Thalamus-Proper removed from FreeSurferColorLUT.txt

Hello MRTrix developers !

I’ve installed the newly released Freesurfer v7.1.0, and it looks like there’s no “Left-Thalamus-Proper” and “Right-Thalamus-Proper” in the FreeSurferColorLUT.txt anymore.

I ran labelconvert in MRTrix 3.0.0, with default values, FreeSurferColorLUT.txt as input LUT, fs_default.txt as output LUT and freesurfer’s aparc+aseg volume image. This raises a warning in the tck2connectome : “The following nodes are missing from the parcellation image: 36, 43 (This may indicate poor parcellation image preparation, use of incorrect of incomplete LUT file(s) in labelconvert, or very poor registration”.

I guess the easiest is to modify the fs_default.txt file to include the “Left-Thalamus” and “Right-Thalamus” strings.

Just wanted to let you know, other people might bump into this as the new version of FreeSurfer gets downloaded…

Thanks for this great tool !
Best regards,
David Romascano

Might also be linked to the issue mentioned here : [labelconvert] bilateral thalamus gone (ie computers with different versions of freesurfer ?)

Welcome David and thanks for the report!

Yes, it looks like the names were actually changed in the FreeSurfer development branch but nobody ever encountered / reported it. Thankfully I put a big fat warning message there so that hopefully people don’t continue with their processing with the thalami stripped.

Short-term for yourself and anybody else who encounters this, modifying the lookup table file locally, either editing the two existing rows to read e.g. “Left-Thalamus” instead of “Left-Thalamus-Proper” or inserting new rows containing the revised names but the same indices and colours, will allow you to continue with processing.

Unfortunately for me, because I need to ensure that this software is compatible with all versions of third-party softwares, I need to deal with some more esoteric issues, as described over on GitHub.

Thanks again