External Email - Use Caution        

Could I get the password for the Ubuntu virtual machine zip file?
If you also have the license file to include as well, that would be great!

Thank you,
Stacey

Stacey M. Schaefer, Ph.D.
Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703



From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edu>
Sent: Tuesday, September 13, 2022 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Digest, Vol 223, Issue 22
 
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Today's Topics:

   1. Re: Follow Up License Freesurfer 5.3 Ubuntu (Wighton, Paul)
   2. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Justina Lee)
   3. Re: Follow Up License Freesurfer 5.3 Ubuntu (fsbuild)
   4. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Wighton, Paul)
   5. Re: Follow Up License Freesurfer 5.3 Ubuntu (Wighton, Paul)
   6. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Justina Lee)
   7. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Wighton, Paul)
   8. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Justina Lee)
   9. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Wighton, Paul)
  10. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Justina Lee)
  11. Re: Freesurfer: fs_install_mcr: Unzip command not found
      (Wighton, Paul)


----------------------------------------------------------------------

Message: 1
Date: Tue, 13 Sep 2022 17:28:39 +0000
From: "Wighton, Paul" <PWIGHTON@mgh.harvard.edu>
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN8PR04MB57952410B3C48F5F89851D4382479@BN8PR04MB5795.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

Hi R?diger,

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ludwig, R?diger <r.ludwig@eni-g.de>
Sent: Tuesday, September 13, 2022 11:32 AM
To: 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 5.3

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

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

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

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Message: 2
Date: Tue, 13 Sep 2022 19:58:56 +0200
From: Justina Lee <justinalee56@gmail.com>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACFPZpufs_ih53YcNOc2u3G9AT9KwOO=VK_FG4XtD9XSzjqAiA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Thank you Paul for your help!


This seems to have solved the issue, as I can now run the command
fs_install_mcr R2019b. It has ended successfully with this end message
stated below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the
command segmentHA_T1.sh. When I try to run this command again it gives me
the following error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab
runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab
2019b.

To do so, please run the following command (you might need root
permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the
usr/local/freesurfer/7.3.2 instead of in the location stated in the error
above. When I try to search this location there is no such existing
directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
the fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a
lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
wrote:

> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> To whom it may concern,
>
>
>
> Apologies for my first post, I was a little bit confounded as to how I can
> reach for help.
>
> I would like to use the segmentation of hippocampal subfields and the
> nuclei of the amygdala.
> Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
>
>
> I am trying to install MATLAB Runtime 2019b to run the command
> segmentHA_T1.sh for the segmentation as described above. The following
> command shows the corresponding error:
>
>
>
> ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr
> R2019b
>
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
> Current
>
>                                  Dload  Upload   Total   Spent    Left
> Speed
>
> 100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:--
> 10.1M
>
> /usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command
> not found
>
>
>
> I am currently struggling to find the solution to this issue. Is the
> installation not in the correct path? Is MATLAB Runtime installed at all?
> Should an already existing matlab file be deleted?
> Any help would be much appreciated.
>
>
>
> Sincerely,
>
> Justina
>
>
>
>
>
>
>
> Sent from Mail
> <https://secure-web.cisco.com/1JF-rDYMVgKJTrVPsWHUacVbsZGxWoxGE8qofNJGanBLzB5H4xG_TSIyr-kKCyfB-OL5ahOLtropBWGT0WNStX9nlY96XmLI4PEcLyxRbpYACqwCkjWGnJ97rPRssexnOq1RJRlrOg_69B_HLSu5yX5bgMIHOh0IfF9pQcTT3TVu3DK8hZxWZSK0gfICgCNrQacXt91cfezI3FeQnjTGxoKqOqzHBsXJaNuI8JxuVMfCrweNj79o9pN5_cVgjrPSCSa5uR_IxkKANQ87K9laDUXpbpf1YpKyxu3k05hdqJLTPSgkt-wfEOgojaS7t3BsJWoxyJ2fHAPhk2SP958H0aA/https%3A%2F%2Fgo.microsoft.com%2Ffwlink%2F%3FLinkId%3D550986>
> for Windows
>
>
> _______________________________________________
> Freesurfer mailing list
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> 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/1uh4d7COjqc1bVLQiDQ6jL1-x2Cu8sxhgIgLz_dog41oDIhM8fTuq3I9l7A0U-S9vXLh2c1HYERWjWRDQ-P2tWah3tgAODl_BVpGrfPQJxSZ8b8tp7bvDrlIRPyYHe8ECeQXKKqR7HYYpsuj0W_eRlliRf3RLFliUMla_Vy1nvCsCWKN59zIJU6vuMQBLr4CA59yuzbdUHZILOlvkicohmO7PykYU9hr5BSqesguhC_1lxDY8I9qdnTi5s4tCkXPSfFtbxb55fm4pVQZ0nnJA_KXGIZRe3MPUbu14WNhHM4FWqJ1XnV2IAma2oaH_RGZ6gdRtBIUdPiGIAx6gluvoiQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <
> https://secure-web.cisco.com/1uh4d7COjqc1bVLQiDQ6jL1-x2Cu8sxhgIgLz_dog41oDIhM8fTuq3I9l7A0U-S9vXLh2c1HYERWjWRDQ-P2tWah3tgAODl_BVpGrfPQJxSZ8b8tp7bvDrlIRPyYHe8ECeQXKKqR7HYYpsuj0W_eRlliRf3RLFliUMla_Vy1nvCsCWKN59zIJU6vuMQBLr4CA59yuzbdUHZILOlvkicohmO7PykYU9hr5BSqesguhC_1lxDY8I9qdnTi5s4tCkXPSfFtbxb55fm4pVQZ0nnJA_KXGIZRe3MPUbu14WNhHM4FWqJ1XnV2IAma2oaH_RGZ6gdRtBIUdPiGIAx6gluvoiQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
>
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------------------------------

Message: 3
Date: Tue, 13 Sep 2022 20:21:21 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
To: freesurfer@nmr.mgh.harvard.edu
Cc: fsbuild@contbay.com, pwighton@mgh.harvard.edu, r.ludwig@eni-g.de
Message-ID: <7e8cc80f2416f5060a4a01b997165c84@trashmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

The glibc version has changed in newer versions of Ubuntu. &nbsp;That and/or changes to encryption related functions is likely preventing the license decoding from working. &nbsp; 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. &nbsp;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.&nbsp; 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. &nbsp;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&nbsp;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; &nbsp;That VM still runs in VirtualBox on todays operating systems.&nbsp;
- R.

On Sep 13, 2022, at 13:28, Wighton, Paul &lt;PWIGHTON@mgh.harvard.edu&gt; wrote:Hi&nbsp;R?diger,This is really interesting..&nbsp; I'm able to reproduce this issue in a docker container.&nbsp; Anyone else who would like to reproduce or look into this issue can use the following containers-&nbsp;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.-&nbsp;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.-&nbsp;The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 and has the latest version of FreeSurfer installed.&nbsp; 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 sol
 ution for this at the moment.&nbsp; 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:&nbsp;freesurfer-bounces@nmr.mgh.harvard.edu &lt;freesurfer-bounces@nmr.mgh.harvard.edu&gt; on behalf of Ludwig, R?diger &lt;r.ludwig@eni-g.de&gt;Sent:&nbsp;Tuesday, September 13, 2022 11:32 AMTo:&nbsp;freesurfer@nmr.mgh.harvard.edu &lt;freesurfer@nmr.mgh.harvard.edu&gt;Subject:&nbsp;[Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu&nbsp;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&nbsp; is&nbsp; ''/opt/apps/freesurfer/5.3/''&nbsp; 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 posit!
 ion we g
et: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---R?diger Ludwig (he/him)IT-ServiceEuropean Neuroscience InstituteA Joint Initiative of the University Medical Center G?ttingen and the Max Planck SocietyGrisebachstr. 537077 G?ttingenTel: +49 551-39 61308Email: r.ludwig@eni-g.deOffice: 0.051_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------

Message: 4
Date: Tue, 13 Sep 2022 18:22:28 +0000
From: "Wighton, Paul" <PWIGHTON@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN8PR04MB579544390194E9A84462675982479@BN8PR04MB5795.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

Hi Justina,

Ok so it looks like the install script is getting further and has extracted the matlab runtime environment into a temporary directory (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is trying to move that temporary directory to a location inside the FreeSurfer directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr R2019b` so that the install script has permissions to write to the FreeSurfer directory?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command fs_install_mcr R2019b. It has ended successfully with this end message stated below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command segmentHA_T1.sh. When I try to run this command again it gives me the following error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the usr/local/freesurfer/7.3.2 instead of in the location stated in the error above. When I try to search this location there is no such existing directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of You Na Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh for the segmentation as described above. The following command shows the corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not found



I am currently struggling to find the solution to this issue. Is the installation not in the correct path? Is MATLAB Runtime installed at all? Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







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Message: 5
Date: Tue, 13 Sep 2022 18:24:23 +0000
From: "Wighton, Paul" <PWIGHTON@mgh.harvard.edu>
Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu
To: fsbuild <fsbuild@contbay.com>, "freesurfer@nmr.mgh.harvard.edu"
        <freesurfer@nmr.mgh.harvard.edu>
Cc: "r.ludwig@eni-g.de" <r.ludwig@eni-g.de>
Message-ID:
        <BN8PR04MB5795189CE8D618836F33C79D82479@BN8PR04MB5795.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

Thanks R, those are very good points.

-Paul
________________________________
From: fsbuild <fsbuild@contbay.com>
Sent: Tuesday, September 13, 2022 2:21 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: r.ludwig@eni-g.de <r.ludwig@eni-g.de>; Wighton, Paul <PWIGHTON@mgh.harvard.edu>; fsbuild@contbay.com <fsbuild@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 <PWIGHTON@mgh.harvard.edu> wrote:

Hi R?diger,

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ludwig, R?diger <r.ludwig@eni-g.de>
Sent: Tuesday, September 13, 2022 11:32 AM
To: 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 5.3

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

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

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

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Message: 6
Date: Tue, 13 Sep 2022 20:28:50 +0200
From: Justina Lee <justinalee56@gmail.com>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACFPZptv6og1pXFjZG+FOEe8bJqgFMfSCZdoR+NmRgoCD9ozUA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Paul,

When I try to run the installation command with sudo, the following error
command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
wrote:

> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Thank you Paul for your help!
>
>
> This seems to have solved the issue, as I can now run the command
> fs_install_mcr R2019b. It has ended successfully with this end message
> stated below:
>
>
>
> mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
> '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
>
>
>
> I think this problem persists with my next issue, which is using the
> command segmentHA_T1.sh. When I try to run this command again it gives me
> the following error:
>
>
>
> ERROR: cannot find Matlab 2019b runtime in location:
>
>
>
> /usr/local/freesurfer/7.3.2/MCRv97
>
>
>
> It is looking for either:
>
>   bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or
>
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>
>
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
>
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2019b.
>
> To do so, please run the following command (you might need root
> permissions):
>
>
>
> fs_install_mcr R2019b
>
>
>
> I have seen that the pathway for fs_install_mcr is located in the
> usr/local/freesurfer/7.3.2 instead of in the location stated in the error
> above. When I try to search this location there is no such existing
> directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.
>
>
>
> Do I need to create a new file for where the runtime should be stored? Or
> create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
> the fs_installl_mcr R2019b be stored under bin for this command to work?
>
> Hope you can continue to help me with my follow-up issue, I appreciate it
> a lot.
>
> Thank you so much.
>
>
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
> wrote:
>
> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> To whom it may concern,
>
>
>
> Apologies for my first post, I was a little bit confounded as to how I can
> reach for help.
>
> I would like to use the segmentation of hippocampal subfields and the
> nuclei of the amygdala.
> Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
>
>
> I am trying to install MATLAB Runtime 2019b to run the command
> segmentHA_T1.sh for the segmentation as described above. The following
> command shows the corresponding error:
>
>
>
> ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr
> R2019b
>
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
> Current
>
>                                  Dload  Upload   Total   Spent    Left
> Speed
>
> 100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:--
> 10.1M
>
> /usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command
> not found
>
>
>
> I am currently struggling to find the solution to this issue. Is the
> installation not in the correct path? Is MATLAB Runtime installed at all?
> Should an already existing matlab file be deleted?
> Any help would be much appreciated.
>
>
>
> Sincerely,
>
> Justina
>
>
>
>
>
>
>
> Sent from Mail
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Message: 7
Date: Tue, 13 Sep 2022 18:32:13 +0000
From: "Wighton, Paul" <PWIGHTON@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN8PR04MB5795D1813960FBB6A4F80FEB82479@BN8PR04MB5795.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="iso-8859-1"

Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr R2019b`?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the matlab runtime environment into a temporary directory (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is trying to move that temporary directory to a location inside the FreeSurfer directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr R2019b` so that the install script has permissions to write to the FreeSurfer directory?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Justina Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command fs_install_mcr R2019b. It has ended successfully with this end message stated below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command segmentHA_T1.sh. When I try to run this command again it gives me the following error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the usr/local/freesurfer/7.3.2 instead of in the location stated in the error above. When I try to search this location there is no such existing directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of You Na Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh for the segmentation as described above. The following command shows the corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not found



I am currently struggling to find the solution to this issue. Is the installation not in the correct path? Is MATLAB Runtime installed at all? Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







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------------------------------

Message: 8
Date: Tue, 13 Sep 2022 20:37:10 +0200
From: Justina Lee <justinalee56@gmail.com>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACFPZpu=rf-kGEU=HVN2hhbNkUinOkK89TB-J-cCPsXkVdyP+w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Paul,

I have entered the command under this directory
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
sudo fs_install_mcr R2019b and the following error persists. (sudo:
fs_install_mcr: command not found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
wrote:

> Hi Justina,
>
> Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
>
> Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
> R2019b`?
>
> -Paul
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Hi Paul,
>
> When I try to run the installation command with sudo, the following error
> command shows:
>
> sudo: fs_install_mcr: command not found
>
> I'm terribly sorry for the inconvenience.
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
> wrote:
>
> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Thank you Paul for your help!
>
>
> This seems to have solved the issue, as I can now run the command
> fs_install_mcr R2019b. It has ended successfully with this end message
> stated below:
>
>
>
> mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
> '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
>
>
>
> I think this problem persists with my next issue, which is using the
> command segmentHA_T1.sh. When I try to run this command again it gives me
> the following error:
>
>
>
> ERROR: cannot find Matlab 2019b runtime in location:
>
>
>
> /usr/local/freesurfer/7.3.2/MCRv97
>
>
>
> It is looking for either:
>
>   bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or
>
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>
>
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
>
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2019b.
>
> To do so, please run the following command (you might need root
> permissions):
>
>
>
> fs_install_mcr R2019b
>
>
>
> I have seen that the pathway for fs_install_mcr is located in the
> usr/local/freesurfer/7.3.2 instead of in the location stated in the error
> above. When I try to search this location there is no such existing
> directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.
>
>
>
> Do I need to create a new file for where the runtime should be stored? Or
> create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
> the fs_installl_mcr R2019b be stored under bin for this command to work?
>
> Hope you can continue to help me with my follow-up issue, I appreciate it
> a lot.
>
> Thank you so much.
>
>
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
> wrote:
>
> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> To whom it may concern,
>
>
>
> Apologies for my first post, I was a little bit confounded as to how I can
> reach for help.
>
> I would like to use the segmentation of hippocampal subfields and the
> nuclei of the amygdala.
> Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
>
>
> I am trying to install MATLAB Runtime 2019b to run the command
> segmentHA_T1.sh for the segmentation as described above. The following
> command shows the corresponding error:
>
>
>
> ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr
> R2019b
>
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
> Current
>
>                                  Dload  Upload   Total   Spent    Left
> Speed
>
> 100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:--
> 10.1M
>
> /usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command
> not found
>
>
>
> I am currently struggling to find the solution to this issue. Is the
> installation not in the correct path? Is MATLAB Runtime installed at all?
> Should an already existing matlab file be deleted?
> Any help would be much appreciated.
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------------------------------

Message: 9
Date: Tue, 13 Sep 2022 18:48:15 +0000
From: "Wighton, Paul" <PWIGHTON@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN8PR04MB5795B409853E7EA8450CC09C82479@BN8PR04MB5795.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' environment, because the install script relies on that.

-Paul
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Hi Paul,

I have entered the command under this directory ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr R2019b and the following error persists. (sudo: fs_install_mcr: command not found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr R2019b`?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Justina Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the matlab runtime environment into a temporary directory (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is trying to move that temporary directory to a location inside the FreeSurfer directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr R2019b` so that the install script has permissions to write to the FreeSurfer directory?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Justina Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command fs_install_mcr R2019b. It has ended successfully with this end message stated below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command segmentHA_T1.sh. When I try to run this command again it gives me the following error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the usr/local/freesurfer/7.3.2 instead of in the location stated in the error above. When I try to search this location there is no such existing directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of You Na Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh for the segmentation as described above. The following command shows the corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not found



I am currently struggling to find the solution to this issue. Is the installation not in the correct path? Is MATLAB Runtime installed at all? Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







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------------------------------

Message: 10
Date: Tue, 13 Sep 2022 20:57:25 +0200
From: Justina Lee <justinalee56@gmail.com>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <CACFPZpv-mj=AiVnvqVD6qL=-RJt2dJ1wMogtMVyU+xr6t4imjQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution       

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
wrote:

> Ah ok, let's try this:
>
> cd /usr/local/freesurfer/7.3.2/bin
> sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
>
> We are appending `./` to fs_install_mcr to tell it it's in the same
> directory.  We are also passing the definition of FREESURFER_HOME into the
> 'sudo'ed' environment, because the install script relies on that.
>
> -Paul
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:37 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Hi Paul,
>
> I have entered the command under this directory ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
> sudo fs_install_mcr R2019b and the following error persists. (sudo:
> fs_install_mcr: command not found)
>
> Could there be a reason for this?
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
> wrote:
>
> Hi Justina,
>
> Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
>
> Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
> R2019b`?
>
> -Paul
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Hi Paul,
>
> When I try to run the installation command with sudo, the following error
> command shows:
>
> sudo: fs_install_mcr: command not found
>
> I'm terribly sorry for the inconvenience.
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
> wrote:
>
> Hi Justina,
>
> Ok so it looks like the install script is getting further and has
> extracted the matlab runtime environment into a temporary directory
> (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
> trying to move that temporary directory to a location inside the FreeSurfer
> directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
> into a 'Permission Denied' error.
>
> Can you try re-installing the matlab runtime by running `sudo
> fs_install_mcr R2019b` so that the install script has permissions to write
> to the FreeSurfer directory?
>
> -Paul
>
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Thank you Paul for your help!
>
>
> This seems to have solved the issue, as I can now run the command
> fs_install_mcr R2019b. It has ended successfully with this end message
> stated below:
>
>
>
> mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
> '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
>
>
>
> I think this problem persists with my next issue, which is using the
> command segmentHA_T1.sh. When I try to run this command again it gives me
> the following error:
>
>
>
> ERROR: cannot find Matlab 2019b runtime in location:
>
>
>
> /usr/local/freesurfer/7.3.2/MCRv97
>
>
>
> It is looking for either:
>
>   bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or
>
>   bin/maci64/libmwlaunchermain.dylib (Mac 64b)
>
>
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
>
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2019b.
>
> To do so, please run the following command (you might need root
> permissions):
>
>
>
> fs_install_mcr R2019b
>
>
>
> I have seen that the pathway for fs_install_mcr is located in the
> usr/local/freesurfer/7.3.2 instead of in the location stated in the error
> above. When I try to search this location there is no such existing
> directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.
>
>
>
> Do I need to create a new file for where the runtime should be stored? Or
> create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should
> the fs_installl_mcr R2019b be stored under bin for this command to work?
>
> Hope you can continue to help me with my follow-up issue, I appreciate it
> a lot.
>
> Thank you so much.
>
>
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu>
> wrote:
>
> Hi Justina,
>
> It looks like the matlab installer is trying to use unzip but it can't
> find it.
>
> Can you try running:
> `sudo apt-get install unzip`
>
> To install unzip then try the matlab installer again?
>
> -Paul
> ------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu <
> freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinalee56@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> To whom it may concern,
>
>
>
> Apologies for my first post, I was a little bit confounded as to how I can
> reach for help.
>
> I would like to use the segmentation of hippocampal subfields and the
> nuclei of the amygdala.
> Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
>
>
> I am trying to install MATLAB Runtime 2019b to run the command
> segmentHA_T1.sh for the segmentation as described above. The following
> command shows the corresponding error:
>
>
>
> ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr
> R2019b
>
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
> Current
>
>                                  Dload  Upload   Total   Spent    Left
> Speed
>
> 100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:--
> 10.1M
>
> /usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command
> not found
>
>
>
> I am currently struggling to find the solution to this issue. Is the
> installation not in the correct path? Is MATLAB Runtime installed at all?
> Should an already existing matlab file be deleted?
> Any help would be much appreciated.
>
>
>
> Sincerely,
>
> Justina
>
>
>
>
>
>
>
> Sent from Mail
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>
>
> _______________________________________________
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------------------------------

Message: 11
Date: Tue, 13 Sep 2022 19:03:58 +0000
From: "Wighton, Paul" <PWIGHTON@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
        not found
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BN8PR04MB5795D1EDC71DB06E4800D3AC82479@BN8PR04MB5795.namprd04.prod.outlook.com>
       
Content-Type: text/plain; charset="us-ascii"

I think we are on the right track, but it looks like there was a space between FREESURFER_HOME and the equal (=) sign? It also looks like there was no space between '$FREESURFER_HOME' and './fs_install_mcr'?

The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Hi Paul,

I have taken your advice and run the command as shown below:

ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME =$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found

The same problem persists yet again :( Does the problem lie somewhere else?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Ah ok, let's try this:

cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

We are appending `./` to fs_install_mcr to tell it it's in the same directory.  We are also passing the definition of FREESURFER_HOME into the 'sudo'ed' environment, because the install script relies on that.

-Paul
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Justina Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Hi Paul,

I have entered the command under this directory ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr R2019b and the following error persists. (sudo: fs_install_mcr: command not found)

Could there be a reason for this?

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?

Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr R2019b`?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Justina Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Hi Paul,

When I try to run the installation command with sudo, the following error command shows:

sudo: fs_install_mcr: command not found

I'm terribly sorry for the inconvenience.

Sincerely,
Justina

On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

Ok so it looks like the install script is getting further and has extracted the matlab runtime environment into a temporary directory (/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is trying to move that temporary directory to a location inside the FreeSurfer directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running into a 'Permission Denied' error.

Can you try re-installing the matlab runtime by running `sudo fs_install_mcr R2019b` so that the install script has permissions to write to the FreeSurfer directory?

-Paul

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Justina Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


        External Email - Use Caution

Thank you Paul for your help!

This seems to have solved the issue, as I can now run the command fs_install_mcr R2019b. It has ended successfully with this end message stated below:



mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to '/usr/local/freesurfer/7.3.2/MCRv97': Permission denied



I think this problem persists with my next issue, which is using the command segmentHA_T1.sh. When I try to run this command again it gives me the following error:



ERROR: cannot find Matlab 2019b runtime in location:



/usr/local/freesurfer/7.3.2/MCRv97



It is looking for either:

  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)



The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):



fs_install_mcr R2019b



I have seen that the pathway for fs_install_mcr is located in the usr/local/freesurfer/7.3.2 instead of in the location stated in the error above. When I try to search this location there is no such existing directory. This can be the same for bin/glnxa64/libmwlaunchermain.so.



Do I need to create a new file for where the runtime should be stored? Or create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the fs_installl_mcr R2019b be stored under bin for this command to work?

Hope you can continue to help me with my follow-up issue, I appreciate it a lot.

Thank you so much.



Sincerely,
Justina

On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu<mailto:PWIGHTON@mgh.harvard.edu>> wrote:
Hi Justina,

It looks like the matlab installer is trying to use unzip but it can't find it.

Can you try running:
`sudo apt-get install unzip`

To install unzip then try the matlab installer again?

-Paul
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of You Na Lee <justinalee56@gmail.com<mailto:justinalee56@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found


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To whom it may concern,



Apologies for my first post, I was a little bit confounded as to how I can reach for help.


I would like to use the segmentation of hippocampal subfields and the nuclei of the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.

I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh for the segmentation as described above. The following command shows the corresponding error:



ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current

                                 Dload  Upload   Total   Spent    Left  Speed

100 2657M  100 2657M    0     0  10.0M      0  0:04:25  0:04:25 --:--:-- 10.1M

/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not found



I am currently struggling to find the solution to this issue. Is the installation not in the correct path? Is MATLAB Runtime installed at all? Should an already existing matlab file be deleted?
Any help would be much appreciated.



Sincerely,

Justina







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