Using ROIs

A region of interest (ROI) is a part of an image or image series that one wants to study closer. One could want to study the cerebellum, and not the complete head.

To study the restricted area or volume, on has to mark out the region of interest on an image. First decide which kind of ROI you want to use. There are five possibilities. There are two geometrical shapes, elliptical and rectangular.Then there are two irregular shaped ROIs, polygonic and freehand. These differ in the way they are created. Finally one can select the pixels needed one by one to build up the ROI. In this tutorial, we will make a polygonic ROI.

1. Give the series a descriptor

Before creating ROIs, it is a good practice to give the image window a Series descriptor if it does not have one already.

1. Right click on the image window. On the popup menu, select Series Descriptor...

2. In the series descriptor, write some text that will identify the image series in the image window

3. Click OK

2. Create a polygonic ROI

The polygonic ROI is made by clicking multiple times on the borderline between what one wants to include and what one wants to exclude on the image, at different places each time. nordicICE will then draw lines between the different points, completing a closed curve.

To make a polygonic ROI:

1. Open an image window, and select the image you want to use.

2. In the Image measurement tools toolbar, click on the triangle besides the icon displaying the current ROI type.

3. In the list that appears, select the Polygon ROI type. Notice that the list is closed.

4. Click on the Polygon icon on the Image measurement tools toolbar. Notice that this opens a new dialog, ROI statistics. Also notice that the dialog title also contains the series descriptor you entered above.

5. Click somewhere on the border between the part of the image.

6. Repeat step 5 somewhere else on the border a number of times. A straight line will be drawn between the last click and the new one. Make sure that the new click is sufficiently close to the previous click that the straight line is a good approximation to the borderline around what you want to include.

7. When you want to close the curve, press the Alt button before you click. Where you click the last time does not matter, The curve will be closed, as if you had clicked on the point you made in step 5.

3. Edit a polygonic ROI

If you are not satisfied with the polygon you have created, you may move any one of the vertices.

To edit a polygonic ROI:

1. Move the mouse over the vertex you want to move. notice that the pointer changes to a hand.

2. Press and drag the vertex to where you want it to be.

3. Release the mouse button.

Statistics about the interior of the area you have marked is available in the ROI statistics window.

4. Store the ROI in the ROI buffer

Sometimes you want multiple ROIs for the same image series. Before you can create a new ROI, you have to store the old ROI. nordicICE has a temporary storage for ROIs called a ROI buffer.

1. Press the Save ROI to buffer button. Notice that a new dialog appears, called ROI buffer. The titlebar also contains the series descriptor for the image series.

Try scrolling through the images in the image window. Notice that the corresponding image number is displayed in the ROI buffer, and that the ROI you created is associated with the image you used when creating the ROI.

5. Create additional ROIs

1. Create additional ROIs by repeating the steps in section 2.

2. Store the new ROIs in the ROI buffer.

6. Save the buffer

The ROIs can be reused on a different set of images in a different session. To be used in a different session, you must store the ROIs

1. In the ROI buffer dialog, press Save buffer... This saves the ROIs, but not the statistics.

2. In the save ROI buffer dialog, locate the folder you want to save the ROIs to, and give the file a name.

3. Close the ROI buffer dialog

4. Close the ROI statistics dialog.

7. Load the buffer

1. In the Measure menu, select the ROI->ROI Buffer->Load... menu item.

2. In the Load multi-ROI (ROI buffer) file dialog select the file you saved in section 6.

Scroll through the images, and check that the ROIs you saved in section 6 are there.