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Dear all,

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

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


On Tue, Nov 7, 2023 at 10:39 AM Fernanda Hansen P. de Moraes <fernandahmoraes@gmail.com> wrote:

Hi, thank you!

 

I’ve made so many tests on thissubject that I deleted the previous recon-all history, it was super long and repetitive. I did run on top of the previous complete recon-all, and then after the wm editing.

 

If you prefer, I can do it all again and send to you.

 

Best,

Fernanda Hansen P. de Moraes

 

fernandamoraes@if.ufrj.br

Física Médica e Doutora em Ciências Médicas

metaBIO - IF UFRJ e Brain Connectivity Unit - Instituto D'Or de Pesquisa e Ensino

 

De: Huang, Yujing
Enviado:Tuesday, November 7, 2023 10:27 AM
Para: Freesurfer support list
Assunto: Re: [Freesurfer] Running autorecon2-wm after wm edits

 

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.

 

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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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