A method and a system for determining an orthodontic treatment for a subject are provided. The method comprises: acquiring a 3D representation of the crown portion of a given tooth; generating a 3D representation of the root portion of the given tooth by: obtaining a location of a root apex of the 3D representation of the root portion; dissecting horizontally the 3D representation of the crown portion to generate a closed curve around the 3D representation of the crown portion, segmenting the closed curve into a plurality of sub-curves; for each one of the plurality of sub-curves, generating a segment of the 3D representation of the root portion; merging the 3D representation of the crown portion with the 3D representation of the root portion, thereby generating the 3D representation of the given tooth; and determining, based on the 3D representation of the given tooth, the orthodontic treatment for the subject.