External Email - Use Caution Ok, thanks! I forgot to mention ut before, but this error only occurs when running it in IOS, in Linux it works fine...
El dv., 14 de maig 2021, 22:52, Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> va escriure: > Yes, but that doesn’t guarantee that the (library) environment is the same > as when you run something from the terminal. > I’m CCing Andrew Hoppes to see if he can assist. > Cheers, > /E > > Juan Eugenio Iglesias > Senior research fellow > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > http://secure-web.cisco.com/1mA1N83HM7Rsjl2L1KkalgrABlubZqRZ_UQ64lxXmRndx2711kiO01TMRaUUuwz9j6XICzNwZFvDHBBBShMS7u6MFR9z8lNlR8iT6I8Twaccigy0ALio3o0IeTnHo9FYwlxAzlnLhn7RNCiRSLpPpQ_PSrDXwlJ_bkyxQ0fgBnMiFtpf5Nb5cQ0_kepO0VkjB2HtF3A4xIXDqvnmmontva138eLK7VW0V3J__3FMAR8wDQpFpKFqbJVKo11fWZjsRIScnCY_VkFMe1SuGmZ5CtQ/http%3A%2F%2Fwww.jeiglesias.com > > On May 14, 2021, at 15:22, Joana Collet i Fàbregas <joana.col...@gmail.com> > wrote: > > External Email - Use Caution > > Dear Juan Eugenio, > > I'm not sure what you mean. In Python I use os.system() to run the > recon-all command from the command line. > Thanks! > > Joana > > El dv., 14 de maig 2021, 21:04, Iglesias Gonzalez, Juan E. < > jiglesiasgonza...@mgh.harvard.edu> va escriure: > >> Dear Joana, >> Is it possibly that Python changes somehow that libraries that are >> loaded, compared with the command line? >> Cheers, >> /E >> >> Juan Eugenio Iglesias >> Senior research fellow >> CMIC (UCL), MGH (HMS) and CSAIL (MIT) >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> http://secure-web.cisco.com/1mA1N83HM7Rsjl2L1KkalgrABlubZqRZ_UQ64lxXmRndx2711kiO01TMRaUUuwz9j6XICzNwZFvDHBBBShMS7u6MFR9z8lNlR8iT6I8Twaccigy0ALio3o0IeTnHo9FYwlxAzlnLhn7RNCiRSLpPpQ_PSrDXwlJ_bkyxQ0fgBnMiFtpf5Nb5cQ0_kepO0VkjB2HtF3A4xIXDqvnmmontva138eLK7VW0V3J__3FMAR8wDQpFpKFqbJVKo11fWZjsRIScnCY_VkFMe1SuGmZ5CtQ/http%3A%2F%2Fwww.jeiglesias.com >> <http://secure-web.cisco.com/148BToGpABivasWCgZR8rJMojzoD19lp4xSo0ku22rTNs46gi8eSQpxJJP6k6M4j5RKqRIKorP1-NtqedAacoQmEWnd8tz7Vpdfvp4n5xyzeV6jiUsTOjsuVZzv-qlc7NyV8dUlH8F8-il7vz5LfdbM8Fc5cE8WMR7k-VMx3r06GDDpq7BuAYFAW3uP54OD40bss37bbnQbVpyCeoZ7nJBWZdd6OefdWUCyQhy6OO9JK6dBHQjwvzXZyflpzJfxOHuNuGSCJc9x6KB1mnmc5tdw/http%3A%2F%2Fwww.jeiglesias.com> >> >> >> On May 14, 2021, at 06:06, Joana Collet i Fàbregas < >> joana.col...@gmail.com> wrote: >> >> External Email - Use Caution >> >> Good morning, >> >> I am a Biomedical Engineering Student at Universitat de Barcelona and I >> am creating a python script that has a Watchdog which detects new patients >> in a specific folder, and we want it to run FS and Hippocampal Subfields. >> The FS runs properly, but when the script arrives to the Hippocampal >> Subfields command, it breaks. >> >> When using the FreeSurfer's Hippocampal Subfields from a python script >> after running FS recon-all right before, the processing is not performed >> due to the error shown in the attatched file. However, when running the >> Hippocampal Subfields from the terminal it does work. >> >> We have even tried to create a watchdog only for the Hippocampal >> Subfields, and when we move a folder obtained after running FS to a >> specific folder, it also runs properly. It is only when it is concatenated >> with FS that it does not work. >> >> We have contacted MathWorks Support, but they told us to reach you. The >> Matlab versions we have are Matlab_R2020a and Matlab_R2014b. >> >> Thanks a lot, >> >> Joana Collet >> <hippocampal-subfields-T1 (1).log><matlab_crash_dump.26817-2 - Jupyter >> Text Editor (1).pdf>_______________________________________________ >> 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/1gJEaZkbH_ux6ref2h-muXqSr9UjSc1lUjmmVv2W1vEQCOaNmVfSH_Y5SYIKwUAl58HzNVhFSE8LEVEhIjBb9PGE89zD88GtRTJkN73Oh7QsHzcuFgbt2OfBFUMwlQ03Qe72LSmmuN0AfJAfF_fluaUdcoGVPkz7H-fgkOKyBXzSFQfe_t0Rh4dpJi3MEnZFyJ5UF1qJFYq2sflnfMdNZ5APk0_GTusGlRXFrmqbY7o8dtmqWdZ3woHH5K_0YESl9QgWwGRnKFwdWLXxsjQCUEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1ZNwealvi1p5F7stWF1RPAb9qsbw9U-FAN7fNadO_R0oPjoIYIEsfGd9sjTXC7QnBjtJMqXEp_AWV8QFL7ENlQ079ucxrSY89_f3RjcPHEy3Sv4wdKHCZrsFYudFvdgXNU1NP6vLxzDiMG2WejeiItyW49K8p3Z29LqCUe32Tit3EZmbK9eSbppg_WRvSKjLPMwZmVp3oMskEfnsGUSMgR8LfhT0kzKntXVSlBRfh_Ccy9QolbN08-rEvOYcAYfy8TGMwe0JdYdqKUK9aPL7vBA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> 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/1gJEaZkbH_ux6ref2h-muXqSr9UjSc1lUjmmVv2W1vEQCOaNmVfSH_Y5SYIKwUAl58HzNVhFSE8LEVEhIjBb9PGE89zD88GtRTJkN73Oh7QsHzcuFgbt2OfBFUMwlQ03Qe72LSmmuN0AfJAfF_fluaUdcoGVPkz7H-fgkOKyBXzSFQfe_t0Rh4dpJi3MEnZFyJ5UF1qJFYq2sflnfMdNZ5APk0_GTusGlRXFrmqbY7o8dtmqWdZ3woHH5K_0YESl9QgWwGRnKFwdWLXxsjQCUEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1ZNwealvi1p5F7stWF1RPAb9qsbw9U-FAN7fNadO_R0oPjoIYIEsfGd9sjTXC7QnBjtJMqXEp_AWV8QFL7ENlQ079ucxrSY89_f3RjcPHEy3Sv4wdKHCZrsFYudFvdgXNU1NP6vLxzDiMG2WejeiItyW49K8p3Z29LqCUe32Tit3EZmbK9eSbppg_WRvSKjLPMwZmVp3oMskEfnsGUSMgR8LfhT0kzKntXVSlBRfh_Ccy9QolbN08-rEvOYcAYfy8TGMwe0JdYdqKUK9aPL7vBA/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* >> http://secure-web.cisco.com/1Ime131OgfbAeI5GMAkZuCfnl-UTXSciV68GJiN7yksFw2S5oLQcZWJ2oSnSRx1Su8KrOq_fLPx7hPnraoCmUs75LIQh7ZWk5uNCeGTSi1SgNTWwegP6TZVIGhkfpHXLUmImmDJlsTO7pZc3Lze1zcHhA1CH5mQ7N5tSGVWwMMsQes95bNjbfKjFycpaUFp-Dike0z0rOYIA59_EyTGM4iPu4t8tevvwEsry9jiXOwdkUzGuAXKb2NelfMC6svdefcRSOVnw94tHaluiEaCAfMw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> <http://secure-web.cisco.com/1LPIYFofpHCLeAMGUT9l-1tpoLMMxCLWOMnsuMuz9kqlmTZIouSwMWx79BnOdQrIE8QPPcsKrtKeOpcNtK9XVB5qt-HYHdqUzGL6L57WuaSbJ5f-GXz_sbtJm_XNlPic3dewisD6zig0XJnOscCnNRMqYpuCIIuUkf1faftLEo5mQpSM6i1zXs1KaU5YWG9GsqC416sAHMkaEOr2E5JLlirPamtVzSk9vvJIEiFWiYJ-IkC7t6bh1sP1hv9x6y6JKz9NbIFMVM0ZgLx3kJwTJOw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> >> . 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Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1gJEaZkbH_ux6ref2h-muXqSr9UjSc1lUjmmVv2W1vEQCOaNmVfSH_Y5SYIKwUAl58HzNVhFSE8LEVEhIjBb9PGE89zD88GtRTJkN73Oh7QsHzcuFgbt2OfBFUMwlQ03Qe72LSmmuN0AfJAfF_fluaUdcoGVPkz7H-fgkOKyBXzSFQfe_t0Rh4dpJi3MEnZFyJ5UF1qJFYq2sflnfMdNZ5APk0_GTusGlRXFrmqbY7o8dtmqWdZ3woHH5K_0YESl9QgWwGRnKFwdWLXxsjQCUEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1gJEaZkbH_ux6ref2h-muXqSr9UjSc1lUjmmVv2W1vEQCOaNmVfSH_Y5SYIKwUAl58HzNVhFSE8LEVEhIjBb9PGE89zD88GtRTJkN73Oh7QsHzcuFgbt2OfBFUMwlQ03Qe72LSmmuN0AfJAfF_fluaUdcoGVPkz7H-fgkOKyBXzSFQfe_t0Rh4dpJi3MEnZFyJ5UF1qJFYq2sflnfMdNZ5APk0_GTusGlRXFrmqbY7o8dtmqWdZ3woHH5K_0YESl9QgWwGRnKFwdWLXxsjQCUEg/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 > http://secure-web.cisco.com/1Ime131OgfbAeI5GMAkZuCfnl-UTXSciV68GJiN7yksFw2S5oLQcZWJ2oSnSRx1Su8KrOq_fLPx7hPnraoCmUs75LIQh7ZWk5uNCeGTSi1SgNTWwegP6TZVIGhkfpHXLUmImmDJlsTO7pZc3Lze1zcHhA1CH5mQ7N5tSGVWwMMsQes95bNjbfKjFycpaUFp-Dike0z0rOYIA59_EyTGM4iPu4t8tevvwEsry9jiXOwdkUzGuAXKb2NelfMC6svdefcRSOVnw94tHaluiEaCAfMw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. >
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