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
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://www.jeiglesias.com
On May 14, 2021, at 06:06, Joana Collet i Fàbregas <joana.collet@gmail.commailto:joana.collet@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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < JIGLESIASGONZALEZ@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/148BToGpABivasWCgZR8rJMojzoD19lp4xSo0ku22rTNs46g...
On May 14, 2021, at 06:06, Joana Collet i Fàbregas joana.collet@gmail.com wrote:
External Email - Use CautionGood 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_R0oPjo...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZNwealvi1p5F7stWF1RPAb9qsbw9U-FAN7fNadO_R0oPjo... 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-1tpoLMMxCLWOMnsuMuz9kqlmTZI... . 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.
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://www.jeiglesias.com
On May 14, 2021, at 15:22, Joana Collet i Fàbregas <joana.collet@gmail.commailto:joana.collet@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. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@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://www.jeiglesias.comhttp://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.collet@gmail.commailto:joana.collet@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.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/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.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/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://www.massgeneralbrigham.org/compliancelinehttp://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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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. < JIGLESIASGONZALEZ@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_UQ64lxXmRndx271...
On May 14, 2021, at 15:22, Joana Collet i Fàbregas joana.collet@gmail.com wrote:
External Email - Use CautionDear 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. < JIGLESIASGONZALEZ@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_UQ64lxXmRndx271... 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.collet@gmail.com> wrote:
External Email - Use CautionGood 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-muXqSr9UjSc1lUjmmVv2W1vEQCOa... 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-muXqSr9UjSc1lUjmmVv2W1vEQCOa... 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-UTXSciV68GJiN7yksFw2S5... 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gJEaZkbH_ux6ref2h-muXqSr9UjSc1lUjmmVv2W1vEQCOa...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gJEaZkbH_ux6ref2h-muXqSr9UjSc1lUjmmVv2W1vEQCOa... 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-UTXSciV68GJiN7yksFw2S5... . 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.
Hi Joana,
I agree with Eugenio that if this is failing from within python, then python is probably messing with your environment. Based on that error log, it’s tough to say whether this is a freesurfer problem or matlab. The fact that it runs fine on linux seems to suggest it’s a macOS-specific issue with calling the matlab runtime library from python. If you’re using anaconda or something, it might be overwriting matlab-runtime linked libraries. I’m not sure how much we can help out here, unfortunately.
Best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Joana Collet i Fàbregas joana.collet@gmail.com Date: Saturday, May 15, 2021 at 11:18 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields
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. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@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) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://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.collet@gmail.commailto:joana.collet@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. <JIGLESIASGONZALEZ@mgh.harvard.edumailto:JIGLESIASGONZALEZ@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://www.jeiglesias.comhttp://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.collet@gmail.commailto:joana.collet@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.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/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.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/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://www.massgeneralbrigham.org/compliancelinehttp://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. _______________________________________________ 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/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.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/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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://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.
freesurfer@nmr.mgh.harvard.edu
-
Hoopes, Andrew -
Iglesias Gonzalez, Juan E. -
Iglesias Gonzalez, Juan E.
-
Joana Collet i Fàbregas