I checked the recon-all script. It looks like unknown-args.txt contains all input arguments not in recon-config.yaml. It doesn’t mean those flags are not recognized.

 

Examining attached recon-all.log, it contains only one recon all submission. ‘-autorecon2-wm’ is used after editing wm volume after running ‘-autorecon2’. It needs to be run on top of earlier recon-all output.

 

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

 

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 7, 2023 7:49 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Running autorecon2-wm after wm edits

 

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Hi, thank you for replying.

 

There is no error on recon-all, apparently. please find attached the log file.

 

 

Thank you very much again.


Fernanda Hansen P. de Moraes

 

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

 

 

On Mon, Nov 6, 2023 at 2:09 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

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

 

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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?

 

Thank you very much in advance,

Fernanda Hansen P. de Moraes

 

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

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