Regions of Interest

To add Regions of Interest (ROIs) to the 3-D display, select Load from ROIs ... from the File menu of the 3-D Viewer: Menu item to load ROIs into the 3-D display

A dialog will now appear, from which you can select both the image on which the ROIs have previously been defined, and the ROI file.

Dialog to select ROIs for 3-D display

First, select the image on which the ROIs were defined by clicking on the Button to open an image icon, by typing in the folder (directory) and file name of the image, or by pressing the right mouse button and selecting from the menu of recently-used images.

Panel to select an input image

Next, select the ROIs that you want to display. Either click on the Button to set the ROI file button, or type in the path to the ROI file name (and press return).

Regions of interest can be displayed in one of two ways:

  • Radio button to show ROIs as a surface As a surface generated and rendered from the regions of interest. In order to successfully generate a surface, there must be ROIs that overlap in adjacent slices of the image. If there are isolated ROIs that only appear in a single slice, no surface can be generated from them. Furthermore, ROIs that do not enclose an area (Line, Curved Lines, Markers and Text) cannot be shown as a surface. If a surface cannot be generated, you will see the message "empty iso-surface" in the status bar of the dialog.
  • Radio button to show ROIs as a outlines As planar polygonal shapes. All types of ROI will be shown in the 3-D display, with the exception of Text ROIs, which will be shown in the same way as Markers (as a small cross).

These two modes of display are illustrated for a set of ROIs outlining the lateral ventricles:

ROIs rendered as a surface, and as polygonal outlines.
ROIs rendered as a 3-D surfaces ROIs rendered as a 3-D outlines
Surface rendered Outlines

You can change the appearance of the surface and outlines by changing the following settings:

  • Opacity. The opacity has a value between 0 (completely transparent) and 1 (completely opaque). Change the opacity using the opacity slider.

    Slider to set the opacity of the rendered ROIs

  • Colour. The default colour with which the surface or outlines are rendered is grey. To change the colour, click on the Button to set the colour of rendered ROIs button and select the new colour from the colour chooser that will pop up.

  • Surface shininess. The surface shininess has a value between 1 and 128. Change the shininess using the Spinner to set the shininess of rendered ROIs spinner. The shininess only affects the appearance if a surface is shown - it does not affect polygonal ROI outlines.

  • Render mode. When ROIs are displayed as a surface, the surface is defined by an array of linked triangles, and can be rendered as:

    • A solid surface. Select a render mode of "Fill".
    • A triangulated mesh. Select a render mode of "Wire frame".
    • A cloud of points. Select a render mode of "Points".

The effect of selecting the Check box to cut away ROIs check-box is dealt with in the section about general controls.

If you click the Button to finish with ROI display button, the ROIs will be removed from the 3-D viewer.