Brainstem visualization

[RaviBot]

Hello!

First off, thank you for developing this incredibly useful package. I'm really excited to use it!

I was wondering if there are plans to add brainstem visualization support for the aseg segmentation? Currently, the FreeSurfer aseg includes brainstem labels, but these don't appear to be rendered in the subcortical plots.

Thank you!
Ravi

[anniegbryant]

Hi Ravi, thank you for your interest in this package! I hope you find it useful 😊

Adding the brainstem is definitely on the "vision board" for this project, as you have suggested. The aseg segmentation in FreeSurfer does indeed include the brainstem, albeit as one contiguous 'brain stem' region. As an alternative, I would love to incorporate the Brainstem Navigator atlas by Marta Biancardi and colleagues at the Martinos Center. For example, this atlas was recently used by Justine Hansen and colleagues in their 2024 Nat Neuro paper "Integrating brainstem and cortical functional architectures" in a way that would be great to incorporate here (excerpt from Figure 1):

They used two-dimensional vector representations in the form of circles; this could be adapted here with polygons that take on the actual structural architecture of the brainstem nuclei, perhaps (excerpt from Figure 2):

For now, this remains on the to-do list for me. In the meantime, if you (or any other interested user!) happen to want to create this two-dimensional vector atlas yourself and contribute it to this package through a PR, this guide would walk you through the process. Will keep you posted on how I'm going with this for sure!

--Annie