Working Group 3 
Brainstem Analyses (Best practices & methods development in segmentation & data processing)

Key objectives of the Working Group
a) establish best practice pipelines for automatic brainstem segmentations in anatomical brainstem data and for analysing functional brainstem data; integrate these into standard analyses toolboxes,
b) establish a research platform for extending available automatic segmentations, improving denoising approaches and integrating additional physiological measurements,
c) establish multivariate genetic architectures of brainstem structures based on more precise segmentations.

Current Projects

Automatic segmentation of brainstem structures:
review and testing of algorithms and software for automatic/semi-automatic segmentation

MRI co-registration focused on the brainstem:
review and testing of best solutions for co-registration of multiple sequences and establishing best practices for quality control

fMRI noise removal, focus on the brainstem:
review of movement and physiological noise correction solutions for the brainstem, HRF estimation, acquisition planning, and quality assessment

Methods for fMRI connectivity that best capture brainstem function and are biologically plausible:
review of static and dynamic functional connectivity methods, traditionally used in the cortex, and how these can be used in the brainstem to recover biologically plausible mechanisms