If the desired workflow has proven to be reproducible (i.e. equivalent VOIs can be generated with a stable set of configuration parameters), there is no need to interactively step through the different stages. Rather, the data can be loaded, all processing steps performed unattended, and then the results inspected and saved. To do so please proceed as follows:
1.Make sure the parameters on the all stages are set appropriately. This can also be ensured by loading a specific protocol file.
2.Load the PET image, and define the crop box if necessary.
3.If there is an MR as well, load the image, and define the crop box.
4.Activate the "Run All" button 
from the lateral taskbar. All steps up to the VOI outlining will be performed.
5.Inspect the relevant intermediate results such as MR segmentation, spatial normalization, rigid matching to ensure the resulting VOIs are meaningful.
6.Save the VOIs and calculate the statistics.
7.Save a protocol file.