[Atlas] Brainnetome subcortical regions

[araikes]

The Brainnetome atlas is already implemented in ggseg but also has subcortical labels (IDs 211-246). Being that you have the Brainnetome data already in fsaverage5 space, I would assume this would be fairly easy to implement (barring the other issues with subcortical space generation). I would attempt but I'm working on our HPC and missing some dependencies.

Brainnetome atlas freesurfer ZIP file: https://pan.cstcloud.cn/s/DQov5gaAR4s
LUT: BN_Atlas_246_LUT.txt
MGZ file: 100307/mri/BN_Atlas_subcortex.mgz

[araikes]

@Athanasiamo Not trying to be pushy but I know sometimes an @ helps for visibility.

[drmowinckels]

Hey.

We actually only have the cortical version, no subcorticals, so its not readily available. We also have not landed on exactly how to "deal" will full-brain atlases (currently, all atlases we have are either subcrotical or cortical), so I need to sit down and make some meaningful decisions on how it will work. So its going to take some time to get done, and I cant promise when :/

[araikes]

Understood.

Could you share whatever scripting was used to transition the FS data provided for Brainnetome's cortical ROIs? With that, in theory, I could try subsetting to just use the subcortical ROIs but then at least it would be in somewhat the same "space."

I'm working on a Singularity image that would have all of the requisite softwares for doing this and this would be a good test if I can replicate how you generated the Brainnetome 3d-to-2d process here.