2D Subcortical Structures

[OliJimbo]

Hello!

I spent some (in hindsight too much) time last week trying to create an atlas for the combined cortical and subcortical atlas pack from PennLINC:

PennLINC AtlasPack

The cortical pipeline worked fine, but it took an embarrassing amount of time to realise that the subcortical structures are not volumetric and so the subcortical pipeline fails.

By labelling the subcortical structures as cortical in the type column it is possible to wrangle some sort of visulisation:

Full brain:

Subcortical only:

If this is more than an edge-case/ general misunderstanding on my part, then is there a way to access axial, sagittal, and coronal views these structures? Or a different way to handle this type of image?

Many thanks,

Oli

[drmowinckels]

hi! Thanks for this! I'm actively working on a version that should improve this. I'll let you know once they land in the repo so yuo can try that.

But I'd like to point out a couple things also:

• full Schaefer 2018 parcellations done: https://ggsegverse.github.io/ggsegSchaefer/
• Diedrichsen SUIT cerebellar flatmap: https://ggsegverse.github.io/ggsegSUIT/

[drmowinckels]

I need to dig into the atlas repo you point to though, to understand how the subcortical regions are stored if not volumetric. Very happy to do so though, as having example data is the best way to progress. Might take me a minute though.

[OliJimbo]

Hi - thanks for looking into this! Looking forward to testing the new version - please let me know if I can help at all in the meantime!