KAHIBARO
23.6. Visualizing Voxelized Geometry
Table of Contents
Checking material assignment
Voxelized geometry in GATE represents anatomy as a 3D grid of voxels that each carry a material and usually a density. Before you trust any simulation that uses a CT or voxel phantom, you must verify that these materials were mapped correctly. Visual inspection is often the fastest way to detect problems long before you look at dose or count results.
In a typical setup, you load a medical image file such as CT or a prebuilt voxel phantom, apply a CT-to-material conversion, and obtain an image-based volume in the geometry. Visualization lets you see whether the resulting material distribution makes sense for a human body or for the specific phantom you are using.
Begin by launching geometry visualization with your voxelized volume enabled. First, confirm that the volume appears at all. If nothing is visible, check that the image path, the voxel volume size, and visibility settings are correct. Once the voxel volume is drawn, use clipping or slicing options in the viewer to examine the interior. Many visualization tools support viewing 2D cross sections in axial, coronal, and sagittal planes within the 3D scene. Use these to compare what you see with the original image that was used to build the voxel geometry.
Material assignment is usually represented by colors. Each material listed in your CT-to-material table or material mapping file is associated with a color in the visualization. Inspect the color legend, or list of logical volumes and materials, to understand which color corresponds to which material. If materials do not have meaningful colors, adjust visualization attributes so that air, lung, soft tissue, bone, and other key materials have clearly distinguishable colors.
Next, look for obvious inconsistencies. Lung regions should appear in the thorax, not in the head or abdomen. Bone should outline the skeleton and not appear in soft tissue regions. If your phantom contains air cavities such as sinuses or trachea, verify that these appear as air material and not as soft tissue. In homogeneous test phantoms such as a water box or a uniform sphere, all interior voxels should share the same material color. If you see unexpected isolated voxels of a different color, this may indicate gaps or misconfigured material thresholds in your mapping.
It is important to compare the voxel geometry directly with the original CT or label image. Load the same slices in a medical image viewer and in the GATE visualization, and step through corresponding planes. The shapes and extents of organs or structures should match. If your CT-to-material mapping uses Hounsfield units, verify that HU ranges were defined so that air is correctly separated from lung, soft tissue, and bone. When several materials share similar HU intervals, a narrow range or incorrect boundary can suddenly convert large parts of the body into the wrong material.
Pay close attention to edge regions, for example at the body contour or at bone interfaces. If density-based mapping is used, verify that lower density tissues such as lung are not accidentally grouped with soft tissue. In some voxel phantoms, distinct labels for organs are converted manually into materials. Visualization is an excellent way to check that each organ label received the intended material name and appears in the correct position.
If you are using multiple voxel volumes, such as a patient CT combined with a separate organ mask or an activity map, check that they overlap as expected. The material volume should enclose or coincide with the other images, and not be shifted or scaled differently. A simple initial test is to temporarily assign extreme colors or high transparency to one of the volumes and see if the overlap looks plausible.
Finally, perform simple sanity checks using material statistics. Some visualization tools can list volume and mass for each material. The total mass of a human-sized phantom should be of the correct order of magnitude, and the relative contributions of air, lung, soft tissue, and bone should be reasonable. Combine these numerical checks with visual inspection for a robust validation of your material assignment.
Always visually confirm that key anatomical regions correspond to the intended materials before relying on any dose or imaging results from voxelized simulations.
Image orientation
Correct image orientation in voxelized geometry is essential. Even if materials are mapped properly, a rotated, mirrored, or shifted phantom will lead to completely wrong dose distributions, beam paths, or imaging geometry. Visualization is the primary tool to verify that the voxel volume is oriented and positioned as intended relative to sources and detectors.
When you place a voxelized volume into the simulation, you typically specify its origin, spacing, and orientation. These come from the image header but must be interpreted correctly in the GATE coordinate system. In visualization, examine the global coordinate axes shown in the viewer. Identify which direction is positive X, Y, and Z. Then mentally or with reference notes relate these to anatomical directions, for example left, right, anterior, posterior, head, and feet. Many medical images follow the patient coordinate system, so you must know how that maps to the simulation coordinates.
Start with simple recognizable features on the image. In a whole-body CT, the head should be above the feet in the axial direction. In brain images, the nose should point anteriorly and the cerebellum should appear posteriorly. Use the visualization to rotate the 3D scene until you can tell whether the phantom is standing upright, lying head-first supine, or has some other orientation. If you are modeling a scanner, verify that the patient position in the voxel volume matches the intended clinical positioning for that modality.
In 2D slice views, orientation errors often appear as left-right flips or rotations by 90 or 180 degrees. For example, the heart might appear on the right side of the chest instead of the left, or the spine might be located anteriorly rather than posteriorly. To detect this, compare slices from the simulation with the same slices in a medical image viewer that uses known orientation labels. Step through several slices and check for symmetry and known anatomical asymmetries.
Table: Common orientation problems and possible visual signs
| Problem type | Visual indication in voxel visualization |
|---|---|
| Left-right flipped | Heart appears on the wrong side, liver and spleen swapped |
| Anterior-posterior | Spine appears in front, sternum appears behind |
| Head-foot swapped | Head structures appear where legs should be and vice versa |
| Rotated 90 degrees | Long axis of body aligned with incorrect global axis |
| Shifted translation | Phantom not centered in field of view, outside beam or detector |
You should also verify the relative orientation between the voxelized geometry and other parts of the simulation. For example, in a CT simulation, the X-ray source and detector should rotate around the patient in a realistic manner. Visualize the gantry rotation with the voxel volume visible. The beam should enter the body from directions consistent with a real CT scanner. In radiotherapy simulations, verify that the treatment beam enters the correct side of the body and passes through the expected anatomical structures before reaching the target.
If your phantom is combined with structures such as external markers, immobilization devices, or supplemental phantoms, check that all of these align correctly. Misalignment can arise from incorrect image origin, spacing, or from mixing coordinate conventions. Visualize their overlap and intersections. When two image-based volumes should coincide, you should see no visible shifts or rotations between their main structures.
Another useful check is to visualize the boundaries of the voxelized phantom together with its bounding box. The box should align with the expected patient coordinate axes and should not be rotated unexpectedly. If your image has non-isotropic spacing, elongated voxels can make the phantom appear stretched or squashed along one direction. Verify that the physical dimensions in each direction match the values in the image header. Use information panels in the visualization, if available, to read back the physical extent and compare with known patient or phantom dimensions.
If you detect orientation problems, correct them at the level of the image-to-geometry conversion, not by arbitrary rotations of the entire scene. Adjust the mapping between image indices and simulation coordinates, including any origin offset, axis reversals, or rotations. After you change the configuration, rebuild the geometry and repeat visualization until the voxelized phantom appears correctly oriented.
Never assume that a voxelized patient or phantom is correctly oriented based only on file headers. Always verify orientation visually against known anatomy and against the intended source and detector geometry.
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