Using VOI Atlas Files

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Using VOI Atlas Files

A VOI atlas is an image file which contains numeric label information for the different anatomic structures as the image information. This VOI information can be loaded into PMOD and used for statistics. The atlas VOI approach has the advantage that the structures can be arbitrarily complex, and that the results of external segmentation programs can easily be used within PMOD. The disadvantage is that the VOI definition cannot be modified. However, in PMOD it is simple to convert atlas VOIs into contour VOIs.

Brain atlas images are representative images of the (human, rat, etc.) brain imaged with a certain modality (PET, SPECT, T1 MR, T2 MR, etc.) showing a normal brain. Usually, the images of many normal subjects are brought into alignment and are then averaged. This results in somewhat blurry template images which show the characteristic pattern of the brain in the particular modality. The template images are used as a basis for the standard analysis of individual images. First, the images are spatially normalized (elastic warping) to the template, and then a set of standard VOIs is applied to the normalized images to obtain regional statistics. Typically, the VOIs in the atlas space are universally applicable, ulike contour VOIs which are program-specific.

The PMOD software includes several human, primate, pig, rat, and mouse atlases with corresponding normalization templates. For using the atlas VOIs a user should first spatially normalize the individual brain images using the corresponding normalization template.