That is probably the best way. Another way would be to run the seg on a set of subjects, run fs-synthmorph-reg on those subjects (non-lin reg to mni152), then map the individuals thal segs to mni, then combine them together. Not sure which one is base. Certainly just running the thal seg on the mni152 is easiest:)

On 1/9/2025 5:51 AM, Melissa Thalhammer wrote:

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Dear Freesurfer experts,

is there a recent recommendation on how to get the thalamic nuclei segmentation into MNI space? I have tried the AAL3 atlas recommended in this previous mail (*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg66907.html https://secure-web.cisco.com/1H8Dmv_kif-oWVc1HwepCKJBjRkpbig-MqiMJUrqPMzzu8xkoQDLTOelzb5LPLsVNs7vay3fJYN5oD8pT-YhFkoLd1lrlJzxcFvdxPwwgG_uwqaz8T_hMp5rLXYkvvLYcDLrLFdiiQGyu4gkdfdLmzR7Y5dV6QSJYMr8v65hL0bQm2MWbHIY2li-A-AD_drjKXfH4LLijMflbcU9e1xm4j41l9UvRtQ0Nei8v2KPMmGzXdJZGCNdR2jbkDUzQVbSTd1FVeQ_3vyhg5mg91ma9Gbb1bcEnfjI71g6IAnthCifMoI4qN_RS2gEZVbYOafaBAK8-8Q0z4-_k_k0H9SEjWQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66907.html) but it contains only 15 instead of 26 nuclei per hemisphere.

I have run recon-all and the ThalamicNuclei pipeline on the MNI-152 subject, which looks decent but wanted to make sure there is no better way?

Thank you!

Best,

Melissa Thalhammer

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