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Visualization: Volume Rendering

The Volume Rendering module provides interactive visualization of 3D image data using a technique known as RayCasting. For official documentation of the panel and functions, see here.

One quick way to render your volume is using the drag and drop function. In the Data module you can drag the mouse skull volume from the image stacks example directly into the 3D widow and Slicer will guess at the settings to render the volume.

While this may be a good starting point, there are a lot of settings you can modify to improve the rendering of your volume in the Volume Rendering module.

  • 3D Slicer uses volume ray casting to computes 2D images from 3D volumetric data sets. Unlike surface reconstruction, there is no estimation of object surfaces or segmentation.
  • The values displayed are calculated using a transfer function that incorporates voxel intensities, material properties, and illumination.
  • The opacity and color of the image can be adjusted by modifying their transfer functions in the Volume Rendering module.

  • Slicer supports both CPU and GPU volume rendering. CPU based will always work, whether you are on a computer without a dedicated graphics card, or on a remote connection (which may not support hardware accelerated graphics), but it can be slow (unless you have dozens of cores in your cpu) and often quality is not great. GPU requires you have a dedicated graphics card with 1GB or more videoRAM and it is much faster, but it has its own limitations (see below).

  • If you have a dedicated graphics card, you may want to set the default visualization method to GPU rendering using the menu option in: Edit->Preferences

  • Always set the rendering quality to normal (this is enabled by defalt, if you opt-in for the SlicerMorph Preferences).

  • The physical limits to the size of the volumes that can be rendered are determined by the graphics card RAM, capabilities of the GPU and its driver. There are many different GPUs. One important technical detail to know, for volume rendering to work correctly, every dimension of the image must be less than the value of the MAX_3D_TEXTURE_SIZE parameter provided by the GPU. In some GPUs (particularly on Macs) this can be 2048, which means you cannot any render any volume that has a dimension larger than this setting.

For fuller discussion on these limits, see the Slicer discourse thread here.

Example: Volume Rendering

  1. Load the MRHead volume from the Sample Data module.
  2. Open the Volume Rendering module. In the Volume field, make sure the volume MRHead is selected. Click the eyeball next to the Volume field to display the image. You can change the 3D Slicer layout to 3D only. (Alternatively, you can drag and drop the MRHead from the Data module into the 3D viewer directly.)

  1. Expand the Advanced tab to view the opacity and color transfer functions. You can click on these functions to move or add additional control points.

  1. Under the Display tab, click on the Select a Preset menu. This menu contains saved transfer functions that work well for common data types. Select MRI Default (row 4, column 5). Try adjusting the color and opacity functions of this suggested display setting. For microCT datasets, presets uCT-8-bit bone, uCT-16-bit bone or uCT-Skull presets often provide an acceptable starting point for volume rendering that can be later better tuned to the data.

  1. See the Panels and their Uses section of Slicer documentation for explanation of each those panels found under the Advanced tab.

Saving your transfer functions

If you design an nice transfer function for your dataset, you can save it to the disk so that you can reuse for similar datasets. You can even convert your favorite transfer functions as 'presets' that are loaded into Slicer. See this thread on this slicer forum about how to enable this functionality. In future you will be able to add your favorite transfer functions as presets (or remove existing presets). You can follow the progress of this feature here

Turtle dataset

With carapace, skull and soft tissue, turtle skull CT (from DICOM tutorial) is a good dataset to practice your volume rendering skills. Try to highlight skull vs soft-tissue and try to visualize both at the same time.