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 anatomical 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, FDG: With this setting the atlas structures are transformed to the anatomical PET space.
   
3. Input, PET: With this setting the atlas structures are transformed to the functional 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 Atlas Structures with Gray Matter

For atlases with population tissue probability maps users can take advantage of restricting the structures to pixels with a high probability belonging to gray matter.

The Mask by GM slider allows defining the lower threshold which is applied to the GM 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 GM probability thresholds (CSF box disabled and WM slider set to 1).

Note that the central structures were not affected by masking in the example above, because the box Mask non-cortical regions 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.

The white matter tissue probability map can be thresholded at a certain level for generating a white matter VOI.

With the CSF box enabled, the CSF threshold slider allows trimming further the GM mask: the higher the threshold the broader the cortical structures become.The illustration below shows masking in the PET space at three decreasing CSF probability thresholds while the GM probability threshold is set to 0.5 and WM probability is set to the value of 1.

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.