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Strain analysis in Segment - User Manual
April 30, 2021
Software platform v3.2 R8757
MEDVISO ABhttp://www.medviso.com
Griffelvagen 3SE-224 67 LundSwedenTel: +46-76-183 6442
Contents
1 Conventions and Abbreviations 1
1.1 Typographic conventions . . . . . . . . . . . . . . . . . . . . 1
1.2 Trademarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.3 Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.4 System requirements . . . . . . . . . . . . . . . . . . . . . . . 3
2 Software overview 5
3 Loading and storing Data - Step by step 7
3.1 Loading data . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
3.1.1 Loading data from database . . . . . . . . . . . . . . 7
3.1.2 Loading data from PACS . . . . . . . . . . . . . . . . 8
3.1.3 Loading data from network disc . . . . . . . . . . . . 9
3.2 Storing data . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
4 Image settings 11
4.1 Manually set image description . . . . . . . . . . . . . . . . . 11
4.2 Image description upon loading . . . . . . . . . . . . . . . . . 11
4.3 Patient details . . . . . . . . . . . . . . . . . . . . . . . . . . 11
5 LV segmentation - Step by step 13
5.1 Automatic LV segmentation . . . . . . . . . . . . . . . . . . . 13
5.2 Manual LV segmentation . . . . . . . . . . . . . . . . . . . . 14
5.3 Erase LV segmentation . . . . . . . . . . . . . . . . . . . . . 14
5.4 Copying LV segmentation . . . . . . . . . . . . . . . . . . . . 15
6 LV segmentation - Step by step 17
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CONTENTS
7 Segmentation of Long Axis Images 197.1 Manual LV segmentation . . . . . . . . . . . . . . . . . . . . 197.2 Manual RV segmentation . . . . . . . . . . . . . . . . . . . . 19
8 Strain Analysis Module 218.1 Strain analysis in cine or tagged images . . . . . . . . . . . . 21
8.1.1 Definition of Mean strain . . . . . . . . . . . . . . . . 218.1.2 Definition of Peak strain . . . . . . . . . . . . . . . . 21
8.2 Automatic strain analysis in short-axis image stacks . . . . . 238.2.1 Torsion . . . . . . . . . . . . . . . . . . . . . . . . . . 26
8.3 Automatic strain analysis in long-axis image stacks . . . . . . 278.4 Strain in Left atria . . . . . . . . . . . . . . . . . . . . . . . . 318.5 Hints for Strain analysis in small animal images . . . . . . . . 328.6 Erase strain data . . . . . . . . . . . . . . . . . . . . . . . . . 338.7 Torsion - Implementation details . . . . . . . . . . . . . . . . 34
9 Strain export options 359.1 Patient exports . . . . . . . . . . . . . . . . . . . . . . . . . . 359.2 Batch exports . . . . . . . . . . . . . . . . . . . . . . . . . . 35
10 Short Commands / Hot keys 37
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1 Conventions andAbbreviations
This chapter describes the typographic conventions and used abbrevia-tions in this manual and in the program.
1.1 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.
1.2 Trademarks
Below are some of the trademarks used in this manual.
— Segment 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).
1.3 AbbreviationsCMR Cardiac Magnetic ResonanceLV Left VentricleRV Right Ventricle
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1.4. SYSTEM REQUIREMENTS
1.4 System requirements
— Operating System: 64-bit Windows 10
— Computer with 8 GB of memory or preferably 16 GB
— Harddisk with at least 5 GB of available space
— Graphics card supporting both DirectX and OpenGL
For users with additional modules not included in the free researchversion:
— Internet connection for software license management
To access full version of machine learning algorithms in Segment:
— CUDA enabled NVIDIA graphics card with 4GB memory or more
— GPU architecture: Turing, Volta, Pascal
— Note: GPU architecture Ampere is not yet supported
Recommendations
— Systems with two screens
— Using SSD disk for reading data
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2 Software overview
An overview of Segment is given in Figure 1. The letters (a-p) in thefigure will be used as references throughout this manual.
Figure 1 – Main graphical user interface. The letters (a-p) in the figure willbe used as references throughout this manual.
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 Loading and storing Data -Step by step
3.1 Loading data
To load patient data from the database, follow Section 3.1.1. To loadpatient data from PACS, follow Section 3.1.2. To load patient data fromnetwork disc, follow Section 3.1.3.
3.1.1 Loading data from database
1. Click on the tool (a), Figure 2 is shown.
Figure 2 – Graphical patient selector.
2. Select patient.
3. Patients can be stored in two formats; DICOM, or Segment format.For images in DICOM format, click Select & Load , Figure 3 is shown.For images in Segment format click Load all .
4. Select image series to load in Figure 3.
5. Click on Load .
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CHAPTER 3. LOADING AND STORING DATA - STEP BY STEP
Figure 3 – Graphical image series selector.
3.1.2 Loading data from PACS
1. Select Import from PACS in the File menu, Figure 4 is shown.
Figure 4 – Interface to import image stacks from PACS.
2. Enter patient or study details and perform search.
3. Select study and series to load.
4. Load the study into Segment by select Open files .
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3.2. STORING DATA
3.1.3 Loading data from network disc
1. Select Open from Disc in the File menu, Figure 5 is shown.
Figure 5 – Image stack loading selector.
2. For analyzed Segment file, select image stack to load and select Load Selected Files .
3. For multiple DICOM files, select Graphical Selector and load image stacksaccording to Figure 3.
4. For one DICOM files, select crop size for the image stack, crop theimage and select Load Selected Files .
3.2 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 As ... in theFile menu (a).
3. To store images including delineation to PACS, select Save to PACS inthe File menu (a).
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4 Image settings
4.1 Manually set image description
1. Right click on the thumbnail for the image stack.
2. Select Select Image Description in the context menu.
4.2 Image description upon loading
The image description is automatically set in the loading process by com-paring information from the DICOM tags with the information in the textfile imagedescription.txt.
1. The text file is found in the folder where Segment is installed.
2. Manually update the text file according to the structure as defined inthe first row in the text file.
4.3 Patient details
Edit patient details by select in the mode.
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5 LV segmentation - Step bystep
5.1 Automatic LV segmentation
[1]
1. Start the LV analysis by select mode (h) and select (i). Anew interface is open, as shown in Figure 6.
Figure 6 – 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 5. LV SEGMENTATION - 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 7 (j).
Figure 7 – LV analysis result.
7. If needed, correction of the LV segmentation can be performed by using
the following tools: , , , , , , , , and
(i).
5.2 Manual LV segmentation
For manual delineation of the LV, the following tools can be used: ,
, , (i).
5.3 Erase LV segmentation
To erase the LV segmentation, select (i) from mode (h).
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5.4. COPYING LV SEGMENTATION
5.4 Copying LV segmentation
To copying the LV segmentation to another image stack, select ImportSegmentation From Another Image Stack from LV menu (a).
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6 LV segmentation - Step bystep
1. Start the RV analysis by select (h) and select (i). A newinterface is open, as shown in Figure 8.
Figure 8 – RV analysis GUI.
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.
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CHAPTER 6. LV SEGMENTATION - STEP BY STEP
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 9 (j).
Figure 9 – RV analysis result.
6. If needed, correction of the RV segmentation can be performed by using
the following tools: , , , , (i).
For manual delineation of the RV, the following tools can be used: ,
, , (i).
To erase the RV segmentation, select (i) under (h).
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.
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7 Segmentation of Long AxisImages
7.1 Manual LV segmentation
For manual delineation of the LV use the or the tool (i). The LVsegmentation should be horseshoe shaped according to Figure 10. The sameprinciple goes for all long-axis images (2CH, 3CH and 4CH).
7.2 Manual RV segmentation
For manual delineation of the RV use the or tool (i). The RVsegmentation should be done in the 4CH view according to Figure 10.
Figure 10 – LV and RV segmentation in 4CH.
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8 Strain Analysis Module
8.1 Strain analysis in cine or tagged images
The strain analysis module uses tagging MR images or cine MR imagesto calculate myocardial strain. The module has been developed in closecollaboration with researchers at KU Leuven in Belgium.
8.1.1 Definition of Mean strain
In the Strain module the mean value of strain in the whole heart is definedas ”Mean strain”. This measures the same character as ”Global strain” fromechocardiography. We are not using the same nomenclature due to the slightdifferences in calculation methods. In echocardiography, ”Global strain” isdefined as (L-L0)/L0 with L the instantaneous length of the endo- or mid-myocardial contour and L0 the length of the contour in end-diastole. InSegment, ”Mean strain” is defined as the mean of all strain value within theentire LV wall.
8.1.2 Definition of Peak strain
Segmental strain at global peak time frame
”Segmental strain at global peak time frame” is defined as the strain valuein each segment at the time point defined as the global peak time frame. Thisis strain at the same time point for all segments. Illustrated in Figure 68
Segmental peak strain for each segment
”Segmental peak strain for each segment” is defined as the peak strain foreach segment. This could be strain at different time points for the differentsegments. In radial direction peak is defined as the maximal value and inlongitudinal/circumferential direction peak is defined as the minimal value.Illustrated in Figure 69
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CHAPTER 8. STRAIN ANALYSIS MODULE
Figure 11 – Illustration of Segmental strain at global peak time frame, whichis the strain values at the vertical blue line in each segment.
Figure 12 – Illustration of Segmental peak strain for each segment, which isthe peak strain in each segment defined by the black cross in the images.
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8.2. AUTOMATIC STRAIN ANALYSIS IN SHORT-AXIS IMAGESTACKS
8.2 Automatic strain analysis in short-axis image stacks
1. Tagging: The automatic strain analysis starts upon loading a taggedimage stack. Segment identifies a tagged image stack according tothe DICOM tag Series Description. The associated Series Descriptionnames can be customized by the user according to Section 4. Manuallystart the automatic strain analysis by Select Tagging Strain Short-axisunder MR menu.Cine: First perform LV segmentation. The automatic strain analysisstarts by Select Feature Tracking Strain Short-axis under MR menu.
2. The strain analysis starts by cropping and upsampling of the imagestack, if needed, as shown in Figure 70.
Figure 13 – Strain cropping interface.
3. The automatic strain registration is then performed in the background.The progress is shown in a progressbar at the bottom of the main inter-face of Segment. During the registration process the user can performsegmentation.Tagging: The segmentation should be performed in one of the firstseven time frames in the tagged image stack, or potential cine imagestack.Cine: The segmentation should be performed in the first time frame
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CHAPTER 8. STRAIN ANALYSIS MODULE
in the cine image stack.This time frame with segmentation will be the initial time frame forthe strain tracking.LV: Perform the LV segmentation according to Figure 71, using meth-ods describe in and Chapter 5.RV: Perform the RV segmentation according to Figure 71, using meth-ods describe in Chapter 6.
Figure 14 – Strain drawing guidance.
4. Ensure the end-diastole (ED) time frame is the first time frame (or closeto). Since the first time frame will be the base for the strain calculationand strain will be defined as 0 in this time frame. You can correct thisby in Segment go to the time frame representing end-diastole, thenselect Set First Timeframe at Current Timeframe in menu Edit.
5. Tagging: Start the strain module by selecting Tagging Strain Short-axis under MR menu (a). The Strain interface is shown (Figure 72).Cine: Start the strain module by selecting Feature Tracking StrainShort-axis under MR menu (a). The Strain interface is shown (Figure72).
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8.2. AUTOMATIC STRAIN ANALYSIS IN SHORT-AXIS IMAGESTACKS
Figure 15 – Strain analysis GUI.
6. LV: Define LV rotation by setting the white line in the middle of theseptum, using the slider, and press Analyse to run the myocardial strainquantification.
7. Verify the strain tracking by using the movie tools.
8. Strain over time and peak strain is shown in the figures to the rightaccording to the selected parameters.
9. You can choose which segments to be presented in the graph with theradiobuttons below the graph.
10. If needed, manual correction can be performed by using the Move
Contour arrows, or moving the LV segmentation interpolation points,in the initial time frame in the strain image stack. Then run the strainquantification again by select Analyse .
11. Manually change the short-axis slices for the bullseye division by selectSet short-axis slices .
12. Tagging: Manually change the initial time frame by select Set initial time frame .
13. Click on export buttons to export result to spreadsheet and save but-tons to store graph and bullseye to image files.
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CHAPTER 8. STRAIN ANALYSIS MODULE
8.2.1 Torsion
For short axis images torsion can be calculated. To derive torsion onemust consider rotation, this is something that also is available in the straingui, aswell as segmental rotation and endocardial and epicardial rotation,Rotation is quantified as the mean angular distance for all the tracking pointsin a chosen group, from the current timeframe to the end diastolic timeframe.With torsion we consider the normalized rotational difference of the heartfor the most basal and apical slices in data. The rotational difference isnormalized with the mean radius divided by the slice distance along thelongaxis. For details on how the torsion measure is obtained see section 8.7.
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8.3. AUTOMATIC STRAIN ANALYSIS IN LONG-AXIS IMAGESTACKS
8.3 Automatic strain analysis in long-axis image stacks
1. Tagging: The automatic strain analysis starts upon loading a taggedimage stack. Segment identifies a tagged image stack according tothe DICOM tag Series Description. The associated Series Descriptionnames can be customized by the user according to Section 4. Manuallystart the automatic strain analysis by Select Tagging Strain Long-axisunder MR menu.Cine: The automatic strain analysis starts by Select Feature TrackingStrain Long-axis under MR menu.
2. Ensure that Image View Plane is set correctly (2CH, 3CH and 4CH),respectively. Otherwise set it according to Section 4.
3. The strain analysis starts by cropping and upsampling of the imagestack, if needed, as shown in Figure 73.
Figure 16 – Strain cropping interface.
4. The automatic strain registration is then performed in the background.The progress is shown in a progressbar at the bottom of the maininterface of Segment. During the registration process the user canperform segmentation. Before performing the segmentation, ensurethat the parameter Number of points along contour in Preferencesis set to at least 160, in order to have a smooth segmentation.
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CHAPTER 8. STRAIN ANALYSIS MODULE
5. Tagging: The segmentation should be performed in one of the firstseven time frames in the tagged image stack, or potential cine imagestack.Cine: The segmentation should be performed in the first time framein the cine image stack.This time frame with segmentation will be the initial time frame forthe strain tracking.LV: Perform the LV segmentation according to Figure 74 by using the
LV endo segmentation tools or in all three long-axis views.RV: Perform the RV segmentation according to Figure 74 by using
the RV endo segmentation tools or in the 4CH view. Settwo annotation points to define the Tricuspidalis valve plane and namethem TV plane. The annotation point tool is found under the Misctoolbox.
Figure 17 – Strain drawing guidance.
6. Ensure the end-diastole (ED) time frame is the first time frame (or closeto). Since the first time frame will be the base for the strain calculationand strain will be defined as 0 in this time frame. You can correct this
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8.3. AUTOMATIC STRAIN ANALYSIS IN LONG-AXIS IMAGESTACKS
by in Segment go to the time frame representing end-diastole, thenselect Set First Timeframe at Current Timeframe in menu Edit.
7. Tagging: Start the strain module by selecting Tagging Strain Long-axisunder MR menu (a). The Strain interface is shown (Figure 75).Cine: Start the strain module by selecting Feature Tracking StrainLong-axis under MR menu (a). The Strain interface is shown (Figure75).
Figure 18 – Strain analysis GUI.
8. Verify the strain tracking by using the movie tools.
9. Strain over time and peak strain is shown in the figures to the rightaccording to the selected parameters.
10. You can choose which segments to be presented in the graph with theradiobuttons below the graph.
11. If needed, manual correction can be performed by using the Move
Contour arrows, or moving the segmentation interpolation points, inthe initial time frame in the tagging image stack. Then run the strainquantification again by select Analyse .
12. Tagging: Manually change the initial time frame by select Set initial time frame .
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CHAPTER 8. STRAIN ANALYSIS MODULE
13. You can toggle between existing views by using the radiobuttons labeledwith the chamber views.
14. Click on export buttons to export result to spreadsheet and save but-tons to store graph and bullseye to image files.
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8.4. STRAIN IN LEFT ATRIA
8.4 Strain in Left atria
To perform strain analysis in the left atria use the RV endo tools. It iswork in progress to add tools specific for left atrial strain, but meanwhile itworks perfectly fine to use the RV endo tools to measure strain in the leftatrial.
1. Start with manually peform left atria segmentation in the first time
frame in the 4CH view using the according to Figure 76.
Figure 19 – Segemntation of left atria to be used for strain analysis.
2. Ensure that Image View Plane is set correctly (4CH). Otherwise set itaccording to Section 4.
3. The automatic strain analysis starts by Select Feature Tracking StrainLong-axis under MR menu.
4. Start the strain module by selecting Feature Tracking Strain Long-axisunder MR menu (a). The Strain interface is shown (Figure 77).
5. Verify the strain tracking by using the movie tools.
6. Strain over time and peak strain is shown in the result panel to theright in the interface labeled with RV.
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CHAPTER 8. STRAIN ANALYSIS MODULE
Figure 20 – Strain analysis GUI.
8.5 Hints for Strain analysis in small animal images
The Strain analysis module is known to work well for analysis of Strainin small animals. However, there are two things to consider:
1. Time resolution The time resolution should be good enough. If youhave less than 15 time frames for the whole cardiac cycle it is recom-mended to upsample the image stack. In Segment you do that by SelectUpsample/Downsaple Temporal under menu Resample image stack undermenu Image tools.
2. Image resolution The strain tracking in human hearts is optimal fora pixel resolution of 0.5 mm. If you have small animal hearts of forexample say 5 times as small as human hearts, you need to upsamplethe image to a pixel resolution of 0.1 mm (0.5/5). In Segment youdo that by Select Upsample/Downsaple Image (In Plane) under menuResample image stack under menu Image tools. Also crop the imageproperly before starting the Strain analysis. Crop it so you only havethe LV and a little bit surrounding around the LV left in the image.
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8.6. ERASE STRAIN DATA
8.6 Erase strain data
Tagging: To erase the strain data, select Clear Tagging Data under MRmenu (a).Cine: To erase the strain data, select Clear Feature Tracking Data under MRmenu (a)
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CHAPTER 8. STRAIN ANALYSIS MODULE
8.7 Torsion - Implementation details
In short axis cardiac images the heart muscle wall of the left chamberis well approximated by a circle. The method finds the axis of rotation,AoR, for the left chamber as the center of a circle fit to the tracking pointsgenerated by the segment strain module. For the circle fitting a least squaresmethod is used.
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9 Strain export options
9.1 Patient exports
For exporting strain results and graphs for one patient, use the Exportfunctions found in the Strain analysis interface numbered 13 in Figure 72.
’
9.2 Batch exports
The batch export script for strain is found under main menu Utility -Export where you find functions for export of Feature Tracking Strain andTagging Strain from multiple files. The result is exported to spreadsheet forfurhter processing.
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10 Short Commands / Hot keys
This chapter describes the hot keys that can be used in Segment.
Stack navigation commands—————————Left arrow Previous frame or pan leftRight arrow Next frame or pan rightUp arrow View next slice in basal directionDown arrow View next slice in apical directionD Go to end diastoleS Go to end systoleShift-D Go to end diastole all visible image stacksShift-S Go to end systole all visible image stacksC Start to play cine thumbnailP Start to play movie
Viewing commands—————————R Refresh screenH Hide/show all contours and markersV Shift mode in panel between montage and one sliceCtrl-A Selects all slicesShift-U Unselect all slicesShift-A View all image stacksShift-1 View one image panelShift-2 View two image panelsAlt-2 View two image panels as rowsShift-3 View three image panelsAlt-3 View three image panels as rowsShift-4 View three image panelsShift-6 View six image panelsAlt-6 View six image panels as rowsShift-9 View nine image panelsCtrl-1 One viewCtrl-2 M-mode viewCtrl-3 Montage viewCtrl-4 Montage row viewCtrl-5 Montage fit viewCtrl-plus Zoom inCtrl-minus Zoom out
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CHAPTER 10. SHORT COMMANDS / HOT KEYS
Segmentation commands—————————- LV -Ctrl-L Perform fully automatic LV segmentationCtrl-M Segment LV endocardiumCtrl-Shift-M Segment LV epicardiumCtrl-R Refine LV endocardiumCtrl-Shift-R Refine LV epicardiumCtrl-F Propagate LV endocardium forward and refineCtrl-Shift-F Propagate LV epicardium forward and refineCtrl-U Copy LV endocardium upwards and refineCtrl-Shift-U Copy LV epicardium upwards and refineCtrl-D Copy LV endocardium downwards and refineCtrl-Shift-D Copy LV epicardium downwards and refineCtrl-E Expand LV EndoCtrl-K Contract LV EndoCtrl-Alt-E Expand LV EpiCtrl-Alt-K Contract LV EpiCtrl-V Exclude papillary muscle from LV endocardiumShift-Alt-R Refine LV endocardium for Alternative LV segmentation method
- RV -Ctrl-Alt-M Segment RV endocardiumCtrl-Alt-R Refine RV endocardiumCtrl-Alt-F Propagata RV endocardium forward, do not refineCtrl-Alt-U Copy RV endocardium upwards and refineCtrl-Alt-D Copy RV endocardium downwards and refine
- Flow -Alt-T Track tool for Flow ROIAlt-R Refine Flow ROIAlt-F Propagate Flow ROI forward and refineCtrl-T Plot flow
- General -O Smooth current segmentationCtrl-Z Undo segmentation
Analysis commands—————————Alt-D Set end diastole at current time frameAlt-S Set end systole at current time frameCtrl-B Bullseye plot
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Translation commands—————————Alt-A Translate contours left (selected slices)Alt-X Translate contours right (selected slices)Alt-W Translate contours up (selected slices)Alt-Z Translate contours down (selected slices)Shift-Alt-A Translate contours and image left (selected slices)Shift-Alt-X Translate contours and image right (selected slices)Shift-Alt-W Translate contours and image up (selected slices)Shift-Alt-Z Translate contours and image down (selected slices)
Tool toggling commands—————————Space Toggle tool in toolbar menu (depending on tool and mode)Shift-L Select LV modeShift-R Select RV modeShift-F Select ROI/Flow modeShift-V Select Scar(Viability) modeShift-M Select MaR modeShift-I Select Misc modeShift-N Select LV Endo penShift-B Select LV Epi penShift-G Select LV Endo interpShift-H Select LV Epi interp
File menu commands—————————Ctrl-N Load next .mat fileCtrl-O Load image stackCtrl-P Open patient data baseCtrl-0 (zero) Reset GUI PositionCtrl-S Save all image stacksCtrl-W Close current image stackCtrl-Shift-W Close all image stacksCtrl-Q Quit program
Mouse commands—————————Mouse wheel Scroll through slicesShift-Mouse wheel Scroll through time framesCtrl-Mouse wheel Scroll through visible thumbnailsAlt-Mouse wheel ZoomLeft+Right mousebutton
Pan / Windowing (dependent on selected tool)
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