Your ‘recon-all -autorecon2-wm -autorecon3’ finished without errors. ‘unknown-args.txt’ is created to filter out arguments not in recon-config.yaml. It doesn’t mean those flags are not recognized.

I don’t know why new surfaces are not created after your editing of wm.mgz. Can you re-send your corrections so someone else can help you?

At the meantime, here is the Freesurfer troubleshooting tutorial page. Hope it can be helpful - https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fernanda Hansen P. de Moraes
Sent: Tuesday, November 21, 2023 7:15 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Running autorecon2-wm after wm edits makes no difference in final surface

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Dear FreeSurfer experts,

I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3 nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. 

How can I create new surfaces and overcome this issue?

Here attached is the complete recon-all log file from the beginning, including all steps attempted. I would be very glad if you could help me overcoming this error to include as much subjects as possible in my project.

Best regards,

Fernanda Hansen P. de Moraes

fernandahmoraes@gmail.com

Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ)
Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino