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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@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 fernandahmor...@gmail.com<mailto:fernandahmor...@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 <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote: Did you get an error when you submit ‘recon-all’? Can you send recon-all.log? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@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<mailto: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 fernandahmor...@gmail.com<mailto:fernandahmor...@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<mailto: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/freesurfer<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://www.massgeneralbrigham.org/complianceline<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://www.massgeneralbrigham.org/complianceline<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>> .
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