Dear Freesurfer community,

I am using the freesurfer version through a singularity container (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://hub.docker.com/r/freesurfer/freesurfer) in a HPC cluster. It all ent well until I extracted the subcortical regions, where I see that for all of my subjects the values of Thalamus-proper are 0. When I look further into it, I see that my FreeSurferColorLUT.txt file only includes Thalamus but not Thalamus-proper.

I found this thread which mentions that the thalamus-proper was removed from recent FreeSurfer versions: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://community.mrtrix.org/t/thalamus-proper-removed-from-freesurfercolorlut-txt/3721/2

Unfortunately, when I try to look for information online on whether they are exactly the same or whether they differ, I only found the FreeSurfer wiki page about the FreeSurferColorLUT(i.e., look up table) which includes this note: “* Thalamus-Proper is the correct segmentation for the Thalamus.” But this is a page from 2015 so might not be up to date anymore. In this thread from 2017it was also discussed that the thalamus-proper is the correct one but it is also stated that name should be changed, so maybe they have done this now.

Basically - do I need to re-run the recon-all with a different freesurfer version to extract Thalamus-proper or has this been replaced by Thalamus now?

Thanks!!