Outlining of Brain Structures

The result of the brain structure transformation is shown on the BRAIN SEGMENTS page. It shows the transformed atlas together with the averaged functional PET.

Result Space

There are two options for evaluating the PET image which can be configured with the Result space box. The information shown on the page is updated as soon as the configuration is changed. It shows the PET image in the selected result space together with the brain structures.

The Result space options are:

1. Atlas: With this setting the PET image is transformed to the MNI space and the original structures of the N30R83 atlas can be applied to it.
   
2. Input, PET Space: With this setting the N30R83 structures are transformed to the PET space.
   
   Note that due to the relatively large size of the PET pixels in this example the structure outlines look rugged. To avoid this effect the PET image should be reconstructed with small pixel sizes.

Intersection of N30R83 Structures with Gray Matter

The original N30R83 structures cover the whole brain. Users can take advantage of a population average gray matter probability map and restrict the structures to pixels with a high probability belonging to gray matter. This operation is controlled by the elements in the masking area.

The slider allows defining the lower threshold which is applied to the probability map for creating the mask. The higher the probability threshold, the thinner the cortical structures become. The illustration below shows masking in the PET space at three increasing probability thresholds.

Note that the central structures were not affected by masking in the example above, because the box Mask basal nuclei was not enabled. If this option is enabled, the central structures are also shrinking. However, because of the low probability levels in that area, the reduction may become too severe. Therefore, masking of the basal nuclei will usually be disabled.

Structure Outlining

Once the result space and gray matter masking have been specified, the brain structures are fully defined and can be outlined to create contour volumes-of-interest. This process is started with the Outline action button.