External Email - Use Caution

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

fernandahmoraes@gmail.com 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

•    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.com

Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1N7zJ9OnjMC__TyipUAwMxskUjlcnWYYSdPBZ4B_n6SAic_... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1KwxzXfk1qtI-kzHoMVtwJPU4Q0KICStiWRDqtl7KUQRJL6... < https://secure-web.cisco.com/1KwxzXfk1qtI-kzHoMVtwJPU4Q0KICStiWRDqtl7KUQRJL6... .

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

External Email - Use Caution 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

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

On Mon, Nov 6, 2023 at 2:09 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1N7zJ9OnjMC__TyipUAwMxskUjlcnWYYSdPBZ4B_n6SAic_JzAthf4UBgffDBddVB3tK2aVeZ7a5K-4NFZUh5pvo9PEZEDMFCETNDkpCkRTgndE5rZOiVUrauxy4xEa3w_cmvsz6Uqaoxh0odoUjhzI_gDF1AmHoxVNvYJWZTsHbnJ4_Rcd7wOCj3PbAXqjdP-RHWAcONknPtPy9BjYopENlclLemD2seyZJVJZWPVC_OzR8glxTu8v1v7zNnBkNT-OnOv0UT8Bn-z1CfYYXzKFCqk17b4fB-hJlrO8PwQDZC1PLS_qOXR7iHxM8GY6ZL/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KwxzXfk1qtI-kzHoMVtwJPU4Q0KICStiWRDqtl7KUQRJL66sPCq0eF3Z0cOeAaikYEpDTtleSRvZ73nDCn-uaKTAAkxo1jgn_SBnvL99kW3TwByZUEQxtchZQcxCcb5WnDRFk80t18Z6YBSoqATlZpROJUG_4XCULwNS-ttBm72wf_9gxklYIVCUQnF70FkcNAxf3BfkBbaF6w0kBvDD1jEFnlE5VLQkRvvYSsC4CLCz1OH4o-sgZijJ40ezsfERE35ZGMDN_pHdnLzJ629_buf45RGSPnZCVr-TJ-Y9N_vbM1GbdcuwDSB6hNNgCB8y/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1KwxzXfk1qtI-kzHoMVtwJPU4Q0KICStiWRDqtl7KUQRJL66sPCq0eF3Z0cOeAaikYEpDTtleSRvZ73nDCn-uaKTAAkxo1jgn_SBnvL99kW3TwByZUEQxtchZQcxCcb5WnDRFk80t18Z6YBSoqATlZpROJUG_4XCULwNS-ttBm72wf_9gxklYIVCUQnF70FkcNAxf3BfkBbaF6w0kBvDD1jEFnlE5VLQkRvvYSsC4CLCz1OH4o-sgZijJ40ezsfERE35ZGMDN_pHdnLzJ629_buf45RGSPnZCVr-TJ-Y9N_vbM1GbdcuwDSB6hNNgCB8y/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .

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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

fernandahmoraes@gmail.com 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 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 YHUANG43@mgh.harvard.edu *Enviado:*Tuesday, November 7, 2023 10:27 AM *Para: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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.

https://secure-web.cisco.com/1x7bqrC7UrIlJmLhjcVbzUgK_CedBVVGszxqmoROGhOn5kx...

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

•    External Email - Use Caution        *
  
  

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

fernandahmoraes@gmail.com

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

•    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.com

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/11p8uU-DWrOCl1TxVUMYTzg7LQGKBtrQKGKhaIQLfsmQzLe... https://secure-web.cisco.com/1N7zJ9OnjMC__TyipUAwMxskUjlcnWYYSdPBZ4B_n6SAic_JzAthf4UBgffDBddVB3tK2aVeZ7a5K-4NFZUh5pvo9PEZEDMFCETNDkpCkRTgndE5rZOiVUrauxy4xEa3w_cmvsz6Uqaoxh0odoUjhzI_gDF1AmHoxVNvYJWZTsHbnJ4_Rcd7wOCj3PbAXqjdP-RHWAcONknPtPy9BjYopENlclLemD2seyZJVJZWPVC_OzR8glxTu8v1v7zNnBkNT-OnOv0UT8Bn-z1CfYYXzKFCqk17b4fB-hJlrO8PwQDZC1PLS_qOXR7iHxM8GY6ZL/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jPqDFzkaHphcjdrRsY7eC9QmOR9nYQzeT_ps87z-7ZEALb... https://secure-web.cisco.com/1KwxzXfk1qtI-kzHoMVtwJPU4Q0KICStiWRDqtl7KUQRJL66sPCq0eF3Z0cOeAaikYEpDTtleSRvZ73nDCn-uaKTAAkxo1jgn_SBnvL99kW3TwByZUEQxtchZQcxCcb5WnDRFk80t18Z6YBSoqATlZpROJUG_4XCULwNS-ttBm72wf_9gxklYIVCUQnF70FkcNAxf3BfkBbaF6w0kBvDD1jEFnlE5VLQkRvvYSsC4CLCz1OH4o-sgZijJ40ezsfERE35ZGMDN_pHdnLzJ629_buf45RGSPnZCVr-TJ-Y9N_vbM1GbdcuwDSB6hNNgCB8y/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1jPqDFzkaHphcjdrRsY7eC9QmOR9nYQzeT_ps87z-7ZEALb... https://secure-web.cisco.com/1KwxzXfk1qtI-kzHoMVtwJPU4Q0KICStiWRDqtl7KUQRJL66sPCq0eF3Z0cOeAaikYEpDTtleSRvZ73nDCn-uaKTAAkxo1jgn_SBnvL99kW3TwByZUEQxtchZQcxCcb5WnDRFk80t18Z6YBSoqATlZpROJUG_4XCULwNS-ttBm72wf_9gxklYIVCUQnF70FkcNAxf3BfkBbaF6w0kBvDD1jEFnlE5VLQkRvvYSsC4CLCz1OH4o-sgZijJ40ezsfERE35ZGMDN_pHdnLzJ629_buf45RGSPnZCVr-TJ-Y9N_vbM1GbdcuwDSB6hNNgCB8y/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .