye analysis - Step bystep
1. Start with manual or automated segmentation of the LV as describedin Chapter 7.
2. Select the image stack to perform bullseye analysis of.
3. Click on the tool (g) to open Bullseye analysis interface, as shownin Figure 20.
Figure 20: Bullseye analysis GUI.
4. Set the slice rotation by dragging the slider so the yellow line is in themiddle of septum. Click on Update . This step is important to have acorrect bullseye plot.
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CHAPTER 10. BULLSEYE ANALYSIS - STEP BY STEP
5. Select the slices to include (marked as yellow lines) in the bullseyeanalysis.
6. Select the parameter to plot.
7. Set the viewing parameters.
8. Click on Export to export data to spreadsheet.
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11 Report generation - Step bystep
1. To generate a patient report, click on (g) to show the report gen-erator.
Figure 21: Report generator.
2. Select measurements and images to include in the report. Items that aregrayed out is not available since measurements or images are missing.
3. Ensure that the appropriate reference values are chosen.
4. Write your impression about the patient.
5. Click on Generate HTML report to generate a HTML report.
6. Click on Send to PACS to send the report to PACS.
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