Creating Regions of Interest

Region of Interest (ROI) Creation

Start the ROI Toolkit from the Toolkits menu:

The ROI Toolkit frame will now appear.

Creating an ROI

In order to create an ROI, you must first select a slice. Double click on one of the slices in the display window. The selected slice will now appear outlined in white.

There are eight types of ROI, which can be created by clicking on the icon in the ROI Toolkit frame:

Text
Marker
Line
Curved line
Rectangular
Elliptical
Irregular, manually drawn
Irregular, contour following

For handy ROI creation you can also bring up the "handy ROI tools" window from the ROI Toolkit: .

This pops up the window show below:

You can move this window around to wherever it is easiest to access, to minimise your movement of the mouse. You can dismiss the window in the way that is usual for your windowing system.

There are different ways to create and edit the different types of ROI. These are detailed below.

Text Annotation

[Keyboard accelerator: point to a selected image slice and press the 't' key.]

To create some text annotation, ensure that you have a slice selected, then click on the icon.

The status bar given you the instructions "click on the selected slice and type text; to finish; Esc to cancel". To define some text annotation, click on your chosen point somewhere in the selected slice. Then type in the text you require, and press the Enter key to finish. Alternatively, just click with the mouse away from the text you have just typed in. To cancel the operation, press the "Escape" key on the keyboard. The text ROI will look like this:

To change the position of some text, click on the text, then click and drag one of the corner handles to move it to a new position.

All text ROIs are displayed with text in the same font size, and with the same font colour. However, the size and colour are configurable using the ROI Toolkit Preferences.

Note: you also rapidly create some text by pointing with the mouse within the selected slice, and pressing the 't' key on your keyboard.

Markers

[Keyboard accelerator: point to a selected image slice and press the 'm' key.]

To create a marker, ensure that you have a slice selected, then click on the icon.

The status bar given you the instructions "click on the selected slice; Esc to cancel". To drop a marker, click on your chosen point somewhere in the selected slice. To cancel the operation, press the "Escape" key on the keyboard. The marker will look like this:

To change the position of the marker, click on the marker, which will then appear with a green "handle" in the centre, shown enlarged below:

To move the marker, click and drag the handle to its new position.

Note: you also rapidly create a Marker by pointing with the mouse within the selected slice, and pressing the 'm' key on your keyboard.

Lines

To create a straight line distance measurement, ensure that you have a slice selected, then click on the

icon.

The status bar given you the instructions "click, hold and drag to define; Esc to cancel". To define a line, click point somewhere in the selected slice and hold the mouse button down; this will be the first end of the line. Drag the mouse to the other end of the line, and release the mouse button. The line will now have been defined. To cancel the operation, press the "Escape" key on the keyboard. The line ROI will look like this:

To change the line, click on it, after which it will then appear with a green "handle" in the centre, as shown below:

To change the line, you can:

Click and drag the centre handle, which moves the line without changing the shape.
Click and drag the cross at either end, which will change the location of that end.
Hold the "shift" key down, and drag one of the crosses at either end. This will rotate the line about the centre point.

Curved Lines

To create a curved line distance measurement, ensure that you have a slice selected, then click on the icon.

The status bar given you the instructions "click or trace points around the shape; Esc to cancel". To define a curved line, you can click the mouse at individual points around the curve, or you can hold the mouse button down to draw the curve. As the ROI is being drawn, it appears as a red outline:

To end the curve, double click with the mouse. To cancel the operation press the "Escape" key on your keyboard.

Note: you can zoom and scroll the image as you are drawing the outline, as usual. To change the curved line, click on it, after which it will then appear with nine "handles", as shown below:

To change the line, you can:

Click and drag the centre handle, which moves the line without changing the shape.

Click and drag the handles at the corners or edges of the bounding box. This stretches the ROI.

Hold the "shift" key down, and drag one of the handles at the corners or edges of the bounding box. This will rotate the line about the centre point.

Edit the individual points that make up the curved line. See See ROI Editing section for more details.

Rectangular ROIs

To create a rectangular ROI, ensure that you have a slice selected, then click on the icon.

This will create a "default" rectangular ROI in the middle of the selected slice:

The rectangular ROI has handles, allowing you to change the shape, size and position of the ROI. These are show enlarged below:

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.

Elliptical ROIs

To create a elliptical ROI, ensure that you have a slice selected, then click on the icon.

This will create a "default" elliptical ROI in the middle of the selected slice:

The elliptical ROI has five handles that allow you change the shape, size and angle of the ROI. Use the centre handle to move the ROI. The other four handles are at the ends of the major and minor axes: click and drag these handles to alter the major and minor axis lengths. In addition, elliptical ROIs can be rotated, by pressing the "Shift" key and dragging one of the axis handles. See ROI Editing section for more details.

Irregular ROIs

Irregular ROIs are drawn manually on the selected slice. Click on the icon to start drawing: the status bar gives the instructions: "click or trace points around the outline; Esc to cancel".

You can click the mouse at individual points around the outline of the feature you want to measure, or you can hold the mouse button down to draw around the outline. As the ROI is being drawn, it appears as a red outline:

To close the outline, and create a completed ROI, double click with the mouse. To cancel the operation press the "Escape" key on your keyboard.

Note: you can zoom and scroll the image as you are drawing the outline, as usual.

Note: for ROIs drawn by hand that have segments of the outline that cross, the "even-odd winding rule" is used to define the interior and exterior portions of the ROI. The figure below shows such a shape:

That which is defined to be the interior of the ROI is coloured in blue. To see how the even-odd rule works, consider the line drawn through the ROI. Each time the line crosses the outline of the ROI, a counter is incremented. When the counter is odd, the line is inside the ROI; when the counter is even, the line is outside the ROI. This rule works for any line drawn through the ROI, and for any direction of traversal of the line.

Contoured ROIs

[Keyboard accelerator: point to the edge of a feature and press the 'c' key.] A contoured ROI follows a contour, or level of intensity, from a point where the mouse is clicked. Optionally, edge detection can be turned on, so that the contouring function automatically finds the edges of image features in the vicinity of the mouse click, and then follows the outline of that feature.

To enable or disable edge detection click on the Edge Detection check box:

Contouring without edge detection

Uncheck the Edge Detection check box, then click on the icon. The status bar gives the instructions: "click on the selected slice at the contour start point; Esc to cancel". Click on the selected slice at the position where you want the contour to start. The algorithm used to find the contour level is explained in the algorithms section.

To cancel the operation press the "Escape" key on your keyboard.

Contouring with edge detection

Ensure that the Edge Detection check box is ticked, then click on the icon. The status bar gives the instructions: "click on an edge the selected slice; Esc to cancel". Click on the selected slice at the edge of an image feature. To cancel the operation press the "Escape" key on your keyboard.

Jim will now have produced a contour, shown in light blue, outlining an image feature. Below is the result of applying edge detection and contouring to the edge of brain lesion. The algorithm used to find an edge is explained in the algorithms section.

Propagation in 3D

Normally, contoured ROIs are only created in the slice in which you click the mouse. However, if you select the check box, then the contour level and initial contour location are propagated to adjacent slices. If a contour at the same contour level are found close to the same location, then a contour will also be created in these slices. The search for the contour level take place in a 5×5 square region of pixels, searching in an outward spiral centred at the contour location. If the contour level is not found within the search area, then propagation stops; otherwise an ROI is created in the adjacent slice, and propagation continues to the next adjacent slice.

Pixel Snap

Turning pixel snap on (by checking the Pixel Snap check box ) causes the outlines of ROIs to snap onto the nearest corners or centres of image pixels. Thus, for example with Pixel Snap turned on, Rectangular ROIs will always contain a whole number of pixels. Without Pixel Snap, ROIs are free to have any shape defined by the user.

The ROIs Toolkit can be set so that the vertices of some ROIs (Line, Curved Line and Irregular ROIs) can snap either to the corners or to the centres of pixels. Change between snapping to centres/corners, by setting your preference in the ROI Preferences dialog.

ROIs created by contouring are unaffected by Pixel Snap.

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