An automated treatment planning system comprising: a planning image memory configured to store a volume diagnostic image; a user interface device configured for a user to input data defining a plurality of regions of interest within the volume diagnostic image; a ROI mapper having a processor configured to: receive the volume diagnostic image and plurality of user-defined regions of interest indicated within the volume diagnostic image; map the plurality of regions of interest of the volume diagnostic image to anatomical structures using a body atlas; wherein said mapping includes: mapping the plurality of regions of interest to the body atlas to determine anatomical locations within the plurality of regions of interest; and mapping each region of interest of the plurality of regions of interest to the body atlas to select correct corresponding anatomical structures; and wherein said selecting includes: selecting the correct corresponding anatomical structures by calculating a similarity metric score between each region of interest of the plurality of regions of interest and each anatomical structure of the body atlas; and wherein the automated treatment planning system further comprises: a planning module configured to generate a treatment plan using the mapped plurality of regions of interest. a planning image memory configured to store a volume diagnostic image; a user interface device configured for a user to input data defining a plurality of regions of interest within the volume diagnostic image; a ROI mapper having a processor configured to: receive the volume diagnostic image and plurality of user-defined regions of interest indicated within the volume diagnostic image; map the plurality of regions of interest of the volume diagnostic image to anatomical structures using a body atlas; wherein said mapping includes: mapping the plurality of regions of interest to the body atlas to determine anatomical locations within the plurality of regions of interest; and mapping each region of interest of the plurality of regions of interest to the body atlas to select correct corresponding anatomical structures; and wherein said selecting includes: receive the volume diagnostic image and plurality of user-defined regions of interest indicated within the volume diagnostic image; map the plurality of regions of interest of the volume diagnostic image to anatomical structures using a body atlas; wherein said mapping includes: mapping the plurality of regions of interest to the body atlas to determine anatomical locations within the plurality of regions of interest; and mapping each region of interest of the plurality of regions of interest to the body atlas to select correct corresponding anatomical structures; and wherein said selecting includes: mapping the plurality of regions of interest to the body atlas to determine anatomical locations within the plurality of regions of interest; and mapping each region of interest of the plurality of regions of interest to the body atlas to select correct corresponding anatomical structures; and wherein said selecting includes: selecting the correct corresponding anatomical structures by calculating a similarity metric score between each region of interest of the plurality of regions of interest and each anatomical structure of the body atlas; and wherein the automated treatment planning system further comprises: a planning module configured to generate a treatment plan using the mapped plurality of regions of interest. a planning module configured to generate a treatment plan using the mapped plurality of regions of interest.