Segmentation Menu

The Segmentation Menu

This menu lets you load, save and clear segmentations, and also call up the `Surface' window to interpolate a smooth surface through the segmentation contours and view a graphical rendering of it. The load, save, clear and surface options are shown in grey when they are not available (because there is no data file loaded or segmentation defined). The `Object selection' option launches a panel to control the appearance and attributes of up to ten different segmented objects: this option is also greyed out when there is no data. Another option brings up the `Thresholds and Gating' panel, which is the gateway to Stradx's semi-automatic segmentation and ECG gating facilities. The final option brings up the `Measurements' window, which displays quantitative information relating to 2D curves drawn in the `Reslice' window and 3D landmarks positioned by the user.

Segmentation contours can be defined by manually tracing their outlines in the `Review' window. To do this, just hold down the left mouse button and follow the desired contour. Just before you get back to the start point (segmentation contours must be closed) release the left mouse button: this closes the loop. You can define as many contours as you like in each frame. The right mouse button deletes the nearest contour.

Alternatively, segmentation contours can be defined one vertex at a time. To do this, switch on the keyboard's `Caps Lock' and then click with the left mouse button at the first vertex position: a cross appears where you clicked (with some operating systems, it is necessary to hold down the `Caps Lock' key while clicking with the mouse). You can now define subsequent vertices by clicking with the left mouse button. Click with the right mouse button to define the final vertex. Remember to switch off the `Caps Lock' when you want to revert to the continuous contour definition mode.

The Review Window

The contours show up as coloured curves in the `Review' window, provided you have not switched them off using the `Segmentation' toggle button above the slider (coincident contours, which may be generated accidentally by thresholding, are easy to spot since they are displayed in a much thicker line width). Remember, also, that you will not be able to define the segmentation contours if you have chosen not to display them.

The middle mouse button can be used to edit segmentation contours. Suppose you wish to replace a small portion of a contour. Use the middle mouse to draw the new section, intersecting the original curve (almost tangentially) at the two points where you wish to splice in the new segment. This is best understood by trying it out, though there are some detailed rules describing the behaviour of the curve editor. If Stradx replaces the wrong portion of curve, simply click once with the middle mouse button to toggle the replaced section.

Edit operations can also be carried out one vertex at a time. The first vertex is defined by clicking the middle mouse button while holding down the control key. Click with the middle mouse button to define subsequent vertices, and the right mouse button for the final vertex.

You can define segmentation contours for up to ten distinct objects using the object selection panel. The procedures described above for the creation, modification and deletion of contours apply only to the currently selected object. To work on the contours of a different object, you must first select the appropriate object in the object selection panel.

Other facilities, which allow semi-automatic segmentation of thresholded data and automatic ECG gating, are described under `Segmentation Thresholds and Gating'.

The Outline Window

The segmentation contours show up as coloured curves in the `Outline' window, provided you have not switched them off by toggling the `Segmentation' button. The display above shows a complete segmentation of the hepatic veins. Remember to click the `All' button in the `Outline' window to see all the contours (or else sweep through them all using the slider). The contours corresponding to the current frame (the one shown above in the `Review' window) are drawn in red. In the display above the outlines have been toggled off. The display below shows the outlines as well.

The Outline Window

When you have created a segmentation you can save it using the `Save segmentation' item on the `Segmentation' menu. You can reload previously saved segmentation files using the `Load segmentation' item. Segmentation files (.sxg suffix) are written in a standard Geomview format, so they can be read by the Geomview 3D visualisation package. However, note that the contours are saved as closed curves in the x-y plane. Stradx calculates their correct 3D positions internally, using the position and calibration information (if available). In the .sxg file, the z-coordinate of every contour vertex is arbitrarily set to the frame number, so the contours appear spread out when viewed in Geomview.

After you've saved a segmentation file, you'll notice the data file name in the main window highlighted in yellow, indicating that you may now wish to save the data file. This is because you've now associated this data file with a particular segmentation file. If you do save the data file, then next time you load the data file the corresponding segmentation file will be loaded automatically.

The `Outline' window also displays the volume of the segmented region in milliliters (calculated using an accurate planimetry technique). This volume estimate tracks the current segmentation, so you should see it change as you add or delete contours in the `Review' window. The exception is when the volume calculation cannot be performed incrementally (for instance, when you load an entirely new segmentation file or open the `Outline' window for the first time), in which case the `Update' button is activated. Click on this button to update the volume estimate, though expect the program to hang for a few seconds while the calculation is taking place.

In the above, we have assumed that the structure to be segmented is sufficiently compact that it fits inside a single sweep of the ultrasound probe. However, Stradx includes special facilities to deal with large structures that can only be covered by multiple sweeps.

Click here to view a QuickTime movie (7 MBytes) showing Stradx being used to estimate the volume of a human bladder, using both the `Outline' and `Surface' windows.