Vessel Segmentation Tutorial
The UI on the sidebar for the Vessel Segmentation module looks like this:
The first thing you need to do is load an image, and then select it as the active volume (at the top of the module's UI).
Then you can change the parameters for preprocessing the image, and press the "pre-process image" button. The preprocessing may take some time to run, depending on the size of the image it may take several minutes but will be much faster if the ITK in Slicer is compiled with GPU acceleration turned on.
Then, you should select the preprocessed image as your active volume. If you are satisfied with how the preprocessing has enhanced the contrast with the vessels in your image, then you can proceed to the next part of the UI (otherwise select the original image again, and try different parameters).
Choose the appropriate radio button for segmenting the hepatic or portal vein. Then, click the "place 2 seeds" button. You should then find a location to mark the start of the vessel segmentation (from the top of the vessel down); the first time you click on the image you will be placing a seed to mark the start and the second time you click you will give a point slightly further down the vessel to indicate a direction for the segmentation.
Once you are happy with the 2 seeds you have placed (you can click the button again to remove them and place them again) you can click the "segment vessels" button to run the segmentation algorithm. You should see the output as both a label map overlayed on the image, as well as a 3D model.
If you get areas where the hepatic and portal overlap, you can use this tool to assign the overlapping areas to one particular vein. If you click the "merge segmentations" button, you will get a merged label map where the overlapping areas are purple. Then, use the radio buttons to select either hepatic or portal and click the "place seed" button and place the seed in the purple overlapp area you wish to assign. In order to finalize assigning that area to one particular vein you must then click the "run seed assignment" button.