Development of a tool for automatic segmentation of the cerebellum in MR images of children

The human cerebellar cortex is a highly foliated structure that supports both motor and complex cognitive functions in humans. Magnetic Resonance Imaging (MRI) is commonly used to explore structural alterations in patients with psychiatric and neurological diseases. The ability to detect regional structural differences in cerebellar lobules may provide valuable insights into disease biology, progression and response to treatment, but has been hampered by the lack of appropriate tools for performing automated structural cerebellar segmentation and morphometry. In this thesis, time intensive manual tracings by an expert neuroanatomist of 16 cerebellar regions on high-resolution T1-weighted MR images of 18 children aged 9-13 years were used to generate the Cape Town Pediatric Cerebellar Atlas (CAPCA18) in the age-appropriate National Institute of Health Pediatric Database (NIHPD) asymmetric template space. An automated pipeline was developed to process the MR images and generate lobule-wise segmentations, as well as a measure of the uncertainty of the label assignments. Validation in an independent group of children with ages similar to those of the children used in the construction of the atlas, yielded spatial overlaps with manual segmentations greater than 70% in all lobules, except lobules VIIb and X. Average spatial overlap of the whole cerebellar cortex was 86%, compared to 78% using the alternative Spatially Unbiased Infra-tentorial Template (SUIT), which was developed using adult images