diff --git a/BlueBerry/Bundles/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox b/BlueBerry/Bundles/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox
index 024eabec99..06afcb812e 100644
--- a/BlueBerry/Bundles/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox
+++ b/BlueBerry/Bundles/org.blueberry.ui.qt.log/documentation/UserManual/blueberrylogview.dox
@@ -1,16 +1,16 @@
/**
\page org_blueberry_ui_qt_log The Logging Plugin
-\imageMacro{Logging.png,"Icon of the Module",2.00}
+\imageMacro{Logging.png,"Icon of the Logging Plugin",2.00}
This plug-in records all logging output of events and progress as specified in the source code with time of occurence, level of importance (Info, Warning, Error, Fatal, Debug), the message given and where it happens. The logging starts once the plug-is started. A screenshot of the provided Logging view is shown next.
\imageMacro{LogView.png,"Screenshot of the Logging Module",16.00}
There are different features available in the view. The filter text field allows for searching all log events containing a certain substring. Using the button "Copy to clipboard" on the bottom right you can copy the current content of the logging view to your clipboard. This enables you to insert the logging information to any text processing application.
You can also show more information on every logging message by activating the two checkboxes. In the simple view, leaving both checkboxes unchecked, you'll see logging messages and logging levels. A brief description of the logging levels can be found in the \ref LoggingPage "logging concept documentation". The checkbox "Category" adds a column for the category. The checkbox "Show Advanced Field" shows method, filename and linenumber where the logging message was emitted as well as the running time of the application. The next figure shows all information which can be shown in the Logging Module.
\imageMacro{LogViewExplain.png,"Details on the Vizualized Logging Information",16.00}
*/
diff --git a/BlueBerry/Bundles/org.blueberry.ui.qt.objectinspector/documentation/UserManual/blueberryobjectinspector.dox b/BlueBerry/Bundles/org.blueberry.ui.qt.objectinspector/documentation/UserManual/blueberryobjectinspector.dox
index d26c5c1079..e445a1011c 100644
--- a/BlueBerry/Bundles/org.blueberry.ui.qt.objectinspector/documentation/UserManual/blueberryobjectinspector.dox
+++ b/BlueBerry/Bundles/org.blueberry.ui.qt.objectinspector/documentation/UserManual/blueberryobjectinspector.dox
@@ -1,8 +1,8 @@
/**
\page org_blueberry_ui_qt_objectinspector The Object Browser
-\imageMacro{ObjectBrowser.png,"Icon of the Module",2.00}
+\imageMacro{ObjectBrowser.png,"Icon of the Object Browser",2.00}
This view is only a debugging tool for berry::Object derived classes.
*/
\ No newline at end of file
diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkColourImageProcessing.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkColourImageProcessing.dox
index bd8d91cf73..284abac1eb 100644
--- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkColourImageProcessing.dox
+++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkColourImageProcessing.dox
@@ -1,34 +1,34 @@
/**
\page org_mitk_views_colourimageprocessing The Colour Image Processing Module
-\imageMacro{ColorImageProcessing.png,"Icon of the Module",2.00}
+\imageMacro{ColorImageProcessing.png,"Icon of the Colour Image Processing Module",2.00}
\section QmitkColourImageProcessingUserManualSummary Summary
This module allows the user to create coloured images from medical images. Generally, these coloured images would be used in presentations, research papers, or as a teaching aide.
\section QmitkColourImageProcessingUserManualOverview Overview
The purpose of this module is to create coloured images, which can then be later used in presentations, research papers, or anything else the user desires. Furthermore, different body sections can be assigned a different colour.
These images are not particularly useful for further image processing, but provide nice, clear, diagrams. Please note that ultrasound images cannot be coloured.
\section QmitkColourImageProcessingUserManualFilters Creating Coloured Images
Open an image in mitk, then click on the colour wheel button. Make sure the image you loaded is selected.
\ Image -> RGBAimage
Clicking on this button creates an RGBA image from your medical image, which should appear in your data manager.
\ Image + mask -> RGBAimage
Before clicking on this button, a mask is needed. A mask is generally created using the segmentation tool. Make sure both the mask and image are selected, then click on the image + mask -> RGBA image button. This creates an
RGBA image that is coloured only in section defined by the mask.
\ Image + mask + color-> RGBAimage
This functions the same way as the Image + mask -> RGBAimage. The difference is that the user can select the colour of the section represented by the mask. This is done by clicking on the colour next to the Image + mask + color-> RGBAimage button
If multiple RGBA images are created with different colours, they can be combined into one image. Ensure that the desired coloured images are selected, then click on the combine RGBA images button.
*/
diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkIsoSurfaceUserManual.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkIsoSurfaceUserManual.dox
index 9e45f7e3fb..5eeb7cc302 100644
--- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkIsoSurfaceUserManual.dox
+++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkIsoSurfaceUserManual.dox
@@ -1,37 +1,37 @@
/**
\page org_mitk_views_isosurface The Iso Surface Module
-\imageMacro{IsoSurfaceIcon.png,"Icon of the Module",2.00}
+\imageMacro{IsoSurfaceIcon.png,"Icon of the Iso Surface Module",2.00}
Available sections:
- \ref QmitkIsoSurfaceUserManualOverview
- \ref QmitkIsoSurfaceUserManualFeatures
- \ref QmitkIsoSurfaceUserManualUsage
- \ref QmitkIsoSurfaceUserManualTroubleshooting
\section QmitkIsoSurfaceUserManualOverview Overview
IsoSurface is a program module for creating surfaces (e.g. polygon structures) out of images. The user defines a threshold that seperates object and background inside the image. Pixels that belong to the object need grey values below the threshold. Pixles with grey values above the threshold will be ignored. The result is a polygon object
that can be saved as an *.stl-object.
\section QmitkIsoSurfaceUserManualFeatures Features
- Creates a surface by thresholding an image
\section QmitkIsoSurfaceUserManualUsage Usage
How to create a surface:
- Load an image into the program, for example by drag & drop
- Look for a meaningful threshold. All pixel grey values of the image that are lower than the threshold will be used to create the surface. All grey values that are higher than the surface will be ignored. You can find the best threshold by using the Volumetry-Functionality or by reading the grey value while clicking on a pixel (see picture 2).
- Insert the threshold into the GUI
- Press the Button "Create Surface"
\imageMacro{IsoSurfaceGUI.png,"Graphical User Interface of Iso Surface",16.00}
\section QmitkIsoSurfaceUserManualTroubleshooting Troubleshooting
*/
diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkRegionGrowingUserManual.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkRegionGrowingUserManual.dox
index c738507ce7..ca5f150f72 100644
--- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkRegionGrowingUserManual.dox
+++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkRegionGrowingUserManual.dox
@@ -1,29 +1,29 @@
/**
\page org_mitk_views_regiongrowing The Region Growing View
-\imageMacro{regiongrowing.png,"Icon of the View",2.00}
+\imageMacro{regiongrowing.png,"Icon of the Region Growing View",2.00}
Available documentation sections:
- \ref QmitkRegionGrowingUserManualOverview
- \ref QmitkRegionGrowingUserManualUsage
\section QmitkRegionGrowingUserManualOverview Overview
The Region growing view provides a programming example, showing developers how to create new views for MITK with a graphical user interface (GUI) that also uses some ITK image filters.
For the programmers: this functionality is the result of tutorial step 9
\section QmitkRegionGrowingUserManualUsage Usage
- you can set a number of seed points by clicking into the render windows while holding down the shift key.
- when clicking "Start region growing", a region growing algorithm starts. This algorithm is gray values based. The gray values are determined from the gray values at all point positions plus/minus a safety margin of 30 (Hounsfield units).
*/
diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleExampleUserManual.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleExampleUserManual.dox
index 26fd79a660..a677ef9105 100644
--- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleExampleUserManual.dox
+++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleExampleUserManual.dox
@@ -1,21 +1,21 @@
/**
\page org_mitk_views_simpleexample The Simple Example module
-\imageMacro{SimpleExample.png,"Icon of the Module",2.00}
+\imageMacro{SimpleExample.png,"Icon of the Simple Example Module",2.00}
\section QmitkSimpleExampleViewUserManualSummary Summary
This module is namely a simple example for simple image interaction.
It offers:
- Sliders to navigate through the different slice stacks (Axial, Sagittal, Coronal) and the time steps
- A "player" for image time series. It automatically steps through all time series with a speed defined by the slider on the right.
- A button "Re-Initialize Navigators" to reinitialize those sliders to their initial position (Slice and time position 0)
- A button "Take Screenshot" to take a screenshot of the chosen window (1=Transveral, 2=Sagittal, 3=Coronal, 4=3D View)
- A button "Take HighDef 3D Screenshot" to take an high resolution screenshot of the 3D scene
- A button "Generate Movie" whichs takes a movie of the chosen window by scrolling either through all slices (Axial, Sagittal, Coronal)
or rotating the 3D scene
- A selection box where the 3D view can be transformed into either a red-blue stereo or a D4D stereo view
*/
diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox
index db9d300506..f2e6f4835b 100644
--- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox
+++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox
@@ -1,44 +1,44 @@
/**
\page org_mitk_views_simplemeasurement The Simple Measurement Module
-\imageMacro{SimpleMeasurementIcon.png,"Icon of the Module",2.00}
+\imageMacro{SimpleMeasurementIcon.png,"Icon of the Simple Measurement Module",2.00}
Available sections:
- \ref QmitkSimpleMeasurementUserManualOverview
- \ref QmitkSimpleMeasurementUserManualFeatures
- \ref QmitkSimpleMeasurementUserManualUsage
\section QmitkSimpleMeasurementUserManualOverview Overview
SimpleMeasurement is a program module that allows to measure distances, angles and paths on a dataset.
\section QmitkSimpleMeasurementUserManualFeatures Features
- The SimpleMeasurement Module is able to measure:
- Distances between two points
- Angles between two lines (defined by three points)
- Distances along a path
\section QmitkSimpleMeasurementUserManualUsage Usage
To use the SimpleMeasurement Module, a data set must first be loaded. This can be done by drag & drop.
Choose the simplemeasurement method you need by pressing the according button.
- Points can be set by "shift-clicking" on the place in the data set.
- Remove points by pressing the del-button on your keyboard.
- You can mark a point by clicking on it with the cursor and moving it while the mouse button is still pressed.
What the different modes mean and how to use them:
- Distances(a): To measure the distance between two points, you have to set two points. The distance will be displayed on the line between the points.
- Angles(b): Angles can be measured between two lines. For that you have to set three points. The angle will be displayed between the two lines.
- Path(c): Distances and angles along a path can be measured by setting at least two (for distance) or three (for angles) or more (for longer paths) points. The distance and the angles for each part will be displayed next to the path.
\imageMacro{SimpleMeasurementGUI.png,"Graphical User Interface of SimpleMeasurement",16.00}
*/
diff --git a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox
index d6580e7e57..73ff748694 100644
--- a/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox
+++ b/Examples/Plugins/org.mitk.example.gui.imaging/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox
@@ -1,8 +1,8 @@
/**
\page org_mitk_views_viewinitialitzation The View Initialization Module
-\imageMacro{viewInitializationIcon.png,"Icon of the Module",2.00}
+\imageMacro{viewInitializationIcon.png,"Icon of the View Initialization Module",2.00}
This view serves as a sandbox for understanding and experimenting with the geometry initialization parameters. For example, to view the axial slices from above instead of from below. It is not intended for end users, but for developers.
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox
index d0df37f777..6d0c80d8ab 100644
--- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox
+++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox
@@ -1,98 +1,98 @@
/**
\page org_mitk_views_datamanager The DataManager
-\imageMacro{QmitkDatamanager_Icon.png,"Icon of the Module",2.00}
+\imageMacro{QmitkDatamanager_Icon.png,"Icon of the Data Manager",2.00}
\tableofcontents
\section QmitkDataManagerIntroduction Introduction
The Datamanager is the central componenent to manage medical data like images, surfaces, etc..
After loading one or more data into the Datamanager the data are shown in the four-view window, the so called Standard View.
The user can now start working on the data by just clicking into the standard view or by using the MITK-modules such as "Segmentation" or "Basic Image Processing".
\imageMacro{QmitkDatamanager_Overview.png,"How MITK looks when started",16.00}
\section QmitkDataManagerLoading Loading Data
There are three ways of loading data into the Datamanager as so called Data-Elements.
The user can just drag and drop data into the Datamanager or directly into one of the four parts of the Standard View.
He can as well use the Open-Button in the right upper corner. Or he can use the standard "File->Open"-Dialog on the top.
A lot of file-formats can be loaded into MITK, for example
- 2D-images/3D-volumes with or without several timesteps (*.dcm, *.ima, *.pic, ...)
- Surfaces (*.stl, *.vtk, ...)
- Pointsets (*.mps)
- ...
The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume.
To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key.
After loading one or more data into the Datamanager they appear as Data-Elements in a sorted list inside the Datamanager.
Data-Elements can also be sorted hierarchically as a parent-child-relation.
For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1).
The order can be changed by drag and drop.
\imageMacro{QmitkDatamanager_ParentChild.png,"Screenshot1",9.61}
The listed Data-Elements are shown in the standard view.
Here the user can scale or rotate the medical objects or he can change the cutting planes of the object by just using the mouse inside this view.
\section QmitkDataManagerSaving Saving Data
There are two ways of saving data from the Datamanger. The user can either save the whole project with all Data-Elements by clicking on "File"->"Save Project"
or he can save single Data-Elements by right-clicking->"Save", directly on a Data-Element.
When saving the whole project, the sorting of Data-Elements is saved as well. By contrast the sorting is lost, when saving a single Data-Element.
\section QmitkDataManagerProperties Working with the Datamanager
\subsection QmitkDataManagerPropertiesList List of Data-Elements
The Data-Elements are listed in the Datamanager.
As described above the elements can be sorted hierarchically as a parent-child-relation.
For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1).
By drag and drop the sorting of Data-Elements and their hierarchical relation can be changed.
\subsection QmitkDataManagerPropertiesVisibility Visibility of Data-Elements
By default all loaded Data-Elements are visible in the standard view.
The visibility can be changed by right-clicking on the Data-Element and then choosing "Toogle visibility".
The box in front of the Data-Element in the Datamanager shows the visibility.
A green-filled box means a visible Data-Element, an empty box means an invisible Data-Element (see Screenshot1).
\subsection QmitkDataManagerPropertiesRepresentation Representation of Data-Elements
There are different types of representations how to show the Data-Element inside the standard view. By right-clicking on the Data-Element all options are listed (see Screenshot2 and Screenshot 3).
- An arbitrary color can be chosen
- The opacity can be changed with a slide control
- In case of images a texture interpolation can be switched on or off. The texture interpolation smoothes the image, so that no single pixels are visible anymore.
- In case of surfaces the surface representation can be changed between points, wireframe or surface.
- Global reinit updates all windows to contain all the current data. Reinit updates a single data item fits the windows to contain this data item.
\imageMacro{QmitkDatamanager_ImageProperties.png,"Screenshot2: Properties for images",10.56}
\imageMacro{QmitkDatamanager_SurfaceProperties.png,"Screenshot3: Properties for surfaces",11.01}
\subsection QmitkDataManagerPropertiesPreferences Preferences
For the datamanager there are already some default hotkeys like the del-key for deleting a Data-Element. The whole list is seen in Screenshot4.
From here the Hotkeys can also be changed. The preference page is found in "Window"->"Preferences".
\imageMacro{QmitkDatamanager_Preferences.png,"Screenshot4",16.00}
\section QmitkDataManagerPropertyList Property List
The Property List displays all the properties the currently selected Data-Element has. Which properties these are depends on the Data-Element. Examples are opacity, shader, visibility. These properties can be changed by clicking on the appropriate field in the "value" column.
\imageMacro{QmitkDatamanager_PropertyList.png,"Screenshot5: Property List",7.85}
*/
diff --git a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox
index e0bbb8306a..fb81cee2d4 100644
--- a/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox
+++ b/Plugins/org.mitk.gui.qt.dicom/documentation/UserManual/QmitkDicom.dox
@@ -1,118 +1,118 @@
/**
\page org_mitk_gui_qt_dicom The Dicom Plugin
-\imageMacro{QmitkDicom_Icon.png,"Icon of Dicom",2.00}
+\imageMacro{QmitkDicom_Icon.png,"Icon of the DICOM Plugin",2.00}
-\note This article requires a basic knowledge of DICOM.
+\note This article requires a basic knowledge of the DICOM Standard.
\tableofcontents
\section org_mitk_gui_qt_dicomOverview Overview
The DICOM editor is an experimental editor which allows for loading of DICOM images as well as server communication.
It features a highly experimental query/retrieve (you need to configure your PACS correspondingly) as well as a DICOM browser.
The DICOM browser allows you to navigate the DICOM folder/cd depending on its metadata (patient/study/series)
and import selected series for viewing in your MITK based application.
It also allows you to store your dicom data in an internal database so you can easily access often used dicom images.
It is based on the commonTK (CTK) DICOM funcionality.
\section org_mitk_gui_qt_dicomDataHandling Data handling
\imageMacro{QmitkDicom_PluginControls.png,"The dicom Plugin controls",7.37}
In the image above you see the start page of the dicom plugin. On top of the start page you see four buttons. The Local Storage,
the Import CD, the Import Folder and the Query Retrieve button. If you press one of these buttons, the dicom plugin will switch to your local dicom image storage or will start importing dicom images
from CD or a folder on your hard drive or it will open the query retrieve screen.
- Click the 'Local Storage' button to open the local storage screen.
- Click the 'Import CD' button to import DICOM data from a CD.
- Click the 'Import Folder' button to import DICOM date from a directory.
- Click the 'Query Retrieve' button to open the query retrieve screen.
\subsection org_mitk_gui_qt_dicomStorage Data storage
\imageMacro{QmitkDicom_PluginExtended.png,"The DICOM data storage",16.00}
If you open the dicom plugin the dicom data storage will be displayed. You are able to see all your stored dicom image data.
You can browse your data by clicking on the left arrow beside the name of your data. There are three levels available.
The first level is the patient level where you can see the patient data. On the second level you can see the dicom studies for the patient.
on the third level you can see all available series refering to it's study.
You can delete the data by selecting it and pressing the delete button.
Be careful if you have selected a patient or a study all refering data be deleted.
So if you delete a patient the patient and all studies and series refered to the patient will be deleted.
If you delete a study all series of the study will be deleted.
If you want to view the dicom data you have to select a series and click on the View button.
The data will appear in the DataManager and will be dispayed.
\imageMacro{QmitkDicom_DisplayDataManager.png,"Viewed image",16.00}
- Click on the arrow on the left of your data to expand or hide dicom data levels.
- Click the 'Delete' button to delete selected DICOM data.
- Click the 'View' button to view DICOM data.
\subsection org_mitk_gui_qt_dicomImport Data import
\imageMacro{QmitkDicom_ImportDialog.png,"The import dialog checked",9.53}
There are two diffrent ways to import DICOM data.
The First one is to directly imort it into your DICOM data storage. To achieve this you should toggle the checkbox 'Copy on import'.
The second approach is, to have a look at the data first before importing it.
To do that you simply don't check 'Copy on import'.
This will leed you to the leed you to the 'External Dicom Data' screen which provides you a preview of the data containing in youre choosen folder.
You can import the data here by selecting it and pressing the 'Download' button.
It is also possible to view DICOM series directly in Mitk by selecting it here and pressing the 'View' button.
- Click 'Import Folder' or 'Import CD' button to open the import dialog.
- Enable the 'Copy on import' checkbox and choose a folder to import into data storage directly.
- Disable the 'Copy on import' checkbox to get to the 'External Dicom Data' screen.
- Click on the arrow on the left of your data to expand or hide dicom data levels.
- Click the 'Download' button to download selected DICOM data to your DICOM data storage.
- Click the 'View' button to view DICOM data.
\section org_mitk_gui_qt_dicomQueryRetrieve Query/Retrieve
\warning This plugin is experimental and not all of the described features behave as expected.
\note The query retrieve plugin only works if the PACS you are calling knows your machine settings.
There are also issues when you are running a firewall.
The query retrieve workflow allows you to get DICOM data from a server.
\imageMacro{QmitkDicom_QueryRetrieve.png,"The query retrieve screen",16.00}
\subsection org_mitk_gui_qt_dicomQuery Query
\imageMacro{QmitkDicom_Nodes.png,"The DICOM network configuration",11.26}
By performing a DICOM query you will ask a server for it's DICOM data.
This requires to setup the DICOM network configuration of your system and the server.
By clicking on 'Add Server' a new plain server field will appear. Now you can give it a name of your choice.
Fill the servers "DICOM name" the AETitle. Type in it's url, it's port and the specific DICOM protocoll you want to use for image transfer.
\note I recommend not to use CGET because most of the PACS systems (Image Servers) don't support that protocoll.
You can configure the DICOM network configuration of your machine by editing the 'Calling AETiltle', the 'Storage AETitle' and The 'Storage Port' text fields.
But normaly you don't have to change your configuration.
\imageMacro{QmitkDicom_FilterWidget.png,"The DICOM search options",3.66}
After you have finished your network configuration and before you start the query you should use the 'Search Options' to specify your query.
Otherwise all data on the server will be queried and you will have to wait for a long time.
You can specify your query by searching for a specific patient name or a study or a serie or a specific DICOM object by it's id.
You are allowed to include or exclude DICOM modalities from your query and you can specify a specific time in which the DICOM images you are searching fo might been captured.
When you finished that you can click the query button and the queried DICOM data will appear.
- Click on the 'Add Server' button.
- Edit 'Name' field.
- Edit 'AETitle' field.
- Edit 'Adress' field.
- Edit 'Port' field.
- Set search options.
- Click on 'Query' button.
\subsection org_mitk_gui_qt_dicomRetrieve Retrieve
\imageMacro{QmitkDicom_Retrieve.png,"The queried DICOM data.",15.22}
After the query you are able to select the queried data and click the 'Retrieve' button.
This will store the queried DICOM data into your DICOM storage.
Click on the 'Local Storage' button and work with your new data.
- Click on the 'Retrieve' button to retrieve the data to your DICOM storage.
- Click on the 'Local Storage' button.
*/
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox
index 37b67bad2d..78c187f6b3 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/Connectomics/ConnectomicsManual.dox
@@ -1,108 +1,108 @@
/**
\page org_mitk_diffusionimagingapp_perspectives_connectomics The Connectomics Perspective
-\imageMacro{connectomics_perspective.png,"Icon of the Perspective",2.00}
+\imageMacro{connectomics_perspective.png,"Icon of the Connectomics Perspective",2.00}
The connectomics perspective is a collection of views which provide functionality for the work with brain connectivity networks. Currently there exist the following views:
\subpage org_mitk_views_connectomicsdata provides network generation either from data or synthetically.
\subpage org_mitk_views_connectomicsnetworkoperations provides functionalies to operate and process on networks and other data.
\subpage org_mitk_views_connectomicsstatistics provides statistical measures for networks.
\section org_mitk_diffusionimagingapp_perspectives_connectomicsNetworkRenderingCustomization Network Rendering Customization
The rendering of the connectomics networks can be customized by changing the associated properties using the property list. A selection of possible options are:
- Connectomics.Rendering.Edges.Filtering - Only render edges above a certain threshold
- Connectomics.Rendering.Edges.Gradient.Parameter - Color the edges according to certain parameters
- Connectomics.Rendering.Edges.Radius.Parameter - Change the radius of the edges according to certain parameters
- Connectomics.Rendering.Nodes.Filtering - Only render nodes above a certain threshold
- Connectomics.Rendering.Nodes.Gradient.Parameter - Color the nodes according to certain parameters
- Connectomics.Rendering.Nodes.Radius.Parameter - Change the radius of the nodes according to certain parameters
- Connectomics.Rendering.Scheme - Switch between the MITK rendering scheme using above properties and the very fast, but less customizable rendering scheme for VTK graphs
\section org_mitk_diffusionimagingapp_perspectives_connectomicsTrouble Troubleshooting
No known problems.
All other problems.
Please report to the MITK mailing list.
See http://www.mitk.org/wiki/Mailinglist on how to do this.
*/
/**
\page org_mitk_views_connectomicsdata The Connectomics Network Data View
-\imageMacro{QmitkConnectomicsDataViewIcon_48.png,"Icon of the View",2.00}
+\imageMacro{QmitkConnectomicsDataViewIcon_48.png,"Icon of the Connectomics Network Data View",2.00}
This view can be used to create a network from a parcellation and a fiber image as well as to create synthetic networks.
\imageMacro{dataview.png,"The user interface",4.85}
To create a network select first a parcellation of the brain (e.g. as provided by freesurfer ) by CTRL+Leftclick and secondly a fiber image ( as created using a tractography view). Then click on the "Create Network" button.
- "Use label of end position of fibers" will create a network containing a node for every label a fiber ends in
- "Extrapolate label" will avoid creating nodes using FreeSurfer white matter labels and instead extrapolate in which grey matter label the fiber would end
Additionally you have the option to create artificial networks, for testing purposes. Currently choices are:
- A regular lattice, where each node is placed in a cubic pattern and only connected to its neighbours
- A heterogenic sphere, where one node is placed in the center and connected to all nodes on the shell
- A random network, where nodes are randomly placed on a spherical shell and randomly connected
*/
/**
\page org_mitk_views_connectomicsnetworkoperations The Connectomics Network Operations View
-\imageMacro{QmitkConnectomicsNetworkOperationsViewIcon_48.png,"Icon of the View",2.00}
+\imageMacro{QmitkConnectomicsNetworkOperationsViewIcon_48.png,"Icon of the Connectomics Network Operations View",2.00}
This view can be used modify networks and related data.
\imageMacro{operationsview.png,"The user interface",4.61}
Select a parcellation and press "Convert to RGBA" to create a RGBA image. By doing this conversion it is much easier to discern the different parcels. Furthermore MITK supports 3D visualization of an RGBA image.
Select a network and press "Create Connectivity Matrix Image" to create a 2D image of the connectivity matrix. By default the weight of a connection is used as grey value. Using the "Rescale" option will rescale the weights so highest one is 255. Using the "Binary" option will result in a binary connectivity matrix.
*/
/**
\page org_mitk_views_connectomicsstatistics The Connectomics Statistics View
-\imageMacro{QmitkConnectomicsStatisticsViewIcon_48.png,"Icon of the View",2.00}
+\imageMacro{QmitkConnectomicsStatisticsViewIcon_48.png,"Icon of the Connectomics Statistics View",2.00}
This view can be used to show statistical analysis of a network.
\imageMacro{statisticsview.png,"The user interface",6.58}
To calculate network statistics select a network in the datamanager. At this time the following statistics are calculated for the entire network:
- The number of vertices in the network
- The number of edges in the network
- The number of edges which have the same vertex as beginning and end point
- The average degree of the nodes in the network
- The connection density the network (the number of edges divided by the number of possible edges)
- The unweighted efficiency of the network ( 1 divided by average path length, this is zero for disconnected graphs)
- The global clustering
Furthermore some statistics are calculated on a per node basis and displayed as histograms:
- The degree of each node
- The (unweighted) betweenness centrality of each node
- The spread of shortest paths between each pair of nodes (For disconnected graphs the shortest paths with infinite length are omitted for readability)
*/
diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox
index 517ed4aba6..b99b98232d 100644
--- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox
+++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox
@@ -1,58 +1,58 @@
/**
\page org_mitk_views_tractbasedspatialstatistics The TBSS View
-\imageMacro{tbss.png,"Icon of the View",2.00}
+\imageMacro{tbss.png,"Icon of the TBSS View",2.00}
\section QmitkTractbasedSpatialStatistics Summary
This view can be used to locally explore data resulting from preprocessing with the TBSS view of FSL
This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general and how to work with the TBSS view of FSL.
If you encounter problems using the view, please have a look at the \ref QmitkTractbasedSpatialStatisticsUserManualTroubleshooting page.
\tableofcontents
\section QmitkTractbasedSpatialStatisticsUserManualOverview Overview
This view is currently under development and as such the interface as well as the capabilities are likely to change significantly between different versions.
This documentation describes the features of this current version.
\section QmitkTractbasedSpatialStatisticsUserManualFSLImport FSL Import
The FSL import allows to import data that has been preprocessed by FSL. FSL creates output images that typically have names like all_FA_skeletonized.nii.gz that are 4-dimensional images that contain registered images of all subjects. By loading this 4D image into the datamanager and listing the groups with the correct number of subjects, in the order of occurrence in the 4D image, in the TBSS-View using the Add button and clicking the import subject data a TBSS file is created that contains all the information needed for tract analysis. The diffusion measure of the image can be set as well.
\imageMacro{fslimport.png,"FSL Import",16.00}
\section QmitkTractbasedSpatialStatisticsUserManualRois Regions of Interest (ROIs)
To create a ROI the mean FA skeleton (typically called mean_FA_skeleton.nii.gz) that is created by FSL should be loaded in to the datamanager and selected. By using the Pointlistwidget points should be set on the skeleton (make sure to select points with relatively high FA values). Points are set by first selecting the button with the '+' and than shift-leftclick in the image. When the correct image is selected in the datamanager the Create ROI button is enabled. Clicking this will create a region of interest that passes through the previously selected points. The roi appears in the datamanager. Before doing so, the name of the roi and the information on the structure on which the ROI lies can be set. This will be saved as extra information in the roi-image. Before the ROI is calculated, a pop-up window will ask the user to provide a threshold value. This should be the same threshold that was previously used in FSL to create a binary mask of the FA skeleton. When this is not done correctly, the region of interest will possible contain zero-valued voxels.
\imageMacro{tbssRoi.png,"Regions of Interest (ROIs)",16.00}
\section QmitkTractbasedSpatialStatisticsUserManualProfiles
y selecting a tbss image with group information and a region of interest image (as was created in a previous stap). A profile plot is drawn in the plot canvas. By clicking in the graph the crosshairs jump to the corresponding location in the image.
\imageMacro{profiles.png,"Profile plots",16.00}
\section QmitkTractbasedSpatialStatisticsUserManualFiberPlotting
It is also possible to use fiber bundles to plot values in images. However, unlike TBSS this only works on 3D volumes (one subject only). To plot the values of a 3D volume using fiber tracking results, we need, fiber data and two planar circles as Regions of Interest that define the region that must be plotted. For every fiber that passes through both ROIs the values at the corresponding positions in the volume are plotted. Every fiber is resampled to the number of segments specified in the GUI. The average value can also be plotted. The subset of the fibers between the ROIs can be cut out by pressing the Cut button.
\imageMacro{trackingplot.png,"Plot of fiber tracts",16.00}
\section QmitkTractbasedSpatialStatisticsUserManualTroubleshooting Troubleshooting
Please report to the MITK mailing list.
See http://www.mitk.org/wiki/Mailinglist on how to do this.
\section QmitkTractbasedSpatialStatisticsUserManualReferences References
1. S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens. Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data. NeuroImage, 31:1487-1505, 2006.
2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004.
*/
diff --git a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox
index 08757baccf..60a919c5fb 100644
--- a/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox
+++ b/Plugins/org.mitk.gui.qt.igtexamples/documentation/UserManual/QmitkIGTTutorial.dox
@@ -1,14 +1,14 @@
/**
\page org_imageguidedtherapytutorial The MITK-IGT Tutorial Module
-\imageMacro{QmitkIGTExamples_ImageGuidedTherapy.png,"Icon of the Module",2.00}
+\imageMacro{QmitkIGTExamples_ImageGuidedTherapy.png,"Icon of the MITK-IGT Tutorial Module",2.00}
\section QmitkIGTTutorialUserManualSummary Summary
This module is not meant as a end-user module. It contains tutorial program code that explains how to use the MITK-IGT component.
It contains only two buttons. The "Start image guided therapy" button will create a virtual tracking device and a virtual tool.
It will move the tool around on random paths in a tracking volume of 200x200x200 mm. The tool is visualized with a cone.
If you do not see a cone moving around, you will need to initialize the rendering views correctly. Use the DataManager view to perform
a global reinit.
*/
diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox
index fe5b8a4884..b526670e21 100644
--- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox
+++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTNavigationToolManager.dox
@@ -1,55 +1,55 @@
/**
\page org_mitk_views_igtnavigationtoolmanager The MITK-IGT Navigation Tool Manager
-\imageMacro{QmitkIGTTracking_IconNavigationToolManager.png,"Icon of the Module",2.12}
+\imageMacro{QmitkIGTTracking_IconNavigationToolManager.png,"Icon of the Navigation Tool Manager",2.00}
\section QmitkMITKIGTNavigationToolManager Introduction
This view allows for creating and editing NavigationToolStorages. These storages contains naviagtion tools of a tracking device, can be saved permanently and used later for any other IGT application.
Available sections:
- \ref QmitkMITKIGTNavigationToolManager
- \ref QmitkMITKIGTNavigationToolManagerToolOverview
- \ref QmitkMITKIGTNavigationToolManagerManagingNavigationToolStorage
- \ref QmitkMITKIGTNavigationToolManagerAddingEditingNavigationTools
\section QmitkMITKIGTNavigationToolManagerToolOverview Navigation Tools Overview
A navigation tool of MITK-IGT represents a tracking tool (e.g. an emt sensor or an optically tracked tool) and it's corresponding data, like it's name and it's surface. A navigation tool is a generalized container for any trackable object in combination with it's additional information. Every navigation tool has different properties which are:
- Name
- Unique identifier
- Tool definition file
- Serial number
- Surface for visualization
- Type of tracking device
- Type of the tool
- Tool landmarks
Note that not all properties are needed for all types of tools. A tool definition file, for example, is only needed by optical tracking tools (e.g. a .rom file for Polaris or a toolfile for the MicronTracker). A tool associated with the aurora system is alwalys identified by it's serial number. You can also detect Aurora tools automatically with the TrackingToolbox view and edit the automatically detected tool storage later with this view.
\section QmitkMITKIGTNavigationToolManagerManagingNavigationToolStorage Managing Navigation Tool Storage
In order to create edit a tool storage container, you can select one of the available tool storages listed in the upper part of the UI. The list shows all tool storages which are available throug the micro services concept of MITK. The list also shows the current tool storage of the IGT tracking toolbox view if it is active. In addition to the listed tool storages, you can load new storages from the hard disc which will then appear in the list and might be edited as all other storage by simply selecting it in the list. You may also save a selected tool storage to the hard disc or create a new one.
In the lower part of the UI you always see the list of tools of the tool storage which is currently selected in the upper part. Use the buttons "add", "edit" and "delete" to manage the contained navigation tools. If you click "edit" or "delete" the operation is applied on the currently selected tool, as shown in the screenshot below.
\imageMacro{QmitkIGTTracking_NavigationToolManagemantStartScreen.png,"Screenshot of the main view of NavigationToolManagent",10.90}
\section QmitkMITKIGTNavigationToolManagerAddingEditingNavigationTools Adding / Editing Navigation Tools
If you add or edit a navigation tool, an input mask, as shown in the screenshot below, appears. The tool identifier is filled automatically, if you change it, remember that it is unique in the current storage. Also, choose a valid surface for every tool, this is nessesary for correct tool visualization. The other information depends on the tracking system type. So choose a tool file for the Polaris or the MicronTracker system and type in a serial number for the Aurora system. Two identical tools with the same serial number are also possible, they are assigned by the order in which they are attached to the device. As long as they also have the same surface as representation, this should not be a problem for most of the use cases.
The tool type is additional information which is not needed by the tracking device but might be needed by further IGT applications. The same applies to the tool landmarks which might be defined for a tool. There are two different types of landmarks which are designed as described here:
- Tool Calibration Landmarks: These landmarks may be used clearly define the tools pose only by using landmarks in the tool coordinate system. E.g., two landmarks for a 5DoF tool and three landmarks for a 6DoF tool. These landmarks may be used, e.g., for a point based registration of a tool from image space to tracking space.
- Tool Registration Landmarks: These landmarks are designed for representing defined landmarks on a tools surface. The number of these landmarks might exeed the number of tool calibration landmarks for reasons of redundancy and averaging. They are used for, e.g., manually registering the pose of a tool by visual markers in a CT scan. If you would use these landmarks to do a point based registration from image space to tracking space later, you might overweight the tool because of two many landmarks compared to other markers.
\imageMacro{QmitkIGTTracking_NavigationToolManagementAddTool.png,"Screenshot of add/edit navigation tool screen",9.19}
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox
index b4b762c87b..bc7c920585 100644
--- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox
+++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkMITKIGTTrackingToolbox.dox
@@ -1,64 +1,64 @@
/**
\page org_mitk_views_igttrackingtoolbox The MITK-IGT Tracking Toolbox
-\imageMacro{QmitkIGTTracking_IconTrackingToolbox.png,"Icon of the module",2.12}
+\imageMacro{QmitkIGTTracking_IconTrackingToolbox.png,"Icon of the MITK-IGT Tracking Toolbox",2.00}
Available sections:
- \ref QmitkMITKIGTTrackingToolboxIntroduction
- \ref QmitkMITKIGTTrackingToolboxWorkflow
- \ref QmitkMITKIGTTrackingToolboxConnecting
- \ref QmitkMITKIGTTrackingToolboxLoadingTools
- \ref QmitkMITKIGTTrackingToolboxAutoDetection
- \ref QmitkMITKIGTTrackingToolboxStartTracking
- \ref QmitkMITKIGTTrackingToolboxLogging
- \ref QmitkMITKIGTTrackingOptions
\section QmitkMITKIGTTrackingToolboxIntroduction Introduction
The MITK-IGT Tracking Toolbox is a view which allows you to connect to a tracking device, track and visualize navigation tools and write the tracked data into a log file. Currently the devices Polaris, Aurora (both Northern Digital Inc. (NDI); Waterloo, Ontario, Canada) and MicronTracker (Claron Technology, Inc.; Toronto, Ontario, Canada) are supported. The MicroBird family (Ascension Technology Corporation, Inc.; Burlington, USA) will hopefully follow soon since it is already supported by the tracking layer of IGT. The logging feature of the Tracking Toolbox supports logging in XML or CSV format.
\imageMacro{QmitkIGTTracking_ScreenshotMitk.png,"MITK Screenshot with the TrackingToolbox activated",16.00}
\section QmitkMITKIGTTrackingToolboxWorkflow General workflow Introduction
A general Workflow with the Tracking Toolbox may be:
- Configuration of a tracking device
- Loading a toolfile which holds tool definitions
- Start tracking
- Logging tracked data
\section QmitkMITKIGTTrackingToolboxConnecting Tracking Device Configuration
The tracking device can be specified in the tracking device configuration section located in the upper area of the tracking tab. As shown in the screenshot below, you choose your tracking device in the drop down menu. If you use a tracking system connected to a serial port, like Aurora or Polaris, you then need to specifiy the serial port. In case of the MicronTracker you only need to ensure that all drivers are installed correctly and integrated into MITK. If you want to check the connection, press "test connection". The results are displayed in the small black box on the right.
\imageMacro{QmitkIGTTracking_ConfigurationWidget.png,"Tracking Device Configuration",8.55}
\section QmitkMITKIGTTrackingToolboxLoadingTools Loading tools
To load tools which can be tracked you need a predefined tracking tool storage. If you use the Aurora system you also have the possibility to automatically detect the connected tools. In this case a tracking tool storage is created by the software (see section below). Otherwise you can use the MITK view NavigationToolManager to define a navigation tool storage. There you can create navigation tools with the corresponding toolfiles, visualization surfaces and so on. Please see NavigationToolManager manual for more details.
Navigation tool storages can be loaded by pressing the button "Load Tools". Please ensure that the tracking device type of the tools matches the chosen tracking device, otherwise you will get an error message if you try to start tracking. All loaded tools will then be displayed in grey as shown in the screenshot below. If you start tracking they will become green if the tools were found and red if they were not found inside the tracking volume.
\imageMacro{QmitkIGTTracking_TrackingToolsWidget.png,"Tracking Tools",9.08}
\section QmitkMITKIGTTrackingToolboxAutoDetection Auto detection of tools (only Aurora)
If the Aurora tracking system is used, a button "Auto Detection" appears. If you press this button the software connects to the system and automatically detects all connected tools. You will then be asked whether you want to save the detected tools as a tool storage to the hard drive. You might want to do this if you want to use or modify this tool storage later. In the automatically detected tool storage the tools are named AutoDetectedTools1, AutoDetectedTools2, and so on. Small spheres are used as tool surfaces. After autodetection the detected tools are loaded automatically even if you did not save them.
\section QmitkMITKIGTTrackingToolboxStartTracking Start/stop tracking
Tracking can simply be started by pressing "Start Tracking". Note that options may not be changed during tracking. Once tracking has started the tracking volume (only if the option is on) and the tools are visualized in the 3D view of MITK.
\section QmitkMITKIGTTrackingToolboxLogging Logging features
If your device is tracking, you are able to log the tracking data by using the logging tab. You first must define a file name. You can then choose whether you want comma seperated (csv) or xml format. Press "Start Logging" to start logging. You can also limit the number of logged frames, which will cause the logging to stop automatically after the given number.
\section QmitkMITKIGTTrackingOptions Options
In the options tab you can enable or disable the visualization of the tracking volume and of the tool quaternions. If enabled, the tool quaternions are shown in the tool information. You can also define the update rate of the tracking data. The update rate should not be set higher than the update rate of the tracking system.
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox
index 3d46273e2f..b6aec950cb 100644
--- a/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox
+++ b/Plugins/org.mitk.gui.qt.igttracking/documentation/UserManual/QmitkNavigationDataPlayer.dox
@@ -1,18 +1,18 @@
/**
\page org_mitk_views_navigationdataplayer NavigationData Player
-\imageMacro{QmitkIGTTracking_IconNavigationDataPlayer.png,"Icon of NavigationData Player",2.00}
+\imageMacro{QmitkIGTTracking_IconNavigationDataPlayer.png,"Icon of the NavigationData Player",2.00}
Available sections:
- \ref NavigationDataPlayerOverview
\section NavigationDataPlayerOverview
The navigation data player plays recorded or artificial navigation data of one ore more tracking tools and visualizes their trajectory. For that purpose select an input file (*.xml only) and select which tracking tool's trajectory should be visualized. If you additionally activate the checkbox "Splines" the trajectory curve will be smoothed via spline interpolation.
Press the button "start" for starting the player and the visualization. If "Sequential Mode" is checked, the navigation data are played sequentially without regarding the recorded time steps.
You can use the resolution field to define which part of the samples you want to use. E.g. 1 = every sample; 2 = every second sample; 3 = every third sample, ...
\imageMacro{QmitkIGTTracking_ScreenshotNavigationDataPlayer.png,"Screenshot of the NavigationData Player",16.00}
*/
diff --git a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox
index 1f9328531e..11373662ad 100644
--- a/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox
+++ b/Plugins/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropper.dox
@@ -1,36 +1,36 @@
/**
\page org_mitk_views_imagecropper The Image Cropper Plugin
-\imageMacro{QmitkImageCropper_Icon.png,"Icon of the Plugin",2.00}
+\imageMacro{QmitkImageCropper_Icon.png,"Icon of the Image Cropper Plugin",2.00}
\tableofcontents
\section QmitkImageCropperUserManualOverview Overview
ImageCropper is a functionality which allows the user to manually crop an image by means of a bounding box. The functionality does not create a new image, it only hides parts of the original image.
\section QmitkImageCropperUserManualFeatures Features
- Crop a selected image using a bounding box.
- Set the border voxels to a specific user defined value after cropping.
\section QmitkImageCropperUserManualUsage Usage
First select from the drop down menu the image to crop. The three 2D widgets show yellow rectangles representing the bounding box in each plane (axial, sagital, coronal), the lower right 3D widget shows the entire volume of the bounding box.\n
- To change the size of bounding box press control + right click and move the cursor up/down or left/right in one of the three 2D views.\n
- To change the orientation of the bounding box press control + middle click and move the cursor up/down or left/right in one of the three 2D views.\n
- To move the bounding box press control + left click and move the cursor to the wanted position in one of the three 2D views.\n
To show the result press the [crop] button.\n
To crop the image again press the [New bounding box!] button.\n\n
All actions can be undone by using the global undo function (Ctrl+Z).\n
To set the border voxels to a specific value after cropping the image, activate the corresponding checkbox and choose a gray value.
\section QmitkImageCropperUserManualTroubleshooting Troubleshooting
*/
diff --git a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox
index 4cfa135346..2267b623d2 100644
--- a/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox
+++ b/Plugins/org.mitk.gui.qt.imagenavigator/documentation/UserManual/QmtikImageNavigator.dox
@@ -1,15 +1,15 @@
/**
\page org_mitk_views_imagenavigator The Image Navigator
-\imageMacro{QmtikImageNavigator_Slider.png,"Icon of the Module",2.00}
+\imageMacro{QmtikImageNavigator_Slider.png,"Icon of the Image Navigator",2.00}
\imageMacro{QmtikImageNavigator_ImageNavigator.png,"Image Navigator",7.47}
Fast movement through the available data can be achieved by using the Image Navigator.
By moving the sliders around you can scroll quickly through the slides and timesteps.
By entering numbers in the relevant fields you can jump directly to your point of interest.
The "Show detail" checkbox enables you to see the world coordinates in millimetres
and the index/voxel coordinates. These may be edited to jump to a specific location.
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox
index b18f55b489..1a6935a94d 100644
--- a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox
+++ b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox
@@ -1,10 +1,10 @@
/**
\page org_surfacematerialeditor The Surface Material Editor
-\imageMacro{QmitkSurfaceMaterialEditor_Icon.png,"Icon of the Module",2.00}
+\imageMacro{QmitkSurfaceMaterialEditor_Icon.png,"Icon of the Surface Material Editor",2.00}
The Surface Material Editor shows the properties of the selected data that are relevant for the selected shader. These properties can be filtered to find a specific property. The preview window shows the representation of a neutral 3D object with the currently selected settings.
\imageMacro{QmitkSurfaceMaterialEditor_Gui.png,"The Surface Material Editor",10.92}
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox
index 921de2063a..f9c2915943 100644
--- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatistics.dox
@@ -1,54 +1,54 @@
/**
\page org_mitk_views_imagestatistics The Image Statistics View
-\imageMacro{QmitkMeasurementToolbox_ImageStatisticsIcon.png,"Icon of the View",2.00}
+\imageMacro{QmitkMeasurementToolbox_ImageStatisticsIcon.png,"Icon of the Image Statistics View",2.00}
\section QmitkImageStatisticsUserManualSummary Summary
This view provides an easy interface to quickly compute some features of a whole image or a region of interest.
This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general.
Please see \ref QmitkImageStatisticsUserManualDetails for more detailed information on usage and supported filters.
If you encounter problems using the view, please have a look at the \ref QmitkImageStatisticsUserManualTrouble page.
\section QmitkImageStatisticsUserManualDetails Details
Manual sections:
- \ref QmitkImageStatisticsUserManualOverview
- \ref QmitkImageStatisticsUserManualUsage
- \ref QmitkImageStatisticsUserManualTrouble
\section QmitkImageStatisticsUserManualOverview Overview
This view provides an easy interface to quickly compute some features of a whole image or a region of interest.
\imageMacro{QmitkMeasurementToolbox_Interface.png,"The interface",9.10}
\section QmitkImageStatisticsUserManualUsage Usage
After selection of an image or a binary mask of an image in the datamanager, the Image Statistics view shows some statistical information. If a mask is selected, the name of the mask and the name of the image, to which the mask is applied, are shown at the top. For time data the current time step is used for the selected mask and the selected image. If the total number of time steps on the selected mask is less than the current time step, the last time step of the mask is used. If a mask is selected, its used time step will be displayed next to its name like this: (t=0).
Check "Ignore zero-valued voxels" to hide voxels with grayvalue zero.
Below it is the statistics window which displays the calculated statistical features (such as mean, standard deviation...).
Beneath the statistics window is the histogram window, which shows the histogram of the current selection.
At top of the histogram window are two radiobuttons. Toggle one of them to either show the histogram as a barchart or as a lineplot.
Use mousewheel to zoom in and out the histogram. With the left mouse button the histogram is pannable in zoomed state.
If the histogram is displayed as a barchart a tooltip is available by hovering over one of the bins. A tooltip is also available, if an intesity profile is created for a path element as mask.
At the bottom of each view is one button. They copy their respective data in csv format to the clipboard.
\section QmitkImageStatisticsUserManualTrouble Troubleshooting
No known problems.
All other problems.
Please report to the MITK mailing list.
See http://www.mitk.org/wiki/Mailinglist on how to do this.
*/
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox
index b73817c4d0..03ddcf8678 100644
--- a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkMeasurement.dox
@@ -1,120 +1,120 @@
/**
\page org_mitk_views_measurement The Measurement View
-\imageMacro{QmitkMeasurementToolbox_MeasurementIcon.png,"Icon of the View",2.00}
+\imageMacro{QmitkMeasurementToolbox_MeasurementIcon.png,"Icon of the Measurement View",2.00}
\section QmitkMeasurementUserManualOverview Overview
The Measurement view enables the user to interact with 2D images or single slices of 3D image stacks and planar figure data types. It allows to measure distances, angels, pathes and several geometric figures on a dataset.
\tableofcontents
The workflow to use this view is:
\imageMacro{QmitkMeasurementToolbox_Workflow.png,"",16.00}
The workflow is repeatedly useable with the same or different measurement figures, which are correlated to the choosen image and can be saved together with it for future use. On pressing the Measurement icon (see picture below the page title) in the view button line the basic appearance of the view is as follws.
\imageMacro{QmitkMeasurementToolbox_BasicScreenEdited.jpg,"",16.00}
The standard working plane is "Axial" but the other standard viewplanes ("Saggital" and "Coronal") are also valid for measurements. To swap between the view planes refer to the application user manual.
\section QmitkMeasurementUserManualFeatures Features
The view as it is depicted below offers the following features in the order of apperance on the image from top to bottom:
\imageMacro{QmitkMeasurementToolbox_MeasurementView.jpg,"",7.60}
The first information is the selected image's name (here: DICOM-MRI-Image) followed by the measurement figures button line with the seven measurement figures. From left to right the buttons are connected with the following functions:
\subsection SubOne Draw Line
Draws a line between two set points and returns the distance between these points.
\subsection SubTwo Draw Path
Draws a path between several set points (two and more) and calculates the circumference, that is all line's length summed up. Add the final point by double left click.
\subsection SubThree Draw Angle
Draws two lines from three set points connected in the second set point and returns the inner angle at the second point.
\subsection SubFour Draw Four Point Angle
Draws two lines that may but must not intersect from four set points. The returned angle is the one depicted in the icon.
\subsection SubFive Draw Circle
Draws a circle by setting two points, whereas the first set point is the center and the second the radius of the circle. The measured values are the radius and the included area.
\subsection SubSix Draw Rectangle
Draws a rectangle by setting two points at the opposing edges of the rectangle starting with the upper left edge. The measured values are the circumference and the included area.
\subsection SubSeven Draw Polygon
Draws a polygon by setting three or more points. The measured values are the circumference and the included area. Add the final point by double left click.
Below the buttonline the statistics window is situated, it displays the results of the actual measurements from the selected measurement figures. The content of the statistics window can be copied to the clipboard with the correspondig button for further use in a table calculation programm (e.g. Open Office Calc etc.).
\imageMacro{QmitkMeasurementToolbox_ImageProcessed.jpg,"",7.56}
The last row contains again a button line to swap from the measurement perspective (activated in the image) to other supported MITK perspectives.
\section QmitkMeasurementUserManualUsage Usage
This Section is subdivided into four subsections:
- Add an image
- Work with measurement figures
- Save the image with measurement information
- Remove measurement figures or image
Let's start with subsection 1
\subsection One Add an image
There are two possible ways to add an image to the programm. One is to grap the image with left mouse click from your prefered file browser and simply drag&drop it to the View Plane field. The other way is to use the
\imageMacro{QmitkMeasurementToolbox_OpenButton.png,"",2.01}
button in the upper left corner of the application. A dialog window appears showing the file tree of the computer. Navigate to the wanted file and select it with the left mouse click. Afterwards just use the dialog's open button.
The wanted image appears in the View Plane and in the Data Manager the images name appears as a new tree node. Now the image is loaded it can be adjusted in the usual way ( zoom in/out: right mouse button + moving the mouse up and down, moving the image: press mouse wheel and move the mouse to the wished direction, scroll through the slices( only on 3D images): scroll mouse wheel up and down).
\imageMacro{QmitkMeasurementToolbox_ImageLoadedScreen.jpg,"",16.00}
After the image is loaded the image's name appears in the Data Manager. By left-clicking on the image name the buttonline becomes activated.
\subsection Two Work with measurement figures
The measurement view comes with seven measurement figures(see picture below), that can be applied to the images.
\imageMacro{QmitkMeasurementToolbox_MeasurementFigureButtonLine.jpg,"",7.22}
The results of the measurement with each of these figures is shown in the statistics window and in the lower right corner of the view plane.
\imageMacro{QmitkMeasurementToolbox_ImageProcessedScreen.jpg,"",6.96}
When applying more then one measurement figure to the image the actual measurement figure is depicted in red and the displayed values belong to this measurement figure. All measurement figures become part of the Data Manager as a node of the image tree.
\subsection Three Save the image with measurement information
After applying the wanted measurement figures the entire scene consisting of the image and the measurement figures can be saved for future use. Therefore just click the right mouse button when over the image item in the Data Manager and choose the item "Save" in the opening item list. Following to that a save dialog appears where the path to the save folder can be set. Afterwards just accept your choice with the save button.
\subsection Four Remove measurement figures or image
If the single measurement figures or the image is not needed any longer, it can be removed solely or as an entire group. The image can't be removed without simultaneously removing all the dependent measurement figures that belong to the image tree in the Data Manager. To remove just select the wanted items in the data manager list by left-click on it or if several items wanted to be removed left click on all wanted by simultaneously holding the ctrl-button pressed.
For more detailed usage of the save/remove functionality refer to the Data Manager User Manual.
",16.00}
*/
diff --git a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox
index 66032f37de..878627bddb 100644
--- a/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox
+++ b/Plugins/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMaker.dox
@@ -1,44 +1,44 @@
/**
\page org_mitk_views_moviemaker The Movie Maker View
-\imageMacro{QmitkMovieMaker_Icon.png,"Icon of the View",2.00}
+\imageMacro{QmitkMovieMaker_Icon.png,"Icon of the Movie Maker View",2.00}
Available sections:
- \ref QmitkMovieMakerUserManualOverview
- \ref QmitkMovieMakerUserManualFeatures
- \ref QmitkMovieMakerUserManualUsage
\section QmitkMovieMakerUserManualOverview Overview
MovieMaker is a functionality for easily creating fancy movies from scenes displayed in MITK widgets.
It is also possible to slide through your data, automatically rotate 3D scenes and take screenshots of widgets.
\section QmitkMovieMakerUserManualFeatures Features
The Movie Maker allows you to create movies and screenshots from within MITK. It can automatically scroll thorugh timesteps and slices while recording a movie. This way, you can record visualizations like a beating heart or a rotating skull.
\section QmitkMovieMakerUserManualUsage Usage
\imageMacro{QmitkMovieMaker_ControlArea.png,"A view of the command area of QmitkMovieMaker",9.84}
\subsection QmitkMovieMakerUserManualWindowSelection Window selection
With the first two drop down boxes, you can choose which window you want to step through and which window you want to record in. Left clicking inside a window will set both drop down boxes to that window, but you can choose different windows for stepping and recording.
The first drop down box defines the window along which slices will be stepped through if stepping is set to spatial (see below). The second denotes the window from which the content will be recorded.
\subsection QmitkMovieMakerUserManualRecordingOptions Recording Options
The slider can be used to step through the slices manually while not recording. Start and stop control a preview of what a video would look like.
The buttons in the bottom part of this section can be used to create movies (windows only) or screenshots. Clicking opens a file %dialog where a name can be selected. After confirmation, a screenshot or movie is created according to the playing options.
\subsection QmitkMovieMakerUserManualPlayingOptions Playing Options
The first section controls whether the movie steps through slices (if a 2D view is selected), rotate the shown scene (if a 3D view is selected), or step through time steps (if set to temporal and a time resolved dataset is selected). If set to combined, a combination of both above options is used, with their speed relation set via the S/T Relation Spinbox.
In the second section the direction of stepping can be set. Options are: Forward, backward and Ping-Pong, which is back-and-forth.The stepping speed can be set via the spinbox(total time in seconds).
Although stepping speed is a total time in sec., this can not always be achieved. As a minimal frame rate of 25 fps is assumed to provide smooth movies, a dataset with only 25 slices will always be stepped through in 1 sec or faster.
*/
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox
index 17dfdb2e03..65f82f63f2 100644
--- a/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox
+++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteraction.dox
@@ -1,47 +1,47 @@
/**
\page org_mitk_views_pointsetinteraction The Point Set Interaction View
-\imageMacro{QmitkPointSetInteraction_Icon.png,"Icon of the View",2.00}
+\imageMacro{QmitkPointSetInteraction_Icon.png,"Icon of the Point Set Interaction View",2.00}
Available sections:
- \ref QmitkPointSetInteractionUserManualOverview
- \ref QmitkPointSetInteractionUserManualDetails
\section QmitkPointSetInteractionUserManualOverview Overview
This functionality allows you to define multiple sets of points, to fill them with points and to save them in so called PointSets.
\imageMacro{QmitkPointSetInteraction_Screenshot.png,"MITK with the QmitkPointSetInteraction functionality",16.00}
This document will tell you how to use this functionality, but it is assumed that you already know how to navigate through the slices of an image using the
four window view. Please read the application manual for more information.
\section QmitkPointSetInteractionUserManualDetails Details
First of all you have to select a PointSet to use this functionality. Therefore, you have to select the point set in the data manager.
If there are currently no point sets in the data tree, you have to first add a new point set to the data tree. This is done by clicking the "Add pointset..."
button.
\imageMacro{QmitkPointSetInteraction_AddPointSet.png,"The Add pointset... dialog",8.64}
In the pop-up dialog, you have to specify a name for the new point set. This is also the node for the new data tree item.
\imageMacro{QmitkPointSetInteraction_CurrentPointSetArea.png,"The Current pointset area",6.52}
The "Current pointset" area contains a list of points. Within this area, all points for the current point set node are listed.
To set points you have to toggle the "Set Points" button, the leftmost of the four buttons on the bottom of the view.
Points can be defined by performing a left mouse button click while holding the "Shift"-key pressed in the four window view.
To erase all points from the list press the next button. The user is prompted to confirm the decision. If you want to delete only a single point, left click on it in the list and then press delete on your keyboard.
With the third button, a previously saved point set can be loaded and all of its points are shown in the list and the four window view.
The user is prompted to select the file to be loaded.
The file extension is ".mps". On the right of this button is the save button.
With this function the entire point set can be saved to the harddrive. The user is prompted to select a filename.
Pointsets are saved in XML fileformat but have to have a ".mps" file extension.
You can select points in the render window, if the "Set Points" button is toggled, with a left mouse button click on them.
If you keep the mouse button pressed, you can move the points by moving the mouse and then releasing the mouse button.
With the delete key you can remove the selected points.
*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox
index 9141b2b83b..7994e52355 100644
--- a/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox
+++ b/Plugins/org.mitk.gui.qt.registration/documentation/UserManual/QmitkPointBasedRegistrationUserManual.dox
@@ -1,106 +1,106 @@
/**
\page org_mitk_views_pointbasedregistration The Point Based Registration View
-\imageMacro{QmitkRegistration_PointBasedIcon.png,"Icon of the View",2.00}
+\imageMacro{QmitkRegistration_PointBasedIcon.png,"Icon of the Point Based Registration View",2.00}
Available sections:
- \ref PointBasedRegistrationUserManualOverview
- \ref PointBasedRegistrationUserManualDetails
\section PointBasedRegistrationUserManualOverview Overview
This view allows you to register two datasets in a rigid and deformable manner via corresponding
PointSets. Register means to align two datasets, so that they become as similar as possible.
Therefore you have to set corresponding points in both datasets, which will be matched. The movement, which has to be
performed on the points to align them, will be performed on the moving data as well. The result is shown in the multi-widget.
\imageMacro{QmitkRegistration_PointBasedRegistration_small.png,"MITK with the PointBasedRegistration view",16.00}
This document will tell you how to use this view, but it is assumed that you already know how to navigate through
the slices of a dataset using the multi-widget.
\section PointBasedRegistrationUserManualDetails Details
First of all you have to open the data sets which you want to register and select them in the Data Manager. You have to select exactly 2 images for registration. The image which was selected
first will become the fixed image, the other one the moving image. The two selected images will remain for registration until exactly two images were selected in the Data Manager again. While
there aren't two images for registration a message is viewed on top of the view saying that registration needs two images. If two images are selected the message disappears and the interaction
areas for the fixed and moving data appears. The upper area is for interaction with the fixed data. Beneath this area is the interaction area for the moving data. On default only the fixed and
moving image with their corresponding pointsets are shown in the render windows. If you want to have other images visible you have to set the visibility via the Data Manager. Also if you want to
perform a reinit on a specific node or a global reinit for all nodes you have to use the Data Manager.
\imageMacro{QmitkRegistration_FixedDataPointBased.png,"The Fixed Data area",7.43}
The "Fixed Data" area contains a QmitkPointListWidget. Within this widget, all points for the fixed data are listed. The label above this list shows the number of points that are already set.
To set points you have to toggle the "Set Points" button, the leftmost under the QmitkPointListWidget. The views in the QmitkStdMultiWidget were reinitialized to the fixed data. Points can
be defined by performing a left click while holding the "Shift"-key pressed in the QmitkStdMultiWidget. You can remove the interactor which listens for left clicks while
holding the "Shift"-key pressed by detoggle the "Set Points" button. The next button, "Clear Point Set", is for deleting all specified points from this dataset. The user is prompted to confirm
the decision. With the most right button, a previously saved point set can be loaded and all of its points are shown in the QmitkPointListWidget and in the QmitkStdMultiWidget. The user is prompted
to select the file to be loaded. The file extension is ".mps". On the left of this button is the save button. With this function all points specified for this dataset and shown in the
QmitkPointListWidget are saved to harddisk. The user is prompted to select a filename. Pointsets were saved in XML fileformat but have to have a ".mps" file extension. You can select landmarks
in the render window with a left mouse button click on them. If you keep the mouse button pressed you can move the landmark to an other position by moving the mouse and then release the mouse
button. With the delete key you can remove the selected landmarks. You can also select landmarks by a double click on a landmark within the QmitkPointListWidget. Using the "Up-Arrow"-button or
the "F2" key you can easily move a landmark upwards and bring it further downwards by pressing "F3" or using the "Down-Arrow"-button. Thus the landmark number can be changed.
The QmitkStdMultiWidget changes its view to show the position of the landmark.
\imageMacro{QmitkRegistration_MovingDataPointBased.png,"The Moving Data area",7.45}
The "Moving Data" area contains a QmitkPointListWidget. Within this widget, all points for the moving data are listed. The label above this list shows the number of points that are already set.
To set points you have to toggle the "Set Points" button, the leftmost under the QmitkPointListWidget. The views in the QmitkStdMultiWidget were reinitialized to the moving data. With the
"Opacity:" slider you can change the opacity of the moving dataset. If the slider is leftmost the moving dataset is totally transparent, whereas if it is rightmost the moving dataset is totally
opaque. Points can be defined by performing a left click while holding the "Shift"-key pressed in the QmitkStdMultiWidget. You can remove the interactor which listens for left
mousebutton click while holding the "Shift"-key pressed by detoggle the "Set Points" button. The next button, "Clear Point Set", is for deleting all specified points from this dataset. The user
is prompted to confirm the decision. With the button on your right hand side, a previously saved point set can be loaded and all of its points are shown in the QmitkPointListWidget and in the QmitkStdMultiWidget.
The user is prompted to select the file to be loaded. The file extension is ".mps". On the left of this button is the save button. With this function all points specified for this dataset and
shown in the QmitkPointListWidget are saved to harddisk. The user is prompted to select a filename. Pointsets were saved in XML fileformat but have to have a ".mps" file extension. You can
select landmarks in the render window with a left click on them. If you keep the mouse button pressed you can move the landmark to an other position by moving the mouse and then
release the mouse button. With the delete key you can remove the selected landmarks. You can also select landmarks by a double click on a landmark within the QmitkPointListWidget. Using the "Up-Arrow"-button or
the "F2" key you can easily move a landmark upwards and bring it further downwards by pressing "F3" or using the "Down-Arrow"-button. Thus the landmark number can be changed.The QmitkStdMultiWidget changes its view to show the position of the
landmark.
\imageMacro{QmitkRegistration_DisplayOptionsPointBased.png,"The Display Options area",7.49}
In this area you can find the "Show Images Red/Green" checkbox. Here you can switch the color from both datasets. If you check the box, the fixed dataset will be
displayed in redvalues and the moving dataset in greenvalues to improve visibility of differences in the datasets. If you uncheck the "Show Images Red/Green" checkbox, both datasets will be
displayed in greyvalues.
Before you perform your transformation it is useful to see both images again. Therefore detoggle the "Set Points" button for the fixed data as well as for the moving data.
\imageMacro{QmitkRegistration_RegistrationPointBased.png,"The Registration area",7.45}
The functions concerning the registration are displayed in the "Registration" area. It not only contains the registration method selection and the registration itself but also offers the possibility
to save, undo or redo the results. Furthermore a display is implemented, which shows you how good the landmarks correspond.
Those features will be explained in following paragraphs.
Using the "Method"-selector, you can pick one of those transformations: Rigid, Similarity, Affine and LandmarkWarping.
Depending on which one you chose, an additional specifier, "Use ICP" can be set, which leads to the following possibilities for registration:
\li Rigid with ICP means only translation and rotation. The order of your landmarks will not be taken into account. E. g. landmark one in the fixed data can be mapped on landmark three in the moving data. You
have to set at least one landmark in each dataset to enable the Register button which performs the transformation.
\li Similarity with ICP means only translation, scaling and rotation. The order of your landmarks will not be taken into account. E. g. landmark one in the fixed data can be mapped on landmark three in the
moving data. You have to set at least one landmark in each dataset to enable the Register button which performs the transformation.
\li Affine with ICP means only translation, scaling, rotation and shearing. The order of your landmarks will not be taken into account. E. g. landmark one in the fixed data can be mapped on landmark three in
the moving data. You have to set at least one landmark in each dataset to enable the Register button which performs the transformation.
\li Rigid means only translation and rotation. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving data. You have to set
at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation.
\li Similarity means only translation, scaling and rotation. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving data.
You have to set at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation.
\li Affine means only translation, scaling, rotation and shearing. The order of your landmarks will be taken into account. E. g. landmark one in the fixed data will be mapped on landmark one in the moving
data. You have to set at least one landmark and the same number of landmarks in each dataset to enable the Register button which performs the transformation.
\li LandmarkWarping means a freeform deformation of the moving image, so that afterwards the landmarks are exactly aligned. The order of your landmarks will be taken into account.
E. g. landmark one in the fixed data will be mapped on landmark one in the moving data. You have to set at least one landmark and the same number of landmarks in each dataset to enable the
Register button which performs the transformation.
The root mean squares difference between the landmarks will be displayed as number, so that you can check how good the landmarks correspond.
The "Undo Transformation" button becomes enabled after performing a transformation and allows you to undo it. After doing this, the "Redo Transformation" button
is enabled and lets you redo, the just undone transformation(no calculation needed)
Saving of the transformed image can be done via the Data Manager.
*/
diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
index a7e277595c..b30dbd73c7 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
+++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox
@@ -1,290 +1,290 @@
/**
\page org_mitk_views_segmentation The Segmentation Plugin
-\imageMacro{QmitkSegmentation_Icon.png,"Icon of the Plugin",2.00}
+\imageMacro{QmitkSegmentation_Icon.png,"Icon of the Segmentation Plugin",2.00}
Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application.
\tableofcontents
\section org_mitk_gui_qt_segmentationUserManualOverview Overview
The Segmentation perspective allows you to create segmentations of anatomical and pathological structures in medical images of the human body.
The perspective groups a number of tools which can be used for:
- (semi-)automatic segmentation of organs on CT or MR image volumes
- semi-automatic segmentation of lesions such as enlarged lymph nodes or tumors
- manual segmentation of any structures you might want to delineate
\imageMacro{QmitkSegmentation_IMGApplication.png,"Segmentation perspective consisting of the Data Manager view and the Segmentation view",16.00}
If you wonder what segmentations are good for, we shortly revisit the concept of a segmentation here.
A CT or MR image is made up of volume of physical measurements (volume elements are called voxels).
In CT images, for example, the gray value of each voxel corresponds to the mass absorbtion coefficient for X-rays in this voxel, which is similar in many %parts of the human body.
The gray value does not contain any further information, so the computer does not know whether a given voxel is part of the body or the background, nor can it tell a brain from a liver.
However, the distinction between a foreground and a background structure is required when:
- you want to know the volume of a given organ (the computer needs to know which %parts of the image belong to this organ)
- you want to create 3D polygon visualizations (the computer needs to know the surfaces of structures that should be drawn)
- as a necessary pre-processing step for therapy planning, therapy support, and therapy monitoring
Creating this distinction between foreground and background is called segmentation.
The Segmentation perspective of the MITK Workbench uses a voxel based approach to segmentation, i.e. each voxel of an image must be completely assigned to either foreground or background.
This is in contrast to some other applications which might use an approach based on contours, where the border of a structure might cut a voxel into two %parts.
The remainder of this document will summarize the features of the Segmentation perspective and how they are used.
\section org_mitk_gui_qt_segmentationUserManualTechnical Technical Issues
The Segmentation perspective makes a number of assumptions. To know what this view can be used for, it will help you to know that:
- Images must be 2D, 3D, or 3D+t
- Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are not supported
- Segmentations are handled as binary images of the same extent as the original image
\section org_mitk_gui_qt_segmentationUserManualImageSelection Image Selection
The Segmentation perspective makes use of the Data Manager view to give you an overview of all images and segmentations.
\imageMacro{QmitkSegmentation_IMGSelection.png,"Data Manager is used for selecting the current segmentation. The reference image is selected in the drop down box of the control area.",5.50}
To select the reference image (e.g. the original CT/MR image) use the drop down box in the control area of the Segmentation view. The segmentation image selected in the Data Manager is displayed below the drop down box. If no segmentation image exists or none is selected create a new segmentation image by using the "New segmentation" button.
Some items of the graphical user interface might be disabled when no image is selected.
In any case, the application will give you hints if a selection is needed.
\section org_mitk_gui_qt_segmentationUserManualManualKringeling Manual Contouring
With manual contouring you define which voxels are part of the segmentation and which are not.
This allows you to create segmentations of any structeres that you may find in an image, even if they are not part of the human body.
You might also use manual contouring to correct segmentations that result from sub-optimal automatic methods.
The drawback of manual contouring is that you might need to define contours on many 2D slices.
However, this is moderated by the interpolation feature, which will make suggestions for a segmentation.
\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling1 Creating New Segmentations
Unless you want to edit existing segmentations, you have to create a new, empty segmentation before you can edit it.
To do so, click the "New manual segmentation" button.
Input fields will appear where you can choose a name for the new segmentation and a color for its display.
Click the checkmark button to confirm or the X button to cancel the new segmentation.
Notice that the input field suggests names once you %start typing and that it also suggests colors for known organ names.
If you use names that are not yet known to the application, it will automatically remember these names and consider them the next time you create a new segmentation.
Once you created a new segmentation, you can notice a new item with the "binary mask" icon in the Data Manager tree view.
This item is automatically selected for you, allowing you to %start editing the new segmentation right away.
\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing
As you might want to have segmentations of multiple structures in a single patient image, the application needs to know which of them to use for editing.
You select a segmenation by clicking it in the tree view of Data Manager. Note that segmentations are usually displayed as sub-items of "their" patient image.
In the rare case, where you need to edit a segmentation that is not displayed as a a sub-item, you can click both the original image AND the segmentation while holding down CTRL or for Mac OS X the CMD on the keyboard.
When a selection is made, the Segmentation View will hide all but the selected segmentation and the corresponding original image.
When there are multiple segmentations, the unselected ones will remain in the Data Manager, you can make them visible at any time by selecting them.
\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling3 Selecting Editing Tools
If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed.
This behavior is disabled while any of the manual segmentation tools are active -- otherwise you might have a hard time concentrating on the contour you are drawing.
To %start using one of the editing tools, click its button the the displayed toolbox.
The selected editing tool will be active and its corresponding button will stay pressed until you click the button again.
Selecting a different tool also deactivates the previous one.
If you have to delineate a lot of images, you should try using shortcuts to switch tools. Just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.).
\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling4 Using Editing Tools
All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or frontal), move the mouse while holding the mouse button and release to finish the editing action.
Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions.
\imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70}
Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed from (Subtract tool) the current segmentation.
Hold down the CTRL / CMD key to invert the operation (this will switch tools temporarily to allow for quick corrections).
\imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68}
Use the slider below the toolbox to change the radius of these round paintbrush tools. Move the mouse in any 2D window and press the left button to draw or erase pixels.
As the Add/Subtract tools, holding CTRL / CMD while drawing will invert the current tool's behavior.
\imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81}
Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it.
When working on an image with a high range of grey values, the selection range can be influenced more strongly by moving the cursor at higher velocity.
Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor.
This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue, e.g. the lungs.
The tool will select more or less pixels (corresponding to a changing gray value interval width) when you move the mouse up or down while holding down the left mouse button.
A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure.
The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below).
\imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28}
\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77}
You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform
small corrective changes. The following figure shows the usage of this tool:
- if the user draws a line which %starts and ends outside the segmenation AND it intersects no other segmentation the endpoints of the line are connected and the resulting contour is filled
- if the user draws a line which %starts and ends outside the segmenation a part of it is cut off (left image)
- if the line is drawn fully inside the segmentation the marked region is added to the segmentation (right image)
\imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"%Actions of the Correction tool illustrated.",13.50}
\imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81}
Left-click inside a segmentation with holes to completely fill all holes.
\imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79}
This tool removes a connected part of pixels that form a segmentation. You may use it to remove so called islands (see picture) or to clear a whole slice at once (hold CTRL while clicking).
\imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"LiveWire Tool",3.01}
The LiveWire Tool acts as a magnetic lasso with a contour snapping to edges of objects.
\imageMacro{QmitkSegmentation_IMGLiveWireUsage.png,"Steps for using LiveWire Tool",16.00}
- (1) To start the Tool you have to double click near the edge of the object you want to segment. The initial anchor point will snap to the edge within a 3x3 region.
- (2) Move the mouse. You don't have trace the edge of the object. The contour will automatically snap to it.
- (3) To fix a segment you can set anchor points by single left mouse button click.
- (4) Go on with moving the mouse and setting anchor points.
- (5) To close the contour double click on the initial anchor point.
- (6) After closing the contour can be edited by moving, inserting and deleting anchor points.
The contour will be transfered to its binary image representation by deactivating the tool.
\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling5 Interpolation
Creating segmentations for modern CT volumes is very time-consuming, because structures of interest can easily cover a range of 50 or more slices.
The Manual Segmentation View offers two helpful features for these cases:
- 3D Interpolation
- 2D Interpolation
The 3D interpolation is activated by default when using the manual segmentation tools. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information.
The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved,
but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary
oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation.
\imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation HowTo",16.00}
You can accept the interpolation result by clicking the "Accept" - button below the tool buttons.
In this case the 3D interpolation will be deactivated automatically so that the result can be postprocessed without any interpolation running in background. During recalculation the interpolated surface is blinking yellow/white. When the interpolation
has finished the surface is shown yellow with a small opacity. Additional to the surface, black contours are shown in the 3D render window. They mark the positions of all the drawn contours which were used for the interpolation.
You can navigate between the drawn contours by clicking on the „Position“ - Nodes in the datamanager which are located below the selected segmentation. If you don't want to see these nodes just unckeck the „Show Position Nodes“ Checkbox and these nodes will be hidden.
If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation.
The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that
- has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND
- is completely clear of a manual segmentation -- i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
Interpolated suggestions are displayed in a different way than manual segmentations are, until you "accept" them as part of the segmentation.
To accept single slices, click the "Accept" button below the toolbox.
If you have segmented a whole organ in every-x-slice, you may also review the interpolations and then accept all of them at once by clicking "... all slices".
\section org_mitk_gui_qt_segmentationUserManualOrganSegmentation Organ Segmentation
\note This feature is only available in our 3M3 Demo Application (http://www.mint-medical.de/productssolutions/mitk3m3/mitk3m3/#downloads) but not in the open source part of MITK
The manual contouring described above is a fallback option that will work for any kind of images and structures of interest.
However, manual contouring is very time-consuming and tedious.
This is why a major part of image analysis research is working towards automatic segmentation methods.
The Segmentation View comprises a number of easy-to-use tools for segmentation of CT images (Liver) and MR image (left ventricle and wall, left and right lung).
\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 Liver on CT Images
On CT image volumes, preferrably with a contrast agent in the portal venous phase, the Liver tool will fully automatically analyze and segment the image.
All you have to do is to load and select the image, then click the "Liver" button.
During the process, which takes a minute or two, you will get visual progress feedback by means of a contour that moves closer and closer to the real liver boundaries.
\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation2 Heart, Lung, and Hippocampus on MRI
While liver segmentation is performed fully automatic, the following tools for segmentation of the heart, the lungs, and the hippocampus need a minimum amount of guidance.
Click one of the buttons on the "Organ segmentation" page to add an average %model of the respective organ to the image.
This %model can be dragged to the right position by using the left mouse button while holding down the CTRL key.
You can also use CTRL + middle mouse button to rotate or CTRL + right mouse button to scale the %model.
Before starting the automatic segmentation process by clicking the "Start segmentation" button, try placing the %model closely to the organ in the MR image
(in most cases, you do not need to rotate or scale the %model).
During the segmentation process, a green contour that moves closer and closer to the real liver boundaries will provide you with visual feedback of the segmentation progress.
The algorithms used for segmentation of the heart and lung are method which need training by a number of example images.
They will not work well with other kind of images, so here is a list of the image types that were used for training:
- Hippocampus segmentation: T1-weighted MR images, 1.5 Tesla scanner (Magnetom Vision, Siemens Medical Solutions), 1.0 mm isotropic resolution
- Heart: Left ventricle inner segmentation (LV Model): MRI; velocity encoded cine (VEC-cine) MRI sequence; trained on systole and diastole
- Heart: Left ventricular wall segmentation (LV Inner Wall, LV Outer Wall): 4D MRI; short axis 12 slice spin lock sequence(SA_12_sl); trained on whole heart cycle
- Lung segmentation: 3D and 4D MRI; works best on FLASH3D and TWIST4D sequences
\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 Other Organs
As mentioned in the Heart/Lung section, most of the underlying methods are based on "training".
The basic algorithm is versatile and can be applied on all kinds of segmentation problems where the structure of interest is topologically like a sphere (and not like a torus etc.).
If you are interested in other organs than those offered by the current version of the Segmentation view,
please contact our research team.
\section org_mitk_gui_qt_segmentationUserManualLesionSegmentation Lesion Segmentation
\note This feature is only available in our 3M3 Demo Application (http://www.mint-medical.de/productssolutions/mitk3m3/mitk3m3/#downloads) but not in the open source part of MITK
Lesion segmentation is a little different from organ segmentation. Since lesions are not part of the healthy body, they sometimes have a diffused border,
and are often found in varying places all over the body.
The tools in this section offer efficient ways to create 3D segmentations of such lesions.
The Segmentation View currently offers supoprt for enlarged lymph nodes.
To segment an enlarged lymph node, find a more or less central slice of it, activate the "Lymph Node" tool and draw a rough contour on the inside of the lymph node.
When releaseing the mouse button, a segmentation algorithm is started in a background task. The result will become visible after a couple of seconds, but you do not have to wait for it.
If you need to segment several lymph nodes, you can continue to inspect the image right after closing the drawn contour.
If the lymph node segmentation is not to your content, you can select the "Lymph Node Correction" tool and drag %parts of the lymph node surface towards the right position (works in 3D, not slice-by-slice).
This kind of correction helps in many cases.
If nothing else helps, you can still use the pure manual tools as a fallback.
\section org_mitk_gui_qt_segmentationUserManualPostprocessing Things you can do with segmentations
As mentioned in the introduction, segmentations are never an end in themselves.
Consequently, the Segmentation view adds a couple of "post-processing" %actions to the Data Manager.
These %actions are accessible through the context-menu of segmentations in Data Manager's list view
\imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58}
- Create polygon %model applies the marching cubes algorithms to the segmentation. This polygon %model can be used for visualization in 3D or other things such as stereolithography (3D printing).
- Create smoothed polygon %model uses smoothing in addition to the marching cubes algorithms, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
- Statistics goes through all the voxels in the patient image that are part of the segmentation and calculates some statistical measures (minumum, maximum, median, histogram, etc.). Note that the statistics are ALWAYS calculated for the parent element of the segmentation as shown in Data Manager.
- Autocrop can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping.
\section QmitkSegmentation_UserManualSurfaceMasking Surface Masking
You can use the surface masking tool to create binary images from a surface which
is used used as a mask on an image. This task is demonstrated below:
\imageMacro{QmitkSegmentation_FromSurfaceBefore.png,"Load an image and a surface.",16.00}
Select the image and the surface in the corresponding drop-down boxes (both are selected automatically if there is just one image and one surface)
\imageMacro{QmitkSegmentation_FromSurfaceAfter.png,"Create segmentation from surface",16.00}
After clicking "Create segmentation from surface" the newly created binary image is inserted in the DataManager and can be used for further processing
\section org_mitk_gui_qt_segmentationUserManualTechnicalDetail Technical Information for Developers
For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions .
*/
diff --git a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox
index 871d5ee270..a484add03e 100644
--- a/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox
+++ b/Plugins/org.mitk.gui.qt.ultrasound/documentation/UserManual/QmitkUltrasound.dox
@@ -1,68 +1,68 @@
/**
\page org_mitk_gui_qt_ultrasound The Ultrasound Plugin
-\imageMacro{QmitkUltrasound_Icon.png,"Icon of Ultrasound",2.12}
+\imageMacro{QmitkUltrasound_Icon.png,"Icon of the Ultrasound Plugin",2.12}
\tableofcontents
\section org_mitk_gui_qt_ultrasoundOverview
This plugin offers a simple interface to create and manage ultrasound devices.
Devices, once configured, will be stored and loaded on the next start of MITK.
One can configure several aspects of the images acquired.
Last but not least, this plugin makes the configured devices available as a microservice,
exposing them for further usage in other plugins.
\section org_mitk_gui_qt_ultrasoundPrerequisites Prerequisites
To make use of this plugin, you obviously require an ultrasound device.
The device must have a video-out of one kind or another. Typical video-outs are: HDMI, DVI, VGA and S-Video.
You also need a Video-Grabber that can acquire the image data from the ultrasound device.
In principal, this plugin is compatible with any grabber that allows the Operating system to access it's functionality.
However, not all grabbers are created equal. Make sure your grabber supports the video-out offered by your ultrasound device and that it can achieve a satisfying framerate.
We have made good experiences with epiphan Grabbers and currently recommend the epiphan DVI2USB 3.0 device which supports HDMI, DVI and VGA, but less costly grabbers certainly are an option.
\section org_mitk_gui_qt_ultrasoundCreateDevice Creating an Device
To configure an ultrasound device, connect the ultrasound device to the grabber and the grabber to the computer. Start the ultrasound device and open the ultrasound plugin. The devicemanager will open.
\imageMacro{QmitkUltrasound_DeviceManagement.png,"MITK Screenshot with the devicemanager activated",7.54}
Any currently configured devices are listed in the box, which accordingly is empty now.
Click "New Device".
\imageMacro{QmitkUltrasound_NewVideoDevice.png,"The 'New Device' form",7.62}
In the appearing form, enter descriptive data on your device in the corresponding fields.
Manufacturer and model will be used to display the device in MITK.
You may choose the video source ID if more than one is available (as is the case on laptops with built-in webcams).
On Windows, try -1 (defaults to the first available source). On Linux and Mac try 0 and 1.
If the wrong camera is address, simply try the next ID.
Most ultrasound images are grey scale, so using a grey scale conversion doesn't take information away from the image, but makes processing images significantly faster.
Only uncheck this box if you require color.
Click Add Device to save your changes.
\imageMacro{QmitkUltrasound_DeviceManagement2.png,"Devicemanager with configured device",7.64}
\section org_mitk_gui_qt_ultrasoundActivateConnect Activation and Connection
A ultrasound device in MITK can be connected and activated. The device you just created automatically is now connected.
A connected device is available to all other plugins in MITK, but does not jet generate image data.
Disconnecting the device causes it to be deleted and not be available anymore.
Click the device, then click "Activate Device". The device is now activated and generates image data continuously.
Click the "US-Imaging Tab"
\imageMacro{QmitkUltrasound_Imaging.png,"US Imaging Tab",7.60}
Select the device and click "Start Viewing". The US-Image should appear.
You can adjust the cropping parameters to reduce the acquired image size which will further increase speed and remove unnecessary information.
All changes are saved and restored whenever MITK is started.
*/
diff --git a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox
index bc0f69919b..5276bd51a8 100644
--- a/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox
+++ b/Plugins/org.mitk.gui.qt.volumevisualization/documentation/UserManual/QmitkVolumeVisualization.dox
@@ -1,143 +1,143 @@
/**
\page org_mitk_views_volumevisualization The Volume Visualization Plugin
-\imageMacro{QmitkVolumeVisualization_Icon.png,"Icon of the Plugin",2.00}
+\imageMacro{QmitkVolumeVisualization_Icon.png,"Icon of the Volume Visualization Plugin",2.00}
\tableofcontents
\section QVV_Overview Overview
The Volume Visualization Plugin is a basic tool for visualizing three dimensional medical images.
MITK provides generic transfer function presets for medical CT data.
These functions, that map the gray-value to color and opacity, can be interactively edited.
Additionally, there are controls to quickly generate common used transfer function shapes
like the threshold and bell curve to help identify a range of grey-values.
\imageMacro{QmitkVolumeVisualization_Overview.png,"",16.00}
\section QVV_EnableVRPage Enable Volume Rendering
\subsection QVV_LoadingImage Loading an image into the application
Load an image into the application by
- dragging a file into the application window.
- selecting file / load from the menu.
Volume Visualization imposes following restrictions on images:
- It has to be a 3D-Image Scalar image, that means a normal CT or MRT.
- 3D+T are supported for rendering, but the histograms are not computed.
- Also be aware that volume visualization requires a huge amount of memory.
Very large images may not work, unless you use the 64bit version.
\subsection QVV_EnableVR Enable Volumerendering
\imageMacro{QmitkVolumeVisualization_Checkboxen.png,"",8.21}
Select an image in datamanager and click on the checkbox left of "Volumerendering".
Please be patient, while the image is prepared for rendering, which can take up to a half minute.
\subsection QVV_LODGPU The LOD & GPU checkboxes
Volume Rendering requires a lot of computing resources including processor, memory and graphics card.
To run volume rendering on smaller platforms,
enable the LOD checkbox (level-of-detail rendering).
Level-of-detail first renders a lower quality preview to increase interactivity.
If the user stops to interact a normal quality rendering is issued.
The GPU checkbox tries to use computing resources on the graphics card to accelerate volume rendering.
It requires a powerful graphics card and OpenGL hardware support for shaders, but achieves much higher frame rates than software-rendering.
\section QVV_PresetPage Applying premade presets
\subsection QVV_Preset Internal presets
There are some internal presets given, that can be used with normal CT data (given in Houndsfield units).
A large set of medical data has been tested with that presets, but it may not suit on some special cases.
Click on the "Preset" tab for using internal or custom presets.
\imageMacro{QmitkVolumeVisualization_InternalPresets.png,"",8.30}
- "CT Generic" is the default transferfunction that is first applied.
- "CT Black&White" does not use any colors, as it may be distracting on some data.
- "CT Cardiac" tries to increase detail on CTs from the heart.
- "CT Bone" emphasizes bones and shows other areas more transparent.
- "CT Bone (Gradient)" is like "CT Bone", but shows from other organs only the surface by using the gradient.
- "MR Generic" is the default transferfunction that we use on MRT data (which is not normalized like CT data).
- "CT Thorax small" tries to increase detail.
- "CT Thorax large" tries to increase detail.
\subsection QVV_CustomPreset Saving and loading custom presets
After creating or editing a transferfunction (see \ref QVV_Editing or \ref QVV_ThresholdBell),
the custom transferfunction can be stored and later retrieved on the filesystem.
Click "Save" (respectively "Load") button to save (load) the threshold-, color- and gradient function combined in a single .xml file.
\section QVV_ThresholdBell Interactively create transferfunctions
Beside the possibility to directly edit the transferfunctions (\ref QVV_Editing),
a one-click generation of two commonly known shapes is given.
Both generators have two parameters, that can be modified by first clicking on the cross and then moving the mouse up/down and left/right.
The first parameter "center" (controlled by horizontal movement of the mouse) specifies the gravalue where the center of the shape will be located.
The second parameter "width" (controlled by vertical movement of the mouse) specifies the width (or steepness) of the shape.
\subsection Threshold
Click on the "Threshold" tab to active the threshold function generator.
\imageMacro{QmitkVolumeVisualization_Threshold.png,"",8.21}
A threshold shape begins with zero and raises to one across the "center" parameter. Lower widths results in steeper threshold functions.
\subsection Bell
Click on the "Bell" tab to active the threshold function generator.
\imageMacro{QmitkVolumeVisualization_Bell.png,"",8.23}
A threshold shape begins with zero and raises to one at the "center" parameter and the lowers agains to zero. The "width" parameter correspondens to the width of the bell.
\section QVV_Editing Customize transferfunctions in detail
\subsection QVV_Navigate Choosing grayvalue interval to edit
\imageMacro{QmitkVolumeVisualization_Slider.png,"",8.23}
To navigate across the grayvalue range or to zoom in some ranges use the "range"-slider.
All three function editors have in common following:
- By left-clicking a new point is added.
- By right-clicking a point is deleted.
- By left-clicking and holding, an exisiting point can be dragged.
- By pressing arrow keys, the currently selected point is moved.
- By pressing the "DELETE" key, the currently selected point is deleted.
- Between points the transferfunctions are linear interpolated.
There are three transferfunctions to customize:
\subsection QVV_GO Grayvalue -> Opacity
\imageMacro{QmitkVolumeVisualization_Opacity.png,"grayvalues will be mapped to opacity.",8.04}
An opacity of 0 means total transparent, an opacity of 1 means total opaque.
\subsection QVV_GC Grayvalue -> Color
\imageMacro{QmitkVolumeVisualization_Color.png,"grayvalues will be mapped to color.",8.81}
The color transferfunction editor also allows by double-clicking a point to change its color.
\subsection QVV_GGO Grayvalue and Gradient -> Opacity
\imageMacro{QmitkVolumeVisualization_Gradient.png,"",8.85}
Here the influence of the gradient is controllable at specific grayvalues.
*/