Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

2022-09-22 Thread fsbuild 
External Email - Use Caution

I can check to see if there is a license in the Freesurfer v5 Ubuntu VM I 
mentioned in the previous email and send it to you to try.   But per my 
last email, I don’t know a way to decode an old license on newer versions of 
the OS where glibc has been updated short of re-compiling what decodes the 
license.   The most practical option may be to run FS 5.3 on a server that 
hosts an old version of Ubuntu that works with your existing license.   
That can be done using a headless VM or container where the image runs off an 
SSD with a hefty amount of RAM assigned to it.  Ubuntu supports QEMU 
virtualization like most linux OS’s and I think you just install those packages 
from the linux repos.  For commercial software, VMware has enterprise 
level server hosting options for these kinds of tasks.

- R.

On Sep 22, 2022, at 06:25, Caspar Schwiedrzik 
 
wrote:External Email - Use 
CautionHi! Would it be 
possible to obtain a license file for Freesurfer v5.3 that is compatible with 
the glibc versions on newer Linux systems? That would go a long way in 
resolving our issues. Thank 
you, Caspar ___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer​
___
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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

2022-09-22 Thread Caspar Schwiedrzik 
External Email - Use Caution

Hi!
Would it be possible to obtain a license file for Freesurfer v5.3 that is 
compatible with the glibc versions on newer Linux systems? That would go a long 
way in resolving our issues.
Thank you,
Caspar
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Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

2022-09-13 Thread Wighton, Paul 
Thanks R, those are very good points.

-Paul

From: fsbuild 
Sent: Tuesday, September 13, 2022 2:21 PM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: r.lud...@eni-g.de ; Wighton, Paul 
; fsbu...@contbay.com 
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu


External Email - Use Caution

The glibc version has changed in newer versions of Ubuntu.  That and/or changes 
to encryption related functions is likely preventing the license decoding from 
working.   Binary backwards compatibility cannot assure old binaries will 
indefinitely run on newer releases of the operating system., e.g., CentOS6 
binaries may not run on CentOS8.  Freesurfer 5.3 was released in 2013 at the 
time of Ubuntu 12 so I would not assume it will run on Ubuntu 18 and/or newer 
versions.  I don['t think LD_LIBRARY_PATH will help with statically linked 
binaries - and sertting it to point to a version could break dynamically linked 
binaries with RPATH strings.  In general it is a bad idea to be running with 
different versions of glibc on the same system.

There is an Ubuntu 12 VM running Freesurfer 5.3 available from 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz<https://secure-web.cisco.com/13_Z5mhms1Dpq_WEjE79lEciW_21298e4jPP1NTDsZfB8Igfsnnu3qYl3BeyM76R9HGTX5lxisLN47qGSSeHCN3PAWPWaLY0swK-cyJZamxaMUeok9Y0urSrvDuG7EXCubWSA3M94NvLmMuwxWo8LWS7hCY67NvQdwSYhtCSqCRyqvpp1Goknf5X8rRc0NCmHs7-L7zGrDXU1W5kOLf63Mk6ffRDL39v9CdhvyvDG9umhsQ0VhOFfdRF6EeAKHLTgPTCv-FmbijBEd2vF73cPSHsNyOyqNt9aB4ywSLhNzB1ro12Z78khyvHF8cXPQ3rz/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz>
   That VM still runs in VirtualBox on todays operating systems.

- R.

On Sep 13, 2022, at 13:28, Wighton, Paul  wrote:

Hi Rüdiger,

This is really interesting..  I'm able to reproduce this issue in a docker 
container.  Anyone else who would like to reproduce or look into this issue can 
use the following containers

- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04 
(glibc v2.23) and everything works as expected in this container.
- The container `pwighton/freesurfer:5..3.0-HCP-focal` is based off of ubuntu 
20.04 (glib2 v2.31) and I am experiencing the same issue you describe.
- The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 
and has the latest version of FreeSurfer installed.  Everything works as 
expected in this container.

So the issue seems to be some interaction between the v5.3 license checking 
code and the crypt() function provided by different versions of glibc, but that 
is just speculation at this point.

I'm sorry I don't have any solution for this at the moment.  You mention you 
are using lmod, would it be possible to define LD_LIBRARY_PATH inside the 
FreeSurfer 5.3 module to point to an older version of glibc?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ludwig, Rüdiger 

Sent: Tuesday, September 13, 2022 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Hello again,

I realized I might have missed some important information in my question about 
freesurfer 5.3 license files a few days ago:

We use Ubuntu 20 with lmod. FREESURFER_HOME  is  ''/opt/apps/freesurfer/5.3/''  
for freesurfer 5.3

When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper 
license file we get the Error:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

After we copy the license file to the proper position we get:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

So the file is obviously read but rejected. We get the same result it with a 
brand new license file, and one that still works for freesurfer 5.3 on our 
CentOS 7 node.
We do not have any problems reading the license file in freesurfer 7.2 or 
freesurfer 7.3

If you need any further information to help us, we am more than willing to 
provide that.

Thank you so much in advance

Ruediger

---
Rüdiger Ludwig (he/him)
IT-Service
European Neuroscience Institute
A Joint Initiative of the University Medical Center Göttingen and the Max 
Planck Society
Grisebachstr. 5
37077 Göttingen

Tel: +49 551-39 61308
Email: r.lud...@eni-g.de
Office: 0.051

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 thi

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

2022-09-13 Thread fsbuild 
External Email - Use Caution

The glibc version has changed in newer versions of Ubuntu.  That and/or 
changes to encryption related functions is likely preventing the license 
decoding from working.   Binary backwards compatibility cannot assure old 
binaries will indefinitely run on newer releases of the operating system., 
e.g., CentOS6 binaries may not run on CentOS8.  Freesurfer 5.3 was 
released in 2013 at the time of Ubuntu 12 so I would not assume it will run on 
Ubuntu 18 and/or newer versions.  I don['t think LD_LIBRARY_PATH will help 
with statically linked binaries - and sertting it to point to a version could 
break dynamically linked binaries with RPATH strings.  In general it is a 
bad idea to be running with different versions of glibc on the same system.
There is an Ubuntu 12 VM running Freesurfer 5.3 available 
from https://secure-web.cisco.com/1X4Gyy7SfMYdVSIKIWMlCS7GCLmcJfLLRdLZo-f9j9-meHNAgQCtdlXlSAbkf0YPgUtG5LlLDHvMUjPREuFaul0mn4dCxScTqVtWZeb4TmW_WO4__aKAR7wBdEkdJYeNFFJGre81boE_tNY6GTULYMtWRUR_fWhz23yTmCNoPZ0zkXOMCS2-f8ieX94kysvRbs_MeQ0cppH8SWAusTZnTyuJCA04ttjmS2Xxf_P73_n5rlLExFEIXxPjRn-3EO9_GCJWkb7krP2M6ZZpQkDH2YBdMpc8FEbFV0WpIc8ambmZr5O1_6vNL1bZmrgCZg8CJ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz%26nbsp;
  That VM still runs in VirtualBox on todays operating systems. 
- R.

On Sep 13, 2022, at 13:28, Wighton, Paul <pwigh...@mgh.harvard.edu> 
wrote:Hi Rüdiger,This is really interesting..  I'm able to reproduce 
this issue in a docker container.  Anyone else who would like to reproduce 
or look into this issue can use the following containers- The container 
`pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16..04 (glibc v2.23) and 
everything works as expected in this container.- The container 
`pwighton/freesurfer:5.3.0-HCP-focal` is based off of ubuntu 20.04 (glib2 
v2.31) and I am experiencing the same issue you describe.- The container 
`pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 and has the 
latest version of FreeSurfer installed.  Everything works as expected in 
this container.So the issue seems to be some interaction between the v5.3 
license checking code and the crypt() function provided by different versions 
of glibc, but that is just speculation at this point.I'm sorry I don't have any 
solution for this at the moment.  You mention you are using lmod, would it 
be possible to define LD_LIBRARY_PATH inside the FreeSurfer 5.3 module to point 
to an older version of 
glibc?-PaulFrom: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Ludwig, Rüdiger 
<r.lud...@eni-g.de>Sent: Tuesday, September 13, 2022 11:32 
AMTo: freesurfer@nmr.mgh.harvard.edu 
<freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Follow Up 
License Freesurfer 5.3 Ubuntu Hello again,I realized I might have missed 
some important information in my question about freesurfer 5.3 license files a 
few days ago:We use Ubuntu 20 with lmod. FREESURFER_HOME  is  
''/opt/apps/freesurfer/5.3/''  for freesurfer 5.3When we try ''mri_convert 
sample-001.mgz sample-001.nii.gz'' without a proper license file we get the 
Error:ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txtAfter we copy the license file to the 
proper position we get:ERROR: Invalid FreeSurfer license key found in license 
file /opt/apps/freesurfer/5.3/license.txtSo the file is obviously read but 
rejected. We get the same result it with a brand new license file, and one that 
still works for freesurfer 5.3 on our CentOS 7 node.We do not have any problems 
reading the license file in freesurfer 7.2 or freesurfer 7.3If you need any 
further information to help us, we am more than willing to provide that.Thank 
you so much in advanceRuediger---Rüdiger Ludwig (he/him)IT-ServiceEuropean 
Neuroscience InstituteA Joint Initiative of the University Medical Center 
Göttingen and the Max Planck SocietyGrisebachstr. 537077 GöttingenTel: +49 
551-39 61308Email: r.ludwig@eni-g.deOffice: 
0.051___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue co

Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

2022-09-13 Thread Wighton, Paul 
Hi Rüdiger,

This is really interesting..  I'm able to reproduce this issue in a docker 
container.  Anyone else who would like to reproduce or look into this issue can 
use the following containers

- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04 
(glibc v2.23) and everything works as expected in this container.
- The container `pwighton/freesurfer:5.3.0-HCP-focal` is based off of ubuntu 
20.04 (glib2 v2.31) and I am experiencing the same issue you describe.
- The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 
and has the latest version of FreeSurfer installed.  Everything works as 
expected in this container.

So the issue seems to be some interaction between the v5.3 license checking 
code and the crypt() function provided by different versions of glibc, but that 
is just speculation at this point.

I'm sorry I don't have any solution for this at the moment.  You mention you 
are using lmod, would it be possible to define LD_LIBRARY_PATH inside the 
FreeSurfer 5.3 module to point to an older version of glibc?

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Ludwig, Rüdiger 

Sent: Tuesday, September 13, 2022 11:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Hello again,

I realized I might have missed some important information in my question about 
freesurfer 5.3 license files a few days ago:

We use Ubuntu 20 with lmod. FREESURFER_HOME  is  ''/opt/apps/freesurfer/5.3/''  
for freesurfer 5.3

When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper 
license file we get the Error:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

After we copy the license file to the proper position we get:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

So the file is obviously read but rejected. We get the same result it with a 
brand new license file, and one that still works for freesurfer 5.3 on our 
CentOS 7 node.
We do not have any problems reading the license file in freesurfer 7.2 or 
freesurfer 7.3

If you need any further information to help us, we am more than willing to 
provide that.

Thank you so much in advance

Ruediger

---
Rüdiger Ludwig (he/him)
IT-Service
European Neuroscience Institute
A Joint Initiative of the University Medical Center Göttingen and the Max 
Planck Society
Grisebachstr. 5
37077 Göttingen

Tel: +49 551-39 61308
Email: r.lud...@eni-g.de
Office: 0.051

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
<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.

[Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

2022-09-13 Thread Ludwig , Rüdiger 
Hello again,

I realized I might have missed some important information in my question about 
freesurfer 5.3 license files a few days ago:

We use Ubuntu 20 with lmod. FREESURFER_HOME  is  ''/opt/apps/freesurfer/5.3/''  
for freesurfer 5.3

When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper 
license file we get the Error:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

After we copy the license file to the proper position we get:
ERROR: Invalid FreeSurfer license key found in license file 
/opt/apps/freesurfer/5.3/license.txt

So the file is obviously read but rejected. We get the same result it with a 
brand new license file, and one that still works for freesurfer 5.3 on our 
CentOS 7 node.
We do not have any problems reading the license file in freesurfer 7.2 or 
freesurfer 7.3

If you need any further information to help us, we am more than willing to 
provide that.

Thank you so much in advance

Ruediger

---
Rüdiger Ludwig (he/him)
IT-Service
European Neuroscience Institute
A Joint Initiative of the University Medical Center Göttingen and the Max 
Planck Society
Grisebachstr. 5
37077 Göttingen

Tel: +49 551-39 61308
Email: r.lud...@eni-g.de
Office: 0.051



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External Email - Use Caution___
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Freesurfer@nmr.mgh.harvard.edu
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 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.