Mapping internal brainstem structures using T1 and T2 weighted 3T images.

Background: Many neurodegenerative diseases affect the brainstem and often do so in an early stage. The overall goal of this project was (a) to develop a method to segment internal brainstem structures from T1 and T2 weighted sequences by taking advantage of the superior myelin contrast of the T1/T2 ratio image (RATIO) and (b) to test if this approach provides biological meaningful information by investigating the effects of aging on different brainstem gray matter structures. Methods: 675 T1 and T2 weighted images were obtained from the Human Connectome Project Aging. The intensities of the T1 and T2 images were re-scaled and RATIO images calculated. The brainstem was isolated and k-means clustering used to identify five intensity clusters. Non-linear diffeomorphic mapping was used to warp the five intensity clusters in subject space into a common space to generate probabilistic group averages/priors that were used to inform the final probabilistic segmentations at the single subject level. The five clusters corresponded to five brainstem tissue types (two gray matters, two mixed gray/white, and 1 csf/tissue partial volume). Results: These cluster maps were used to calculate Jacobian determinant maps and the mean Jacobians of 48 brainstem gray matter structures extracted. Significant linear or quadratic age effects were found for all but five structures. Conclusions: These findings suggest that it is possible to obtain a biologically meaningful segmentation of internal brainstem structures from T1 and T2 weighted sequences using a fully automated segmentation procedure.