Start the ROI Toolkit from the Toolkits
menu:
The ROI Toolkit frame will now appear.
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:
There are different ways to create and edit the different types of ROI. These are detailed below.
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;
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.
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:
Note: you also rapidly create a Marker by pointing with the mouse within the selected slice, and pressing the 'm' key on your keyboard.
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 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 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:
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:
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:
To enable or disable edge detection click on the Edge Detection check
box:
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.
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.
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.
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.