whereami atlas ith most number of names (especially in thalamus)

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1

Hi,

I want to map certain x y z values to a brain region. Most of them are in Thalamus. So I would like to use an atlas that can differentiate between them and not give Thalamus for all of them. Can you recommend which one I should use? I am using the whereami function.

I tried the HCP atlas, but it had no match for a lot of voxels in the thalamus.

Thanks,
Prateek Sasan

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There are several atlases available with subthalamic structures.

Keuken atlas with 3 age ranges (included here with our modal smoothing optionally):
https://afni.nimh.nih.gov/pub/dist/atlases/keuken/
https://www.ncbi.nlm.nih.gov/pubmed/24650599

Pauli atlas
https://www.nature.com/articles/sdata201863
https://neurovault.org/collections/3145/

More complicated ways -
THOMAS atlas (must install git-lfs package for download and then several packages to generate parcellations)
https://github.com/thalamicseg/thomas_new

A version for Parkinson Disease subjects:
https://www.nitrc.org/projects/atag_pd

Vinod Kumar made this available to me (2mm voxel size):
https://www.sciencedirect.com/science/article/pii/S1053811917305955?via%3Dihub
https://github.com/vinkrishna/Thalamic-Functional-Atlas (I have started to put a simple form of the atlas if anyone would like to try)

Thalamus (available with FreeSurfer)
https://www.sciencedirect.com/science/article/pii/S1053811918307109?via%3Dihub
https://surfer.nmr.mgh.harvard.edu/fswiki/ThalamicNuclei

MAPBOT
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474778/