Table of Content

We take a look at several tools to more precisely segment structures of anatomical interest. These include Mask Bounding Box, Region Growing on Mask and Eraser Mask.

Setting region of interest

We start with a scan of the torax (opened after click on Open Image button or command RMOpenImage). We want to segment a specific rib.


We open the Image Analysis tab (button Image Analysis or command RMImageAnalysis) and select a threshold that shows the ribs and torax bones properly. We then go to the Segmentation tab (button Segmentation or command RMSegmentation). We press the button Mask from Threshold (Manual Segmentation subsection) to convert the thresholded area into an editable mask.

Picking a seed point over a mask obtained from Mask from Threshold.

We push the button Pick Seed Point (Region Growing Segmentation subsection), select a slice and pick a point that is inside the structure we want to segment. We then check the checkbox On Mask under the button Surface from Region Growing, and click Surface from Region Growing to have a first guess of the surface that will contain our target structure.

Region Growing Surface, with On Mask checked.

We can now delete the surface or hide it in the layer manager (it belongs to a layer called Region Growing). The layer manager is in the tabs located at the right of the Rhino interface (or we can show it by typing the command Layer).

Bounding Box Mask

We press the button Create under the field Bounding Box, in the Manual Segmentation subsection in Segmentation tab. A red box appears over the image and clips the mask, in such a way that only the mask located inside the box is shown and used for segmentation. This box belongs to a layer called Bounding Box, and hence can be shown, hidden or locked as with Rhino layers (see the layer manager or type command Layer).

Bounding Box.

We select the box and move it so that it contains the structure we want to segment. We can translate, scale and rotate it (preferably in this order) with the gumball handles, which are a set of colored arrows (for translation), dots (for scaling) and arcs (for rotation). To see the gumball we need to have checked the Gumball option in the Rhino bottom interface, located between SmartTrack and Record History. Whenever we have a good guess, we click again over Surface from Region Growing (with On Mask checked on and the seed point we had selected before) and we will retrieve a surface that is smaller than the one we had before.

If we are not satisfied with it, we can delete it (use command SelMesh to quickly select meshes in the Rhino scene), move the bounding box, press Surface from Region Growing and iterate as many times as needed until we have a proper isolated structure.

Eraser Mask

With the bounding box we managed to significantly shrink our segmented surface, but there are details that are difficult to extract with a box. In the surface above, we have two ribs that are connected, but we want to extract only one of them. To do so, we have to disconnect them by manually removing the tissue that joins them together. We use for that the Eraser button, located in Manual Segmentation subsection (Segmentation tab).


Once pressed Eraser, a window appears with similar layout as the Paint Mask tools (Paint and Delete buttons, size and shape of the paint picker, Fill Between Slices, Show Mask and mask color). These tools let us create a mask that is different from the one we are editing in Manual Segmentation. The difference is that, once we press the Apply button, this mask will be subtracted from the Manual Segmentation mask.
We then go through the image and paint area to be removed, in this case to separate one rib from the other. Once we are done, we click Apply and then extract a new surface in Surface from Region Growing (with On Mask and Close Surface checked). If we separated them properly, the isolated structure will appear. Before running this last step, it is important to check that the layer Region Growing does not have a previous surface on it (in that case, we can delete the content of the layer or rename it to prevent overlapping with the new surface).

After erasing.

Like with the bounding box, we can iterate many times with the eraser to remove material. In this case we use it to polish the structure to be segmented.


Once we have finished, we can extract the rib as a closed mesh that is 3D printable.

At left the whole torax bone structure with the overlapping rib. At right the isolated rib surface.