Segment CT Instructions For Use - English

Segment CT Instructions For Use - English April 23, 2018 Software platform v2.2 R6353

MEDVISO AB http://www.medviso.com Griffelvägen 3 SE-224 67 Lund Sweden Tel: +46-76-183 6442 ii

Contents 1 Terms and conditions 1 1.1 Regulatory status........................ 1 1.2 Conditions for use........................ 1 1.3 Indications for use........................ 1 2 Conventions and Abbreviations 3 2.1 Typographic conventions.................... 3 2.2 Trademarks............................ 3 2.3 Abbreviations.......................... 3 3 Getting started 5 3.1 System requirements....................... 5 3.2 Installation............................ 5 3.2.1 Installing Matlab Compiler Runtime......... 5 3.2.2 Installing Segment CT................. 7 3.3 Starting Segment CT...................... 7 3.4 Uninstallation.......................... 7 3.5 Software overview........................ 7 3.6 First time running Segment CT................. 9 3.6.1 Setting preferences................... 9 3.6.2 Setting window positions................ 9 3.6.3 Patient database.................... 9 3.6.4 PACS connection.................... 9 4 Loading and storing Data - Step by step 11 4.1 Loading data........................... 11 4.1.1 Loading data from database.............. 11 4.1.2 Loading data from PACS................ 12 iii

CONTENTS 4.1.3 Loading data from network disc............ 13 4.2 Storing data........................... 13 5 Image viewing tools 15 5.1 Viewing options......................... 15 5.2 Crop image stack......................... 15 5.3 Zoom............................... 15 5.4 Adjust contrast.......................... 15 5.4.1 Manual adjustment................... 15 5.4.2 Automatic adjustment................. 16 5.5 Measure distance......................... 16 6 3D Segmentation module 17 6.1 3D Segmentation - Step by step................ 18 6.2 Segmentation tools (panel a).................. 19 6.3 Object tools (panel j)...................... 20 6.4 View modes (panel b)...................... 21 6.5 Sort out tool........................... 22 6.6 Split tool............................. 22 6.7 Smoothing tool.......................... 22 6.8 Vessel tool............................ 23 6.9 Preview / generate STL file................... 25 7 Cardiac reconstruction - Step by step 27 8 LV segmentation - Step by step 29 8.1 Automatic LV segmentation................... 29 8.2 Manual LV segmentation.................... 30 8.3 Erase LV segmentation..................... 30 9 RV segmentation - Step by step 31 9.1 Manual RV segmentation.................... 31 9.2 Erase RV segmentation..................... 31 10 LV Perfusion analysis - Step by step 33 11 ROI analysis - Step by step 35 11.1 Manual ROI analysis...................... 35 11.2 Erase ROI segmentation..................... 35 iv

CONTENTS 12 Bullseye analysis - Step by step 37 13 Report generation - Step by step 39 v

1 Terms and conditions This manual contains Instructions For Use, to safely be able to use Segment CT. 1.1 Regulatory status Segment CT bears the CE marking of conformity and is certified according to the ISO 13485 standard. Segment CT is based almost entirely on the software Segment which is FDA approved with FDA 510(k) number K090833. An application for FDA approval for Segment CT is work in progress. Users are also required to investigate the regulatory requirements pertinent to their country or location prior to using Segment CT. It is in the users responsibility 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 is a tool to provide relevant clinical data. The clinician is solely responsible for interpretation of clinical data and taking decisions how to manage the patients. The software should be used to read images from CT Scanners. Images can be supplied either by CD s or by using DICOM standard to transfer files directly from the scanner or PACS systems. 1.3 Indications for use Segment CT is a software that display and analyzes DICOM-compliant cardiovascular images acquired from CT scanners. Segment CT is designed for review, quantification and reporting of cardiovascular structures using multi-slice and multi-frame CT images. Segment CT provides validated and reproducible data for supporting the evaluation of cardiac function. Images and associated data analysis can be stored, communicated, rendered, and displayed within the system and across PACS system. The data produced 1

CHAPTER 1. TERMS AND CONDITIONS by Segment CT is intended to be used to support qualified cardiologist, radiologist or other licensed professional healthcare practitioners for clinical decision making. It is a support tool that provides relevant clinical data as a resource to the clinician and is not intended to be a source of medical advice or to determine or recommend a course of action or treatment for a patient. 2

2 Conventions and Abbreviations This chapter describes the typographic conventions in this manual and in the program. 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 Abbreviations CT Computed Tomography LV Left Ventricle ROI Region of Interest RV Right Ventricle 3

3 Getting started 3.1 System requirements Windows 10 (64 bit). Computer with 16 GB of memory or more. Harddisk with at least 1 GB of available space. Graphics card, CUDA enabled with 4GB memory or more. versions of the software will use GPU for faster computations. Future 3.2 Installation For first time installation, start with installing Matlab Compiler Runtime (Section 3.2.1) and thereafter installing Segment CT (Section 3.2.2). For upgrading, only install Segment CT (Section 3.2.2). To be able to perform the installation you need to have administrator privileges on the machine. 3.2.1 Installing Matlab Compiler Runtime 1. Download the MCR file and double click it. The file can be downloaded from Medviso AB homepage (http://medviso.com/download2/). 2. Follow the instructions in Figures 1-4. Figure 1: Click on Run. 5

CHAPTER 3. GETTING STARTED Figure 2: Click on OK. Figure 3: Click on Install. Figure 4: Click on Next. 6

3.3. STARTING SEGMENT CT 3. Reboot the computer. 3.2.2 Installing Segment CT 1. The latest Segment CT version can be downloaded from Medviso AB homepage (http://medviso.com/download2/). Download the file install Segment CT 2px Ryyyy double click it and follow the instructions. You need a password to download the software, which you should have received at the time of purchase. If you have lost the password, please contact sales@medviso.com. 2. For new installations you need to add your license code for Segment CT. Add your license by enter your license code in the installation process. You can also add your license code after installation by starting Segment CT and select Generate License under the Help menu in Segment CT. Note that you have to run the software as Administrator to be able to add the license code in Segment CT. A third way of adding your license is to add a license file (named code.lic) to the same folder as where Segment CT is installed. If you do not have a license code, please contact sales@medviso.com. 3.3 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 Figure 5 should be displayed. If it is not displayed, then the software is not correctly installed. 3.4 Uninstallation To uninstall Segment CT, remove all files in the folder C:/Program/Segment CT or C:/Program Files/Segment CT. User preferences are stored in the Application Data and the subfolder Segment CT under each user account. To uninstall the Matlab Compiler Runtime, use the Windows functionality Install or Remove Programs in the control panel menu. 3.5 Software overview An overview of Segment CT is given in Figure 6. The letters (a-o) in the figure will be used as references throughout this manual. 7

CHAPTER 3. GETTING STARTED Figure 5: Startup window for Segment CT. Figure 6: Main graphical user interface. The letters (a-o) in the figure will be used as references throughout this document. 8

3.6. FIRST TIME RUNNING SEGMENT CT To learn more about each tool, hold the mouse over the icon in the software and a help text will be displayed. 3.6 First time running Segment CT The first time Segment CT is started, it runs a setup process which can take a while, so be patient. To complete the setup, set preferences and window positions as described in Sections 3.6.1 and 3.6.2. 3.6.1 Setting preferences It is recommended to set the preferences of which folders to use to avoid browsing each time you want to load or save a file. It is invoked by using the Preferences menu (a). Set Data, Export and CD folders. 3.6.2 Setting window positions The position of the main window for Segment CT can be set by dragging the window to an optional position and size. The size and position will be saved so 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 move outside the screen. In this case you could press Shift-Ctrl-R to reset GUI positions. This is also available under the File menu (a). 3.6.3 Patient database We recommend that you start by using our example patient database. Download the file Patientdatabase.zip from Medviso AB homepage (http://medviso.com/download2/). The file is quite large (1.4 GB). Unpack the file and place the contents in a folder. It is recommended to place it in a subfolder where Segment CT is installed. In Segment CT you need to set the location of the patient database. Click on Preferences and click on Advanced System and DICOM Settings. A new user interface appears and click on Database Folder, select the folder where the file patientdatabase.mat resides. 3.6.4 PACS connection Setting up PACS connection and Segment Server usually requires help from your local PACS support, and we recommend that you contact us to setup 9

CHAPTER 3. GETTING STARTED a telephone / web-based video conference to make this process as smooth as possible. The Database and PACS connection manual and the Sectra PACS plugin manual is found at Medviso AB homepage (http://medviso.com/products/cmr/resources/). The Sectra PACS plugin may require additional Microsoft Visual C++ components that can be downloaded from Medviso AB homepage (http://medviso.com/download2/). 10

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 patient data from PACS, follow Section 4.1.2. To load patient data from network disc, follow Section 4.1.3. 4.1.1 Loading data from database 1. Click on the tool (a), Figure 7 is shown. Figure 7: Graphical patient selector. 2. Select patient. 3. Patients can be stored in two formats; DICOM, or Segment CT format. For images in DICOM format, click Select & Load, Figure 8 is shown. For images in Segment CT format click Load all. 11

CHAPTER 4. LOADING AND STORING DATA - STEP BY STEP 4. Select image series to load in Figure 8. Figure 8: 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 9 is shown. Figure 9: Interface to import image stacks from PACS. 12

4.2. STORING DATA 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 10 is shown. Figure 10: Image stack loading selector. 2. Select image stack to load. 3. For DICOM files, select crop size for the image stack and crop the image. 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). 13

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). 5.2 Crop image stack 1. Click on Misc 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 (e) to zoom in and zoom out in the image stack. 5.4 Adjust contrast 5.4.1 Manual adjustment 1. Select image stack. 2. Select the tool (i). 3. Adjust the contrast and brightness by right click and drag the mouse in the image stack (right-left for contrast and up-down for brightness). 15

CHAPTER 5. IMAGE VIEWING TOOLS 5.4.2 Automatic adjustment The automatic contrast and brightness adjustment is based on the intensity values inside the LV segmentation. If no LV segmentation exist, default HU values are used in the adjustment. To automatically adjust contrast and brightness in the selected image stack, select (e). To automatically adjust contrast and brightness in all loaded image stacks, select (e). 5.5 Measure distance 1. Click on Misc mode (h). 2. Select the tool (i). 3. Measure a distance by dragging the mouse from start to end point in the image stack. 16

6 3D Segmentation module The module allows to perform a 3D segmentation for 3D printing purposes, or to export to CAD/CFD analysis software for patient-specific modelling. The segmentation process is to convert the image volume into a set of distinct objects by assigning which voxels in the image belongs to which objects. Before printing or exporting, the objects are converted to surfaces. 3D Segmentation module is started with the icon tab. found under the 3D Print An overview of the module is given in Figure 11. To learn more about each tool, hold the mouse over the icon in the software and a help text will be displayed. In the standard 4 panel view the image with segmentation overlay is displayed in the three standard views; (transversal view, coronal view, sagittal view, and a panel showing object likelihood. Figure 11: Overview of graphical user interface. The letters (a-j) in the figure will be used as references throughout this chapter. 17

CHAPTER 6. 3D SEGMENTATION MODULE 6.1 3D Segmentation - Step by step This section outlines the typical steps involved when creating a 3D model. Details on how each of the tool works is given in Section 6.2. 18 1. Create a vision. The first step is to create a vision on how the finished printed object should look. What parts of the image volume should be included? How should the objects be connected so that the printed model does not fall apart? Creating a vision together with the colleages that will used the finished model is essential, for sucessful usage of the technology. 2. Crop the image volume. This makes the entire workflow faster and easier. Cropping is performed with the crop tool. Crop relatively tight around object of interest. Objects from different cropped regions can be combined in exporting step as the software remembers position of objects also after crop operations. 3. Adjust object likelihood function. Object likelihood is a mapping function that maps voxel intensities to likelyhood of the object to be segmented. Use either predefined mapping functions or manually adjust the curve. Type of mapping function can be changed by selecting one of the three mappint functions: Pos - Positive, Neg - Negative, Gauss - Gaussian. Object likelihood is adjusted in panel h. 4. Create object. There are two main methods to segment an object, either draw the object in 3D using the 3D draw tool object using the pick tool., or pick the 5. Separate objects. Often objects are connected and needs to be separated. There are two main methods to split an object into two objects. A) Use the split tool, or B) Use set operations of objects to remove one object from another object. 6. Manual adjustments. Manual segmentation tools are described in Section 6.2. The suggested workflow is to work with one object at a time. Do your manual adjustment for one object before you start

6.2. SEGMENTATION TOOLS (PANEL A) processing the next object. In the end of the process you can merge and split objects as desired. 7. Fill objects. In general, it is not necessary that the objects filled for 3D printing, however filling is highly recommended as A) Smoothing of non filled objects may erase sections of the object, B) filled object generates simpler surfaces and better control of support structures for 3D printing. Fill of objects is done using the fill tool. 8. Smooth object. Before exporting the object smoothing is desirable. For details, see Section 6.7. 9. Export / preview. When the segmentation of the desired anatomical objects is complete, start the export/preview tool. For details, see Section 6.9. 6.2 Segmentation tools (panel a) Segmentation tools are generally applied to current object shown in panel h, except for some tools that creates new objects. 2D/3D. (hot-key 2, 3) Selects if tools are applied in 2D or 3D. 3D paint tool. Hold down mouse and drag small sections of the object at a time. Crosshair tool. Put crosshair to mark point in 3D. Local threshold. A local threshold operation is performed within the pen tip radius. This tool can be used to locally paint regions according to object probability. Pen radius in mm is adjusted in panel g. Draw tool, add region to segmentation. adjusted in panel g. Pen radius in mm is Erase tool, remove region from segmentation. Pen radius in mm is adjusted in panel g. Pick tool (hot-key p), left click in image to pick an object and add to current object. In 2D mode use shift and mouse wheel to pick objects at crosshair position from multiple slices. 19

CHAPTER 6. 3D SEGMENTATION MODULE Keep tool (hot-key k), left click in image to keep a part of the current object and create a new object. Typically useful with vessel tool. Split tool, splits the current object. For details, see Section 6.6. Box tool, add segmentation / remove segmentation inside 3D box. This tool can be used to crop objects and to add support structures for models. Crop tool, crop image volume. Fill tool (hot-key 2D: f, 3D: F), fill object in 2D/3D. Active contour tool (hot-key a). Applicable in 2D. Adjusts and smooth contour using active contour algorithm. Use Ctrl-mouse wheel to go to next slide and apply active contour tool. Threshold image volume. This creates a new object by thresholding. Threshold is adjusted by object likelihood function. Vessel tool, opens a new user interface. For details, see Section 6.8. Delete segmentation, delete segmentation from current object. Undo (hot-key Ctrl-Z), undo last drawing command. 6.3 Object tools (panel j) Working with objects is a good way to divide the segmentation task in smaller steps. The segmentation process typically creates many objects, and it is highly recommended to rename objects with understandable names and delete temporarily created objects as it may be hard to remember the content of each object. Objects may also be of use in the segmentation process by using set operations,,, to combine objects algebraically. In particular this is extra powerful when the objects have been created using different object likelihood mappings. Sort out object. Removes non connected parts. For details, see Section 6.5. Smooth object. For details, see Section 6.7. Erode object. creates a new object that is one voxel thinner than the parent object. 20

6.4. VIEW MODES (PANEL B) Dilate object. creates a new object that is one voxel thicker than the parent object. Hollow. Make a filled object hollow. Minus. Takes first object minus the second, and creates a new object. Not. Inverts the object, and creates a new object. Union. Joins two or more objects, and creates a new object. Cut. Takes the intersection of two or more objects, and creates a new object. Move up. Move object up in list. Move down. Move object down in list. New object. Create a new object. Copy object. Copy the selected object to a new object. Rename object. Rename the selected object. Delete object. Deletes the selected object. 6.4 View modes (panel b) Standard view with, transversal view, sagittal view, coronal view, and object likelihood image. To switch between active view use, or the hot keys (hot-key t = transversal view, hot-key s = sagittal view, hot-key c = coronal view.) Display - transversal view & likelihood image. (hot-key T) Display - sagittal view & likelihood image. (hot-key S) Display - coronal view & likelihood image. (hot key C) Refresh tools/view. Zoom out. Zoom in. Display segmentation countour (green line) Display segmentation as red overlay. Display segmentation in a 3D view. 21

CHAPTER 6. 3D SEGMENTATION MODULE Preview / generate STL file. For details, see Section 6.9. 6.5 Sort out tool Select. This tool is used to remove non connected parts of an object by keeping only the largest or n largest connected parts. The user interface is shown in Figure 12. The number of parts in the object are shown. Default option is to keep only the largest part (or n parts), or you can select to keep all parts larger than a specified volume. Each kept part is created as new object. Figure 12: User interface for Sort out. 6.6 Split tool Select. Put crosshair on the object you want to keep and right click on object you want to cut away. If possible put cross hair and right click on opposide side of a clear and visible cut region. If possible put the cross hair on solid parts such as the bone to indicate clearly parts that should not be deleted. If you want to keep both the objects, but only split them apart, make a copy of the object prior to splitting, work to split out one and use the algebraics function to get both desired objects. 6.7 Smoothing tool Select. User interface for Object smoothing is shown in Figure 13. How to apply smoothing step-by-step: 22

6.8. VESSEL TOOL 1. Adjust smoothing with editbox or slider 2. Press Apply smoothing to apply the smoothing and create a new smoothed object. Figure 13: User interface for Object smoothing. Top plot shows the spatial extent of the smoothing filter and the bottom panel shows an example of different smoothed objects in one dimension with 1,2, 4, 7 pixels width. 6.8 Vessel tool Select. Start by adjusting the object likelihood to enhance the vessels of interest maximally. Often if you want to enhance vessls, close to bones as illustrated in Figure 14, then use the Gaussian mapping as illustrated in the figure. Next start the vessel enhancement tool Figure 15.. The user interface is shown in In the user interface select start and end scale for the vessel enhancement. For large vessels it is recommended to use the 3D draw tool. Click 23

CHAPTER 6. 3D SEGMENTATION MODULE Figure 14: Adjust object likelihood to enhance vessels. Figure 15: User interface for vessel enhancement. 24

6.9. PREVIEW / GENERATE STL FILE Finish to create a new vessel enhancement object. Often from this object it is advantagous to use the keep tool final object. Then use to pick vessels to include in the to merge the kept objects. Often you also may want to use the tool to merge the detected vessels with a larger vessel manually draw as the vessel enhancement may fail precisely when a small vessel branches of a large vessel. 6.9 Preview / generate STL file Select. The user interface to generate STL-files is shown in Figure 16. Figure 16: Preview / generate STL file user interface. Step-by-step: 1. Select object to add to preview. 2. Select color with Color. 3. If desired, adjust transparity. 25

CHAPTER 6. 3D SEGMENTATION MODULE 4. Click Add object. 5. Repeat step 1-4 for all desired objects. 6. Inspect the visual output from all angles. 7. If the completed model is acceptable, then click Create STL, otherwise go back and edit the segmentation. When the 3D segmentation module is closed all objects are retained. Use the standard save functions in Segment CT to store segmentation and image volume to disc or patient database. 26

7 Cardiac reconstruction - Step by step To be able to perform automatic segmentation of the left ventricle and right ventricle, as described in 8 and 9, the original transversal CT image stack must 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 right mouse click to define LV epicadial apex (one red point). Use shift-click on the mouse to define pulmonary valve (one magenta point). 3. Click on RV Slice and LV Slice to toggle between the slices where you have placed the RV point and the LV points, respectively. 4. Click on Generate orthogonal image. This generates a orthogonal image, as defined by the dotted red line in the Original image panel. 27

CHAPTER 7. CARDIAC RECONSTRUCTION - STEP BY STEP 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/or automatic RV segmentation on the generated short-axis image stack. 8. Click on Generate Short-axis Stack to generate the short-axis image stack to the main Segment CT interface. 9. If you already have been generated a short-axis stack and only would like to store the defined reonstruction points, click on Save Point Positions. 28

8 LV segmentation - Step by step 8.1 Automatic LV segmentation 1. The automatic LV segmentation is applied to a reconstructed shortaxis stack, generated by cardiac reconstruction as described in Chapter 7. The LV slices to be included in the automatic LV segmentation is defined 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 volumes curve can be reviewed (k) and the measured LV volumes are presented, according to Figure 18 (j). Figure 18: LV analysis result. 4. If needed, correction of the LV segmentation can be performed by using the following tools:,,,,,, and (i). 29

CHAPTER 8. LV SEGMENTATION - STEP BY STEP 8.2 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 the operation is only applied to the current time frame. 8.3 Erase LV segmentation To erase the LV segmentation, select Clear All LV Segmentation from LV menu (a). 30

9 RV segmentation - Step by step 9.1 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 the operation is only applied to the current time frame. 9.2 Erase RV segmentation To erase the RV segmentation, select Clear All RV Segmentation from RV menu (a). 31

10 LV Perfusion analysis - Step by step 1. Start with manual or automated segmentation of the LV as described in Chapter 8. 2. Select the image stack to perform LV perfusion analysis of. 3. Select LV Perfusion from Analysis menu to start the analysis and open the perfusion analysis interface, as shown in Figure 19. Figure 19: LV perfusion analysis GUI. 4. Set the slice rotation by dragging the slider so the yellow line is in the middle of septum. This step is important to have a correct bullseye plot. 5. Select the parameter to plot. Perfusion Index (PI) for a myocardial region is defined as P I = Intensity myocardium Intensity bloodpool, where the blood pool intensity is the mean in each slice. Transmural Perfusion Ratio (TPR) for a subendo region is defined as T P R = Intensity subendo mean(intensity subepi, where the mean ) subepi intensity is the mean for the whole mycoardium. Transmural Fat is defined as regions in the myocardium with a HU within [-30 100]. 33

CHAPTER 10. LV PERFUSION ANALYSIS - STEP BY STEP Calcium can only be quantified in image stacks with a slice thickness of 3 mm. Calcified regions are defined as regions in the myocardium with a HU within [110 150]. 6. Set the viewing parameters. 7. Bullseye division for the 17 segment model is shown both in the longaxis view and in the short-axis view as colorcoded lines and frames, respectively. 8. You can pin-point corresponding region in both the short-axis view and the bullseye plot by a single left click on the mouse. 9. Click on Export bullseye to export data to spreadsheet. 34

11 ROI analysis - Step by step 11.1 Manual ROI analysis 1. Click on ROI mode (h). 2. If the checkbox Single Frame Mode (m) is selected, then the operation is only 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 according to Figure 20 (a). 11.2 Erase ROI segmentation Delete selected ROIs by selecting Delete Selected ROIs, and all ROIs by selecting Clear All ROIs in the ROI menu (a). 35

Figure 20: ROI analysis GUI.

12 Bullseye analysis - Step by step 1. Start with manual or automated segmentation of the LV as described in Chapter 8. 2. Select the image stack to perform bullseye analysis of. 3. Click on the tool (g) to open Bullseye analysis interface, as shown in Figure 21. Figure 21: Bullseye analysis GUI. 4. Set the slice rotation by dragging the slider so the yellow line is in the middle of septum. Click on Update. This step is important to have a correct bullseye plot. 5. Select the slices to include (marked as yellow lines) in the bullseye analysis. 6. Select the parameter to plot. 37

CHAPTER 12. BULLSEYE ANALYSIS - STEP BY STEP 7. Set the viewing parameters. 8. Click on Export to export data to spreadsheet. 38

13 Report generation - Step by step 1. After performing measurements, click on (g) to show the report generator. Figure 22: Report generator. 2. Select the desired sections to include in the report. Sections that are grayed out is not available since measurements, or images are missing. 3. Select the images to include in the report. 4. Ensure that the appropriate reference values are chosen. 5. Write your impression about the patient. 6. Click on Generate HTML report to generate a HTML report. 7. Click on Send to PACS to send the report to PACS. 39