External Email - Use Caution

Yes, sure. This is the file Thanks.

Il giorno gio 8 feb 2024 alle ore 17:03 Huang, Yujing < YHUANG43@mgh.harvard.edu> ha scritto:

Can you re-send recon-all.log as attachment?

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Francesco Lomi *Sent:* Thursday, February 8, 2024 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mpr2mni305 failed

•    External Email - Use Caution        *
  
  

Hello everybody,

I'm new on Freesurfer and I've installed the software on my Ubuntu 20.04 machine. The installation should be fine. just tried to run recon-all on my subject data but i got stuck on the following error you can see on the screenshot:

Any idea on how to fix this?

Thank you in advance

Best,

Francesco _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1oLKwPYSbTYlGnepioqQaD2illAO2qSWmkeXO7C-Me2Lumi... 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/1elkiEyubIJHl1S0yvValvt8P_T8Y1MaY8FxHdpaeA7HV3L... < https://secure-web.cisco.com/1elkiEyubIJHl1S0yvValvt8P_T8Y1MaY8FxHdpaeA7HV3L... . 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.

External Email - Use Caution

Unfortunately I've tried to change the directory but I've encountered the same error, as shown in the log file. Best, Francesco

Il giorno gio 8 feb 2024 alle ore 17:59 Huang, Yujing < YHUANG43@mgh.harvard.edu> ha scritto:

This is from your recon-all.log:

“

setenv SUBJECTS_DIR /home/ubuntu/freesurfer/subjects

FREESURFER_HOME /home/ubuntu/freesurfer

Actual FREESURFER_HOME /home/ubuntu/Freesurfer

“

Your SUBJECTS_DIR points to your Freesurfer install directory - /home/ubuntu/freesurfer/subjects. I’m not sure if this is the reason for the failure. But it is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions.

Can you re-set SUBJECTS_DIR and try again?

Best,

Yujing

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Francesco Lomi *Sent:* Thursday, February 8, 2024 11:44 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] mpr2mni305 failed

•    External Email - Use Caution        *
  
  

Yes, sure. This is the file

Thanks.

Il giorno gio 8 feb 2024 alle ore 17:03 Huang, Yujing < YHUANG43@mgh.harvard.edu> ha scritto:

Can you re-send recon-all.log as attachment?

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Francesco Lomi *Sent:* Thursday, February 8, 2024 10:58 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mpr2mni305 failed

•    External Email - Use Caution        *
  
  

Hello everybody,

I'm new on Freesurfer and I've installed the software on my Ubuntu 20.04 machine. The installation should be fine. just tried to run recon-all on my subject data but i got stuck on the following error you can see on the screenshot:

Any idea on how to fix this?

Thank you in advance

Best,

Francesco

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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/1B2FjuIeWZOriXnDx-1419Fl6KtNIb_NbX0s_C4_lf8gzQr... https://secure-web.cisco.com/1oLKwPYSbTYlGnepioqQaD2illAO2qSWmkeXO7C-Me2LumiP4rBWYJehJ4zf-547A-rtYmWGn_DyYsc6kP2dpS1A1a-oOCUbb9oqQMZ2nYxotRJE2zcYaP7s-pnSPC8SYtyIMZJuACKxErzY8oxIjPZ_2kwNgjXJQ8b0Kce3L0PZnWZ0jzDRcRzK74uYpQ2uMrVzQfojrXHfy2to4yzeOVm7vmaukod8PapbGlu1O2i2yhHH7ia0e3HPuRnNli9uqCkkUld-YFNLVm-SskSRZt7MD1Yr-cmuj8T1MbrqF-LglwLw-9o1IhWXZCxsA_4Py4oSmmANfyG2cbfIqhEe01Q/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/1xPqwFFuQ9HJTEj8ZB8k4S3h2po9oeuc9q67VE5qZy5ZXgF... https://secure-web.cisco.com/1elkiEyubIJHl1S0yvValvt8P_T8Y1MaY8FxHdpaeA7HV3Lc-BYK2vaTFS-QAEv1EQi7J4sc6McygO52ZxgjV9sgz8_czkrK9MV7sMXuSIQfBdMuiS93DIAo6KzX0OV3KzWvNkdvOBTIZxGwd7x55Pv96G1aqQdvN0fX9uQZ0GBawS_LuNa60PcLTiSQOg6khWO_DM0nVFFAUgi73ugyILSAqJeLYqFdmcRnlqo6KKFiR2it2HG9EPtEW7NwH1KzUfg3e1J8EO3E9994yFOjibsMWbU9Dg_c4gG0dG1K3Vo2ctS1Zuz_Pf_tPvkBVxFVNzR_x02ew56sRzt45MV4BmA/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/1xPqwFFuQ9HJTEj8ZB8k4S3h2po9oeuc9q67VE5qZy5ZXgF... https://secure-web.cisco.com/1elkiEyubIJHl1S0yvValvt8P_T8Y1MaY8FxHdpaeA7HV3Lc-BYK2vaTFS-QAEv1EQi7J4sc6McygO52ZxgjV9sgz8_czkrK9MV7sMXuSIQfBdMuiS93DIAo6KzX0OV3KzWvNkdvOBTIZxGwd7x55Pv96G1aqQdvN0fX9uQZ0GBawS_LuNa60PcLTiSQOg6khWO_DM0nVFFAUgi73ugyILSAqJeLYqFdmcRnlqo6KKFiR2it2HG9EPtEW7NwH1KzUfg3e1J8EO3E9994yFOjibsMWbU9Dg_c4gG0dG1K3Vo2ctS1Zuz_Pf_tPvkBVxFVNzR_x02ew56sRzt45MV4BmA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1B2FjuIeWZOriXnDx-1419Fl6KtNIb_NbX0s_C4_lf8gzQr... 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/1xPqwFFuQ9HJTEj8ZB8k4S3h2po9oeuc9q67VE5qZy5ZXgF... < https://secure-web.cisco.com/1xPqwFFuQ9HJTEj8ZB8k4S3h2po9oeuc9q67VE5qZy5ZXgF... . 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.