Segment 3DPrint Instructions For Use - Englishmedviso.com/documents/segment3dp/segment3dpinstructions... · 2020-03-04 · 1 Terms and conditions This manual contains Instructions

Segment 3DPrintInstructions For Use - English

March 4, 2020

Software platform v3.0 R7900

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 . . . . . . . . . . . . . . . . . . . . . . . . 21.4 Intended patient population . . . . . . . . . . . . . . . . . . . 21.5 Applicable medical conditions . . . . . . . . . . . . . . . . . . 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 3DPrint . . . . . . . . . . . . . . . . . . . . 133.5 Uninstallation . . . . . . . . . . . . . . . . . . . . . . . . . . 143.6 Software overview . . . . . . . . . . . . . . . . . . . . . . . . 143.7 First time running Segment 3DPrint . . . . . . . . . . . . . . 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 3D Segmentation module 256.1 3D Segmentation - Step by step . . . . . . . . . . . . . . . . 256.2 Segmentation tools (panel a) . . . . . . . . . . . . . . . . . . 276.3 Object tools (panel k) . . . . . . . . . . . . . . . . . . . . . . 296.4 View modes (panel b) . . . . . . . . . . . . . . . . . . . . . . 306.5 Sort out tool . . . . . . . . . . . . . . . . . . . . . . . . . . . 306.6 Split tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306.7 Smoothing tool . . . . . . . . . . . . . . . . . . . . . . . . . . 316.8 Vessel tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316.9 Preview / generate STL file . . . . . . . . . . . . . . . . . . . 336.10 Storing segmentation . . . . . . . . . . . . . . . . . . . . . . 34

7 CT Cardiac analysis - Step by step 357.1 Cardiac reconstruction . . . . . . . . . . . . . . . . . . . . . . 357.2 LV analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

7.2.1 Automatic LV segmentation . . . . . . . . . . . . . . 367.2.2 Manual LV segmentation . . . . . . . . . . . . . . . . 367.2.3 Erase LV segmentation . . . . . . . . . . . . . . . . . 377.2.4 Validation of LV segmentation . . . . . . . . . . . . . 37

7.3 RV analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387.3.1 Manual RV segmentation . . . . . . . . . . . . . . . . 387.3.2 Erase RV segmentation . . . . . . . . . . . . . . . . . 387.3.3 Validation of RV segmentation . . . . . . . . . . . . . 38

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CONTENTS

8 MR Cardiac analysis - Step by step 398.1 LV analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

8.1.1 Automatic LV segmentation [1] . . . . . . . . . . . . 398.1.2 Manual LV segmentation . . . . . . . . . . . . . . . . 408.1.3 Erase LV segmentation . . . . . . . . . . . . . . . . . 408.1.4 Copying LV segmentation . . . . . . . . . . . . . . . 418.1.5 Validation of LV segmentation . . . . . . . . . . . . . 418.1.6 Summary of LV segmentation validation . . . . . . . 41

8.2 RV analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418.2.1 Automatic RV segmentation [1] . . . . . . . . . . . . 418.2.2 Manual RV segmentation . . . . . . . . . . . . . . . . 438.2.3 Erase RV segmentation . . . . . . . . . . . . . . . . . 438.2.4 Validation of RV segmentation . . . . . . . . . . . . . 438.2.5 Summary of RV segmentation validation . . . . . . . 43

9 ROI analysis - Step by step 459.1 Manual ROI analysis . . . . . . . . . . . . . . . . . . . . . . 459.2 Erase ROI segmentation . . . . . . . . . . . . . . . . . . . . . 459.3 Validation of the ROI analysis . . . . . . . . . . . . . . . . . 45

9.3.1 Summary of ROI validation . . . . . . . . . . . . . . 47

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1 Terms and conditions

This manual contains Instructions For Use, to safely be able to use Segment3DPrint.

1.1 Regulatory status

Segment 3DPrint bears the CE marking of conformity and is certified ac-cording to the ISO 13485 standard.

Users are required to investigate the regulatory requirements pertinent totheir country or location prior to using Segment 3DPrint. It is in the usersresponsibility to obey these statues, rules and regulations.

1.2 Conditions for use

• The software may only be used by medically trained professionals.

• The software should be used to read medical images in DICOM format.Images can be supplied either by CD’s or by using DICOM standardto transfer files directly from the scanner or PACS systems.

• The software is a tool to provide relevant clinical data. Anatomicalmodels developed using the software is to be used as a resource tothe clinician and the clinician is solely responsible for interpretation ofclinical data and taking decisions how to manage the patients.

• The user is responsible for installing Segment 3DPrint. Medviso pro-vide online assistance in the installation process if needed. To installSegment 3DPrint you need to be Administrator on the computer toinstall on.

• Users should participate in an online training session held by Medvisoprior to use Segment 3DPrint. This is provided by Medviso as a partof the software trial process.

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CHAPTER 1. TERMS AND CONDITIONS

1.3 Indications for use

Segment 3DPrint is a software for visualization and image segmentation ofmedical images. The software aims to transfer imaging information from amedical imaging system such as a Computer Tomography (CT) scanner orMagnetic Resonance (MR) scanner to an output file or for visualization. Itis intended to generate anatomical 3D models for education or evaluatingsurgical treatment options. Segment 3DPrint is intended to be used by med-ically trained professionals for the patient population and medical conditionsgiven in the Instructions for Use for the device.

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 image and the upper limitations is to fit in the medicalscanner

Height No limitations. The lower limitations lay in the resolution ofthe image and the upper limitations is to fit in the medicalscanner

Health Possible contrast agent contraindications and general inappro-priateness of radiation or magnetic field dependt on used med-ical scanner for image acquisition

Patient state Patient is not user

1.5 Applicable medical conditions

The medical purpose of Segment 3DPrint is to generate patient-specific anatom-ical models for increased understanding of anatomy to be used for

• Education

• Communication

• Surgical planning / procedures evaluating surgical treatment options

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1.6. SAFETY INSTRUCTIONS

1.6 Safety Instructions

The computer where Segment 3DPrint is installed should have

• anti-virus protection installed to protect against cyber attacks

• login to access Segment 3DPrint to ensure that only accredited usersuse the device

• backup on patient data to ensure no data is lost

In the preferences for Segment 3DPrint the user can activate user login tothe device 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 3DPrint 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 VentricleMR Magnetic ResonanceROI 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

• CUDA enabled graphics card with 4GB memory or more

• Internet connection for software license management

• 3-button computer mouse

• 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 3DPrint version can be down-loaded from Medviso AB homepage (http://medviso.com/download2/). Youneed a password to download the software, which you should have receivedat the time of purchase. If you have lost the password, please [email protected]. Download the Installation file, double click it and fol-low the instructions in the 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 4: Select Yes. Click on Next.

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Figure 5: Click on Install.

Figure 6: Wait for completed process.

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3.2. INSTALLATION

For upgrading, only install Segment 3DPrint according to Figure 7 - 8.


Figure 8: Click on Install.

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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 3DPrint.Add your license code after installation by starting Segment 3DPrint andselect Generate License under the Help menu in Segment 3DPrint. Notethat you have to run the software as Administrator to be able to add thelicense code in Segment 3DPrint. If you have lost the license code, pleasecontact [email protected].

3.4 Starting Segment 3DPrint

To start the program, double click the file C:/Program Files/Segment 3DPrint/segment3dp.exe,or your shortcut to it. When starting the software, the image in Figure 11should be displayed. If it is not displayed, then the software is not correctlyinstalled.

Figure 11: Startup window for Segment 3DPrint.

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3.5 Uninstallation

To uninstall Segment 3DPrint, remove all files in the folder C:/Program/Medviso/Segment3DPrint or C:/Program Files/Medviso/Segment 3DPrint. User prefer-ences are stored in the Application Data and the subfolder Segment 3DPrint

under each user account. To uninstall the Matlab Compiler Runtime, usethe Windows functionality Install or Remove Programs in the control panelmenu.

3.6 Software overview

An overview of Segment 3DPrint is given in Figure 12. The letters in thefigure will 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 3DPRINT

3.7 First time running Segment 3DPrint

The first time Segment 3DPrint is started, it runs a setup process whichcan take a while, so be patient. To complete the setup, set preferences andwindow positions 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 3DPrint can be set by drag-ging the window to an optional position and size. The size and positionwill be saved so that next time Segment 3DPrint is launched the same po-sition will be used. In case where one have switched to another monitor,Segment 3DPrint may move outside the screen. In this case you could pressShift-Ctrl-R to reset GUI positions. This is also available under the Filemenu (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 3DPrintformat. For images in DICOM format, click Select & Load , Figure 14 isshown. For images in Segment 3DPrint 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 3DPrint 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


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 3D Segmentation module

The module allows to perform a 3D segmentation for 3D printing purposes, orto export to CAD/CFD analysis software for patient-specific modelling. Thesegmentation process is to convert the image volume into a set of distinctobjects by assigning which voxels in the image belongs to which objects.Before printing or exporting, the objects are converted to surfaces.

3D Segmentation module open after clicking 3D PRINT tab. An overview ofthe module is given in Figure 17. To learn more about each tool, hold themouse over the icon in the software and a help text will be displayed. Thestandard 4 panel view dispaly the image with segmentation overlay in thethree standard views; (transversal view, coronal view, sagittal view), and thefourth panel showing object likelihood.

Figure 17: Overview of graphical user interface. The letters (a-k) in thefigure will be used as references throughout this chapter.

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.

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CHAPTER 6. 3D SEGMENTATION MODULE

1. Create a vision. The first step is to create a vision on how thefinished printed object should look. What parts of the image volumeshould be included? How should the objects be connected so that theprinted model does not fall apart? Creating a vision together with thecolleages that will used the finished model is essential, for sucessfulusage of the technology.

2. Crop the image volume. This makes the entire workflow faster and

easier. Cropping is performed with the crop tool . Crop relativelytight around object of interest. Objects from different cropped regionscan be combined in exporting step as the software remembers positionof objects also after crop operations.

3. Adjust object likelihood function. Object likelihood is a mappingfunction that maps voxel intensities to likelihood of the object to besegmented. Use either predefined mapping functions or manually ad-just the curve. Type of mapping function can be changed by selectingone of the three mappint functions: } Pos - Positive, } Neg - Nega-

tive, } Gauss - Gaussian. Object likelihood is adjusted in panel i, andobject likelihood view is presented in panel (g).

4. Create object. There are both automatic, semi-automatic and man-

ual methods to segment an object using , . , and . Allsegmentation tools are described in Section 6.2

5. Separate objects. Often objects are connected and needs to be sep-arated. There are two main methods to split an object. A) Use the

split and erase tool , or B) Use set operations of objects to remove

one object from another object .

6. Manual adjustments. Manual segmentation tools are described inSection 6.2. The suggested workflow is to work with one object ata time. Do your manual adjustment for one object before you startprocessing the next object. In the end of the process you can mergeand split objects as desired.

7. Fill objects. In general, it is not necessary to have solid objects for3D printing, however filling is highly recommended as A) Smoothingof non filled objects may erase sections of the object, B) filled object

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6.2. SEGMENTATION TOOLS (PANEL A)

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 anatomicalobjects is complete, start the export/preview tool. For details, seeSection 6.9.

6.2 Segmentation tools (panel a)

Segmentation tools are generally applied to current object shown in panel i,except for some tools that creates new objects.

2D/3D. (hot-key 2, 3) Selects if tools are applied in 2D or 3D.

Crosshair tool. Put crosshair to mark point in 3D.

Wand tool. Magic wand from mouse click. Clicking on the areaperforms automatic segmentation according to probability mapthreshold.

Threshold image volume. This creates a new object by thresh-olding. Threshold is adjusted by object likelihood function.

3D paint tool. Hold down mouse and drag small sections of theobject at a time.

Local threshold. A local threshold operation is performed withinthe defined pen radius. This tool can be used to locally paint regionsaccording to object probability. Pen radius in mm is adjusted inpanel g.

Draw tool, add region to segmentation. Pen radius in mm isadjusted in panel g.

Erase tool, remove region from segmentation. Pen radius in mmis adjusted in panel g.

Active contour tool (hot-key a). Applicable in 2D. Adjusts andsmooth contour using active contour algorithm. Use Ctrl-mousewheel to go to next slide and apply active contour tool.

Fill tool (hot-key 2D: f, 3D: F), fill object in 2D/3D.

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Split and erase tool, splits the current object and cuts awayundesired part. For details, see Section 6.6.

Pick tool (hot-key p), left click in image to pick an object and addto current object. In 2D mode use shift and mouse wheel to pickobjects at crosshair position from multiple slices.

Keep tool (hot-key k), left click in image to keep a part of thecurrent object and create a new object. Typically useful with vesseltool.

Vessel tool, opens a new user interface for vessel segmentation.For details, see Section 6.8.

Support structure tool, creates support structure between twoconsecutive points.

Add Text tool, adds label to object.

Box tool, add segmentation / remove segmentation inside 3D box.This tool can be used to crop objects and to add support structuresfor models.

Place annotation point tool (hot-key p), right click at the de-sired position to set a point. This tool can be used to set up thesupport structure.

Clear point tool, clears all annotation points.

Cut in 3D menu, drop down menu to select cut plane.

Cut in transversal plane tool, cuts segmentation in transversalplane and creates two cut planes: lower and upper.

Cut in sagittal plane tool, cuts segmentation in sagittal planeand creates two cut planes: left and right.

Cut in coronal plane tool, cuts segmentation in coronal planeand creates two cut planes: anterior and posterior.

Cut in obliquel plane tool, cuts segmentation in oblique planeand creates two cut planes.It is needed first to set up at least threepoints to place plane for cutting.

Crop tool, crop image volume.

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6.3. OBJECT TOOLS (PANEL K)

6.3 Object tools (panel k)

Working with objects is a good way to divide the segmentation task insmaller steps. The segmentation process typically creates many objects, andit is highly recommended to rename objects with understandable names anddelete temporarily created objects as it may be hard to remember the con-tent 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 usingdifferent object likelihood mappings.

Sort out object. Removes non connected parts. For details, seeSection 6.5.

Smoothes object. For details, see Section 6.7.

Erode object. Creates a new object that is one voxel thinner thanthe parent object.

Dilate object. Creates a new object that is one voxel thicker thanthe parent object.

Close object. Closes the borders of the object.

Hollow. Makes a filled object hollow.

Minus. Takes first selected object minus the second selected ob-ject, and creates a new object.

Not. Inverts the object, and creates a new object.

Union. Joins two or more selected objects, and creates a newobject.

Cut. Takes the intersection of two or more selected objects, andcreates a new object.

Move up. Moves object up in list.

Move down. Moves object down in list.

New object. Creates a new object.

Copy object. Copies the selected object to a new object.

Rename object. Renames the selected object.

Delete object. Deletes the selected object.

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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 (t = transversal view, s = sagittal view, 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)

Display segmentation contour (green line)

Display segmentation as red overlay

Display segmentation in a 3D view

Preview / generate STL file. For details, see Section 6.9

Delete segmentation

Delete all

6.5 Sort out tool

Select . This tool is used to remove non connected parts of an objectby using of three following options: (1) by keeping only the largest or (2)by keeping N the parts larger then threshold as separate objects or (3) byremoving N parts smaller than the threshold. The user interface is shown inFigure 18. The number of parts in the object are shown. Default option isto keep only the largest part. You can select to keep all parts larger thana specified threshold, then each kept part is created as new object. Youcan also remove N parts smaller then threshold, without creating separateobjects for each kept part.

6.6 Split tool

Select . Put crosshair on the object you want to keep and right click onobject you want to cut away. If possible put cross hair and right click onopposide side of a clear and visible cut region. If possible put the cross hairon solid parts such as the bone to indicate clearly parts that should not bedeleted. If you want to keep both the objects, but only split them apart,

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6.7. SMOOTHING TOOL

Figure 18: User interface for Sort out.

make a copy of the object prior to splitting, work to split out one and usethe subtruction function (described in 6.3) to get both desired objects.

6.7 Smoothing tool

Select . Smoothing surface window is shown in Figure 19. How to applysmoothing step-by-step:

1. Adjust smoothing with editbox or slider

2. Press Apply to apply the smoothing and create a new smoothed object.

6.8 Vessel tool

Select . Start by adjusting the object likelihood to enhance the vesselsof interest maximally. Often if you want to enhance vessls, close to bones asillustrated in Figure 20, then use the Gaussian mapping as illustrated in the

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Figure 19: Smooth surface window. On the left segmentation before smooth-ing, on the right segmentation after smoothing.

figure.

Figure 20: Adjust object likelihood to enhance vessels.

Next start the vessel enhancement tool . The user interface is shown inFigure 21.

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 . ClickFinish to create a new vessel enhancement object. Often from this object

it is advantagous to use the keep tool to pick vessels to include in the

32

6.9. PREVIEW / GENERATE STL FILE

Figure 21: User interface for vessel enhancement.

final object. Then use to merge the kept objects. Often you also may

want to use the tool to merge the detected vessels with a larger vesselmanually draw as the vessel enhancement may fail precisely when a smallvessel branches of a large vessel.

6.9 Preview / generate STL file

Select . The user interface to generate STL-files is shown in Figure 22.

Step-by-step:

1. Select object to add to preview.

2. Select color with Color .

3. If desired, adjust transparity.

4. Click Add object .

33


Figure 22: Preview / generate STL file user interface.

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 , otherwisego back and edit the segmentation.

6.10 Storing segmentation

When the 3D segmentation module is closed all objects are retained. Usethe standard save functions in Segment 3DPrint to store segmentation andimage volume to disc or patient database.

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7 CT Cardiac analysis - Step bystep

7.1 Cardiac reconstruction

To be able to perform automatic segmentation of the left ventricle and rightventricle, as described in 7.2 and 7.3, 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 23.

Figure 23: 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 7. CT CARDIAC ANALYSIS - 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 3DPrint 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 .

7.2 LV analysis

7.2.1 Automatic LV segmentation

1. The automatic LV segmentation is applied to a reconstructed short-axis stack, generated by cardiac reconstruction as described in Chapter7. 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 24 (j).

4. If needed, correction of the LV segmentation can be performed by using

the following tools: , , , , , , and (i).

7.2.2 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.

36

7.2. LV ANALYSIS

Figure 24: LV analysis result.

7.2.3 Erase LV segmentation

To erase the LV segmentation, select Clear All LV Segmentation from LV menu(a).

7.2.4 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.

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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CHAPTER 7. CT CARDIAC ANALYSIS - STEP BY STEP

7.3 RV analysis

7.3.1 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.

7.3.2 Erase RV segmentation

To erase the RV segmentation, select Clear All RV Segmentation from RVmenu (a).

7.3.3 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.

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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8 MR Cardiac analysis - Stepby step

8.1 LV analysis

8.1.1 Automatic LV segmentation [1]

1. Start the LV analysis by select mode (h) and select (i). Anew interface is open, as shown in Figure 25.

Figure 25: LV analysis GUI.

2. Select the slices covering the left ventricle by left-click to select mostbasal slice and right-click to select most epicardial apical slice.

3. Review the slice selection in the long-axis views.

4. Ensure that the center cross is in the middle of the LV.

5. Start the automatic LV segmentation.

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CHAPTER 8. MR CARDIAC ANALYSIS - STEP BY STEP

6. 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 26 (j).

Figure 26: LV analysis result.

7. If needed, correction of the LV segmentation can be performed by using

the following tools: , , , , , , , , and

(i).

8.1.2 Manual LV segmentation

For manual delineation of the LV, the following tools can be used: , ,

, (i).

8.1.3 Erase LV segmentation

To erase the LV segmentation, select (i) from mode (h).

40

8.2. RV ANALYSIS

8.1.4 Copying LV segmentation

To copying the LV segmentation to another image stack, select Import Seg-mentation From Another Image Stack from LV menu (a).

8.1.5 Validation of LV segmentation

1. J. Tufvesson, E. Hedstrom, K. Steding-Ehrenborg, M. Carlsson, H.Arheden, E. Heiberg, Validation and development of a new automaticalgorithm for time resolved segmentation of the left ventricle in mag-netic resonance. Biomed Res Int, 2015:970357.

8.1.6 Summary of LV segmentation validation

The result in [1] showed a mean differences between automatic LV segmen-tation by Segment CMR and manual delineation were EDV -11 mL, ESV 1mL, EF -3 %, and LVM 4 g in a set of 50 patients.

No uncertainty/error information is showed in the software together withthe LV measurements.

8.2 RV analysis

8.2.1 Automatic RV segmentation [1]

1. Start the RV analysis by select mode (h) and select (i). Anew interface is open, as shown in Figure 27.

2. Set RV center and select the slices covering the right ventricle by left-click to select most basal slice and most apical slice.

3. Review the slice selection and center line in the long-axis views.

4. Start the automatic RV segmentation.

5. The segmentation result is presented in the main window where vol-umes curve can be reviewed (k) and the measured RV volumes arepresented, according to Figure 28 (j).

6. If needed, correction of the RV segmentation can be performed by using

the following tools: , , , , (i).

41


Figure 27: RV analysis GUI.

42

8.2. RV ANALYSIS

Figure 28: RV analysis result.

8.2.2 Manual RV segmentation

For manual delineation of the RV, the following tools can be used: , ,

, (i).

8.2.3 Erase RV segmentation

To erase the RV segmentation, select (i) from mode (h).

8.2.4 Validation of RV segmentation

1. M. A. Aneq, E. Nylander, T. Ebbers, and J. Engvall, Determinationof right ventricular volume and function using multiple axially rotatedMRI slices, Clin Physiol Funct Imaging 31(3) pp. 233-9, 2011.

8.2.5 Summary of RV segmentation validation

The result in [1] showed a differences between semi-automatic RV segmen-tation by Segment CMR and the phantom data volumes of 1 ml (0.5%), -3ml (2.3%) and 3 ml (2.3%), respectively. For the test in the 23 patients,the Right ventricular end-diastolic (EDV), end-systolic (ESV) and stroke

43


volumes (SV) determined in the rotated long-axis (RLA) were 179,1 ± 29.3;80.1 ± 17.1; 99.3 ± 16.9 ml and in the short-axis (SA) were 174.0 ± 21.1; 78.8± 13.6; 95.3 ± 14.5 ml, with P-values for the difference from 0.17 to 0.64 (ns).

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


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 29 (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.

45

CHAPTER 9. ROI ANALYSIS - STEP BY STEP

Figure 29: ROI analysis GUI.

46

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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Segment 3DPrint Instructions For Use - Englishmedviso.com/documents/segment3dp/segment3dpinstructions... · 2020-03-04 · 1 Terms and conditions This manual contains Instructions