Editing Regions of Interest

Editing Regions of Interest (ROIs)

Using the handles

The shape of an ROI can be altered in several ways, but most commonly by dragging the "handles" that are around the outline of an ROI. To see the handles on an ROI, first select the ROI by clicking on the outline (ensure first that you are in Edit Mode). ROI handles are shown enlarged below for a Rectangular ROI.

To change an ROI, click and drag one of the handles:

Use the centre handle to move an ROI.
Use an edge handle to stretch an ROI vertically or horizontally.
Use a corner handle to stretch an ROI both vertically and horizontally.

To change an Elliptical ROI, click and drag either:

The centre handle to move the ROI.
The handle at the end of the major or minor axis to alter the axis length.

Rotating ROIs

The following types of ROI can be rotated:

Straight Line.
Curved Line.
Elliptical.
Irregular (either manually drawn or contour).

These ROIs can be rotated by holding down the "Shift" key and dragging one of the corner or edge handles. When rotating an Elliptical ROI, a pair of red crossed lines appears, showing the new orientation of the major and minor axes of the ellipse.

As the ROI is being rotated, the status bar shows:

the angle between the line and the horizontal for straight Line ROIs.
the angle of the major axis for Elliptical ROIs.
the angle of the current rotation for Curved Line and Irregular ROIs.

When the mouse is released, the status bar shows the final rotation angle.

Vertex handles on Irregular and Curved Line ROIs

You can move the individual vertices of an Irregular or Curved Line ROI, using its vertex handles. To see the vertex handles, first select an irregular or curved line ROI, and then use the ROI toolkit Edit Outline from the Edit menu (or use the keyboard accelerator "Control-O"). The ROI will then appear like this:

When an ROI has a lot of handles, not all the handles may be visible. Only a selection of handles is shown, such that the visible handles do not overlap. As you zoom in on the ROI, more and more handles can be seen, since they do not overlap at high zoom. This makes editing the outline of Irregular ROIs quicker, since coarse changes can be made at low zoom before zooming in for fine-detail changes.

An ROI seen at low zoom - only a selection of the vertices has a handle shown.

The same ROI, with higher zoom - more handles are visible.

To change the outline, use the mouse in the following way:

Click and drag a vertex handle to change its position. Other non-visible handles are also dragged along.
Press the "Shift" key and click on a vertex to delete it.
Press the "Control" key and click on a vertex to add a new pair of vertices either side of it.

Note: you can zoom and scroll the image as you are editing the ROIs.

Using the Eraser

Irregular ROIs may also be edited using the "Eraser" tool. When an Irregular ROI is selected and editable, the tool becomes active: .

You will typically use the eraser tool to remove part of an Irregular ROI that has been produced by contour following, where the contour follows the image feature for most of its outline, but then deviates towards another image feature. For example, below is an attempt to outline a small brain lesion in the frontal white matter using edge detection and contouring. The outline has deviated into the second (almost confluent) periventricular lesion below.

To remove the left hand "limb" of the ROI, click on the icon, and draw an erasing line that separates the ROI from the unwanted limb. Points erased will appear as a white line.

After the erasure, the original ROI will be split into two, as shown below. Any unwanted ROIs can now be selected and deleted.

All points on the ROI outline beneath the eraser line will be deleted. If this results in two or more breaks in the ROI outline, then the original ROI will be divided into two or more ROIs. For the purposes of audit, the original ROI will be retained as the largest of the remaining ROIs (the remaining ROI with the largest number of outline points). Any additional ROIs will be treated as new ROIs.

Another example of the use of the Eraser is to separate contours that are joined by a small "bridge". In the following example, after attempting to outline the brain by following a contour, the brain was joined to the scalp by a very small bridge of tissue:

Here is a close up of the bridge during erasure:

Using a small eraser width (1 pixel), the Eraser was used to divide the brain from the scalp contour, resulting in the two contours below:

The unwanted scalp contour was then selected and deleted.

Using the Eraser to Extend an ROI

You can also use the eraser to extend an irregular ROI's boundary. To do this, start drawing the eraser line inside an ROI, loop the line outside the ROI, and the then end with the line back inside the ROI. This loop that you form will extend the boundary of the ROI, as illustrated below.

The original ROI.

The erasor line, starting and ending inside the ROI, but looping outside.

The extended ROI, includes the area enclosed by the loop.

Eraser Width

The width of the eraser line is measured in screen pixels, and is set from the selector .

ROI Deletion

To delete an ROI, first select it, then either choose Cut from the ROI Toolkit Editmenu, the keyboard accelerator "Control-X", or press the delete key.

Other ROI Edit Operations

Other ROI editing operations are available in the ROI Toolkit Edit menu:

Cut (accelerator: Control-X). Deletes an ROI, but places it on the ROI clipboard. If more than one ROI is selected, operation applies to all selected ROIs.

Copy (accelerator: Control-C). Copies an ROI to the ROI clipboard. If more than one ROI is selected, operation applies to all selected ROIs.

Paste (accelerator: Control-V). Paste ROI(s) in the clipboard to the selected slice.

Select All (accelerator: Control-A). Selected all ROIs in the selected slice.

Paste All Slices. Paste ROI(s) in the clipboard to the all slices of the image.

Edit Outline. Shows the Vertex handles of an irregular ROI, allowing the outline to be edited.

Note: Sometime when you create ROIs or copy/paste them, you will see a message stating that an ROI already exists in the slice and has not been created. The ROI Toolkit does not allow a regions of the same type and shape to appear twice in the same slice. This is to prevent unintentional duplication of ROIs that lie exactly on top of each other, so that the user would be unaware of one of the ROIs. If this happened, then area and volume measurement might give the erroneous results because of these "hidden" ROIs.

Note: When you have a selected slice, you can cycle through the ROIs by pressing the ">" and "<" keys. As you press the ">" key the next ROI in the selected slice is selected. As you press the "<" key the previous ROI in the selected slice is selected. Deleted ROIs cannot be selected in this way.

ROI Edit Undo

When you add or change ROIs and make a mistake or the result is unsatisfactory, the operation can be undone. To undo the last operation, select Undo from the Edit menu:

, or use the keyboard accelerator "Control-Z".

Note that the maximum number of undo operations is set in the user preferences of the ROI toolkit.

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