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Using Mask Files

Standard templates can only be created and applied if it is possible to reliably map the organ of interest to a standard anatomy. Otherwise, masks created by some sort of thresholding or segmentation are often useful in individual analyses. Such binary masks can also be used for statistics calculations in PMOD.

To load a mask for VOI analysis first select the Template tab, and then Mask. A loading button becomes active and allows to loading a binary file. If the data in the file is not binary a dialog window appears

for defining the Binarization Level [%] and the names for the mask and the background.

Binary VOI Mask

A mask template only contains two VOIs, the Mask pixels In, and all background pixels Out. Most of the times only the In region will provide reasonable values, but the Out region can also be evaluated on demand.

The same operations are supported as for the template VOIs: statistics can be calculated in the mask VOIs, contour VOIs can be defined in parallel and masked, and mask VOIs can be converted do contour VOIs by the Outline selected button. A notable application of masking is the restriction of contour VOIs to the gray matter pixels which can easily be achieved if a gray matter segment is available from a matched MRI data set. An example of restricting a contour VOI shown on a PET to gray matter is illustrated below.