Manual Segmentation

Lesions can be segmented manually. This part of the documentation is a copy of the corresponding part of DTItrack manual. This segmentation procedure has to be realized on the 2D delineation view on the left.

Select a slice where you would like to start drawing a lesion (to change slice, you can press keys and ). You can zoom in for more precision.

Now choose the ROI color in the color selector. Note that the ``label 0'' (black) color will erase a region (make it as no-ROI).

Press ``j'' to activate the ``Lesion segmentation mode'', you will see a purple cross somewhere in the view. Maintain a left-click and move the mouse to define the contour of the ROI for this slice. The contour is shown in green. You must maintain your click until you reach the first point of the contour (the purple cross). You can also use an alternative mode: by middle-clicking, you can define several control points to draw the ROI contour. When you have enough control points, Ctrl+middle-click on the first control point to finish the drawing. You can then right-click on one of these contol points to move it. You can add a control point by pressing Shift+right-click between two existing control points. You can delete a control point by pressing Ctrl+right-click on it.

Once you have finished with the contour drawing, you must validate it by pressing ``v'', you will see that the region you just define is now filled by the color by the one you chose in the color selector.

Figure 6.11: Step by step procedure for ROI generation. Repeat this procedure for several slices until you are satisfied with the ROI. This illustration has been realized for the DTITrack manual but the procedure to segment a lesion is similar.

Put a 2D view in full screen and zoom in to the region of interest. Choose a color in the color selector.

Press ``j'' to activate the ROI generation mode. A purple cross will appear on the view.

Mode 1: Left-click and maintain to freely draw the ROI contour. Release the mouse only when you reach the first cross.

Mode 2: Middle-click to draw the ROI with control points. Ctrl+middle-click on the first cross to finish the contour.

Right click on a point to move it. Shift+right-click between points to add one. Ctrl+right-click on a point to delete it.

Once your contour drawn, Press ``v'' to validate it. The region is then colorized. Use Label 0 color (black) to erase a region.

- As said above, this mode can be activated and disactivated by pressing ``j''. When it is activated, no interaction is possible in the 2D view, but you can still change slice by pressing or .
- See figure 6.11 for a step by step illustration.