The Brainstem Navigator Toolkit v1.0: An Atlas of Brainstem Nuclei and Coregistration Tutorial in Younger Adults

Motivation: Brainstem and diencephalic nuclei are small (e.g., volume range: 10-300 mm³), making precise coregistration of atlas labels essential to avoid displacement in native space images. Goal(s): To develop a comprehensive suite of coregistration routines (scripts and tutorial) capable of accurately aligning brainstem nuclei atlas labels to 3Tesla/7Tesla structural, diffusion, and functional MRI data. Approach: We created an in-depth tutorial to guide users in applying the Brainstem Navigator atlas labels automatically and precisely to MRI data of individual subjects (or vice-versa). Results: The Brainstem Navigator toolkit, including these coregistration routines, is now publicly available on NITRC as version 1.0. Impact: The Brainstem Navigator toolkit v1.0 includes a probabilistic atlas of 31 brainstem nuclei and comprehensive coregistration routines for 3Tesla/7Tesla MRI. This toolkit facilitates precise structural, diffusion, and functional MRI coregistration, significantly advancing research into brainstem-related disorders and neuroscientific inquiries.