The PMOD VOI interface provides a facility easily create the infrastructure of an atlas from a VOI definition. Once a VOI set has been outlined which should become the regions of a new atlas, the 
button on the Group panel can be activated. It opens the dialog window illustrated below which requests the user to specify an Atlas name, the location Path of the structure (proposing the default atlas location), and optionally template images which will be available for the spatial normalization. They typically correspond to different modalities or different image contrasts (MR pulse sequence, PET tracer), always with the anatomy corresponding to the region definition.
Note that the label list text file which is created needs to be edited in order to implement a tree structure, unless the VOIs are just modified outlines of an existing atlas.