Freesurfer fsaverge is in MNI305 space. Try

mri_label2label --srcsubject <> --srclabel <.label> --trgsubject fsaverage --trglabel <fsaverage.label> --hemi rh --regmethod surface

These are some helpful links

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yang Yifan
Sent: Friday, February 14, 2025 5:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer coordinates

        External Email - Use Caution        

Hi Yujing,

Many thanks for your reply! The email didn’t come through to my inbox and I just found it in the online archive.

Regarding the coordinate conversion, I had a look at the link but didn’t find MNI 305 related information. It would be very helpful if you could be more specific about the command to run. Thanks!

Best wishes,

Vivian

From: Yang Yifan <vivian_yyf@outlook.com>
Date: Wednesday, 5 February 2025 at 13:03
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: FreeSurfer coordinates

Hi FreeSurfer Developers,

I’m conducting manual ROI labelling on each participant’s inflated surface (after going through the ‘recon-all’ command), but I wasn’t very sure if the coordinates in the corresponding .label files are in MNI 305 space. At the top of the plain text files it’s showing ‘vox2ras=TkReg’.

If they are not in MNI 305, could you please explain a bit about what coordinate system is used here and how I could convert that into MNI 305?

Thank you very much!

Best wishes,

Vivian