Hi Andy,

Based on my understanding from GIFTI specification, your .gii are functional files. I’m not sure if mris_convert supports it.

I’m curious how you got the .gii files.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Andy Kim
Sent: Thursday, January 5, 2023 3:05 AM
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] How to convert surface-based atlas to annotation?

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Dear FreeSurfer Developers,

To analyze functional connectivity, I first got Shen 268 surface-based atlas from Neurovault. Now I want to extract average time series data from my subjects based on the atlas but I have no idea how to make annotation.

All I have is .gii left and right hemispheres atlas files. When I tried mris_convert, it says: DA[0] has coordsys with intent NIFTI_INTENT_NONE (should be NIFTI_INTENT_POINTSET).

Could you please give me any tips for making an annot file from surface-based atlas? Thank you in advance.

Kind Regards,

Andy (Junghyun) Kim