Thanks for the feedback, Noam. Despite living in the same real-world coordinates (RAS), the different volumes in recon-all-clinical have indeed different headers, which may lead to problems if your downstream method does not work in RAS. We will look into producing volumes that are oriented like FS, instead of diagonal / positive vox2ras ;-) for the time being, reorienting the way you did should fix the issue 😊 Best wishes, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com From: Noam Peled noam@findneuro.com Date: Wednesday, March 25, 2026 at 11:22 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all-clinical (FS 8.1): MEG/EEG coregistration issue - inverted BEM normals from norm.mgz geometry
External Email - Use Caution Dear FreeSurfer team,
I'm writing to report a coordinate-frame issue when using recon-all-clinical (FreeSurfer 8.1) with downstream MEG/EEG coregistration and BEM workflows (MNE-Python), along with findings from testing across multiple subjects.
I have a MEG processing pipeline that has worked reliably using standard recon-all (FreeSurfer 7.3). After switching to recon-all-clinical (FS 8.1) on the same data, the EEG/MEG sensors appear completely displaced from the scalp surface during coregistration.
I tested the watershed BEM generation across 8 subjects using recon-all-clinical output and found the following: - Using norm.mgz (the SynthSR-derived volume from recon-all-clinical) for watershed BEM consistently produces surfaces with inverted normals. The norm.mgz has a non-standard geometry compared to what the standard pipeline produces. - Using a separately conformed T1 (via mri_convert --conform on the original input) for watershed BEM produces correct topology and passes all validation checks. - The cortical surfaces from recon-all-clinical live in norm.mgz space. However, when using the conformed T1 watershed for BEM, 7 out of 8 subjects showed 99-100% source retention, indicating the coordinate frames are close enough for practical use. - Simply symlinking T1.mgz to norm.mgz fixes the coordinate alignment but introduces the inverted normals problem, so this is not a viable workaround.
1. Is this a known issue? 2. Is there a more principled approach than the workaround above for reconciling the coordinate frames between the clinical pipeline surfaces and the conformed BEM surfaces?
Thanks! Noam Peled