3D Volume Rendering¶
What is Volume Rendering ?¶
Volume Rendering (VR) is a well known visualization method for the 3D visualization of medical images. It is based on transparency and coloration of voxels. Indeed, a medical image is composed of a set of voxels, each voxel having a grey level that represents a physical property of the tissue (absorption of X ray in case of CT for instance). A voxel being a pixel in 3D, it is a square if slice thickness = pixel size or a rectangular box if slice thickness is different from the pixel size, which represents most clinical images of the thoracic-abdominal area (the most frequent voxel size being typically around 0.5 x 0.5 x 5 mm3, 0.5 x 0.5 x 2 mm3 or 0.5 x 0.5 x 1 mm3). Without transparency and without color, the 3D view of voxels permits to see only border voxels. To see inside voxels, it is therefore necessary to put border voxels in transparency as shown on the following image VR-DEF.jpg.
The remaining problem is thus to select voxels that we want to see, and voxels that have to be put in transparency. Such a selection, called “segmentation” in computer sciences and consisting in delineating anatomical or pathological structures, is complex and time consuming. Another solution is to automatically replace all grey levels by colors, and add for each grey level an associated transparency level. This transformation is summarized in a transfer function that gives for each grey level a color and a transparency level. For instance, bones being the highest grey level in a CT, it is sufficient to put all voxels with a grey level under 230HU in full transparency, to put all voxels with a grey level beyond 400 HU with no transparency and to perform a progressive decrease of transparency between these two grey level values. We can do the same with the color map from dark to white. We obtain thus the result illustrated on the following image VR-TF-DEF.jpg. In this figure, the transfer function is illustrated on the right. It is printed on the grey level histogram that provides the number of voxels having this grey level for each grey level of the image.
Fast use of VR : basic tools¶
The VR-Render visualization mode is started by pressing the F2 shortcut, or by selecting the “Volume rendering view” in the Window menu. Activation creates 3 windows in the “Image visualization” area: a Volume rendering window, a Transfer function editor window and a 2D MPR view window called Negato1 (see next image). VR-Render has been developed in order to be used in a fast way. Automated transfer functions (TF) have therefore been included in the software allowing users to save time by only selecting these transfer functions. This selection is performed in the TF selector box of the “Transfer function editor”.
As shown for medical use, the current software includes several pre-computed CT-scan transfer functions allowing to visualize bones, kidneys, liver, lungs, muscles, skin and vessels (see next image). More automated transfer functions provide standard transfer functions currently used in other applications. It is important to notice that in VR-Render 0.8 the color table of the transfer functions is applied on the Negato1 view. It can be highly useful to have a better medical image reading.
It is possible to manipulate the Volume Rendering view with the same command than with the 2D MPR view, which means by using the mouse SCROLLER or by using the combination of the “**SHIFT**” key and pressing the RIGHT button for the zoom, by pressing the LEFT button and moving the mouse for the rotation, and by combining the SHIFT key and pressing the LEFT button for translation. In this case, a movement in any direction creates a translation in the same direction. The reset of translations and zooms is performed with the R key.
It is also possible to go directly to frontal, sagittal and axial views by using the “Window” menu and by selecting “Frontal view”, “Sagittal view” and “Axial view” options. In this same menu, the “Snapshot rendering view” option allows to take a picture of the Volume rendering view.
Another important interest of VR-Render is the ability to visualize only a part of the image by applying a cutting plane on the global image. We have proposed two major kinds of cutting planes (see image F2-CUTTING.jpg). The first one is the standard axial, sagittal and frontal cutting plane. The second one is a mobile cutting plane that can be placed anywhere in the volume. The selection of cutting planes (and unselection) is done with the “Window” menu or via shortcuts : “O” for the “View clipping Box” option providing three main axes and “P” for “View clipping Plane”.
The clipping box provides 6 cutting planes: two axial, two frontal and two sagittal ones. The displacement of a cutting plane is then performed by pressing the left mouse button on the corresponding center sphere of this plane. When selected, the plane changes color and the sphere turns red. Displacement is then realized by moving the mouse. It is possible to remove the clipping box planes by selecting the “Reset clipping box” option in the “Window” menu or by using the shortcut “Ctrl O”. This cutting box can also be reduce through a kind of in an out zoom by selecting the central volume sphere by a right button pressing, and then by adding a “Shift” pressing and an up (zoom out) and down (zoom in) movement of the mouse. In the same way, the cutting box can be translated by selecting the central volume sphere by pressing the left button, and then by adding a “Shift” pressing and a movement of the mouse.
Furthermore, the clipping plane provides one cutting plane that can be moved thanks to the displacement and orientation of a vector that is normal in this cutting plane. The displacement is then performed by pressing the left mouse button on one of the two extremities of the vector. When selected, the vector turns red. Displacement is then realized by moving the mouse. When the cutting plane cuts the box, a red intersection appears. It is then possible to directly move the plane into the direction of the normal vector by pressing the left mouse button on one of its borders and by displacing it. It is finally possible to remove the clipping box planes by selecting the “Reset clipping plane” option in the “Window” menu or by using the shortcut “Ctrl P”.
