External Email - Use Caution        

Hi Andrei,

Glad to know it worked. I also encountered the problem before and found the solution in the script itself.

Best regards,

Kiyotaka


On Sun, Mar 20, 2022 at 12:32 AM Andrei Bieger <andreibieger@gmail.com> wrote:

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Greetings, Professor Nemoto,

Your solution worked like a charm. Thank you very much!

Best regards
Andrei


Em sáb., 19 de mar. de 2022 às 12:03, Kiyotaka Nemoto <kiyotaka@nemotos.net> escreveu:

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Hi Andrei,

You need to use sudo to use the script because it tries to install files under $FREESURFER_HOME.
curl fails because the script tries to download a file in $FREESURFER_HOME where you don't have permission to write without sudo.
You also need to set FREESURFER_HOME for the sudo environment.

The command below should work for you.

sudo FREESURFER_HOME=$FREESURFER_HOME $FREESURFER_HOME/bin/fs_install_mcr R2014b

Hope this helps,

Kiyotaka


On Sat, Mar 19, 2022 at 11:32 PM Andrei Bieger <andreibieger@gmail.com> wrote:

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Hello, everyone,

I`m having trouble installing the MatLab Runtime 2014b as required for running the new hippocampal subfields pipeline. The "fs_install_mcr 2014b" command returns me the message below:

andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ fs_install_mcr 2014b
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100    10  100    10    0     0      2      0  0:00:05  0:00:04  0:00:01     2
Archive:  installer.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of installer.zip or
        installer.zip.zip, and cannot find installer.zip.ZIP, period.

Then I tried running the specific line of the script to download the file so I could take a look at it:

andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$     curl --location MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://ssd.mathworks.com/supportfiles/downloads/$MCR_VER/deployment_files/$MCR_VER/installers/$OS_TAG/MCR_${MCR_VER}_${OS_TAG}_installer.zip -o installer.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100    10  100    10    0     0    161      0 --:--:-- --:--:-- --:--:--   161
andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ file installer.zip
installer.zip: ASCII text
andrei@andrei-VirtualBox:~/Programs/freesurfer/7.2.0/bin$ unzip installer.zip
Archive:  installer.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of installer.zip or
        installer.zip.zip, and cannot find installer.zip.ZIP, period.

It does not recognize it as a .zip file, and the Ubuntu Archive Manager won`t recognize it either: "An error occurred while loading the archive."
I know this is more of a Linux/Matlab issue than a freesurfer one. But I wonder if anyone else is facing this issue? Might that be a problem with the curl package, Matlab support to older Runtime versions or my Linux distro?

Thank you!

--
Andrei Bieger
_______________________________________________
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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
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 <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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.


--
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyotaka@nemotos.net
_______________________________________________
Freesurfer mailing list
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
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 <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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.


--
Andrei Bieger
_______________________________________________
Freesurfer mailing list
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
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 <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
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.