General segmentation of the human brain involves defining anatomical structures by "primary" borders, corresponding to signal intensity transitions at brain-CSF or gray-white matter interfaces, or by "secondary" borders, which are knowledge-based anatomic subdivisions within a gray or white matter field that are not defined unambiguously by signal intensity transitions [Filipek et al. 1994].
The following is a list of neuroanatomical structures or the boundaries that contain them that are segmented at the MGH CMA: Cerebral Exterior and White matter, Cerebellum Exterior & White Matter, Caudate, Hippo-Amygdala, Insula, Operculum, Pallidum, Putamen, Thalamus, Brain Stem, Ventricle (lateral, 3rd and 4th), Globus Pallidus, and Cortical Parcellations.
The completely manual method for segmentation would be to draw the desired borders directly onto the raw image. This would take too much time and be prone to errors, especially due to fatigue.
Iso-intensity contours can be used to outline structures. The user can pick an intensity by pointing to a pixel that seems to be on the border of a structure or the intensity can be chose by hand or by using a histogram.