Regions Of Interest (ROI)

The cropping box might be limited in terms of geometry. In order to extract a fiber bundle more precisely, you can define regions in the image where you want to visualize fibers that go through them. These regions are called Regions Of Interest (ROIs). We describe in this section a step by step procedure to define and use ROIs.

Put a 2D view in full screen (for instance FA map) and select a slice where you would like yo start drawing a ROI(to change slice, you can press keys and ). You can zoom in for more precision. Please see Sec. 3.3.1 for 2D view interactions. 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 ``ROI generation 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 3.12: Step by step procedure for ROI generation. Repeat this procedure for several slices until you are satisfied with the ROI. You need then to validate it by clicking ``Validate ROIs'' button in the tool bar.

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.

Repeat step 2 on other slices, until you are satisfied. Once you have finished, you have to validate your ROI definition by pressing ``validate ROIs''. The ROI will automatically be turn into as an isosurface in the 3D view.

You can repeat this procedure as many times as you want in order to define several ROIs. Don't forget to change the color otherwise they will be considered as the same ROI. You can save the ROI by clicking the ``Save ROIs'' button (left icon). You will then be able to load them for future use with the ``Add ROIs'' button (middle icon). You can reset all the ROIs by clicking ``Reset ROIs'' (right icon).

- 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 .
- Don't forget to savwe the ROIs, not to loose yout work.
- See figure 6.11 for a step by step illustration.

Once you have finish generating the ROIs, you can track the fibers with respect to these ROIs. Typically, A ROI is fully defined with its color, no matter if it is composed by several disconnected regions. The fiber tracking process (see Sec. 3.4.3) will restrict the display to the fibers that go through every ROI wihtout exception (i.e through every color). You can now use the cropping box to further extract the bundle of interest.