Cerebellar isolation, parcellation, and conformal surface mapping

The topographic organization of motor, sensory and cognitive functions in the human cerebellum is poorly understood, and, owing to its anatomical organization, most of the folial surface is hidden from view. In order to facilitate surface-based analysis of functional activation within the cerebellar cortex, we constructed a “pipeline” for extracting, labelling and conformally mapping the cortical surface. Methods The pipeline utilizes a cerebellar template volume isolated from a high-resolution, high-contrast-to-noise Tl-weighted MRI brain volume [l] and parcellated according to Schmahmann et al. [2]. See Figure 1. Isolation of a cerebellar subvolume was landmark driven; the posterior commissure, obex and apex of the fourth ventricle defined a standard orientation [3]. A template-to-source warp facilitiated removal of the cerebrum. The brainstem was then removed from the cerebellum by a computerized cut-plane that stepped though the volume until it reached the lingula, sparing wrap-around cerebellar tissue. The final perimeter of the cut surface served as the boundary for flatmapping to a plane. Parcellation was effected by warping the template cerebellum to a source subvolume, applying the resulting transform to the template parcellation, and editing the labels to correct errors due to poorly resolved fissures and/or variable fissuration. Marching Cubes was used to extract an isovalue surface from individual cerebellar subvolumes; however, these surfaces commonly exhibited undesirable Figure 1. Cerebellar template with fissure