diff --git a/Modules/Bundles/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox index 2ab0ad220c..4112df75ad 100644 --- a/Modules/Bundles/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.imagecropper/documentation/UserManual/QmitkImageCropperUserManual.dox @@ -1,41 +1,41 @@ /** \bundlemainpage{org.imagecropper} The Image Cropper Module \image html icon.png "Icon of the Module" Available sections: - \ref QmitkImageCropperUserManualOverview - \ref QmitkImageCropperUserManualFeatures - \ref QmitkImageCropperUserManualUsage - \ref QmitkImageCropperUserManualTroubleshooting \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 (transversal, 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 oriantation of bounding box press control + middle 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/Modules/Bundles/org.mitk.gui.qt.imagestatistics/documentation/UserManual/QmitkImageStatistics.dox b/Modules/Bundles/org.mitk.gui.qt.imagestatistics/documentation/UserManual/QmitkImageStatistics.dox index 5e4246f6d6..dfb3b2b63d 100644 --- a/Modules/Bundles/org.mitk.gui.qt.imagestatistics/documentation/UserManual/QmitkImageStatistics.dox +++ b/Modules/Bundles/org.mitk.gui.qt.imagestatistics/documentation/UserManual/QmitkImageStatistics.dox @@ -1,44 +1,44 @@ /** \bundlemainpage{org.imagestatistics} The Image Statistics Module \image html ImageStatistic_48.png "Icon of the Module" \section QmitkImageStatisticsUserManualSummary Summary This module 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 module, 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 module, please have a look at the \ref QmitkImageStatisticsUserManualTrouble page. \section QmitkImageStatisticsUserManualDetails Details Manual sections: - \ref QmitkImageStatisticsUserManualOverview - \ref QmitkImageStatisticsUserManualUsage - \ref QmitkImageStatisticsUserManualTrouble \section QmitkImageStatisticsUserManualOverview Overview This module provides an easy interface to quickly compute some features of a whole image or a region of interest. \image html Screenshot1.png "The interface" \section QmitkImageStatisticsUserManualUsage Usage -After selection of an image or a binary mask of an image in the datamanader the Image Statistics module shows some statistical information. If a mask is selected the name of the mask and the name of the image this mask is applied to are shown at the top. +After selection of an image or a binary mask of an image in the datamanader, the Image Statistics module 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. -Below that are the statistics window, which displays the calculated statistical features (such as mean, standard deviation...) and the histogram. +Below it is the statistics window which displays the calculated statistical features (such as mean, standard deviation...) and the histogram. At the bottom of the module are two buttons. 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/Modules/Bundles/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox b/Modules/Bundles/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox index cfb70bdcda..d08eaf2920 100644 --- a/Modules/Bundles/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox +++ b/Modules/Bundles/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox @@ -1,10 +1,10 @@ /** \bundlemainpage{org.surfacematerialeditor} The Surface Material Editor \image html SurfaceMaterialEditorIcon.png "Icon of the Module" -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. +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. \image html QmitkSurfaceMaterialEditorGui.png "The Surface Material Editor" */ \ No newline at end of file diff --git a/Modules/Bundles/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox index 0c425ab865..7bb71ca167 100644 --- a/Modules/Bundles/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.moviemaker/documentation/UserManual/QmitkMovieMakerUserManual.dox @@ -1,45 +1,45 @@ /** \bundlemainpage{org.moviemaker} The Movie Maker Module \image html icon.png "Icon of the Module" 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. + 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 \image html QmitkMovieMakerControlArea.png "A view of the command area of QmitkMovieMaker" \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 one, but you can choose different windows for stepping and recording. +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 which content will be recorded. +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 +\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, according to the playing options, is created. +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 +\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. Via the spinbox, stepping speed can be set (total time in seconds). +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/Modules/Bundles/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox index cd31b651df..d724b1e41e 100644 --- a/Modules/Bundles/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.pointsetinteraction/documentation/UserManual/QmitkPointSetInteractionUserManual.dox @@ -1,38 +1,38 @@ /** \bundlemainpage{org.pointsetinteraction} The Point Set Interaction Module \image html pointset_interaction.png "Icon of the Module" 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. \image html QmitkPointSetInteraction.png "MITK with the QmitkPointSetInteraction functionality" 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..." +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. \image html AddPointSet.png "The Add pointset... dialog" -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. +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. \image html CurrentPointSetArea.png "The Current pointset area" -The "Current pointset" area contains a list of points. Within this area, all points for the current point set node are listed. T 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 mousebutton click while holding the "Shift"-key pressed in the four window view. +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 harddisk. The user is prompted to select a filename. Pointsets were saved in XML fileformat but have to have a ".mps" file extension. +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 release the mouse button. With the delete key you can remove the selected points. +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/Modules/Bundles/org.mitk.gui.qt.regiongrowing/documentation/UserManual/QmitkRegionGrowingUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.regiongrowing/documentation/UserManual/QmitkRegionGrowingUserManual.dox index 3b4d4ff23c..2ac0861e8c 100644 --- a/Modules/Bundles/org.mitk.gui.qt.regiongrowing/documentation/UserManual/QmitkRegionGrowingUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.regiongrowing/documentation/UserManual/QmitkRegionGrowingUserManual.dox @@ -1,29 +1,29 @@ /** \bundlemainpage{org.regiongrowing} The Region Growing Module \image html icon.png "Icon of the Module" Available documentation sections: - \ref QmitkRegionGrowingUserManualOverview - \ref QmitkRegionGrowingUserManualUsage \section QmitkRegionGrowingUserManualOverview Overview -The Region growing module provides mainly a programming example, showing developers how to create new bundle for MITK with graphical user interface (GUI) and which is also using some ITK image filters. +The Region growing module provides a programming example, showing developers how to create new bundles 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 */ diff --git a/Modules/Bundles/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox b/Modules/Bundles/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox index 82f5f4536c..83616b0c80 100644 --- a/Modules/Bundles/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox +++ b/Modules/Bundles/org.mitk.gui.qt.segmentation/documentation/UserManual/org_mitk_gui_qt_segmentation.dox @@ -1,263 +1,263 @@ /** \bundlemainpage{org.segment} The Segmentation Module \image html segmentation.png "Icon of the Module" -Some of the below described features are not available in the open-source part of the MITK-3M3-Application. +Some of the features described below are not available in the open-source part of the MITK-3M3-Application. Available sections: - \ref org_mitk_gui_qt_segmentationUserManualOverview - \ref org_mitk_gui_qt_segmentationUserManualTechnical - \ref org_mitk_gui_qt_segmentationUserManualImageSelection - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling1 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling2 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling3 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling4 - \ref org_mitk_gui_qt_segmentationUserManualManualKringeling5 - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation2 - \ref org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 - \ref org_mitk_gui_qt_segmentationUserManualLesionSegmentation - \ref org_mitk_gui_qt_segmentationUserManualPostprocessing - \ref org_mitk_gui_qt_segmentationUserManualSurfaceMasking \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 for +The perspective groups a number of tools which can be used for: \image html org_mitk_gui_qt_segmentationIMGapplication.png Segmentation perspective consisting of the Data Manager view and the Segmentation view 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 +However, the distinction between a foreground and a background structure is required when: Creating this distinction between foreground and background is called segmentation. The Segmentation perspective of MITKApp 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. +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 +\section org_mitk_gui_qt_segmentationUserManualTechnical Technical Issues The Segmentation perspective makes a number of assumptions. To know what this module can be used for, it will help you to know that: -\section org_mitk_gui_qt_segmentationUserManualImageSelection Image selection +\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. -\image html org_mitk_gui_qt_segmentationIMGselection.png Data Manager is used for selection of the current segmentation. The reference image is selected in the drop down box of the control area. +\image html org_mitk_gui_qt_segmentationIMGselection.png Data Manager is used for selecting the current segmentation. The reference image is selected in the drop down box of the control area. -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 that has been 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. +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. +In any case, the application will give you hints if a selection is needed. -\section org_mitk_gui_qt_segmentationUserManualManualKringeling Manual contouring +\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 +\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 and consider them the next time you create a new segmentation. +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, so that you can %start editing the new segmentation right away. +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 +\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 usually segmentations are 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 on the keyboard. +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 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 Data Manager, you can make them visible at any time by selecting them. -If you want to see all segmenations at the same time, just clear the selection by clicking outside all the tree items in Data Manager. +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. +If you want to see all segmenations at the same time, just clear the selection by clicking outside all the tree items in the Data Manager. -\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling3 Selecting editing tools +\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling3 Selecting Editing Tools If you are familiar with MITKApp, 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 +\subsection org_mitk_gui_qt_segmentationUserManualManualKringeling4 Using Editing Tools -All of the editing tools work by the same principle: you press the mouse (left button) anywhere in a 2D window (any of the orientations transversal, sagittal, or frontal), move the mouse while holding the mouse button and release to finish the editing action. -All tools work on the original slices of the patient image, i.e. with some rotated/tilted MR image volumes you need to perform a "reinit" option in Data Manger before you are able to use 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 transversal, sagittal, or frontal), move the mouse while holding the mouse button and release to finish the editing action. +All tools work on the original slices of the patient image, i.e. with some rotated/tilted MR image volumes you need to perform a "reinit" option in the Data Manger before you are able to use the editing tools. 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. -\image html org_mitk_gui_qt_segmentationIMGiconAddSubtract.png Add and Subtract tools +\image html org_mitk_gui_qt_segmentationIMGiconAddSubtract.png Add and Subtract Tools 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 key to invert the operation (this will switch tools temporarily to allow you quick corrections). +Hold down the CTRL key to invert the operation (this will switch tools temporarily to allow for quick corrections). -\image html org_mitk_gui_qt_segmentationIMGiconPaintWipe.png Paint and Wipe tools +\image html org_mitk_gui_qt_segmentationIMGiconPaintWipe.png Paint and Wipe Tools 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 while drawing will invert the current tool's behavior. -\image html org_mitk_gui_qt_segmentationIMGiconRegionGrowing.png Region Growing tool +\image html org_mitk_gui_qt_segmentationIMGiconRegionGrowing.png Region Growing Tool -Click at one point in a 2D slice widget to add an image region by the region growing tool to the segmentation. Moving up the cursor while holding the left mouse button widens the range for the included grey values, moving it down narrows it. +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 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 "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). +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). \image html org_mitk_gui_qt_segmentationIMGleakage.png Leakage correction feature of the Region Growing tool -\image html org_mitk_gui_qt_segmentationIMGiconCorrection.png Correction tool +\image html org_mitk_gui_qt_segmentationIMGiconCorrection.png Correction Tool 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: -\image html org_mitk_gui_qt_segmentationIMGcorrectionActions.png %actions of the Correction tool illustrated +\image html org_mitk_gui_qt_segmentationIMGcorrectionActions.png %Actions of the Correction tool illustrated. -\image html org_mitk_gui_qt_segmentationIMGiconFill.png Fill tool +\image html org_mitk_gui_qt_segmentationIMGiconFill.png Fill Tool Left-click inside a segmentation with holes to completely fill all holes. -\image html org_mitk_gui_qt_segmentationIMGiconErase.png Erase tool +\image html org_mitk_gui_qt_segmentationIMGiconErase.png Erase Tool 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). \subsection org_mitk_gui_qt_segmentationUserManualManualKringeling5 Interpolation Creating segmentations for modern CT volumes is very time-consuming, because strucutres of interest can easily cover a range of 50 or more slices. The Segmentation view offers a helpful feature for these cases: "Interpolation" creates suggestions for a segmentation whenever you have a slice that 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 a every-x-slices way, you may also review the interpolations and then accept all of them at once by clicking "... all slices". +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 +\section org_mitk_gui_qt_segmentationUserManualOrganSegmentation Organ Segmentation 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). +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 +\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation1 Liver on CT Images -On CT image volumes, preferrably with contrast agent in the portal venous phase, the Liver tool will fully automatically analyze and segment the image. +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 +\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. +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 visual feedback of the segmentation progress. +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: -\subsection org_mitk_gui_qt_segmentationUserManualOrganSegmentation99 Other organs +\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 offered by the current version of the Segmentation view, +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 +\section org_mitk_gui_qt_segmentationUserManualLesionSegmentation Lesion Segmentation -Lesion segmentation is a little different from organ segmentation, because lesions are not part of the healthy body, sometimes having a diffuse border, -and oftenly they are found if varying places all over the body. +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. +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 Data Manager. +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 -\image html org_mitk_gui_qt_segmentationIMGDataManagerContextMenu.png Context menu items for segmentations +\image html org_mitk_gui_qt_segmentationIMGDataManagerContextMenu.png Context menu items for segmentations. \section org_mitk_gui_qt_segmentationUserManualSurfaceMasking 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 tast is demonstrated below: +is used used as a mask on an image. This task is demonstrated below: \image html segmentationFromSurfaceBefore.png Load an image and a surface. Select the -image and the surface in the corresponding drop-down boyes (both is selected automatically +image and the surface in the corresponding drop-down boxes (both are selected automatically if there is just one image and one surface) \image html segmentationFromSurfaceAfter.png After clicking "Create segmentation from surface" the newly created binary image is inserted in the DataManager and can be used for further processing */ diff --git a/Modules/Bundles/org.mitk.gui.qt.simplemeasurement/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox b/Modules/Bundles/org.mitk.gui.qt.simplemeasurement/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox index e527e494bb..925c583962 100644 --- a/Modules/Bundles/org.mitk.gui.qt.simplemeasurement/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox +++ b/Modules/Bundles/org.mitk.gui.qt.simplemeasurement/documentation/UserManual/QmitkSimpleMeasurementUserManual.dox @@ -1,44 +1,44 @@ /** \bundlemainpage{org.simplemeasurement} The Simple Measurement Module \image html SimpleMeasurementIcon.png "Icon of the Module" Available sections: - \ref QmitkSimpleMeasurementUserManualOverview - \ref QmitkSimpleMeasurementUserManualFeatures - \ref QmitkSimpleMeasurementUserManualUsage \section QmitkSimpleMeasurementUserManualOverview Overview -SimpleMeasurement is a program module that allows to measure distances, angels and pathes on a dataset. +SimpleMeasurement is a program module that allows to measure distances, angles and paths on a dataset. \section QmitkSimpleMeasurementUserManualFeatures Features \section QmitkSimpleMeasurementUserManualUsage Usage -To use the SimpleMeasurement Module, at first a data set must be loaded. That can be done by drag & drop. +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. What the different modes mean and how to use them: \image html SimpleMeasurementGUI.png Graphical User Interface of SimpleMeasurement */ diff --git a/Modules/Bundles/org.mitk.gui.qt.viewinitialization/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox b/Modules/Bundles/org.mitk.gui.qt.viewinitialization/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox index d0357a26e3..e0e919fdac 100644 --- a/Modules/Bundles/org.mitk.gui.qt.viewinitialization/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox +++ b/Modules/Bundles/org.mitk.gui.qt.viewinitialization/documentation/UserManual/org_mitk_gui_qt_viewinitialization.dox @@ -1,8 +1,8 @@ /** \bundlemainpage{org.viewinitialitzation} The View Initialization Module \image html viewInitializationIcon.png "Icon of the Module" -This view serves as a sandbox for experimenting with and understanding the geometry initialization parameters. For example to view the transversal slices from above instead of from below. It is not intended for end users, but for developers. +This view serves as a sandbox for understanding and experimenting with the geometry initialization parameters. For example, to view the transversal slices from above instead of from below. It is not intended for end users, but for developers. */ \ No newline at end of file