From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, May 16, 2021 at 9:59 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulcus represented in wm.mgz filled in lh.white

It is possible. Try running defect-seg to see where the defects are. Run it with --help to get more info

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Hi freesurfer experts,

 

I have some cases where sulci near the occipital pole are reflected in the wm.mgz, but are filled in the white surface.

Attached is a capture showing the sulcus near the image center, where the crosshairs are located.

 

Might the topology fixer have filled in this sulcus, to reduce topological errors?

This was generated using recon-all -all, freesurfer 6.0, ubuntu 18.04.3.

 

Thanks,

 

Donna

 

 

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