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 <pwigh...@mgh.harvard.edu>
wrote:

> Ah ok, let's try this:
>
> cd /usr/local/freesurfer/7.3.2/bin
> sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
>
> We are appending `./` to fs_install_mcr to tell it it's in the same
> directory.  We are also passing the definition of FREESURFER_HOME into the
> 'sudo'ed' environment, because the install script relies on that.
>
> -Paul
> ------------------------------
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:37 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
>         External Email - Use Caution
>
> Hi Paul,
>
> I have entered the command under this directory 
> ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
> 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 <pwigh...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@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 <pwigh...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@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 <pwigh...@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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@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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> attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/11dt0fJlRbQeHUzvxO4FxFVtrd5qpQOtnPZPVe8HwTqmiWTz_MyZVEk4mwzDqO10hIQcHqLK_4a8uc05z37PxXEdNsEPZrJk5GcUBUx8jjKsOCpa7Po622eMwGT_nS40ltoiKkZzUAKJ0Cy9sUT02hH9TfW_WPnlBMbzg3WodjY5qMYcwPYEMEEUPCIa0-07bqETa4OHTZyt4WizinLfTuPCrLSitsVjkcxpwvdKYsrpAIU0cb51NFvIBw-n2GcdqLZu4iroTgGIJ5t60Gl1AYgxgF77s8TW7eC3v24sZV4u3q15TRx5UT4_FKo-lUUq1/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <https://secure-web.cisco.com/1NTIn-Iz9YXM_1TaOsPXGWl7SK3uYiZ0n3TBJo4d63r6yF7ojf3C3NQQ_Rpp5Fu0tEfcGr07YeXQ5zqhGdiXTa1zvV-mWP6PmqdvyflbgxtaHVDCWDiswyCZzjPx3OcEs8XAzP2xqDDKm3dUUfM21kmOlq8pFz1nmF7VifSzmV_sU8WLq34OUpT80CTGmLDqpUVB0nhqgIr5yBM8rqDjnb1XzzT7dO3cwjV0pxmoSBUo5GFiufIwfBic2chan90fd4Qh1JPjluPAm4Hjn7f6pinX6jiVZgLkPD0B_jKALS_ZMHvgsHAGeZSgEcI2_Q7OV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> <*MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/11dt0fJlRbQeHUzvxO4FxFVtrd5qpQOtnPZPVe8HwTqmiWTz_MyZVEk4mwzDqO10hIQcHqLK_4a8uc05z37PxXEdNsEPZrJk5GcUBUx8jjKsOCpa7Po622eMwGT_nS40ltoiKkZzUAKJ0Cy9sUT02hH9TfW_WPnlBMbzg3WodjY5qMYcwPYEMEEUPCIa0-07bqETa4OHTZyt4WizinLfTuPCrLSitsVjkcxpwvdKYsrpAIU0cb51NFvIBw-n2GcdqLZu4iroTgGIJ5t60Gl1AYgxgF77s8TW7eC3v24sZV4u3q15TRx5UT4_FKo-lUUq1/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <https://secure-web.cisco.com/1NTIn-Iz9YXM_1TaOsPXGWl7SK3uYiZ0n3TBJo4d63r6yF7ojf3C3NQQ_Rpp5Fu0tEfcGr07YeXQ5zqhGdiXTa1zvV-mWP6PmqdvyflbgxtaHVDCWDiswyCZzjPx3OcEs8XAzP2xqDDKm3dUUfM21kmOlq8pFz1nmF7VifSzmV_sU8WLq34OUpT80CTGmLDqpUVB0nhqgIr5yBM8rqDjnb1XzzT7dO3cwjV0pxmoSBUo5GFiufIwfBic2chan90fd4Qh1JPjluPAm4Hjn7f6pinX6jiVZgLkPD0B_jKALS_ZMHvgsHAGeZSgEcI2_Q7OV/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
> .
>
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> https://secure-web.cisco.com/1pWKJlHuMIikPrFeRgJx8bdHDce7Euxy381Zk3zv1LqW7Unu1y9WGED_evKPtfjP1trQrSc3wJ1TDgXEv7xvAnmXsbyLL2iBRTQ-XWyUAtzfzCzjHxYuSWMp7ZXavsPLJEuhnYtSCkQyoix7GzJb3k39b40iJ61Tu4X6bXASsKpmo_Ql-NvPfJRS6dt3LDaRg8asjI2j3Thn8lejen02YFNw1-DtzVseNcf-Y9J7xW0A3iA9bQ53no2Dm7QKOcGQq7josAhLmv2ywG6h2cJrodY9FruLgnsE9F_Gja68p85vdxO8Xs7GQbzCf1_mxI_DG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
> is addressed.  If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/11dt0fJlRbQeHUzvxO4FxFVtrd5qpQOtnPZPVe8HwTqmiWTz_MyZVEk4mwzDqO10hIQcHqLK_4a8uc05z37PxXEdNsEPZrJk5GcUBUx8jjKsOCpa7Po622eMwGT_nS40ltoiKkZzUAKJ0Cy9sUT02hH9TfW_WPnlBMbzg3WodjY5qMYcwPYEMEEUPCIa0-07bqETa4OHTZyt4WizinLfTuPCrLSitsVjkcxpwvdKYsrpAIU0cb51NFvIBw-n2GcdqLZu4iroTgGIJ5t60Gl1AYgxgF77s8TW7eC3v24sZV4u3q15TRx5UT4_FKo-lUUq1/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/11dt0fJlRbQeHUzvxO4FxFVtrd5qpQOtnPZPVe8HwTqmiWTz_MyZVEk4mwzDqO10hIQcHqLK_4a8uc05z37PxXEdNsEPZrJk5GcUBUx8jjKsOCpa7Po622eMwGT_nS40ltoiKkZzUAKJ0Cy9sUT02hH9TfW_WPnlBMbzg3WodjY5qMYcwPYEMEEUPCIa0-07bqETa4OHTZyt4WizinLfTuPCrLSitsVjkcxpwvdKYsrpAIU0cb51NFvIBw-n2GcdqLZu4iroTgGIJ5t60Gl1AYgxgF77s8TW7eC3v24sZV4u3q15TRx5UT4_FKo-lUUq1/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>
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