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) > 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 > 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 > 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 > http://secure-web.cisco.com/1LPIYFofpHCLeAMGUT9l-1tpoLMMxCLWOMnsuMuz9kqlmTZIouSwMWx79BnOdQrIE8QPPcsKrtKeOpcNtK9XVB5qt-HYHdqUzGL6L57WuaSbJ5f-GXz_sbtJm_XNlPic3dewisD6zig0XJnOscCnNRMqYpuCIIuUkf1faftLEo5mQpSM6i1zXs1KaU5YWG9GsqC416sAHMkaEOr2E5JLlirPamtVzSk9vvJIEiFWiYJ-IkC7t6bh1sP1hv9x6y6JKz9NbIFMVM0ZgLx3kJwTJOw/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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