This paper describes a novel approach to in-vivo measurement of brain surface folding in clinically acquired neonatal MR image data, which allows evaluation of surface curvature within subregions of the cortex. This paper addresses two aspects of this problem. Firstly: normalization of folding measures to provide area-independent evaluation of surface folding over arbitrary subregions of the cortex. Secondly: automated parcellation of the cortex at a particular developmental stage, based on an approximate spatial normalization of previously developed anatomical boundaries. The method was applied to seven premature infants (age 28-37 weeks) from which gray matter and gray-white matter interface surfaces were extracted. Experimental results show that previous folding measures are sensitive to the size of the surface of analysis, and that the area independent measures proposed here provide significant improvements. Such a system provides a tool to allow the study of structural development in the neonatal brain within specific functional subregions, which may be critical in identifying later neurological impairment.