Determination of PET functional volume in an infected rabbit. CT and PET images are acquired from the scanner (step 1). Affine registration of images is conducted to achieve a one-to-one voxel correspondence between CT and PET images (except when the images are in registration due to simultaneous acquisition) (step 2). Lung segmentation is achieved using an interactive region growing (IRG) algorithm (step 3). The segmented lung is used as a binary mask in whole body PET imaging in order to bound functional uptake only pertaining to the lungs (PET M) (step 4). Significant uptake regions of PET M are delineated using an adaptive thresholding method (step 5). Resulting segmentation of uptake regions (PET S) and segmented regions with PET intensity values (PET T) are used for quantification and monitoring of the disease extent.