The coordinates reported in .label are in Freesurfer tkregister RAS space. You can use mri_label2label to map them to MNI 305 space https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yang Yifan
Sent: Wednesday, February 5, 2025 8:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FreeSurfer coordinates

        External Email - Use Caution        

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