This section assumes that the reader has competed the region competition based segmentation tasks in the previous section. The instructions offered in this section are less detailed than previous sections, since the reader would have gained sufficient experience using the tool in the preceding sections. The first task in this section is to use edge-based snakes to segment the ventricles in our image. In this step we will perform the preliminary tasks: clearing the previous segmentation, selecting the appropriate label and entering SNAP mode.
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This section shows you how to interact with a three-dimensional image in SNAP. It assumes that you have successfully loaded an image following the instructions in the previous section. This section requires approximately 10 minutes to complete. After loading a grey image , SNAP puts itself into manual segmentation mode.
The control panel for this mode is displayed to the right. These interaction modes are called tools for short. The contents of the tool options sub-panel depend on the tool that is currently selected in the IRIS toolbox. The segmentation label sub-panel is used to select the labels used for manual and automatic segmentation, and the 3D toolbox provides additional tools used to interact with the three-dimensional rendering of the segmented structures.
Let's focus our attention on the three of the four dark windows that are displaying slices of the volumetric image the fourth window is used for 3D display and will be discussed later. These three slice windows display three views of the image volume, in the orthogonal axial, coronal, and sagittal planes. Notice that a scrollbar is located next to each slice window.
Under each scrollbar is located a slice counter, which shows the index of the displayed slice and the total number of slices in the direction perpendicular to the slice. A key feature of SNAP is that the three slices are not viewed independently, but rather linked by a common cursor. As you manipulate the scroll bars, you will notice that the blue lines in the other two slice windows are moving. These blue lines indicate the intersection between orthogonal slices. As we will see shortly, the common cursor makes it easy to examine the volumetric image near any particular voxel.
Crosshairs mode is used to quickly focus all three slide views onto a location in the image. When you click on one of the slices, the other two slices are adjusted so that the pixel where you clicked becomes the point of intersection of the three slices. Thus, you can easily examine the orthogonal views of the image in the neighborhood of any pixel.
You can also hold down the left mouse button and move the mouse around the slice for faster navigation. Remember that you can use the scroll wheel of your mouse to change the slice currently displayed in the slice window under the mouse. This lets you move around the image in three dimensions, without moving the mouse away from the slice window! You will notice that the common cursor formed by the blue dashed lines always points to the same voxel in all three slice views.
The grey level intensity of the voxel and the segmentation label corresponding to it are displayed in the tool options sub-panel of the control panel:. Since we have not done any segmentation yet, the segmentation label at every voxel has numeric value 0 and is called "Clear". The action of clicking on a voxel in the image to check its greylevel intentensity value is called probing.
We will make use of probing later in this tutorial. In other SNAP modes where the left mouse button is used for other tasks, you can still move the crosshairs by using the middle mouse button, or by holding the Alt key on the keyboard and using the left mouse button. Click and hold the right mouse button anywhere in one of the slice windows, and drag the mouse up to zoom into the slice.
Drag the mouse down to zoom out. Click and hold the left mouse button anywhere in one of the slice windows, and drag the mouse in any direction to pan around the image. Click the Reset View button located below each slice window to restore the original zoom level, as illustrated below. By default, SNAP lets you change the zoom in all three slice windows independently.
However, it is often desireable to make sure that each of the three slices is displayed using the same zoom level. The tool options sub-panel, which is shown below, allows you to link the zoom level between the three slice views, as well as to specify zoom level explicitly.
Tick the "Zoom slices together" check-box in the tool options sub-panel. Try zooming in and out in one of the slice windows by dragging the mouse as before. Notice how the other slices zoom in accordingly. The slices will zoom to double the default zoom level. Click the "Reset 2D views" button. The zoom level will return to default in all three slices.
When slices are zoomed together, the number of pixels on the computer screen corresponding to a unit of length in the space of the 3D image is the same in all three slice windows. When slices are zoomed independently, the a distance in image space may correspond to different distances in the slice windows. The MRI image that we have loaded in the last section of this tutorial has fairly low contrast.
It is difficult to see some of the structures in the image. SNAP provides a windowing dialog for adjusting the mapping between intensities in the 3D image and the intensities of the displayed slices. This dialog consists of a plot area on the left and several controls and buttons on the right.
The plot area displays the current mapping between image intensities and display intensities as a think red line with four embedded yellow diamonds. These diamonds are called control points and can be used to change the shape of the mapping.
Also, the plot area shows in blue the histogram of the intensities in the grey image. Notice that most of the intensities fall in the lower third of the intensity range. So, to improve the contrast, we will adjust the mapping accordingly. Notice how the red line changes, and the displayed slices change contrast. You can also directly manipulate the curve by moving the control points. Move the mouse over one of the yellow control points, hold down the left mouse button and move the mouse to update the mapping.
The number shown in the text box labeled 'Level' is the image intenisty of the leftmost control point. The number shown in the text box labeled 'Window' is the difference between the rightmost and leftmost control points. The slider 'Control Points' allows you to change the number of the control points, increasing the control over the shape of the mapping curve.
By default, SNAP shows the axial slice in the upper left, the sagittal in the upper right, and the coronal slice in the lower right. You can change the order of the display using the 'Display Options' dialog. Select Options Display Options The display options dialog will appear. This is useful if you are preparing a manuscript or a presentation and want to make sure that elements such as crosshairs are clearly visible.
Section 3. Viewing the 3D Image. Step 1. Examining the Control Panel. Use the scrollbars to change the currently displayed slice in one of the three slice windows. If your mouse has a scroll wheel, you can use it to change the slice instead. Make sure that the mouse cursor is inside of the slice window that you want to interact with.
Select Options Intensity Curve The windowing dialog will appear. Choose the 'Layout' tab. Experiment with selecting different display configurations.
Press 'Apply' to put the selected configuration into effect. Press 'Close' to close the dialog. Choose the 'Appearance' tab. Choose one of the available user inteface elements and adjust its color, line thickness, etc. Press 'Apply' to make changes. Press 'Reset' to restore default settings.
Tutorial: Getting Started with ITK-SnAP
This section describes how SNAP can be used for manual segmentation. You will learn about working with segmentation labels, painting regions ontwo-dimensional slices of the image, and saving and loading segmentation results. This section requires approximately 10 minutes to complete. To segment an anatomical structure in SNAP means to assign a label to each voxel in the structure. A label is a number between 0 and Associated with each label is a name and a set of display settings, such as the color used to display the label.
This section gives step by step instructions on segmenting an image using the region competition snake in last section's terminology, snake evolution that uses the region feature image. This section assumes that you are working with the image MRIcrop-orig. We will segment the caudate nucleus and the ventricles in this image. This section also assumes that you are using the label file MRIcrop-seg.
This section of the tutorial introduces the basic concepts behind the automatic segmentation component of SNAP. There are no action items in this section, just an explanation of the theory and terminology that must be understood to use SNAP effectively. All examples in this section will be made using two-dimensional images. The concepts, however, extend to three dimensions in a straight forward way.
This section contains a list of loosely organized list of SNAP features that can make it a more powerful tool than it may appear at first look. Click below to jump to a specific tip:. SNAP includes an image information window that can be brought up at any time. The window displays dimensions of the image, voxel size, current cursor location and other useful information. When performing manual segmentation, it may be useful to dedicate a larger area of the screen to a single slice of the 3D image. SNAP allows you to replace the standard four-view layout three slice views and a 3D view with a single-view layout.