Volume nodes describe data sets that can be thought of as stacks of 2D images that form a 3D volume. Volume nodes describe where the images are stored on disk, how to render the data (window and level), and how to read the files. This information is extracted from the image headers (if they exist) of volume files at the time the MRML file is generated. Consequently, MRML files isolate MRML browsers from understanding how to read the myriad of file formats for medical data.

Model nodes describe polygonal data. They indicate where the model is stored on disk, and how to render it (color, opacity, and so forth). Models (3D surfaces) are assumed to have been constructed with the orientation and voxel dimensions of the original segmented volume.

The output of a rigid-body registration is a rotation and translation expressed mathematically as a transformation matrix. These transforms can be inserted into MRML files as Matrix nodes. Each matrix affects volumes and models that appear below it in the MRML file. Multiple matrices can be concatenated together.

A Transform is not a node with attributes, but a construct for building MRML files. A Transform encapsulates the Matrix nodes inside it, such that they are invisible to nodes outside the Transform.

Color nodes define colors by describing not only the actual color value, but also its name and a list of label values. One attribute of model nodes is the name of the associated color. When Slicer displays label maps, it colors each voxel by looking up the color associated with that label value. Thus, when label maps appear on reformatted slices, their colors automatically match the corresponding surface models in the 3D view.

Option nodes allow browser-specific information to be stored in a MRML file. For example, Slicer uses Option nodes to store the user's 3D viewpoint information, since there currently is no View node in MRML 2.0.