Did you get an error when you submit ‘recon-all’? Can you send recon-all.log?
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fernanda Hansen P. de Moraes Sent: Monday, November 6, 2023 11:33 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Running autorecon2-wm after wm edits
External Email - Use Caution 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?
Thank you very much in advance, Fernanda Hansen P. de Moraes
fernandahmoraes@gmail.commailto:fernandahmoraes@gmail.com Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino