Step 3: Segment lesions

We will use the Segmentation to annotate the loaded PET SUV image with the segmentations of the lesions.

Select the Segmentation plugin in the toolbar or by choosing the Segmentation entry at Window->Show View in menu bar. On the ride side of the application the Segmentation plugin appears.

In the Data Selection box you can find two image selectors. In the Patient Image selector our image should be already selected. Click on the button next to the Segmentation selector.

Now a dialog appears where you can choose a name for your segmentation, e.g. Neoplasm, primary. A suggestion list provides you presets with different colors. Of course you can choose your favorite color instead. Confirm your decision by clicking Ok. A new DataNode is in the Data Manager and the Segmentation selector in the plugin has now the new segmentation selected.

Various segmentation tools are available, from basic manual contouring, to thresholding and more advanced automated tools. We provide also a interpolation for 2D and 3D. For more information and help please press F1.

MITK initialize the metadata for this segment by default:

• Category: overall category of the segmentation.

• Type: more specific description of the segmentation.

• Anatomic region: where applicable, location of the segmented structure.

In our example Segmentation type: "Neoplasm, Primary" which belongs to the "Morphologically Altered Structure" category.

Try it yourself: Repeat the same sequence of steps to segment the Secondary lesion!