Manual Delineation with Slicer 3D

Senan Doyle
January 19, 2009

1 Introduction
The following instructions pertain to Slicer Version 3.4. Additional information on manual segmentation with
Slicer can be found at http://www.na-mic.org/Wiki/index.php/Slicer3:Training

1.1 Load Volume

1. File → Add Volume ...
2. Select volume and press Apply

1.2 Change Viewer Settings

1. Press Layout Icon (see below)

2. Select layout of your choice. Red slice only layout displays a single modality, while multiple modalities
can be viewed simultaneously with the Four up layout, for example.
3. Several useful settings can be found by pressing the button below, such as visibility of the label layer on
each modality. The label layer is viewed on all modalities; delineation in one modality is instantly visible
in the others. It is useful to select show label volume outlines here.

4. Choose the correct view (axial, coronal, sagittal). Note that these may be identified incorrectly, and so
the true axial view may be found under coronal, for example.
5. Zoom by clicking the right mouse button and moving the mouse.
6. Use the scroll wheel to change slice number.

1.3 Turn off Interpolation and Change Contrast

1. From Modules List, select Volumes (see below)

1
 2. In the Display tab on the left panel, Uncheck the Interpolate box.
3. In the Display tab on the left panel, you will also find the image histogram and contrast settings.

1.4 Manual Delineation

1. From Modules List, select Editor
2. Click Create Label Map
3. Set Label to 1. To erase regions, paint over them with the 0 label.

4. Click Enable Volume Check Points to allow large mistakes to be corrected.

5. Choose a tool to identify the lesion. The size of the brush can be changed in this box.
6. A very useful tool is the Level Tracing tool, which incudes all neighbouring points of the same intensity.

1.5 Save Label Map

1. From File List, select save