Labeling Regions of Interest
You can use the tools available on the ROI Painter panel, shown below, to quickly and easily label voxels that correspond to a feature or structure of interest.
ROI Painter panel
You should note that the behavior of an ROI Painter tool is determined by the selected settings — Add, Remove, 2D/3D mode, and Use range (see ROI Painter Tool Settings) — and the type of view in which you work (see Labeling Regions of Interest in 2D Views and Labeling Regions of Interest in 3D Views).
Labeling Regions of Interest in 2D Views
This topic describes how to label regions of interest with the ROI Painter tools in 2D views.
How to Label a Region of Interest in 2D Views
- Scroll through the image stack and adjust the view so that the area you plan to segment is shown clearly onscreen (see Using the Manipulate Tools and Window Leveling).
- Click the Segment tab on the left side of the workspace to access the ROI Painter panel.
- Do one of the following:
- Create a new ROI, if required (see Creating New Regions of Interest).
- Select the region of interest you intend to modify in the Data Properties and Settings panel.
- Define a range, optional.
In this context, any voxel with a value outside of the range will not be selectable (see Defining Intensity Ranges).
- Select the tool with which you plan to work and the tool settings (see ROI Painter Tool Settings).
- Label the image, as required (see Working with the ROI Painter Tools in 2D Views).
Editing Regions of Interest with the Brush Tools
If required, you can automatically re-assign labeled voxels from one region to interest to another with the Brush tools. For example, in cases in which an automated bone segmentation resulted in voxels corresponding to trabecular bone erroneously labeled as cortical bone or vice versa. In the example below, some trabecular regions (highlighted in blue) were assigned to cortical bone (highlighted in yellow).
Automated segmentation result
You can also choose to work in Exclusive mode with the Brush tools. In this mode, only the labeled voxels belonging to the selected regions of interest will be affected when painting. This option is available on the ROI Painter panel as shown below.
ROI Painter panel
How to Edit Regions of Interest with the Brush Tools
- Select the 2D view in which you plan to edit the regions of interest.
- Select the required regions of interest on the Data Properties and Settings panel.
The selected ROIs are identified as (A) and (B).
- Select a 2D or 3D Brush on the ROI Painter panel.
- Select the Exclusive option, if required.
In this mode, painting will only be applied to the labeled voxels of the selected regions of interest. Unlabeled voxels will not be painted.
- Do the following, as required:
- Add and re-assign labeled voxels to ROI (A) from ROI (B) by holding down Left Ctrl (or your configured Add with key) and then painting.
As shown below, only voxels highlighted in yellow are re-assigned to those highlighted in blue when painting in Exclusive mode.
- Remove and re-assign labeled voxels from ROI(A) to ROI(B) by holding down Left Shift (or your configured Remove with key) and then painting.
- Add and re-assign labeled voxels to ROI (A) from ROI (B) by holding down Left Ctrl (or your configured Add with key) and then painting.
Labeling Regions of Interest in 3D Views
In some cases, you may want to label regions of interest in 3D views. When working in 3D views with the ROI Painter tools, you should note that only visible voxels will be selectable and that visibility can be controlled through window leveling and with opacity.
How to Label a Region of Interest in a 3D View
- Select the required 3D view and adjust the rendering so that only the area you plan to segment is shown onscreen (see Using the Manipulate Tools and Window Leveling).
- Click the Segment tab on the left side of the workspace to access the ROI Painter panel.
- Do one of the following:
- Create a new ROI (see Creating New Regions of Interest).
- Select the region of interest you intend to modify in the Data Properties and Settings panel.
- Make sure that the region of interest you plan to modify is set to visible in 3D.
If required, click the 3D icon on the right side of the item in the Data Properties and Settings panel to display the ROI.
- Select the tool with which you plan to work and the tool settings (see ROI Painter Tool Settings).
- Select a working area in the drop-down menu on the ROI Painter panel.
- None… Lets you work on all voxels within the shape of the region of interest
- Dataset… Lets you work on all visible voxels of the selected image data. You can adjust window leveling to help isolate objects that you need to select (see Window Leveling).
- Region of interest… Lets you work on all voxels of the selected region of interest or multi-ROI.
- Label the image, as required (see Working with the ROI Painter Tools in 3D Views).
